Ty Jacobs’ Bio Study GuideTable of contents Intro to biomolecules 1 Water 3 Carbohydrates 8 Lipids 13 Nucleic acids 17 Proteins 22 Eukaryotic cell structure 34 Prokaryotic cell structure 44 Prokaryotes vs Eukaryotes 49 Cell and molecular Viruses and Prions 50 biology Diffusion and Osmosis 53 Substrate Transport 56 Cell signalling 58 Energy in the cell 64 Glycolysis 70 Pyruvate decarboxylation 75 Oxidative phosphorylation 80 Photosynthesis 86 Other sources of energy 93 Cell cycle and cancer 95 Mitosis and meiosis 100 Origins of life 107 Cell/Molecular biology lab 113 Genetics 115 Evolution 156 The biosphere 173 Evolution and Behavior 184 ecology Population ecology 190 Community ecology 195 Conservation biology 205 Archaea and bacteria 141 Diversity of life Prokaryotes and Protists 208 Plant and fungal diversity 218 Invertebrate diversity 229 Vertebrate diversity 245 Plant structure and function 252 Developmental Animal reproduction 282 biology Embryonic development 291 Body organization & tissues 301 Respiratory systems 305 Anatomy and Circulatory systems 314 physiology Digestive systems 324 Excretory systems 334 Nervous systems 342 Immune systems 354 Muscular systems 364 Sensory systems 371 Skeletal systems 373 Integumentary systems 377 Endocrine systems 380 1 • Life's molecular diversity is based on the properties of carbon ◦ Why is carbon great? ▪ Carbon is unparalleled in its ability to from large and complex molecules due to its capacity to make 4 bonds. ▪ Almost all of the molecules in the cell are composed of carbon. Carbon based molecules are called organic compounds. ◦ How can carbon molecules vary? ▪ The chain of carbon atoms in an organic molecule is called a carbon skeleton. • Length: carbon skeletons vary in length • Branching: skeletons may be unbranched or branched • Double or triple bonds: skeletons may have double or triple bonds • Rings: skeletons may be arranged in rings (i.e. cyclohexane, benzene) ▪ Compounds composed of only hydrogen and carbon atoms are called hydrocarbons. ▪ Two molecules might have the same molecular formulas, but different three-dimensional shapes due to the locations of certain bonds. • Compound with the same formula but different structural arrangements are called isomers. • A few chemical groups are key to the functioning of biological molecules ◦ Chemical groups that are important to reactivity and structure are called functional groups. The table below shows the 6 most popular functional groups found in biomolecules. • Cells make a huge number of large molecules from a limited set of polymers ◦ What are macromolecules? ▪ Molecules of major classes (i.e. carbohydrates, proteins, lipids, nucleic acids) are called macromolecules. ▪ Cells make most of their macromolecules by joining together smaller molecules into chains called polymers. The building blocks of polymers are called monomers. ▪ Types of monomers: 2 • Carbohydates: monosaccharides • Nucleic acids: nucleotides • Proteins: amino acids • Lipids: glycerol and fatty acids ◦ Making polymers ▪ Cells link monomers together to form polymers by a dehydration reaction, a reaction that removes a molecule of water. ▪ For each monomer added to a chain, a water molecule is released. ▪ Dehydration reactions are the same regardless of the specific monomers and the type of polymer the cell is producing. ◦ Breaking polymers ▪ Cells not only make macromolecules but also have to break them down. This digestion process is called hydrolysis. • Essentially the reverse of a dehydration reaction, hydrolysis involves adding a water molecule to break a bond. ▪ One water molecule is used up every time a bond between two monomers is broken. ◦ The diversity of polymers ▪ Remarkably, a cell makes all its thousands of different macromolecules from a small list of ingredients—about 40 to 50 common components and a few others that are rare. ▪ The key to the great diversity of polymers is arrangement—variation in the sequence in which monomers are struck together. ▪ The variety in polymers account for the uniqueness of each organism. 3 1. Weak Interactions in Aqueous Systems a) Hydrogen bonding gives water its unusual properties Each hydrogen atom of a water molecule shares an electron pair with the central oxygen atom. The H-O-H bond angle is 104.5 degrees. The oxygen nucleus attracts electrons more strongly than does the hydrogen nucleus; that is, oxygen is more electronegative. The result of this unequal electron sharing is two electric dipoles in the water molecule, one along each of the H-O bonds; each hydrogen atom bears a partial positive charge and the oxygen atom bears a partial negative charge equal in magnitude. As a result, there is an electrostatic attraction between the oxygen atom of one water molecule and the hydrogen of another, called a hydrogen bond. It is a weak bond, about 10% covalent and 90% electrostatic. Hydrogen bonds in water have a very short lifetime, but they are constantly breaking and forming. The sum of all the hydrogen bonds between water molecules confers great internal cohesion on liquid water. The nearly tetrahedral arrangement of the orbitals about the oxygen atom allows each water molecule to form hydrogen bonds with as many as four neighboring water molecules. Hydrogen bonds account for a higher melting point because much thermal energy is required to break a sufficient portion of hydrogen bonds to destabilize the crystal lattice of ice. During melting or evaporation, the entropy of the system increases as the water molecules become less orderly. b) Water forms hydrogen bonds with polar solutes Hydrogen bonds form between an electronegative atom (the hydrogen acceptor, usually oxygen or nitrogen) and a hydrogen atom covalently bonded to another electronegative atom (the hydrogen donor) in the same or another molecule. Hydrogen bonded to carbons do not participate in hydrogen bonding. 4 important hydrogen bonds in our body: Between the hydroxyl group of an alcohol and water Between the carbonyl group of a ketone and water Between peptide groups in polypeptides Between complementary bases of DNA 4 Hydrogen bonds are strongest when the bonded molecules are oriented to maximize electrostatic reaction, which occurs when the hydrogen atom and the two atoms that share it are in a straight line—that is, when the acceptor atom is in line with the covalent bond between the donor atom and H. c) Water interacts electrostatically with charged solutes Compounds that dissolve easily in water are hydrophilic whereas nonpolar solvents that does not dissolve easily in water are hydrophobic. Water easily dissolves charged molecules; it destabilizes the charge by surrounding the individual ions. Water has a very high dielectric constant, a physical property that reflects the number of dipoles in a solvent. By this being high, it is effective in screening electrostatic reactions between dissolved ions. 5 d) Water readily dissolves polar solutes Because water is a polar molecule, it can readily dissolve other polar solutes (like dissolves like). e) Water is the solvent of life Water readily dissolves ionic and polar solvents. Many organic molecules are either ionic or polar (i.e. proteins, sugars, etc.) As the solvent inside all cells, in blood, and in plant sap, water dissolves an enormous variety of solutes necessary for life. f) Nonpolar gasses are poorly soluble in water. g) Nonpolar compounds force energetically unfavorable changes in the structure of water. When water is mixed with a nonpolar compound, two phases form; neither liquid is soluble in the other. The nonpolar compounds interfere with the hydrogen bonding among water molecules. Dissolving hydrophobic molecules in water produces a measurable decrease in entropy. Water molecules in the immediate vicinity of a nonpolar solute are constrained in their possible orientations as they form a highly ordered cage-like shell around each solute molecule. The number of ordered water molecules, and therefore the magnitude of of the entropy decrease, is proportional to the surface area of the hydrophobic solute enclosed within the cage of water molecules. Amphipathic compounds contain regions that are polar and regions that are nonpolar. When an amphipathic compound is mixed with water, the polar, hydrophilic region interacts favorably with water and tends to dissolve, but the nonpolar, hydrophobic region tends to avoid contact with water. The nonpolar regions cluster together to present the smallest hydrophobic area to the aqueous solvent, and the polar regions are arranged to maximize their interaction with the solvent. These structures are called micelles. The forces that hold the nonpolar regions of the molecules together are called hydrophobic interactions. 2. Ionization of Water, Weak acids, and weak bases a) Pure water is slightly ionized When any acid is dissolved in water, they contribute H+ by ionizing; bases consume H+ by becoming protonated. The total hydrogen ion concentration from all sources is measurable and is expressed as the pH of the solution. Hydrogen ions formed in water are immediately hydrated to form hydronium ions (H3O+). Hydrogen bonding between water molecules makes the hydration of dissociating protons virtually instantaneous. No individual proton moves very far through the solution, but a series of proton hops between hydrogen-bonded water molecules causes the net movement of a proton over a long distance in a remarkably short time. As a result of the high ionic mobility of H+, the acid-base reactions in aqueous solutions are exceptionally fast. b) The pH and blood When the pH of the blood often falls below the normal value of 7.4, this condition is called acidosis. When the pH of the blood is higher than normal, the condition is called alkalosis. 3. Cohesion vs Adhesion and Capillary Action a) Cohesion Cohesion – water is attracted to other water molecules. Defined as the “stickiness” that water molecules have for eachother. 6 Cohesion makes a water droplet a drop. liquid. Water's hydrogen bonds moderate temperature a) Water's high specific heat The ability of water to stabilize temperature stems from its relatively high specific heat. water is less dense as a solid than as a liquid. 4. lots of heat is required to make this happen. This means that water will change its temperature less than other liquids when it absorbs or loses a given amount of heat. creating a three-dimensional crystal. c) Capillary action Capillary action is the movement of water within the spaces of a porous material against the flow of gravity. 5. This keeps water molecules relatively far apart from one another. each molecule forms stable hydrogen bond with their neighbors. Since hydrogen bonds are strong. water atoms constantly break and re-form hydrogen bonds. which causes a decrease in density. This disorder causes water molecules to be packed tightly in a given space. b) Adhesion Adhesion – water is attracted to other substances (namely polar ones). In liquid form. or solid. b) Unlike most substances. . This is due to adhesion and cohesion. The specific heat of a substance is defined as the amount of heat that must be absorbed for 1g of that substance to change its temperature by 1 degree Celsius. This is because of hydrogen bonding. Ice is less dense than liquid water a) Water exists on Earth in the form of a gas (water vapor). As water freezes. The high specific heat of water can be due to its hydrogen bonding. Heat must be absorbed to break hydrogen bonds. 7 . The two families of monosaccharides are aldoses and ketoses a. III. Carbohydrate monomers are monosaccharides. What are carbohydrates? I. “hemi” meaning that the alcohol and the aldehyde or ketone are all in the same molecule. c. b. one of the carbon atoms is double-bonded to an oxygen atom to form a carbonyl groups. All of the monosaccharides contain one or more chiral carbon atoms. C6H12O6). If the carbonyl group is at the end of a carbon chain. They generally have the moleuclar formulas that are some multiple of CH2O (i. b. If the carbonyl group is at any other position. the monosaccharide is a ketose (ketone).e. Note that the carbon that differs among the two molecules is NOT the anomeric carbon. In this form. B. Monosaccharides have asymmetric centers a. the monosaccharide is an aldose (aldehyde). such as the starch molecules we consume in pasta and potatoes. II. all monosaccharides with five or more carbon atoms in the backbone occur predominantly as cyclic structures in which the carbonyl group has formed a covalent bond with the oxygen of a hydroxyl group along the chain. In aqueous solution. i. IV. meaning that two stereoisomeric configurations (denoted alpha and beta) can be produced. Monosaccharides are the simplest carbohydrates a. D/L configuration is based on the chiral center most distant from the carbonyl carbon. just know there are two different stereoisomers. Monosaccharides and Disaccharides I. attacking either the “front” or the “back” of the carbonyl carbon. The name carbohydrate refers to a class of molecules ranging from the small sugar molecules dissolved in soft drinks to large polysaccharides. . each of the other carbon atoms has a hydroxyl group. The formation of these ring compounds is the result of a general reaction between alcohols and aldehydes or ketones to form derivatives called hemiacitals or hemiketals. ii. You don't need to distinguish between alpha and beta. The alcohol can add in either one of two ways. The reaction with the first molecule of alcohol creates an additional chiral center (the carbonyl carbon). The backbones of common monosaccharides are unbranched carbon chains in which all the carbon atoms are linked by single bonds. i. 8 A. The common monosaccharides have cyclic structures a. (The molecules shown above are both D-stereoisomers) c. Those with the OH on the left is the L-stereoisomer and those with the OH on the right is the D-stereoisomer. Two sugars that differ only in the configuration around one carbon atom are called epimers. Six-membered ring compounds are called pyranoses (formed from aldohexoses) and 5- membered ring compounds are called furanoses (formed from aldopentoses and ketohexoses). c. which is formed when a hydroxyl group of one sugar molecule reacts with the anomeric carbon of the other. Disaccharides contain a glycosidic bond a. Water is removed as a byproduct. (picture) Alpha 1--> 4 linkage: both monomers are alpha anomers and the glycosidic linkage takes place between C-1 of one anomer and C-4 of the second anomer. The numbering of a glycosidc linkage refers to the carbons from each monomer that are involved in the bond. A glycosidic linkage is named after the anomers of monosaccharides (alpha or beta units) involved in the linkage. and the carbonyl carbon is called the anomeric carbon. V. Isomeric forms of monosaccharides that differ only in their configuration about the anomeric carbon are called anomers. . b. Disaccharides consist of two monosaccharides joined covalently by an O-glycosidic bond. In the picture below C1 in all 3 molecules is the anomeric carbon. 9 d. e. Glycogen is a polymer of alpha1→4 linked subunits of glucose. with alpha1→6 linked branches. When glycogen is used as an energy source. Glycogen is the main storage polysaccharide of animal cells. c. II. Introduction a. differ from each other in the identity of their recurring monosaccharide units. Homopolysaccharides contain only a single monomeric species. i. in the types of bonds linking the units. i. and in the degree of branching. Polysaccharides I. i. Reacts positively with iodine to turn purple. Starch in plant cells and glycogen in animal cells are the most important storage polysaccharides. ii. Starch contains two types of glucose polymer. Some homopolysaccharides are stored forms of fuel a. Heteropolysaccharides contain two or more different kinds. ii. They are both heavily hydrated. but glycogen is more extensively branched (every 8-12 residues) and more compact than starch. ii. amylose and amylopectin. in length of their chains. Amylopectin consists of highly branched chains (branch points occurring every 24 to 30 residues). b. also called glycans. . glucose units are removed one at a time. 10 C. because they have many exposed OH groups available to hydrogen-bond with water. i. b. Amylose consists of long. unbranched chains of D-glucose residues connected by alpha1→4 linkages. Polysaccharides. The glucose residues are connected by alpha1→4 linkages and the branch points are connected by alpha1→6 linkages. Polysaccharides do not have defining molecular weights. Penicillin and related antibiotics kill bacteria by preventing synthesis of the cross links. Cellulose is a fibrous. The only chemical difference from cellulose is the replacement of the hydroxyl group C-2 with an acetylated amino group. It is a linear. ii. extended chain. water-insoluble substance. 11 III. i. It is the principal component of the hard exoskeletons of arthropods. the exact structure depends on species. found in the cell walls of plants. this gives the polymer a linear. peptidoglycan. tough.Bacterial and algal cell walls contain structural heteropolysaccharides a. is a heteropolymer of alternating beta1→4 linked N-acetylglucosamine and N-acetylmuramic acid residues. cross-linked by short peptides. unbranched homopolysaccharide. Each monomer is turned 180 degrees around the glycosidic bond. i. i. ii. Cellulose contains many intrachain and interchain hydrogen bonds. The linear polymers lie side by side in the cell wall. IV. ii. iv. The supermoleuclar structure has high tensile strength and low water content (no place for water hydrogen bonds) b. but no interchain covalent bonds. Chitin is a lnear homopolysaccharide composed of N-acetylglucosamine residues in a (beta1→4) linkage. leaving the cell wall to weak to resist osmotic lysis. The rigid component of bacterial cell walls. Some homopolysaccharides serve structural roles a. iii. . All the glucose residues have a beta configuration. d. Types of glycoconjugates a. Proteoglycans are macromolecules of the cell surface or ECM where one or more sulfated GAG chains are joined covalently to a membrane protein or a secreted protein. They are usually found on the outer face of the plasma membrane. They bind to ECM proteins through electrostatic interactions (GAGs are very negative). Glycoproteins. c. i. enormous supramolecular assemblies of many core proteins bound to a single molecule of hyaluronan. the extracellular matrix (ECM). 12 V. i. Glycosphingolipids are plasma membrane components in which the hydrophilic head groups are oligosaccharides. b. Glycoconjugates: Proteoglycans. Proteoglycans are glycoasminoglcyan—containing macromoleucles of the cell surface and ECM a. Glycosaminoglycans are heteropolysaccharides of the extracellular matrix a. A glycoconjugate is a carbohydrate covalently joined to a protein or a lipid (these molecules are biologically active). These heteropolysaccharides are called glycosaminoglycans (GAG). The extracellular space in the tissues of multicellular animals is filled with a gel-like material. II. . and Glycophingolipids I. The ECM is composed of an interlocking network of heteropolysaccharides and fibrous proteins. Some proteoglycans can form proteoglycan aggregates. which holds cells together and provides a porous pathway for the diffusion of nutrients and oxygen to individual cells. D. they are unique to animals and are not found in plants. Glycoproteins have one or more several oligosaccharides of varying complexity joined covalently to a protein. Storage Lipids I. and the compounds that contain them. f. In some fatty acids. . At room temperature. ii. unsaturated fatty acids have way lower melting points. Fatty acids are hydrocarbon derivatives. Fatty acids with these kinks cannot pack together as tightly as saturated fatty acids. --CH=CH--CH2--CH=CH-- e. As a result. the double bond is between C- 9 and C-10 and the other double bonds of polyunsaturated (multiple double bonds) fatty acids are usually at C-12 and C-15. i. They are carboxylic acids with hydrocarbon chains ranging from 4 to 36 carbons long. Polyunsaturated fatty acid double bonds are separated by a methylene group meaning. The most commonly occurring fatty acids have even number of carbon atoms in an unbranched chain of 12 to 24 carbons. h. The even number of carbons are a result of bio synthesis from acetate (2 carbon unit) c. the most stable conformation is the fully extended form. free rotation around each carbon-carbon bond gives the hydrocarbon chain great flexibility. 13 A. the chain contains one or more double bonds (unsaturated). i. Fatty Acids are Hydrocarbon Derivatives a. In unsaturated fatty acids. g. i. are largely determined by the length and degree of unsaturation of the hydrocarbon chain. a cis double bond forces a kink in the hydrocabon chain. Melting points are also strongly influenced by the length and degree of unsaturation of the hydrocabon chain. in which the steric hindrance of neighboring atoms is minimized. b. In water. saturated fatty acids are waxy and unsaturated fatty acids are oily. In most monounsaturated (one double bond) fatty acids. The physical properties of the fatty acids. The carboxylic acid group is polar (and ionized at neutral pH) and accounts for the slight solubility of short-chain fatty acids in water. i. these molecules can pack together tightly in nearly crystalline arrays. In the fully saturated compounds. The longer the fatty acyl chain and the fewer the double bonds. The nonpolar hydrocarbon chain accounts for the poor solubility of fatty acids in water. the lower is the solubility in water. in others. and their interactions with each other are therefore weaker. this chain is unbranched and fully saturated (contains no double bonds). d. ii. rather than carbohydrates. b. Structural lipids in membranes I. aqueous media in the ECM whereas the hydrophobic tails point toward the inside to prevent interactions with polar molecules. The simplest lipids constructed from fatty acids are the triacylglycerols. Triacylglycerols a. where it will interact with the polar. Second. because triacylglycerols are hydrophobic and therefore unhydrated. First. and oxidation of tryacylglycerols yields 2x more energy. the carbon atoms of fatty acids are more reduced than those of sugars. Phospholipids are the main building block of plasma membranes. Triacylglycerols provide stored energy and insulation a. B. essentially insoluble in water. ii. Because the polar hydroxyls of glycerol and the polar carboxylates of the fatty acids are bound in ester linkages. The hydrophobic section are 2 fatty acid chains connected to glycerol. meaning that they contain hydrophobic sections and hydrophilic sections. . which are composed of three fatty acids each in ester linkage with a single glycerol. i. Phospholipids a. the hydrophilic head points toward the surface. III. Most triacylglycerols are are mixed. they contain two or three different fatty acids. hydrophobic molecules. the organism that carries fat as fuel does not have to carry the extra weight of water of hydration that is associated with sugars. The hydrophillic section is the phosphate group attached to the glycerol. triacylglycerols are nonpolar. There are two significant advantages to using tryacylglycerols as stored fuels. 14 II. Phospholipids are amphipathic. i. as the oxidation of carbohydrates. In a typical plasma membrane. c. iii. substances that act only on the cells near the point of hormone synthesis instead of being transported in the blood to act on cells in other tissues or organs. b. C. Depending on the type of phospholipase. open form. Cartoenoids. Leukotrienes contain three conjugated double bonds. no cyclic structure. c. ii. Overproduction of lenukotrienes causes asthmatic attacks. emulsifying dietary fats to make them more readily accessible to digestive lipases. e. Sterols are structural lipids present in the membranes of most eukaryotic cells. Waxes are esters of fatty acids and monodhydroxylic alcohols. Three classes: i. three with 6 carbons and one with 5. IV. Porphyrins are 4 fused pyrrole rings usually in a complex with a metal heme. Phospholipases degrade phospholipids and into lysophospholipid. Thromboxanes have a 6-membered ring also containing an ether. Porphyrins. d. Carotenoids are fatty acid carbon chains with conjugated double bonds and 6 carbon rings at each end. The steroid nucleus is almost planar and relatively rigid. Two types: a. a. the most major sterol in animal tissues. Examples would be chlorophyll and hemoglobin. Lanolin is a waxy secretion of wool bearing animals. different products are generated II. Structure is defined by the “steroid nucleus” (4 fused rings). Eicosanoids carry messages to nearby cells a. with a polar head group (the hydroxyl group at C-3) and a nonpolar hydrocarbon body (the steroid nucleus and the hydrocarbon side chain at C-17). II. Prostaglandins (PG) contains a 5-carbon ring originating from the chain of arachidonic acid. Used as protective coating or exoskeleton. They are pigmented molecules in animals and plants. Eicosanoids are paracrine hormones. Waxes. Sterols have four fused carbon rings a. c. III. is amphipathic. ii. White fat cells have a large lipid droplet composed of triacylglycerides with a small . Cholesterol. the 20-carbon polyunsaturated fatty acid. i. All eicosanoids are derived from arachidonic acid. III. and adipose cells I. 15 b. the fused rings do not allow rotation around C-C bonds. Phospholipids and sphingolipids are degraded in lysosomes i.Adipose cells are fat storing cells. They are produced by platelets and act in the formation of blood clots and the reduction of blood flow to the site of a clot. b. They are powerful biological signals. Bacteria cannot synthesize sterols. Bile acids are polar derivatives of cholesterol that act as detergents in the intestine. Thin-layer chromatography a. II. As the solvent rises on the plate by capillary action. III. Thin-layer chromatogrpahy on silicic acid employs the same principle as adsorption chromatography. such as silica gel is packed into a glass column. it carries lipids with it. Gas-liquid chromatography resolves mixtures of volatile lipid derivatives a. by washing the column with solvents of progressively higher polarity. f. Gas-liquid chromatography separates volatile components of a mixture according to their relative tendencies to dissolve in the inert material packed in the chromatography column or to volatilize and move through the column. b. c. A small sample of lipids dissolved in chloroform is applied to near one edge of the plate. in order of increasing polarity. D. Lipids can be fractionated by chromatographic procedures based on different polarities of each class of lipid. carried by a current of an inert gas such as helium. In adsorption chromatography.Mass spectrometry reveals complete lipid structure a. d. to which it adheres. The polar lipids bind tightly to the polar silicic acid. Lipids containing unsaturated fatty acids develop a yellow or brown color when exposed to iodine. IV. b. an insoluble. but the neutral lipids pass directly through the column and emerge in the first chloroform wash. scattered lipid droplets. and lots of mitochondria. d. The separated lipids can be detected by spraying the plate with a dye or by exposing the plate to iodine fumes. The polar lipids are then eluted. polar material. the entire setup is enclosed in a chamber saturated the solvent vapor. Brown fat cells have lots of cytoplasm. . The less polar lipids move farthest. as they have less tendency to bind to the silicic acid. which is dipped in a shallow container of an organic solvent or solvent mixture. e. 16 layer of cytoplasm. A thin layer of silica gel is spread onto a glass plate. b. Working with lipids I. Adsorption chromatography separates lipids of different polarity a. c. and the lipid mixture is applied to the top of the column. Mass spectrometric analysis of lipids establishes the length of a hydrocarbon chain or the position of double bonds. Messenger RNAs are intermediaries. A segment of DNA that contains the information required for the synthesis of a functional biological product. RNAs have a broader range of functions. i. Ribosomal RNAs are components of ribosomes. pyrimidine and purine. whether protein or RNA. carrying genetic information from one or a few genes to a ribosome. Genome is the collection of all the genes in an organism. where the corresponding proteins are synthesized. ii. and the phosphate is esterified to the 5' carbon. Transcriptome vs. i. The molecule without a phosphate group is called a nucleoside. iii. ii. Nucleotides have three characteristic components: (1) a nitrogenous base. . N-B-glycosyl bond is formed by the removal of the elements of water (OH from the pentose and the H from the base). tissue. 17 A. Transfer RNAs are adapter molecules that faithfully translate the information in mRNA into a specific sequence of amino acids. Introduction a. The base of a nucleotide is joined covalently (at N-1 of pyrimidines and N-9 of purines) in an N-B-glycosyl bond to the 1' carbon of the pentose. Genome i. c. ii. b. or organism. b. Some basics I. The nitrogenous bases are derivatives of two parent compounds. Transcriptome is the collection of all the RNA transcripts in a cell. and (3) one or more phosphates. (2) a pentose. is referred to as a gene. II. and several types are found in cells: i. Nucleotides and nucleic acids have characteristic bases and pentoses a. the complexes that carry out the synthesis of proteins. d. Both types of pentoses are in their B-furanose (closed five-membered ring) form. i. . ii. b. backbones of nucleic acids consist of alternating phosphate and pentose residues. creating a phosphodiester linkage. but the second common pyrimidine is not the same in both: it is thymine in DNA and uracil in RNA. Both DNA and RNA contain two major purine bases. All phosphodiester linkages have the same orientation giving the nucleic acid a specific directionality which goes from a 5' to a 3' direction (refers to the end of the strand). i. III. Thus. Nucleic acids have two kinds of pentoses. adenine and guanine. Nucleotides in both DNA and RNA are covalently linked together through phosphate- group “bridges. Phosphodiester bonds link successive nucleotides in nucleic acids a. Deoxyribonucleotides are the structural units of DNA (base + phosphate + deoxyribose) and ribonucleotides are the structural units of RNA (base + phosphate + ribose). 18 c. The backbones of both DNA and RNA are hydrophilic. and two major pyrimidines. DNA contains 2'-deoxy-D-ribose and RNA contains D-ribose. In both DNA and RNA one of the pyrimidines is cytosine.” in which the 5'-phosphate group of one nucleotide unit is joined to the 3'-hydroxyl group of the next nucleotide. The pentose ring is not planar but occurs in one of a variety of conformations generally described as “puckered.” e. The properties of nucleotide bases affect the 3D structure of nucleic acids a. c. One result of this is that pyrimidines and purines are nearly to very planar. A = T G=C A+G=T+C b. d. Chargaff's rules i. The base composition of DNA generally varies from one species to another. Purine and pyrimidine bases are hydrophobic and relatively insoluble in water at near- neutral pH of the cell. The stacking provides a combination of van der Waals and dipole-dipole interactions and helps minimize contact of the bases with water. Nucleic acid structure I. i. ii. The bases hydrogen bond with one another: this is the most important mode of interaction between two complementary strands of nucleic acid. facing the surrounding water. and nucleic acids are characterized by a strong absorption at wavelengths near 260 nm. These strands are antiparallel to one another (one in 5' to 3' direction and the other is in 3' to 5' direction). nutritional state. Pyrimidines and purines are weakly basic compound and are thus called bases. iv. 19 i. G bonds to C = 3 hydrogen bonds B. IV. i. DNA specimens isolated from different tissues of the same species have the same base composition. DNA is a double helix that stores genetic information a. The hydrophilic backbones are on the outside of the double helix. f. The pairing of the two strands creates a major groove and minor groove on the surface of a duplex. A bonds to T = 2 hydrogen bonds ii. c. iii. or changing environment. . i. Electron delocalization among atoms in the ring gives most of the bonds partial double- bond character. d. The base composition of DNA in a given species does not change with an organism's age. b. e. Two helical DNA chains are wound around the same axis to form a right-handed double helix. Hyrophobic stacking interactions in which two or more bases are positioned with the planes of their rings parallel (like a stack of coins) helps create the 3D structure. The 5' end lacks a nucleotide at the 5' position and the 3' end lacks a nucleotide at the 3' position. All nucleotide bases absorb UV light. c. Structural variation in DNA reflects 3 things: (1) different possible conformations of the deoxyribose. Z-DNA is a left-handed helix and there is barely a minor groove. II. 20 e. and (3) free rotation about the C-1'-N glycosyl bond. It is a right-handed double helix. A common type of DNA sequence is a palindrome: the sequence is spelled identically when read either forward or backward. thymine is found in the other). DNA can occur in different 3D forms a. Certain DNA sequences adopt unusual structures a. A-form DNA is favored in solutions that are devoid of water. The backbone takes on a zigzag appearance. The b-form DNA is the most stable structure for DNA molecule under physiological conditions. 10. Palindromes are repeats in opposite strands. but the helix is wider and their number of base pairs per helical turn is 11. b. The sequence of DNA from each strand is complementary to each other (wherever adenine occurs in one chain. Z-DNA have been found in bacteria and eukaryotes.5 base pairs per helical turn when in aqueous solution. (2) rotation about the contiguous bonds that make up the phosphodeoxyribose backbone. Z-form DNA has 12 base pairs per helical turn and the structure appears more slender and elongated. III. f. They create special structures: . d. It may play a role in regulating the expression of some genes. 21 i. Weak interactions. formed from ATP in a reaction catalyzed by adenylyl cyclase. b. When only a single DNA (or RNA) strand is involved. Another regulatory nucleotide. ii. ii. the closer the evolutionary relationship between two species. Hydrolysis of the nucleoside phosphates provides the chemical energy to drive many cellular reactions. . It inhibits the synthesis of rRNA and tRNA molecules needed for protein synthesis. b. i. V. When an inverted repeat occurs within each individual strand of the DNA (on the same strand). The single strand tends to assume a right-handed helical conformation dominated by base-stacking interactions.Many RNAs have more complex 3D structures a. ii. Second messengers tend to be nucleotides. Nucleic acids from different species can form hybrids a. i. The 3D structure of RNA is very complex. the more extensively their DNAs will hybridize. Hybrid duplexes are which segments of one species DNA strand form base-paired regions with segments of another species DNA strand. Z-form has been synthesized in the lab) e. the sequence is called a mirror repeat. preventing the uncessary production of nucleic acids. RNA can base-pair with complementary regions of either DNA or RNA. i. It reflects a common evolutionary heritage. (B-form is not observed. Other functions of nucleotides I. C. especially base-stacking interactions help stabilize RNA structures. the structure is called a hairpin. Nucleotides carry chemical energy in cells a. and triphosphates. ppGpp. The product of transcription of DNA is always single-stranded RNA. Some nucleotides are regulatory molecules a. d. Double stranded RNA is usually found in the A-form. The phosphate group covalently linked at the 5' hydroxyl of a ribonucleotide may have one or two additional phosphates attached. One of the most common is cyclic AMP or cAMP. When both strands of duplex DNA are involved. is produced in bacteria in response to a slowdown in protein synthesis during amino acid starvation. The resulting molecules are referred to as nucleoside mono-. II. IV. di-. it is called a cruciform. c. which influence the solubility of the amino acids in water. For all amino acids except glycine. Tryptophan All of the aromatic amino acids are relatively nonpolar and can participate in hydrophobic interactions. Glutamine . particularly their polarity. Asparagine. L-amino acids are those with an alpha-amino group on the left whereas D-amino acids have the alpha-amino group on the right. amino acids have two possible stereoisomers. Valine. c) Amino acids can be classified by R group Amino acids can be simplified by grouping the amino acids into 5 main classes based on the properties of their R groups. Proline. Aromatic R groups Phenylalanine. Uncharged R Groups Serine. Polar. Alanine. Nonpolar. Tyrosine. L system. They have a carboxyl group and an amino group bonded to the same carbon atom (the alpha carbon). Methionine The R groups in this class of amino acids are nonpolar and hydrophobic. This means that the alpha-carbon is a chiral center and thus. Isoleucine. the alpha carbon is bonded to four different groups. Threonine. The two forms are enantiomers and the stereoisomers are optically active—that is. Alipathic R Groups Glycine. they rotate plane-polarized light. Can absorb UV light. Leucine. They differ from each other in their side chains. Amino acids a) Amino acids share common structural features All 20 of the common amino acids are alpha-amino acids. The absolute configurations of simple sugars and amino acids are specified by the D. These proteins tend to stabilize protein structure by means of hydrophobic interactions. Cysteine. 22 1. or R groups. or tendency to interact with water at biological pH. b) Major type of proteins in the body The amino acid residues in proteins are L stereoisomers The amino acid residues in protein molecules are exclusively L stereoisomers. 5(pKa1 + pKa2) pH > pI. designated pI. the amino acid residue at the end with a free alpha-amino group is the amino-terminal (or N-terminal) residue. The S-S bond is strongly hydrophobic. or zwitterion. Amino acids are thus amphoteric. which can act as either an acid or base. it exists in solution as the dipolar ion. pI = 0. in which two cysteine molecules or residues are joined by a disulfide bond. which has a free carboxyl group. Cysteine is readily oxidized to form a covalently linked dimeric amino acid called cystine. 23 These amino acids contain functional groups that form hydrogen bonds with water. Peptides and proteins a) Peptides are chains of amino acids A peptide is two or more amino acid molecules covalently linked together. molecule will have a negative charge (“amino acid” will act like acid and donate H+ into the more basic solution) pH < pI. is the carboxyl terminal (C-terminal) residue. Positively charged (basic) R groups Lysine. These bonds play a special roles of many proteins by forming covalent links between parts of a polypeptide molecule or between two polypeptide chains. The characteristic pH at which the net electric charge is zero is called the isoelectric point or isoelectric pH. Arginine. The amino acids are held together by a peptide bond. histidine may be positively charged or uncharged at 7.0 Negatively charged (acidic) R groups Aspartate + glutamate Random important information Most flexible amino acid = glycine Most constrained amino acid = proline d) Amino acids can act as acids or bases When an amino acid lacking an ionizable R group is dissolved in water at neutral pH. In a peptide. . Histidine Histidine has an ionizable side chain with a pKa near neutrality. the greater the net electric charge of the amino acid. e) Titration curves predict the electric charge of amino acids An important piece of information derived from the titration curve of an amino acid is the relationship between its net charge and the pH of the solution. The the farther the pH of the solution is from the isoelectric point. 2. molecule will have a more positive charge (“amino acid” will act like base and accept H+ from the more acidic solution) At its isoelectric point. the Amino acid is least soluble in water and does not migrate in an electric field. the residue at the other end. and other properties. When this is suspended in a much larger volume of buffered solution. The extract is subjected to treatments that separate the proteins into different fractions based on a property such as size or charge. If at least two polypeptide chains are identical. 24 b) Biologically active peptides and polypeptides occur in a vast range of sizes and compositions Some proteins consist of a single polypeptide chain. binding affinity. the membrane allows the exchange of salt but not proteins. The protein. Working with proteins a) Proteins can be separated and purified It is important to purify proteins before the protein's properties and activities can be determined. a process referred to as fractionization. releasing the proteins into a solution called a crude extract. then the protein is said to be oligomeric. and the identical units are referred to as protomers. A porous solid material with the appropriate chemical properties (the stationary phase) is held in a column. but others. called multisubunit proteins. The first step in purification is to break open the cells. Column chromatography takes advantage of differences in protein charge. have two or more polypeptides associated noncovalently. dissolved in the same . The purified extract is placed in a bag or tube made up of some semipermeable membrane. size. A solution containing the protein of interest usually must further be altered before subsequent purification steps are possible. 3. Dialysis is a procedure that separates proteins from small solutes by taking advantage of the proteins' larger size. and a buffered solution (the mobile phase) migrates through it. Carried out in a gel that helps slow the migration of proteins approximately in proportion to their charge-to-mass ratio. is layered on top of the column. The affinity of each protein for the charged groups on the column is affected by the pH (which determines the ionization state of the molecule) and the concentration of completing free salt ions in the surrounding solution. . Large proteins emerge fro the column sooner than small ones. The beads in the column have a covalently attached chemical group called a ligand—a group or molecule that binds to a macromolecule such as a protein. The solid phase consists of cross-linked cavities of a particular size. When a protein mixture is added to the column. The expansion of the protein band in the mobile phase is caused by both separation of proteins with different properties and by diffusional spreading. proteins with a net positive charge migrate through the matrix more slowly than those with a net negative charge. In the mobile phase. Separation can be optimized n band in the mobile phase (the protein solution) is caused both by separation of proteins with different properties and by diffusional spreading. any protein with affinity to the ligand binds to the beads. and those with bound cationic groups are called anion exchangers. The column matrix is a synthetic polymer (resin) containing bound charged groups. the resolution of two types of proteins with different net charges generally improves. Size-exclusion crhomatography separates proteins according to size. Affinity chromatography is based on binding affinity. In cation-exchanged chromatography. and its migration through the matrix is retarded. Small proteins enter the cavities and are slowed by their more labyrinthine path through the column. those bound with anionic groups are called cation exchangers. because the migration of the former is retarded more by interaction with the stationary phase. rendering the overall charge from the protein insignificant and conferring on each protein a similar charge-to-mass ratio. An electrophoretic method commonly employed for estimation of purity and molecular weight makes use of sodium dodecyl sulfate (SDS). the proteins are visualized by adding a blue color dye. b) Proteins can be separated and characterized by electrophoresis Electrophoresis helps separate proteins based on the migration of charged proteins in an electric field. Can be also sued to determine isoelectric point and molecular weight. Individual proteins migrate faster or more slowly through the column depending on their properties. Electrophoresis in the presence of SDS therefore separates proteins almost exclusively After electrophoresis. The protein then percolates through the solid matrix.4 times its weight of SDS. Proteins can be visualized meaning a researcher can quickly estimate the number of different proteins in a mixture or the degree of purity of a particular protein preparation. Ion-exchange chromatography—exploits differences in the sign and magnitude of the net electric charge of proteins at a given pH. the solid matrix has negatively charged groups. As the length of the column increases. 25 buffered solution that was used to establish the mobile phase. SDS bound contributes a large net negative charge. Large proteins cannot enter the cavities and so take a shorter path through the column. A protein will bind about 1. Disulfide bridges are NOT broken down during allosteric interactions. leaving all other peptide bonds intact. Proteins must have multiple stable conformations—this reflects the changes that must take place in most proteins as they bind to other molecules or catalyze reactions. When water surrounds a hydrophobic molecule. or solvation layer. d) Mass spectrometry offers an alternative method to determine amino acid sequences Mass spectrometry can provide a highly accurate measure of the molecular weight of a protein. and the proteins are separated by SDS gel electrophoresis. . Isoelectric focusing is a procedure used to determine the isoelectric point (pI) of a protein. Overview of Protein Structure a) Introduction The spatial arrangement of atoms in a protein or any part of a protein is called its conformation. This results an a favorable increase in entropy. On carefully examining the contribution of weak interactions to protein stability. The possible conformations a protein include any structural state it can achieve without breaking covalent bonds. c) Protein chemistry is enriched by methods derived from classical polypeptide sequencing The Edman degradation procedure labels and removes the only amino-terminal residue from a peptide. because each group no longer presents its entire surface to the solution. Proteins in any of their functional. folded conformations are called native proteins. we find that hydrophobic interactions generally predominate. In general. Proteins are first separated by isoelectric focusing in a thin strip gel. the optimal arrangement of the hydrogen bonds results in a highly structured shell. This creates an unfavorable decrease in entropy. The most stable conformation is the one that is the most thermodynamically stable. Disulfide bonds are typically found in extracellular proteins because the environment is more oxidizing (inside the cell it is more reducing). The gel is then laid horizontally on a second gel. each protein migrates until it reaches the pH that matches its pI so proteins will be at different points on the gel. The chemical interactions that stabilize the native conformation include disulfide bonds and weak interactions. vertical separation reflects differences in molecular weight. also known as having the lowest Gibbs free energy. the extent of the solvation layer decreases. the protein conformation with the lowest free energy (the most stable conformation) is the one with the maximum number of weak interactions. b) A protein's conformation is stabilized largely by weak interactions Stability is defined as the tendency to maintain a native conformation. Two-dimensional electrophoresis is combining isoelectric focusing and SDS electrophoresis sequentially. Weak interactions that predominate as a stabilizing force in a protein structure because there are so many. 4. When nonpolar groups cluster together. Horizontal separation reflects differences in pI. A pH gradient is established by allowing a mixture of low molecular weight organic acids and bases to distribute themselves in an electric field across the gel. 26 Position on the band is used to determine molecular weight. of water around the molecule. When a protein mixture is applied. away from water. remains the same or nearly the same throughout the segment. 5. Where a regular pattern is not found. Amino acid sequences of most proteins contain a significant content of hydrophobic amino acid side chains.6 amino acid residues. the polypeptide backbone is wound around an imaginary axis drawn longitudinally through the middle of the helix. Most of the structural patterns reflect two simple rules: (1) hydrophobic residues are largely buried in the protein interior. It is also important that any polar or charged groups in the protein interior have suitable partners for hydrogen bonding or ionic interactions. Each helical turn includes 3. Why does the alpha helix form more readily than many other possible conformations? The structure is stabilized by a hydrogen bond between the hydrogen atom attached to the electronegative nitrogen atom of a peptide linkage and the electronegative . the secondary structure is sometimes referred to as undefined or a random coil. b) The alpha helix is a common protein secondary structure In the alpha helix. without regard to positioning of its side chains or its relationship to other segments. and the R groups of the amino acid residues protrude outward from the helical backbone. thus reducing the number of hydrogen-bonding and ionic groups that are not paired with a suitable partner. phi and psi. The presence of hydrogen-bonding groups without partners in the hydrophobic core of a protein can be destabilizing. A regular secondary structure occurs when each dihedral angle. and (2) the number of hydrogen bonds and ionic interactions within the protein is maximized. Protein secondary structure a) Introduction Secondary structure is the chosen segment of a polypeptide chain and describes the local spatial arrangement of its main-chain atoms. 27 Hydrophobic amino acid side chains therefore tend to cluster in a protein's interior. away from water. The twist of an alpha helix ensures that the critical interactions occur between an amino acid side chain and the side chain three to four residues away on either side of it. The position of an amino acid residue relative to its neighbors is also important. every peptide bond participates in such hydrogen bonding. negatively charged amino acids are often found near the amino terminus of the helical segment. A final factor affecting the stability of an alpha helix is the identity of the amino acid residues near the ends of the alpha-helical segment of the polypeptide. Alanine shows the greatest tendency to form alpha helices. The opposite is true at the carboxyl-terminal end of the helical segment. 28 nitrogen atom of a peptide linkage. where they have a stabilizing interaction with the positive charge of the helix dipole. For this reason. The order of the amino acid side chains can stabilize or destabilize the alpha-helical structure. permitting the formation of an ion pair. Within the alpha helix. resulting in a net dipole across the helical axis that increases with helix length. These dipoles are aligned through the hydrogen bonds of the helix. c) Amino acid sequence affects stability of the alpha helix Each amino acid residue in a polypeptide has an intrinsic propensity to form an alpha helix (some are more likely to form an alpha helix. some less likely). Positively charged amino acids are often found three residues away from negatively charged amino acids. . a positively charged amino acid at the amino- terminal end is destabilizing. A small electric dipole exists in each peptide bond. 29 d) The beta conformation organizes polypeptide chains into sheets The beta conformation is defined by backbone of a polypeptide chain extending into a zigzag rather than a helical structure. is called a beta sheet. Hydrogen bonds form between adjacent segments of the polypeptide within the sheet. The individual segments that form a beta sheet are usually nearby on the polypeptide chain but can also be quite distant from each other in the linear sequence of the polypeptide. The location of bends in the polypeptide chain and the direction and angle of these . they may be in different polypeptide chains. all of which are in the beta conformation. Protein tertiary and quaternary structures a) Introduction The overall three-dimensional arrangement of all atoms in a protein is referred to as the protein's tertiary structure. Amino acids that are far apart in the polypeptide sequence and are in different types of secondary structure may interact within the completely folded structure of a protein. Hydrogen bonds are linear in the antiparallel conformations 6. The arrangement of several segments side by side. The adjacent polypeptide chains in a Beta sheet can be either parallel or antiparallel. such as Pro. Ser. and globular proteins. . 30 bends are determined by the number and location of specific bend-producing residues. The arrangement of these protein subunits in three-dimensional complexes constitutes quaternary structure. Thr. Some proteins contain multiple subunits. with polypeptide chains arranged in long strands or sheets. There are two major groups in which many proteins are classified: fibrous proteins. and Gly. with polypeptide chains folded into a spherical or globular shape. 31 . etc. Most multimers have identical subunits in symmetrical arrangements. Nuclear magnetic resonance Advantages: NMR is carried out on macromolecules in solution and it can illustrate the dynamic side of protein structure. The repeating structural unit in a multimeric protein is called a protomer. e) Some proteins or protein segments are intrinsically disordered Intrinsically disordered proteins have properties that are distinct from classical structured proteins. a conformation that is usually biologically functional. 7. which permits close packing. How do proteins fold into its native 3D conformation? a) Protein folding is the physical process by which a protein chain acquires its native 3- dimensional structure. A multisubunit protein is referred to as a multimer. The supertwists are left-handed. are wrapped about each other to form a supertwisted coiled coil. They are all insoluble in water. are supertwisted about each other. Collagen Collagen helix is a unique secondary structure (like an alpha helix with key differences). Fibrous proteins share properties that give strength and/or flexibility to the structures in which they occur. nails. The tight wrapping provides a lot of strength. X-ray diffraction is done best in tandem with NMR. . and instead are characterized by high densities of charged amino acid residues. The physical environment in a crystal is not like in a living cell. A multimer with just a few subunits is often called an oligomer. d) Protein Quaternary Structures range from simple dimers to large complexes Many proteins have multiple polypeptide subunits. These cross-links are disulfide bonds. Two strands of alpha-keratin. b) Each protein exists as an unfolded polypeptide or random coil when translated from a sequence of mRNA to a linear chain of amino acids. Only certain atoms have the kind of nuclear spin that gives rise to an NMR signal. 32 b) Fibrous proteins are adapted for a structural function. as they tend to disrupt ordered structures. Alpha-keratin Alpha-keratin is found only in mammals (make up hair. Pro residues are also prominent. The twisting is right-handed. The alpha- keratin helix is a right-handed alpha helix. They lack a hydrophobic core. after the beam has been diffracted by the electrons of the atoms. It is left-handed and has three amino acid residues per turn.). c) Methods for determining 3-D structure of a protein X-ray diffraction The spacing of atoms in a crystal lattice can be determined by measuring the intensities and locations of spots produced on photographic film by a beam of x rays of given wavelength. opposite in the sense to the alpha helix. so the protein can look different. Three separate polypeptides. called alpha chains. The surfaces where the two alpha helices touch are made up of hydrophobic amino acids. The strength of fibrous proteins is enhanced by covalent cross-links between polypeptide chains and between adjacent chains in a supramolecular assembly. oriented in parallel (with the same amino termini at the same end. 8. cleavage of subunits. misfolding.000 to 25. and aggregation. although some occurs in the rough endoplasmic reticulum lumen (specifically proper folding and formation of disulfide bonds) 5 principal modification: formation of disulfide bonds. How is this possible? b) Protein post-translational modification (PTM) increases the functional diversity of the proteome by the covalent addition of functional groups or proteins. The human genome comprises between 20. or degradation of entire proteins. scientists have discovered that the human proteome (collection of all the proteins in a cell) is vastly more complex than the human genome. e) Chaperonins are proteins that provide favorable conditions for the correct folding of other proteins. specific proteolytic cleavages. 33 c) Proteins are folded and held together by several forms of molecular interactions (weak interactions. Chaperonins prevent protein unfolding. Most of the modifications take place in the golgi complex. addition and processing of carbohydrates. Post-translational modification of proteins a) Within the last few decades. etc. d) If the protein is not in the lowest energy conformation it will continue to move and adjust until it finds its most stable state. disulfide bonds.000 genes but the human proteome is estimated at over 1 million. assembly into multimeric proteins . proper folding. The biggest factor in a protein's ability to fold is the thermodynamics of the structure.). sphingolipids. ▪ Molecules must be absorbed while other molecules must be eliminated. lipids adopt a fluid state ▪ Most stable state is called liquid ordered state (this is at intermediate temps). ▪ It can be thought that cells and organelles are “big vesicles” ◦ Membrane fluidity ▪ Membrane fluidity depends on temperature At low temperatures. and glycerophospholipids ▪ non-polar elements face each other internally and polar head groups face outward ◦ Hydrophobic interactions in water ▪ Glycerophospholipids and sphingolipids spontaneously form bilayers when placed in a polar solution like water. ▪ Thus. it turns into the liquid disordered state (not as . If the membrane becomes too hot. ▪ Cell membranes are made up of sterols. the surface area to volume ratio gets smaller. This is done to minimize the surface area of contact between the nonpolar areas of the molecule and the polar liquid. the lipids solidify into a paracrystal At higher temperatures. 34 Why are cells so small? ◦ The answer lies in the surface area-to-volume ratio. not enough material will be able to cross the membrane fast enough to accommodate the increased cellular volume. For most cells. pointing down to one another. so they form a (liposome) vescile. the passage of all materials must occur through the plasma membrane. if a cell grows beyond a certain limit. ▪ Cells must constantly interact with their surrounding environment to survive. This means that the relative amount of surface area available to pass materials to a unit volume of the cell steadily decreases. Cellular membranes ◦ Introduction ▪ Fluid mosaic model of membranes because it is a patchwork of different types of molecules and these molecules move rapidly within the lipid bilayer ▪ Cell membranes are permeable for non-polar compounds. ▪ In a bilayer. The tails on the end of the bilayer are exposed to water. ▪ As a cell gets larger. whereas the hydrophobic tales on are on the inside. but not for polar compounds. polar head groups are on the outside. large molecules. ▪ Adhesion proteins attach cells to neighboring cells. It is a very broad category of proteins. ▪ Cell walls are not found in animal cells. Sterols increase ordering of unsaturated fatty acids and decrease ordering of saturated fatty acids ▪ If the membrane has more unsaturated fatty acids. or markers for cell-cell recognition. . ▪ Lipids in the plasma membrane are free to move around across. Mechanically-gated ion channels respond to environmental stimuli such as pressure. it solidifies into a paracrystal. polar molecules) move through the passive membrane. If you can fit you can go through Aquaporin increase rate of H2O passing. the transition temperature is lowered. ◦ Membrane proteins ▪ Channel proteins: provide passageway through membrane for hydrophilic substances. Can be done passively. a barrier to infection. protists. 35 stable). Cell Wall ◦ Cell Wall found in plants. ▪ Sterols broaden the transition range between paracrystal and liquid disordered state. a secondary structure develops beneath the primary one. ▪ Porins allow passage of certain ions and small polar molecules through the membrane. Sometimes. then allow the passage of certain molecules through. providing anchors for internal filaments and tubules (stability) ▪ Receptor proteins are the binding sites for hormones and other trigger molecules. ▪ Recognition proteins (glycoproteins) are peripheral proteins on the extracellular side of the plasmamembrane that helps other cells distinguish it from foreign cells. ◦ Glycocalyx: a carbohydrate coat that covers the outer face of cell wall of some bacteria and outer face of plasma membrane of some animal cells. polysaccharides in archaea. or actively by coupling movement with the hydrolysis of ATP. which will cause the channel to open. ▪ Carrier proteins bind to specific molecules. Consists of glycolipids (attached to plasma membranes) and glycoproteins (such as recognition proteins). ▪ Ion channels help move ions across the membrane. ▪ Transport proteins help move molecules (ions. peptidoglycans in bacteria. and bacteria. ◦ Provides support to the cell. Two different types: Voltage gated ion channels respond to differences in membrane potential Ligand gated ion channels require a chemical to bind to a receptor site. ▪ Made up of cellulose in plants. change shape. Tend to not be specific. vibration. etc. temperature. If the membrane becomes too cold. they are just large passages. The oligosaccharide chain attached to the protein serves as this recognition tag. fungi. chitin in fungi. May provide adhesive capabilities. Converts chemical energy from ATP into mechanical energy of movement. and polysaccharides secreted by cells. 36 Extracellular matrix ◦ Found in animals: areas between adjacent cells occupied by fibrous structural proteins. ◦ Cells adhere to the ECM in two ways: ▪ focal adhesions – connection of the ECM to actin filaments in the cell ▪ hemidesmosomes – connection of ECM to intermediate filaments Cytoskeleton ◦ Cytoskeleton is a network of specialized proteins that provides a framework for maintenance of cell shape. cells of the larynx. Spindle fibers for mitosis and meiosis are made up of microtubules. and will interfere with mitosis. ◦ Flagella and cilia are microtubule-containing extensions that project from some cells. and trachea would be greatly effected. Are in a 9x3 array. Thinnest of the three types. ▪ Motile cillia usually occur in large numbers on the cell surface. ▪ Common structures: collagen (most common). provide support and motility for cellular activities. and cell motility. ▪ Intermediate filaments: provide support for maintaining cell shape (keratin) Locomotion ◦ Microtubule organizing enters (MTOCs) Structures from which microtubules emerge. ◦ Protein filaments are the basic units for maintenance of cell's shape. Cell motility generally requires interaction of the cytoskeleton with motor proteins. sperm cells. Plants. ◦ Some types of cell motility involve the cytoskeleton. adhesion proteins. 9 pairs + 2 singlets in center ▪ Microtubule assembly of cilium or flagellum is anchored in the cell by a basal body. Colchinine inhibits microtubule activity. laminin ◦ Provides mechanical support and helps bind adjacent cells. ▪ Microtubules: made up of the protein tubulin. although they lack centrioles. If a person is born with a genetic defect that produces abnormal microtubules. ▪ Fagella are usually limited to just one or a few per cell. Involved in muscle contraction. ▪ Cytoplasmic streaming refers to the circular motion of cytosol and organelles around . Include centrioles and basal bodies (are at the base of each flagellum and cillium and organize their development). ▪ Both are in a 9+2 array. Involved in cell movement and movement of organelles. do have MTOCs. ◦ Intracellular circulation ▪ Brownian movement: particles spread out randomly throughout cytoplasm due to kinetic energy. integrin + fibronectin. and are longer than cillia. Dyenin is a protein associated with a flagellum. Three types: ▪ microfilaments: made up two intertwined strands of actin. Thickest of the three types. ▪ Desmosomes (adhesion junction): function like rivets. Endomembrane system ◦ The endomembrane system is composed of the different membranes that are suspended in the cytoplasm within a eukaryotic cells. RNA). Separates the contents of the nucleus from the cytoplasm. or organelles. the golgi apparatus. and the cell membrane. ◦ There are three main types of cell juntions in animal cells: ▪ Tight junctions: Plasma membranes of the neighboring cells are tightly pressed against each other. the endoplasmic retriculum. continuous passageway from the plasma membrane to the nuclear membrane. They form long strands called chromosomes. ▪ Regulate the passage of macromolecules (proteins. ▪ When a cell is not dividing. ◦ Extracellular circulation ▪ Molecules from the external environment can diffuse into cells. and other mateirals to all parts of the cell. Nucleus ◦ The nucleus contains the DNA. which consists of DNA tightly twisted around proteins. molecules travel through a circulatory system to move from one cell to another one that is far away. These connections unify most of the plant into one living continuum. bound together by specific proteins. lysosomes. ATP. ▪ Gap Junctions: provide direct connection between cytoplasm of one cell and cytoplasm of neighboring cell via channels called connexins. nutrients. the genetic material of the cell. but permit free passage of water. ▪ Endoplasmic reticulum provides a direct. fastening cells together into strong sheets. 37 larg fungal and plant cells through the mediation of actin filaments in the cytoskeleton. vesicles. ▪ In more complex animals. ◦ These membranes divide the cell into functional and structural compartments. Cell Junctions ◦ Plant cell walls are perforated with plasmodesmata: channels that connect plant cells. This movement aids in the delivery of organelles. and other small molecules. organelles of the endomembrane system include: the nuclear membrane. chromatin appears as a diffuse mass and you can't determine . ◦ In eukaryotes. ◦ Inside the nuclear envelope is the chromatin. ions. and genetic information. ◦ The nuclear envelope surrounds the nucleus with a double membrane with multiple pores. Cytosol = broth. Proteins made from these types of ribosomes are usually destined for insertion into membranes or for export from the cell. Composed of intermediate filaments and membrane associated proteins. Endoplasmic Reticulum ◦ The Endoplasmic reticulum (ER) is an extensive network of membrane tubules and sacs called cisternae. This is the dense fiber network of most cells. Cytoplasm = veggie-stew. ◦ There is much evidence for a nuclear matrix. Internal compartment of the ER surrounded by the membranes is called the ER lumen. ◦ Cytosol is the aqueous substance that everything is suspended in. As the cell prepares to divide. Cytosol + organelles + everything else that is suspended. ER runs adjacent to the nucleus. the chromosomes move farther away to the point where they can be distinguished from one another. Cytosol vs Cytoplasm ◦ Cytoplasm is the streaming movement within a cell. . ◦ The nuclear side of the envelope is lined by the nuclear lamina. ◦ Cells that have high rates of protein synthesis have large numbers of ribosomes. ▪ bound ribosomes are attached to the outside of the endoplasmic reticulum or the nuclear envelope. 38 one chromosome from another. Proteins made from these types of ribosomes function within the cytosol. proteins. ◦ Ribosomes build proteins in to cytoplasmic locations: ▪ free ribosomes are suspended in the cytosol. The nucleolus accomplishes the manufacture of ribosomes. Ribosomes ◦ Ribosomes are complexes made up of ribosomes RNA and protein. Provides mechanical support and regulates cellular events such as DNA replication and cell division. IT JUST DESCRIBES THE FLUID. a framework of protein fibers extending throughout the nuclear interior. Participates in chromatin organization. It includes everything suspended between the cell wall and the nucleus. ◦ The nucleolus is the central portion of the cell nucleus and is composed of chromosomal RNA. and DNA. They carry out protein synthesis. Many of these secretory proteins are glycoproteins. 39 ◦ Two distinct types of ER: ▪ The smooth ER outer surface lacks ribosomes. Golgi Apparatus ◦ Many transport vesicles travel to the Golgi apparatus after leaving the ER. as the receiving and the shipping departments of the Golgi apparatus. respectively. and some modifications of the vesicles. Another function of the rough ER is to build parts that add to the plasma membrane. The membrane of each cisterna in a stack separates its internal space from the cytosol. Functions of the smooth ER include: lipid and sterol synthesis. The rough ER is continuous with the outer nuclear membrane. and storage of calcium ions. and shipping. these act. detoxification of drugs and poisons. . ▪ Vesicles adds its comments to the Golgi apparatus on the cis side and the vesicles leave the Golgi apparatus on the trans side. The golgi apparatus is like a warehouse for receiving. sorting. ▪ The rough ER outer surface is studded with ribosomes. ◦ Consists of flattened membranous sacs—cisternae. The main function of the rough ER is to generate proteins and package them for secretion. ◦ The two sides of a Golgi stack are referred to as the cis and trans face. The vast majority of protein post-translational modifications happen here. 40 Lysosomes ◦ A lysosome is a membranous sac of hydrolitic enzymes that many eukaryotic cells use to digest marocmolecules and damaged organelles. not animal cells. ◦ Lysosomes are found in animal cells. ◦ Lysosomes internal evironment is acidic because its enzymes function best in those pH levels. and phosphatases are found in lysosomes. ◦ Glycosidases. ◦ Functions in phagocytosis. . ◦ Vacuoules are mostly found in plant cells. aryl sulfatases. thereby maintaining the appropriate internal osmolarity. NOT in most plant cells. ◦ Functions in autophagy. When a cell engulfs good. A damaged organelle becomes surrounded by a double membrane. Perform a variety of functions in different kinds of cells. catalyzing digestion. Vacuoules ◦ Vacuoules are large vesicles derived from the ER or Golgi apparatus. ◦ Many unicellular eukaryotes in living in fresh water have contractile vacuoules that pump out excess water out of the cell. and the lysosome fusees with the vesicle. ◦ Food vacuoules are formed by phagocytosis. the lysosome fuses with the food vacoule and then catalyzes digestion. which develops by the coalescence of smaller vacuoules. ◦ Specialized peroxisomes called glyoxysomes are found in fat-storing tissues of plant seeds. Contain enzymes that initiate the conversion of fatty acids to sugar. and it is the main repository of inorganic ions. ◦ In plant cells. . which seedlings use as source of energy. producing hydrogen peroxide as a by-product. peroxisomes modify by-products of photorespiration. This is discussed in the genetics unit (see mitochondrial inheritance) ◦ Structure and function of the mitochondria is discussed in the chapter on the citric acid cycle. ◦ Lecuoplasts can specialize to store starch/lipids/proteins or serve biosynthetic functions ◦ Chromoplasts store carotenoids Ribosomes ◦ Structure and function of chloroplasts are discussed in the genetics unit. Mitochondria ◦ Exceptions to the universality of the genetic code is seen with mitochondria. Peroxisomes ◦ The peroxisome is a specialized metabolic compartment bounded by a single membrane. They contain enzymes that remove hydrogen atoms from various substrates and transfer them to oxygen. Plastids ◦ Found in plant cells ◦ Chloroplast: structure of chloroplasts are discussed in the photosynthesis chapter. 41 ◦ Mature plant cells generally contain a large central vacuoule. Solution inside the central vacuoule is called cell sap. 42 . 43 . ▪ Endospore can live in harsh conditions. ▪ The original cell produces a copy of its chromosome and surrounds that copy with a tough. mulitlayered structure. . Outer membrane- peptidoglycan layer-plasma membrane. forming the endospore. with an outer membrane that contains lipopolysaccharides. ◦ Certain bacteria have developed resistant cells called endospores to withstand hard conditions. ◦ Cell wall of many prokaryotes is surrounded by a sticky layer of polysaccharide or protein. ▪ Gram negative bacteria have a thin peptidoglycan wall and are structurally more complex. ◦ Peptidoglycan is a polymer composed of modified sugars cross-linked by short polypeptides. it turns back into a normal cell. Contain teichoic acid chains. ◦ Cell walls are typically made up of peptidoglycan in eubacteria and polysaccharides in archaebacteria. ▪ Both structures help prokaryotes to adhere to their substrate or to other individuals. When conditions get better. ▪ Called a capsule if it is dense and well-defined or a slime layer if it is not well organized. ◦ Two main types: ▪ Gram positive bacteria have a thick peptidoglycan wall. 44 Cell wall ◦ Prokaryotic cell walls give structural integrity and shape and serve to anchor flagellae. Motility ◦ About half of all prokaryotes are capable of taxis. 45 ◦ Some prokaryotes stick to their substrate or to one another by hairlike appendages called fimbriae. ◦ 1 chromosome that is circular. ◦ Prokaryotic ribosomes are slightly smaller than eukaryotic ribosomes. ◦ A typical prokaryotic cell have much smaller rings of independently replicating DNA molecules called plasmids. but slightly different than mitosis. a process very similar to. Binary fission is a type of asexual reproduction. ▪ Fimbriae are usually shorter than more numerous than pili. Organization of DNA ◦ genome of prokaryote usually has considerably less DNA. ▪ Chemotaxis means changing movement in response to chemicals. a directed movement toward or away from a stimulus. most carrying only a few genes. ◦ restriction endonuclease is a bacterial protein that cleaves foreign DNA at specific sites Reproduction ◦ Reproduce by binary fission. a region of the cytoplasm that is not enclosed by a membrane. ◦ Chromosome is located in the nucleoid. whereas eukaryotes have linear chromosomes. ◦ They are small and have short generation times. ◦ Differences between binary fission and mitosis: ▪ Binary fission occurs among prokaryotes (cells that do not have a nucleus) whereas Mitosis occurs among eukaryotes (cells that do have a nucleus) ▪ binary fission does not include spindle formation and sister chromatids in its process making it faster means of cell division than mitosis . ◦ Chromosomes of prokaryotes are associated with many fewer proteins than are the chromosomes of eukaryotes. phages carry prokaryotic genes from one host cell to another. conjugation = how to introduce variation in prokaryotes ◦ In transformation. the genotype and possible phenotype of a prokaryotic cell are altered by the uptake of foreign DNA from its surroundings. When the phage replicate its . This results from accidents that occur during the phage replication cycle. 46 ▪ Binary fission does not have the 4 distinct cellular phases that are seen in mitosis Transformation. transduction. ◦ In transduction. When that virus injects the DNA into a new host. Ability to do this results from a piece of DNA on the plasmid called the F factor. Hfr cell.cell. DNA is transferred between two prokaryotic cells. 47 own DNA in a host cell and then packages new phages. ◦ In conjugation. the DNA cannot replicate but now is injected into the prokaryote. some phages may have accidentally uptook non-viral DNA or DNA that is partially viral or partially host. F+ cell). (Look at picture for more information) . (F. Appear in upper part of test tube but not very top. ◦ Facultative anaerobes use O2 if it is present but also can carry out fermentation or anaerobic respiration if it is an anaerobic environment. 48 Prokaryotes are diverse in metabolism ◦ Obligate aerobes must use oxygen for cellular respiration and cannot grow without it. Appear at very bottom of test tube. Appear in top of test tube. ◦ Obligate anaerobes cannot use O2. ◦ Microaerophiles need oxygen because they cannot ferment or respire anaerobically but are poisoned at very high O2 concentrations. Aerotolerant organisms do not require oxygen because they metabolize energy anaerobically. they are poisoned by it. . Appear mostly at top because aerobic respiration is better. Can be found spread evenly throughout the test tube. translation occurs in cytoplasm Cellular respiration ◦ Prokaryotes ▪ Occurs on plasma membrane ◦ Eukaryotes ▪ Occurs in mitochonrida Cell theory (5 parts) ◦ all living things are composed of cells ◦ the cell is the basic functional unit of life ◦ the chemical reactions of life take place inside the cell ◦ cells only arise from pre-existing cells ◦ cells carry genetic information in the form of DNA (passed from parent cell to daughter cell) . 49 DNA replication ◦ Prokaryotes ▪ Only one origin of replication per DNA molecule ▪ Occurs inside the cytoplasm ◦ Eukaryotes ▪ Multiple origin of replication sites per DNA molecule ▪ Occurs inside nucleus Transcription/Translation ◦ Prokaryotes ▪ Transcription and translation occur simultaneously ◦ Eukaryotes ▪ Transcription occurs in nucleus. ◦ Stage 1: Virus attaches to the host cell. ◦ Viral envelopes are membranes surrounding viruses that contain host cell phospholipids and glycoproteins. double stranded RNA. Lytic cycle ◦ A phage that replicates only by the lytic cycle is called a virulent phage. Could be rod-shaped. . ▪ The genome is usually organized as a single linear or circular molecule of nucleic acid. single stranded DNA. ◦ Stage 2: Virus injects DNA into host cell. or more complex in shape. 50 Viruses introduction ◦ Viruses are infectious particles consisting of little more than genes packed in a protein coat. ◦ The protein shell enclosing the viral genome is called a capsid. polyhedral. ◦ Viruses only replicate in host cells. This aids the virus in entering the host cell. ◦ Stage 3: Viral DNA directs production of viral proteins and copies of the viral genome by host and viral enzymes. ◦ Viruses that infect bacteria are called bacteriophages. These viruses usually bind to teichoic acid chains of gram-positive bacteria as means to cell attachment. or single stranded RNA. Host cell's DNA is hydrolyzed. ◦ Phages that can reproduce by lytic and lysogenic cycle are called temperate phages. ▪ Capsids are built from a large number of protein subunits called capsomeres. ◦ Viruses are nonliving because they cannot reproduce on their own. Structure of viruses ◦ Virus genomes can be double stranded DNA. The number of species a particular virus can infect is called the host range of the virus. The cell swells and bursts. ◦ Certain stress factors activates the prophage DNA to begin the lytic cycle. The host cell incorporates itself into the host DNA and lays dormant. releasing new virus particles. ◦ Step 5: Virus directs production of an enzyme that damages the cell wall. the phage DNA will begin creating itself and will follow the lytic cycle from here- on out. until it re-enters the lysogenic cycle. allowing to fluid and enter. Bacterium reproduces normally. Lysogenic cycle ◦ A prophage is a virus who has injected its DNA into the host cell and the DNA incorporated itself into the host chromosome. . ◦ Phage injects DNA into the host cell. 51 ◦ Step 4: New viruses are put together. copying the prophage DNA long with it. When this happens. Prions ◦ Prions are proteins that are unique in their ability to reproduce on their own and become infectious. 52 RNA viruses ◦ RNA viruses are called retroviruses. . ◦ These viruses are equipped with an enzyme called reverse transcriptase. They are misfolded versions of proteins in the brain that cause normal proteins to misfold too. which transcribes an RNA template into DNA. There will be a net movement of water out of the cell. ▪ Can be done with input of energy (coupled with ATP hydrolysis) – active diffusion. Molecules can only move in the direction of the concentration gradient. The cell may shrivel up and die. ▪ Can be done without the input of energy – passive diffusion. ◦ In a hypertonic environment. there is said to be an electrochemical gradient. ▪ If a concentration gradient (difference in concentration between two sides of a membrane) and a membrane potential exists between two sides of a membrane. Osmosis ◦ Osmosis is the spontaneous movement of water from areas of low osmolarity to high osmolarity. ▪ Diffusion can also occur if there is a difference in charge (electrical potential difference) between two different areas—this is called a membrane potential. ◦ In an isotonic environment. ◦ In a hypotonic environment. There will be no net movement of water across the plasma membrane. ◦ Facilitated diffusion is the process of moving polar. Cotransport ◦ A cotransport protein can couple the “downhill” diffusion of a solute to the “uphill” transport of a second substance against its own concentration gradient. the external osmolarity is lower than the internal osmolarity . Diffusion will occur down the electrochemical gradient. Depends on solute concentration and membrane permeability. 53 Facilitated diffusion ◦ Diffusion is the spontaneous movement of particles from an area of high concentration to low concentration. the external osmolarity is equal to the internal osmolarity of the cell. large. Volume of the cell is stable. Molecules can move against the concentration gradient. and ionic molecules through the plasma membrane via protein channels. ◦ Osmolarity is defined as the total amount of solutes in moles divided by liters of solution. the external osmolarity is greater than the internal osmolarity of the cell. ◦ Tonicity is the ability of a surrounding solution to cause a cell to gain or lose water. Water moves in the direction from higher water potential to lower water potential (picture on next page). Also called osmotic potential. ▪ The protoplast is the living part of the cell. the cell becomes turgid (normal state). There will be a net movement of water into the cell. This is expressed by the water potential equation: Ψ = Ψs + Ψp ▪ The solute potential (Ψs) of a solution is directly proportional to its molarity. ▪ When in a hypertonic solution. Water potential ◦ Water potential is a measurement that combines the effects of solute concentration and pressure. ▪ When in a hypotonic solution. Water moves from regions of higher water potential to regions of lower water potential. so that changes how the cell responds to changes in osmolarity. and the cell wall against the protoplast. the cell becomes plasmolyzed. ◦ Water potential is abbreviated as Ψ and is measured in units of megapascal (Mpa) ▪ Ψ = 0 Mpa for pure water at sea level and at room temperature ◦ Both pressure and solute concentration affect water potential. The shell may get too big and lyse. ▪ Pressure potential (Ψp) is the physical pressure on a solution ◦ Turgor pressure is the pressure exerted by the plasma membrane against the cell wall. ◦ Plant cells have a cell wall. . ▪ Potential refers to water's capacity to perform work. ▪ When in an isotonic solution. 54 of the cell. which also includes the plasma membrane ◦ Consider a U-shaped tube where the two arms are separated by a membrane permeable only to water. It determines the direction of movement of water. the cell becomes flaccid. 55 Types of transport molecules ◦ Uniport transports one solute at a time. . ◦ Co-transport involves moving two different molecules. ◦ Symport transports the solute and another molecule in the same direction at the same time ◦ Antiport transports the solute and another molecule in different directions at the same time. ◦ Three types: phagocytosis. and then suspended within small vesicles. ◦ Primarily used for absorption of extracellular fluids. ◦ Clathrin participates in endocytosis by forming a polyhedral lattice around coated pits. The endosome is called a phagosome. An endocytotic process occurs and the ligand is ingested. Exocytosis ◦ Exocytosis is the energy-consuming process by which a cell directs the contents of secretory vesicles out of the cell membrane and into the extracellular space. amoeba. “cell drinking. ◦ Happens sporadically. bacteria) from the extracellular fluid. 56 Endocytosis ◦ In endocytosis. etc. forming an invagination.” is a mode of endocytosis in which small particles are brought into the cell. macrophages. and receptor mediated endocytosis Receptor mediated endocytosis ◦ Receptor mediated endocytosis is an endocytotic mechanism in which specific molecules are ingested into the cell. ◦ Occurs in certain specialized cells such as neutrophils.e. pintocytosis. The specificity results from a receptor-ligand interaction. Phagocytosis ◦ Phagocytosis results in the ingestion of living matter (i. Receptors on the plasma membrane of the target tissue will specifically bind to ligands on the outside of the cell. the cell enguls some of its extracellular fluid including material dissolved or suspended in it. Pintocytosis ◦ Pintocytosis. A portion of the plasma membrane is invaginated and pinched off forming a membrane-bounded vesicle called an endosome. . ◦ During cellular stress the process of Autophagy is upscaled and increased. . 57 Autophagy ◦ Autophagy is a normal physiological process in the body that deals with destruction of cells in the body. Cellular stress is caused when there is deprivation of nutrients and/or growth factors. ◦ It maintains homeostasis or normal functioning by protein degradation and turnover of the destroyed cell organelles for new cell formation. ◦ Thus Autophagy may provide an alternate source of intracellular building blocks and substrates that may generate energy to enable continuous cell survival. Particular receptor in a cell “may listen” to one signal but not the other. ◦ Integration: when two signals have opposite effects on a metabolic characteristic. ◦ Adaptation/desensitization: Receptor activation triggers a feedback circuit that shuts off the receptor or moves it from the cell surface. both receptor pathways will converge on the “same” molecule and will cause a common response. ◦ Amplification: when enzymes activate systems.” A signal will not be heard in each and every cell type. Integrated means at some point. ◦ Modularity: proteins with multivalent affinities from diverse signaling complex form interchangeable parts. even closely related ones ▪ they change with cellular and environmental conditions Gated ion channels ◦ generally found in excitable cells ◦ Usually move ions by facilitated diffusion very quickly (these channels cannot be saturated) ◦ Gated ion channels are one of two signaling systems which actually move molecules through the membrane ◦ The membrane has a very asymmetric ion distribution (creates membrane potential) Sodium-potassium pump ◦ energy source: ATP hydrolysis ◦ 3 Na+ leaves. the regulatory outcomes results from the integrated input of both receptors. the number of affected molecules increases geometrically in an enzyme cascade. 58 5 common features of signal transducing systems ◦ Specificity: signal molecule fits binding site on its own complementary receptor. 2 K+ comes in (moves one positive charge to the outside) ◦ Generates a membrane potential (electrochemical gradient) . other signals do not fit. Signal transduction generalizations ◦ Signal transduction pathways have unique features: ▪ differ between cell types. the receptor may not be present in every cell so a cell may not be able to “listen to a certain signal. In addition. A single signaling molecule can activate a large number of target molecules. Phosphorylation provides reversible proteins of interaction. Hormones reach virtually all body cells. Once activated. ◦ Endocrine (hormonal) signaling: specialized endocrine cells secretes hormones into body fluids. Its cytoplasmic side binds an inactive G protein. the protein becomes active. This activates the G protein. ▪ Step 2: The activated G protein dissociates from the receptor. the protein is inactive. causing a GTP to displace the GDP. ▪ Step 3: The changes in the enzyme and G protein are only temporary because the G protein also functions as a GTPase enzyme—it then hydrolyzes GTP to GDP and Pi. and then binds to the enzyme. 59 Changes in membrane potential ◦ polarization: a difference in charge across a membrane. stimulating the target cell. ◦ Synaptic signaling: A nerve cell releases neurotransmitter molecules into a synapse. a protein that binds the energy-rich molecule GTP. altering the enzyme's conformation. ▪ Step 1: When the appropriate signaling molecule binds to the extracellular side of the receptor. diffuses along the membrane. (Binding is reversible). It now is available for reuse. When GDP is bound to the protein. results in a positive or negative Vm ◦ depolarization: a decrease in the absolute value of Vm (membrane potential moves closer to 0) ◦ hyperpolarization: an increase in absolute value of Vm (membrane potential moves farther from 0) Three types of cell signals ◦ Paracrine signals: A secreting cell acts on nearby target cells by secreting molecules of a local regulator. the receptor is activated and changes shape. G protein-coupled receptors ◦ A G protein-coupled receptor is a cell-surface trans membrane receptor that works with the help of a G protein. . When GTP is bound to the protein. the enzyme can trigger the next step leading to a cellular response. ▪ Step 3: Dimerization activates the tyrosine kinase region of each monomer. the receptors exist as individual units refer to as monomers. thus activating the protein. each tyrosine adds a phosphate from an ATP molecule to a tyrosine on the tail of the other monomer. forming a complex known as a dimer. ▪ Step 1: before the signaling molecule binds. Each protein binds to a specific phosphorylated tyrosine. leading to a cellular response. ▪ Step 2: the binding of a signaling molecule causes two receptor monomers to associate closely with each other. . ▪ Step 4: Now that the receptor is fully activated. Each activated protein triggers a transduction pathway. it is recognized by specific relay proteins inside the cell. 60 Receptor tyrosine kinases ◦ Receptor tyrosine kinases catalyzes the transfer of phosphate groups from ATP to the amino acid tyrosine on a substrate proteins. specific ions flow through the channel and rapidly change the electrochemical gradient of the cell. 61 Ligand-gated ion channel ◦ Ligand-gated ion channel is a type of membrane receptor containing a region that can act as “gate” when the receptor changes shape. the gate closes and ions no longer enter the cell. ▪ Step 2: when the ligand binds to the receptor and the gate opens. They have a different pathway than other ligands: ▪ Step 1: hormone diffuses into the cell through the plasma membrane ▪ Step 2: hormone binds to an intracellular receptor in the cytoplasm or nucleus. ▪ Step 3: when the ligand dissociates from the receptor. Steroid hormones ◦ Steroid hormones are nonpolar: they can diffuse through the plasma membrane without a problem. ▪ Step 1: Ligand-gated ion channel receptor remains closed until a ligand binds to the receptor. stimulating the transcription of the gene into mRNA . ▪ Step 3: the bound protein acts as a transcription factor. This binding activates the protein. water-soluble molecules that act in a signal transduction pathway. raising cytosolic Ca2+ levels. ◦ Binding of epinephrine to the plasma membrane elevates the cytosolic concentration of cyclic AMP (cAMP). ◦ Step 5: The calcium ions activate the next protein in one or more signaling pathways. leading to activation of phospholipase C ◦ Step 2: Phospholipase C cleaves a plasma membrane phospholipid called PIP2 into DAG (diacylglycerol) and IP3 (inositol triphoshoate). non-protein. . /DAG functions as a 2nd messenger in other pathways. ◦ The effect of increased cAMP levels is the activation of protein kinase A. causing it to open. IP3 and Ca2+ pathway ◦ Step 1: signaling molecule binds to a receptor. ◦ Step 4: Calcium flows out of the ER (down the concentration gradient). 62 cyclic AMP and second messengers ◦ Second messengers are small. ◦ Step 3: IP3 quickly diffuses through the cytosol and binds to an IP3-gated calcium-ion channel in the ER membrane. converts ATP to cAMP in response to an extracellular-signal. ◦ Phosphodiesterase is the enzyme that breaks down cAMP. ◦ A membrane-bound enzyme called adenylyl cyclase. 63 . it is the energy that can be transformed to power the work of the cell. some energy becomes unusable. ◦ Two basic forms of energy: ▪ kinetic energy: the energy of motion Heat. bu tit cannot be created or destroyed. that is. the greater its entropy. . ▪ System refers to the matter under study and refer to the rest of the universe (everything outside of the system) as the surroundings. or thermal energy. ◦ Scientists use a quantity called entropy as a measure of disorder. it exchanges both energy and matter with its surroundings. Chemical energy is the potential energy available for a chemical reaction. Energy can be transferred and transformed. is a type of kinetic energy associated with the random movement of atoms or molecules. a disordered form of energy. ◦ According to the second law of thermodynamics. energy conversions increase the entropy (disorder) of the universe. unavailable to do work. It is the most important type of energy for living organisms. can be harnessed to power photosynthesis ▪ potential energy: energy that matter possesses as a result of its location or structure Molecules possess potential energy because of the arrangement of electrons in the bonds between their atoms. ▪ An organism is an open system. or randomness. ◦ The first law of thermodynamics (law of energy conservation) states that energy in the universe is constant. a type of kinetic energy. Energy transformations ◦ Thermodynamics is the study of energy transformations that occur in a collection of matter. In most energy transformations. some energy is converted to heat. Chemical reactions either release or store energy ◦ An exergonic reaction is a chemical reaction that releases energy. ▪ If energy cannot be destroyed. 64 Forms of energy ◦ Energy is defined as the capacity to change or to perform work. ▪ The more randomly arranged a collection of matter is. then why can't organisms simply recycle their energy? It turns out that during every transformation. Light. powers nearly all forms of cellular work. Notice below when the bond to the third group breaks. The energy for chemical reactions is stored in ATP. a phosphate group leaves ATP. is an example of an endergonic process. . the process by which plant cells make sugar using the energy from ATP. ▪ The energy of catabolic reactions is used to drive anabolic reactions. These like charges are crowded together. becomes ADP (adenosine diphosphate). ◦ Endergonic reactions yield products that are rich in potential energy. making the bonds connecting the phosphate groups unstable. ▪ Anabolism refers to chemical reactions in which simpler substances are combined to form more complex molecules. cells release energy from fuel molecules. ATP can readily be broken down by hydrolysis. ▪ They start out with reactant molecules that contain relatively little potential energy. the hydrolysis of ATP is exergonic. The structure of ATP is shown below. it releases energy. ATP drives cellular work by coupling exergonic and endergonic reactions ◦ ATP. ◦ The amount of additional energy stored in the products equals the difference in potential energy between the reactants and the products. The total of an organism's chemical reactions is called metabolism. ▪ Catabolism refers to chemical reactions that result the breakdown of more complex organic molecules into simpler substances. Every working cell in an organism carries out thousands of endergonic and exergonic reactions. The triphosphate part is a chain of three phosphate groups. Each phosphate group is negatively charged. and energy is released. The adenosine part of ATP consists of adenine (a nitrogenous base that's found in DNA) and ribose. 65 ▪ An exergonic reaction begins with reactants whose covalent bonds contain more energy than those in the products. Photosynthesis. The reaction releases to the surroundings an amount of energy equal to the difference in potential energy between the reactants and the products ▪ Cellular respiration is exergonic. or adenosine triphosphate. the addition of water. Anabolic reactions usually require energy. Energy is absorbed from the surroundings as the reaction occurs. ▪ Thus. ▪ A metabolic pathway is a series of chemical reactions that either builds a complex molecules or breaks down a complex molecule into simpler compounds. so the products of an endergonic reaction contain more chemical energy than the reactants did. a 5-carbon sugar. ◦ There are three types of cellular work: ▪ Chemical work – phosphorylation of reactants provide energy to drive the endergonic of synthesis of products ▪ Mechanical work. so that the “downhill” part of a reaction can begin. transfer of a phosphate group to a membrane protein allowing through the passage of a large. polar solute). ▪ We can think of activation energy as the amount of energy needed for reactant molecules to move “uphill” to a higher-energy. transfer of phosphate group to special motor proteins in the muscle cell causes the proteins to change shape and pull on protein filaments. ▪ Most cellular work depends on ATP energizing molecules by phosphorylating them. ◦ Activation energy protects the highly ordered molecules of your cells from spontaneously breaking . there is an energy barrier that must be overcome before the reaction itself can proceed. 66 ◦ How does the cell couple the hydrolysis of ATP (exergonic) with an endergonic reaction? ▪ It usually does so by transferring a phosphate group from ATP to some other molecule by a process called phosphorylation. This energy barrier is known as activation energy (EA). The energy released from hydrolysis of ATP back into ADP and Pi drives endergonic reactions. How do enzymes work? ◦ In every chemical reaction. Energy from exergonic reactions drives the conversion of ADP + Pi (inorganic phosphate) into ATP. (i.e. Work can be sustained because ATP is a renewable energy source that cells regenerate.e. in turn causing the cell to contract) ▪ Transport work. (i. unstable transition state. Because an enzyme is a protein. etc. Without an enzyme. ▪ The specific reactant that an enzyme acts on is called the enzyme's substrate. dipole-dipole interactions. .). and that shape determines the enzyme's specificity. ▪ An enzyme is very selective in the reaction it catalyzes. an enzyme has a unique 3D shape. ◦ Step 1: The enzyme starts with an empty active site ◦ Step 2: A substrate (sucrose in this example) enters the active site. ▪ The active site changes shape slightly. ◦ Step 3: The strained bond of the substrate reacts. the activation energy might never be reached. molecules that function as biological catalysts. A substrate fits into the region of an enzyme called an active site. the bonds in a reactant are contorted into the higher-energy. This induced fit may contort substrate bonds or place chemical groups of the amino acids making up the active site in position to catalyze the reaction. attaching through intermolecular attractive forces (hydrogen bond. 67 down but life depends on countless chemical reactions that must occur quickly and precisely for a cell to survive. and the substrate is converted to the products. increasing the rate of a reaction without being consumed by the reaction. ▪ Enzymes are specific because their active site fit only specific substrate molecules. ▪ With the aid of an enzyme. embracing the substrate more snugly. unstable transition state from which the reaction can proceed. The catalytic cycle of an enzyme ◦ Follow the picture of an enzyme sucrase catalyzing the hydrolysis of sucrose into fructose and glucose. An enzyme speeds up a reaction by lowering the activation energy needed for a reaction to begin. How can the specific reactions that a cell requires get over that energy barrier? ▪ The answer to the dilemma lies in enzymes. e. and another round of cycle can begin. ◦ Cells use inhibitors as important regulators of cellular metabolism. If a cell is producing more of a product than it needs. specific non-polypeptide unit required for the biological function of some proteins. ◦ A noncompetitive inhibitor does not enter the active site. it is called a coenzyme. ▪ The cofactors of some enzymes are inorganic (i. an enzymes shape is central to its function. ▪ Competitive inhibition can be overcome by increasing the concentration of the substrate. Many of a cell's chemical reactions are arranged in metabolic pathways. ◦ Deviations from these conditions (i. and its binding changes the shape of the enzyme so that the active site no longer fits the substrate. heme group. prosthetic groups ◦ Many enzymes require nonprotein helpers called cofactors. iron).e. ▪ The optimal pH for most enzymes is near neutrality. Its active site is now available for another substrate molecule. change temperature. altering its specific shape and destroying its function. making it more likely that a substrate molecule rather than an inhibitor will be nearby when an active site becomes vacant. ◦ A prosthetic group is a tightly bound. instead. pH. and this 3D shape is affected by the environment.e. ▪ Most human enzymes work best close to body temperature at 35-40 degrees Celsius. there are optimal conditions under which it is most effective. a place called an allosteric site. vitamins) Enzyme inhibitors ◦ A chemical that interferes with an enzyme's activity is called an inhibitor. Cofactors vs. pepsin in your stomach works best at pH = 2). ◦ A competitive inhibitor reduces an enzyme's productivity by blocking substrate molecules from entering the active site. There are exceptions (i.e. ◦ For every enzyme. 68 ◦ Step 4: The enzyme releases the products and emerges unchanged from the reaction. ▪ If the cofactor is an organic molecule. in the range of 6-8. . salinity) can cause the enzyme to denature. it binds to the enzyme somewhere else. which loosely bind to the active site and function in catalysis. Optimal conditions for enzymes ◦ As with all protein's. (i. Freed up electrons are picked up by electron transport proteins. ▪ The energy of the electrons is used to generate ATP.e. Therefore. Freed up electrons are picked up by electron transport proteins. FAD. 2 molecules of ATP are produced by a process called substrate-level phosphorylation. This is called feedback inhibition. . 1 molecule of ATP is produced by substrate-level phosphorylation. ◦ Steps: ▪ (1) Glycolysis takes place in the cytoplasm glucose is oxidized into 2 molecules of pyruvate. Freed up electrons are picked up by electron transport proteins. also known as chemiosmosis. Overview of cellular respiration ◦ Cells need to generate energy to fuel anabolic pathways and other cellular processes. In this process. forming ATP. The active transport of H+ creates an electrochemical gradient between the intermembrane space and the mitochondrial matrix. ◦ The movement of ions across a selectively permeable membrane down their electrochemical gradient is known as chemiosmosis. electrons are stripped away from glucose in chemical reactions. ▪ (3) Citric acid cycle actetyl-CoA is fully oxidized. The electrochemical gradient becomes large enough to the point where the hydrogen ions will begin moving down their electrochemical gradient (from the intermembrane space back into the mitohcondrial matrix) through FoF1 ATPase (the enzyme that catalyzes the reaction of ADP + Pi → ATP). ◦ Movement of H+ ions through FoF1 ATPase provides a proton-motive force that drives the synthesis of ATP. Oxidation refers to the loss of electrons. NAD) and then are transported to the mitochondria and are given to the electron transport chain. ◦ An electrochemical gradient refers to an electrical potential and a difference in concentration across a membrane. ▪ Glucose is broken down by being oxidized. ▪ The freed up electrons are picked up by electron transport proteins (i. ▪ (2) Pyruvate decarboxylation takes place in the mytochondrial matrix The molecules of pyruvate are oxidized into acetyl-CoA so they can be shunted into the citric acid cycle. an enzyme transfers a phosphate group fro ma substrate molecule directly to ADP. Energy from the electrons are used to pump hydrogen ions (H+) from the mitochondrial matrix out to the intermembrane space. ▪ (4) Oxidative phosphorylation Electron transport proteins that previously picked up electrons in steps 1-3 drop off electrons at the electron transport chain (ETC). The main way cells achieve this is by breaking down glucose into energy. 69 the product may act as an inhibitor of one of the enzymes in an earlier pathway. Oxygen accepts the low energy electrons to complete the process. glycogen) ▪ when there is plenty of excess energy ◦ (2) glycolysis ▪ generates energy via oxidation of glucose ▪ short-term energy needs ◦ (3) pentose phosphate pathway ▪ generates NDAPH via oxidation of glucose ▪ for detoxification and the bio synthesis of lipids and nucleotides ◦ (4) synthesis of structural polysaccharides Glycolysis: overview in the evolution of life ◦ glycolysis probably was one of the earliest energy-yielding pathways ◦ it was developed before photosynthesis. fatty acid oxidation. when the atmosphere was still anaerobic. pentose phosphate pathway. gluconeogenesis ▪ rough ER: protein synthesis ▪ smooth ER: lipid and steroid biosynthesis central importance of glucose ◦ glucose is an excellent fuel ▪ yields good amount of energy upon oxidation (energy then is used to perform cellular processes and synthesize biomolecules) ▪ can be sufficiently stored in polymeric form (starch.Metabolic pathways in eukaryotic cells occur in specific compartments ◦ reason behind this is that different metabolites can operate in different locations and in different pathways ◦ in eukaryotic cells (memorize this): ▪ mitochondrion: citric acid cycle. glycogen) ▪ many organisms and tissues can meet their energy needs on glucose only ◦ glucose is a versatile biochemical precursor Four major pathways of glucose utilization ◦ (1) storage ▪ can be stored in the polymeric form (starch. electron transport oxidative phosphorylation. 70 . ◦ It is the anaerobic conversion of glucose into pyruvate by a sequence of enzyme-catalyzed . amino acid breakdown ▪ cytosol: glycolysis. fatty acid biosynthesis. 6-bisP is highly unfavorable under standard conditions.6-biphosphate is committed to become pyruvate and yield energy ◦ this process uses the energy of ATP ◦ highly thermodynamically favorable/irreversible ◦ phosphofructokinase-1 is highly regulated because this is a committed step STEP 4: Aldol Cleavage of F-1.6-bP ◦ Fructose 1.6-biphosphate → dihydorxyacetone phosphate (DHAP)+ glyceraldehyde 3- phosphate (GAP) ◦ catalyzed by aldolase ◦ Rationale: ▪ cleavage of a six-carbon sugar into two three-carbon sugars ▪ high-energy phosphate sugars are three-carbon sugars ◦ cleave of Frc 1. and glucokinase in prokaryotes ◦ hexokinase = induced fit (binding of glucose and Mg*ATP induces a large conformational change which brings the active site residues together) ◦ Rationale: ▪ traps glucose inside the cell (adding phosphate gives molecule negative charge) ▪ lowers intracellular glucose concentration to allow further uptake of glucose ◦ ATP-bound Mg2+ facilitates this process by shielding the negative charges on ATP ◦ highly thermodynamically favorable/irreversible (regulated by substrate inhibition) STEP 2: phosphohexose isomerization ◦ Glucose-6-phosphate → Fructose-6-phosphate ◦ catalyzed by phosphohexose isomerase ◦ Rationale: ▪ C-1 of fructose is easier to phosphorylate by PFK-1 ▪ Allows for symmetrical cleavage by aldolase ◦ Converts the aldose glucose into the ketose fructose ◦ Slightly thermodynamically unfavorable/reversible ▪ product concentration kept low to drive forward STEP 3: 2nd priming phosphorylation ◦ Fructose 6-phosphate + ATP→ Fructose 1.6-biphosphate ◦ catalyzed by phosphofructokinase-1 (PFK-1) ◦ Rationale: ▪ further activation of glucose ▪ allows for 1 phosphate/3-carbon sugar after step 4 ◦ First committed step of glycolysis ▪ fructose 1. 71 reactions ▪ pyruvate can be further aerobically oxidized ▪ pyruvate can be used as a precursor in biosynthesis STEP 1: Phosphorylation of Glucose ◦ Glucose + ATP → Glucose-6-phosphate + ADP ▪ nucleophilic oxygen at C-6 of glucose attacks the last (gamma) phosphate of ATP ▪ uses up the energy of ATP ◦ catalyzed by hexokinase in eukaryotes. but only slightly under physiological conditions ▪ GAP (glyceraldehyde 3-phosphate) concentration is kept low to pull reaction forward . 3-bisphosphoglycerate is a high energy compound. so DHAP must be converted to GAP ◦ thermodynaically unfavorable/reversible ▪ GAP concentration kept low to pull reaction forward ◦ ****NOTE steps 6-10 happen twice since 2 GAP molecules are generated********* STEP 6: Oxidation of GAP ◦ glyceraldehyde 3-phosphate + Pi + NAD+ → 1.3-bisphosphoglycerate + ADP → ATP + 3-phosphoglycerate ◦ catalyzed by phosphoglycerate kinase ◦ Rationale: substrate-level phosphorylation to make ATP ◦ catalyzed by phosphoglycerate kinase (PGK) ▪ kinases transfer phosphate groups from ATP to various substrates) ◦ 1. 72 STEP 5: triose phosphate interconversion ◦ dihydroxyacetone phosphate → glyceraldehyde 3-phosphate ◦ catalyzed by: triose phosphate isomerase ◦ rationale: ▪ allows glycolysis to proceed by one pathway ◦ GAP is the substrate for the next enzyme.3-bisphosphoglycerate + NADH + H+ ◦ catalyzed by: glyceraldehyde 3-phosphate dehydrogenase (GAPDH) ◦ rationale: ▪ generation of a high-energy phosphate compound ▪ incorporates Pi which allows for net production of ATP via glycolysis ◦ first energy-yielding step in glycolysis (forms NADH) ◦ thermodynamically unfavorable/reversible ▪ coupled to next reaction to pull forward STEP 7: 1st production of ATP ◦ 1. It can donate the phosphate group to ADP to make ATP ◦ Highly thermodnamically favorable/reversible ▪ Is reversible because of coupling to GAPDH reaction STEP 8: Migration of the phosphate ◦ 3-phosphoglycerate → 2-phosphoglycerate ◦ catalyzed by phosphoglycerate mutase (mutases catalyze migration of functional groups) ◦ rationale: be able to form high-energy phosphate compound ◦ thermodynamically unfavorable/reversible ▪ reactant concentration kept high by PGK to push forward STEP 9: dehydration of 2-PG to PEP ◦ 2-phosphoglycerate → phosphoenolpyruvate + H2O ◦ catalyzed by enolase ◦ rationale: generate a high-energy phosphate compound ◦ 2-phosphoaglycerate is not a good enough phosphate donor → this is why step 8 happens ◦ slightly thermodynamically unfavorable/reversible ▪ product concentration kept low to pull forward STEP 10: phosphotransfer from PEP ◦ phosphoenolpyruvate + ADP→ pyruvate + ATP ◦ catalyzed by pyruvate kinase (requires divalent metals for activity) ◦ second substrate level phosphorylation: generates another ATP molecule . to acetaldehyde and reducing it to ethanol. By regenerating NAD+. ▪ Pyruvate → acetyldehyde + CO2 catalyzed by pyruvate decarboxylase ▪ Acetaldehyde + NADH + H+ → ethanol + NAD+ catalyzed by alcohol dehydrodgenase ▪ two-step reduction of pyruvate to ethanol. By regenerating NAD+. ▪ lactate builds up in muscle during strenuous exercise → the acidification of muscle prevents its continuous strenuous work ▪ the lactate can be transported to the liver and converted back to glucose (cori cycle) ◦ 3) ethanol fermentation (no oxygen is present) → Done in yeast only ▪ rationale: NAD+ is regenerated by transferring e. 73 ◦ rationale: ▪ substrate-level phosphorylation to make ATP ▪ produces 2 ATP ◦ Loss of phosphate from PEP yields an enol that tautomerizes into ketone ◦ Tautomerization: ▪ effectively lowers the concentration of the reaction product ▪ drives the reaction toward ATP formation ◦ highly thermodynamically favorable/irreversible Balanced equation of glycolysis ◦ C6H12O6 + 2 ADP + 2 Pi + 2NAD+ → 2 pyruvate + 2 NADH + 2 H+ + 2 ATP + 2 H2O Pyruvate has 3 fates: ◦ 1) TCA cycle (oxygen is present) ◦ 2) lactic acid fermentation (no oxygen is present) → occurs in humans (muscles) and other organisms ▪ pyruvate + NADH + H+ → l-lactate + NAD+ ▪ rationale: NAD+ is regenerated by transferring e. irreversible ▪ Note that acetaldehyde is the final electron acceptor ▪ humans do not have pyruvate dehydrogenase for ethanol metabolism . it can be re-used in glycolysis.to pyruvate and reducing it to lactate. it can be re-used in glycolysis. rising in bread . 74 ▪ CO2 is responsible for carbonation in beer. ◦ Pyruvate + CoA-SH + NAD+ ----> Acetyl-CoA + NADH + CO2 ▪ enzyme: pyruvate dehydrogenase complex (PDC) (E1 + E2 + E3) PDC is a large multi-enzyme complex short distance between catalytic sites all channeling of substrates from one catalytic site of another. This minimizes side reactions. fulfill a function. and dissociate ▪ the function of CoA is to accept and carry acetyl groups Step 1: Condensation ◦ Acetyl-CoA + Oxaloacetate + H2O ----> CoA-SH + Citrate ◦ enzyme: citrate synthase (induced fit = wont be active until all substrates bind to it) ◦ rate-limiting step of citric acid cycle ◦ activity largely depends on concentration of oxaloacetate ◦ highly thermodynamically favorable/irreversible ▪ regulated by substrate availability and product inhibition . (Pyruvate decarboxylation) conversion of pyruvate to acetyl-CoA ◦ net reaction: oxidative decarboxylation of pyruvate ▪ Rationale: acetyl-CoA can enter the citric acid cycle and yield energy. lipoyllysine and FAD are prosthetic groups ◦ structure of Coenzyme A ▪ recall that coenzymes or co-substrates are not a permanent part of the enzyme's structure. they associate. ▪ TPP. Acetyl-CoA can also be used to synthesize storage lipids. 75 In eukaryotes. The goal of the citric acid cycle is to fully oxidize the pyruvate molecule so the energy from the freed up electrons can be used to make ATP. ◦ oxidative phosphorylation occurs in the inner membrane ◦ Memorize the parts of the mitochondria in the picture below. citric acid cycle occurs in mitochondria ◦ glycolysis occurs in cytoplasm ◦ citric acid cycle occurs in the mitochondrial matrix. which can be converted to ATP ◦ slightly thermodynamically favorable/reversible ▪ product concentration kept low to pull forward Step 6: the third oxidation ◦ succinate + FAD -----> fumarate + FADH2 ◦ enzyme: succinate dehydrogenase ◦ bound to mitochondrial inner membrane ◦ part of complex II in the electron-transport chain ◦ near equilibrium/reversible . a tertiary alcohol. isocitrate is a secondary alcohol and is a good substrate for oxidation. ◦ Addition of H2O to cis-aconitate is stereospecific ◦ thermodynamically unfavorable/reversible ▪ product concentration kept low to pull forward step 3: decarboylation #2 and formation of NADH ◦ Isocitrate + NADP+ ----> alpha-ketoglutarate + NADPH + H+ + CO2 ◦ NADPH + NAD+ ---> NADH + NADP+ ◦ enzyme: isocitrate dehydrogenase ◦ oxidative decarboxylation: lose a carbon as co2 and generate NADH ◦ oxidation of the alcohol to a ketone: transfers a hydride to NAD ◦ cytosolic isozyme uses NADP+ as a cofactor ◦ highly thermodynamically favorable/irreversible ▪ regulated by product inhibition and ATP step 4: decarboxylation #3 and formation of NADH ◦ alpha-ketoglutarate + CoA-SH + NAD+ → Succinyl-CoA + NADH + H+ + CO2 ◦ enzyme: alpha-ketuoglutarate dehydrogenase ◦ last oxidative decarboxylation: ▪ net full oxidation of all carbons of glucose after two turns of the cycle carbons not directly from glucose because carbons lost came from oxaloacetate ▪ succinyl-CoA is another high-energy thioester bond ▪ highly thermodynamically favorable/irreversible regulated by product inhibition Step 5: formation of GTP ◦ succinyl-CoA + GDP + Pi ---> GTP + CoA-SH + Succinate ◦ enzume: succinyl-CoA synthetase ◦ synthases catalyze condensation reactions where no nucleotides are involved ◦ synthetases: condensation reactions that use nucleotides ◦ substrate level phosphorylation ◦ energy of thioester allows for incorporation of inorganic phosphate ◦ Produces GTP. However. is a poor substrate for oxidation. 76 Step 2: transformation of 6 carbon unit to isocitrate ◦ citrate ----> cis-Aconitate + H2O ▪ enzyme = aconitase ◦ cis-aconiate +H2O ----> Isocitrate ▪ enzyme: aconitase ◦ citrate. 77 ▪ product concentration kept low to pull forward step 7: hydration ◦ Fumarate + OH.----> carbanion transition state ◦ carbanion transition state + H+ ---> L-malate ◦ enzyme: fumarase ◦ stereospecific: ▪ addition of water is always trans and forms L-malate ▪ OH.adds to fumarate. then H+ adds to the carbanion ◦ slightly thermodynamically favorable/reversible ▪ product concentration kept low to pull reaction forward last step ◦ L-malate + NAD+ ---> NADH + H+ + Oxaloacetate ◦ enzyme: malate dehydrogenase ◦ final step of cycle ◦ regenerates oxaloacetate for citrate synthase ◦ highly thermodynamically unfavorable/reversible ▪ oxaloacetate concentration kept VERY low by cytrase synthase pulls the reaction forward CAC intermediates are amphibolic (Anaplerotic reactions) ◦ intermediates in citric acid cycle can be used in other biosynthetic pathways (removed form cycle) ◦ must replenish intermediates in order for the cycle and central metabolic pathway to continue ◦ 4-carbon intermediates are formed by carboxylation of 3-carbon precursors ... They use reducing equivalents of NADPH and energy (ATP). 6 NADPH and make 1 GAP Calvin cycle step 1: CO2-fixation ◦ 3 ribulose 1. 14C-labeled amino acids and sugars found explanation: green algae are able to convert CO2 into small organic compounds (CO2 assimilation) ▪ Observation 2: within 5 sec of incubation of 14CO2. and proteins and other organic molecules.5 bisphosphate (most do this) ▪ stored as starch in chloroplast for later use ▪ translocated to cytosol and converted to sucrose (transported to non-photosynthesizing parts) Calvin cycle step 3: regeneration ◦ 5 Glyceraldehyde-3-phosphate + 3 ATP ----> 3 Ribulose 1.snabonline.5 BisP to generated 3 molecules of 3-phosphoglycerate calvin cycle step 2: reduction ◦ 6 3-phosphoglycerate + 6 ATP + 6 NADPH + 6 H+ ----> 6 Glyceraldehyde-3-phosphate + 6 ADP + 6 NADP+ +6 Pi ◦ mechanism: reversal of glycolysis with the exception that NADPH is used instead of NADH ▪ Unlike GAPDH from cytoplasmic gluconeogenesis. stromal enzyme uses NADPH as co-factor ◦ fates of GAP: ▪ Used to regenerate ribulose 1. labeled 3-phosphoglycerate (3PG) was detected explanation: 3PG is a stable intermediate and is formed by carboxylation of carbon intermediate ◦ Click the link for a great animation about the experiments: http://www. 78 Calvin's experiments ◦ Calvin: incubated green algae with 14CO2 isotope and traced the metabolic fate of 14C isotope ▪ Observation 1: within less than a minute. 9 ATP.com/Content/TopicResources/Topic5/Activities/Interactives/5_6/5-- 6. ◦ Autotrophic organisms use CO2 as sole source for biosynthesis of starch. Called reductive pentose phosphate pathway (from hexose to pentose) A stoichiometry problem: ◦ 3 CO2 + 9 ATP + 6 NADPH + 6 H+ ---> 1 GAP + 9 ADP + 8 Pi + 6 NADP+ (calvin cycle) ◦ But you are short 1 Pi from balancing! ◦ The 9th Pi is added from the cytosol .swf Carbon assimilation pathway: the calvin cycle (dark reaction) ◦ Plants reduce CO2 into sugars through the calvin cycle.5B-P carboxylase) (most abundant protein in biosphere) ◦ carboxylation of ribulose 1. which is generated during photosynthesis to reduce CO2 to carbon intermediates!!!! ◦ Calvin cycle doesn't happen in the dark because reducing equivalents and ATP are not provided in the absence of photosynthesis ◦ 3 turns of calvin cycle consume: 3 CO2. cellulose.5-bisphosphate + 3 ADP ◦ very similar to the non-oxidative part of the pentose phosphate pathway except that it proceeds in the opposite direction. lipids.5 bisphosphate + 3 CO2 ----> 6 3-phosphoglycerate ◦ enzyme: rubisco (ribulose 1. 79 Pi/Triose antiporter ◦ DHAP (produced from calvin cycle) leaves stroma into cytosol through the Pi-triose antiporter. The stripped Pi then moves back into the stroma via the same transporter and this balances out the calvin cycle. ◦ Antiport is also used to transfer NADPH and ATP produced by photosystems into the cytosol . DHAP gets dephosphroylated when it eventually turns into sucrose. lipids.NADH:Ubiquinone Oxidoreductase ◦ Structural features: ▪ transfers electrons from NADH → ubiquinone ▪ Embedded in membrane ▪ one domain extends into matrix (docking station for NADH) ◦ Mechanistic features: ▪ couples 2 reactions: electron transfer and proton translocation across inner mitohondrial membrane ▪ (1) Transfers 2 electrons from NADH to ubiquinone ▪ (2) Transfers 4 protons through inner mitochondrial membrane per 2 electrons ▪ Exergonic (1) drives endergonic (2) . electrons are donated by NADH and FADH2 ▪ takes place in mitochondria for eukaryotes Brief review of universal electron carriers ◦ oxidative phosphorylation is based on electron carriers ◦ dehydrogenases collect electrons from catabolic pathways and transfer them to: ▪ nicotamide nucleotides: NAD+ and NADP+ ▪ Flavin nucleotides: FAD and FMN Universal electron carriers 1: Ubiquinone ◦ Ubiquinone (coenzyme Q) ▪ remains in lipid bilayer ▪ very mobile ▪ shuttles electrons between various carriers ▪ Accepts 1 or 2 electrons Universal electron carriers 2: Cytochromes ◦ Electron carrier proteins ◦ most are integral proteins of inner mitochondrial membrane ◦ Accepts 1 electron only complex 1. 80 Overview ◦ oxidative phosphorylation: ▪ catabolism of carbohydrates. amino acids converge on cellular respiration ▪ oxygen is reduced to H2O. bond) passes electrons from acyl- CoA to electron transfer flavoprotein (ETF) ◦ ETF will eventually complete electron transfer to Q: ▪ FAD → electron transfer flavoprotein → ETF:ubiquinone oxidoreductase → ubiquinone (Q) Other bypasses of complex 1 ◦ glycerol-3-phosphate from fat degradation or reduction of dihydroxyacetone phosphate (glycolysis) ◦ oxidized by glycerol 3-phosphate dehydrogenase (outer surface of membrane) dehydrogenase channels electrons to ubiquinone (Q) via FAD . 81 complex 2 – succinate dehydrogenate ◦ Transfers electrons from succinate → FADH2 → ubiquinone ◦ Succinate dehydrogenase is the only membrane-bound enzyme in the Krebs Cycle ◦ Electrons from succinate do not have enough energy to allow proton pumping → cannot be funneled through complex 1 Other bypasses of complex 1 ◦ first step of fatty acid breakdown (formation of -C=C. FADH2. Cu+) ▪ Pumps 4H+ through the membrane for every pair of electrons passed to cytochrome c (2 needed) ▪ Cytochrome c passes electrons to complex IV ◦ Net equation: QH2 + 2 cyt c1 (oxidized) + 2H+ (inside) ---> Q + 2 cyt c1 (reduced) + 4H + (outside) ▪ 2 H+ comes from the conversion of QH2 back to Q . QH2) to 1-electron carrier (cytochromes. 82 complex 3 – cytochrome bc1 ◦ structure: ▪ also known as ubiquinone:cytochrome c oxidoreductase ▪ transfers electrons from ubiquinone → cytochrome c ▪ transports 2 protons through inner membrane ◦ mechanism: ▪ Function: switch from 2-electron carrier (NADH. Energy is stored as a proton-motive force ◦ 2 components: ▪ 1) chemical potential due to [H+] gradient across membrane ▪ 2) electrical potential due to separation of charge (H+) ◦ protons spontaneously flow down electrochemical gradient driving ATP synthesis ATP synthesis ◦ proton motive force provides energy to drive ATP synthesis (ADP + Pi → ATP) ◦ Requires ~50 kJ/mol under cellular conditions ◦ ATP synthesis results from coupling proton flux to phosphorylation . 83 cytochrome IV – cytochrome oxidase ◦ structure ▪ transfers electrons from cytochrome c → O2 ▪ reduces 1 O2 to 2 H2O ◦ mechanism ▪ for every 4 electrons passing through complex IV: ▪ One O2 is converted to 2 H2O using 4 H+ from matrix ▪ involves single-electron transfers (cytochrome c) ▪ all intermediates remain bound to complex ▪ all intermediates are highly reactive radicals and can cause damage if released ETC – balance sheet ◦ For each electron pair: ▪ 4 H+ are pumped out by complex I ▪ 4 H+ are pumped out by complex III ▪ 2 H+ are pumped out by complex IV ▪ 10 H+ total using NADH ◦ pumping out H+ generates electrochemical gradient. (step 1) . ATP) ◦ gamma subunit binds only 1 Beta subunit ◦ rotation of gamma subunit (driven by proton motive force) forces beta subunits to cycle through conformations rotational catalysis model for ATP synthesis ◦ movement of protons down electrochemical gradient through c ring induces rotation of ring and gamma stalk in plane of membrane (green circle in middle) ◦ rotation of gamma stalk causes beta subunits to associate with gamma in a cyclic fashion ◦ FOCUS ON THE PURPLE UNIT ONLY: ▪ 1) Subunit begins in the Loose conformation. This is the conformation that will bind the ADP and Pi. ADP/Pi. 84 The ATP synthase paradox ◦ Proton motive force is required to released tightly bound ATP rather than to synthesize it!!!!! ATP synthase consists of two functional domains ◦ Fo: contains a passive proton pore ◦ F1 contains nine subunits (5 types) ▪ 'head' consists of altering alpha and beta subunits ▪ beta subunits contain catalytic site ◦ stator connects Fo and F1 F1 structure and dynamics ◦ Each beta subunit adopts a different conformation ◦ each conformation binds different ligands (none. blue subunit. (step 2 and Step 3) ▪ 3) Gamma stalk rotates and changes the conformation of the subunit from the Tight conformation to the Open conformation. In one 360 degree rotation. eukaryotes ◦ In eukaryotes. ◦ direction of rotation determines outcome: ▪ direction 1: PMF-driven ATP synthesis ▪ direction 2: ATP-driven H+ pump ATP hydrolysis ◦ ATP breakdown to ADP is a hydrolysis reaction! Stoichiometry of ATP synthesis – historical view ◦ number of electrons moved and number of ATP molecules formed are whole numbers (integers) ◦ values of these numbers are derived from P/O ratios ◦ Phosphates transferred (P) : oxygen oxidized (O) ◦ Ratios were NADH = 3. Why? ▪ Prokaryotes have no mitohcondria so they do not need to transfer pyruvate into the mitochondrial matrix. (step 4) ◦ Note that there are three different subunits per ATP synthase (purple subunit. ADP and Pi bind to form ATP. They use cell membrane for oxidative phosphorylation. succinate = 2 (Numbers you need to know for DAT) Prokatyotes vs. However. which is done via active transport. This means that in one 360 degree rotation. the total energy from glucose is about 38 ATP. the total energy from glucose is about 36 ATP. thus costing ATP. 3 ATP is formed. and yellow subunit). in eukaryotes. . This causes ATP to be released from ATP synthase. In the tight conformation. each different color subunit goes through all different conformations (as described above). 85 ▪ 2) Gamma stalk rotates and changes the conformation of the subunit from the Loose conformation to the Tight conformation. ◦ Note that prokaryotes do not do TCA cycle because they don't have mitochondria. planar rings resembling heme w/ phytol side-chain ◦ Mg 2+ (not iron) is at center of tetrapyrrol ring ◦ strongly absorb light due to conjugated double bonds in ring ◦ spectra of chlorophylls a and b are not identical . membrane-surrounded vesicles or sacs. ◦ The calvin cycle occurs in the stroma whereas photophosphorylation occurs on the thylakoid membranes. and an inner membrane that encloses the internal compartment. Chromophores: Light-absorbing molecules ◦ light absorption: absorbing a photon raises chromophore (electrons) to a higher energy level ◦ Photon energy must match exactly energy gap between ground state and excited state ◦ excited state is unstable and short-lived ◦ Excited chromophore eventually returns to ground state ◦ energy is released as light (emission). heat. the aqueous phase enclosed by the inner membrane. 86 Overview of the two stages of photosynthesis ◦ (1) light dependent photophosphorylation (topic for this chapter) ▪ energy from light is absorbed by chlorophyll and other pigments ▪ absorbed energy is used: to generate ATP and to transfer electrons from water to NADP+ (oxygen is produced) ◦ (2) carbon assimilation/carbon fixation (the calvin cycle—previously discussed) ▪ uses products of light reactions ▪ NADPH and ATP reduce CO2 ▪ new organic carbon is converted into triose phosphates. ◦ This compartment contains many flattened. and starch Structure of plant chloroplasts ◦ chloroplasts are surrounded by two membranes. sucrose. the thylakoids. contains most of the enzymes for the carbon-assimilation reactions. ▪ Embedded in the thylakoid membrane are the photosynthetic pigments and enzyme complexes that carry out the light reactions and ATP synthesis. or (biological) work ◦ This is the “idea” behind photosynthesis Primary Photosynthetic Pigments 1: chlorophylls ◦ Green pigments in thylakoid membranes ◦ Contain polycylic. ◦ The stroma. usually arranged in stacks called grana. an outer membrane that is permeable to small molecules and ions. binding proteins and membrane components Secondary Pigments ◦ Accessory (secondary) pigments: carotenoids present in thylakoid membranes ◦ secondary pigments absorb light outside the range of chlorophylls Primary and secondary photopigments ◦ spectra are complimentary: each 'antenna' absorbs in a specific wavelength range → pigments cover whole visible spectrum Chlorophylls channel energy from sunlight to reaction centers ◦ photosystems: pigments/proteins arranged into functional units ◦ all pigments absorb light as photons ◦ only a few chlorophylls convert light energy into chemical energy ◦ these are part of photochemical reaction centers ◦ rest of pigments transmits light energy to reaction centers → light-harvesting (antenna) molecules . 87 ◦ chlorophylls are always associated with binding proteins ◦ chlorophyll + binding protein = light harvesting complexes (LHCs) ◦ proteins orient chlorophyll in 3D space ◦ Energy transfer requires contact between pigments. P680 and P700 ▪ are complementary ▪ resemble the two bacterial systems ◦ each chloroplast has hundreds of each system in thylakoid membranes ◦ Photosystem 2 (PSII): ▪ contains equal amounts of chlorophylls a and b ▪ P680 reaction center ▪ contributes to proton gradient across thylakoid membrane ◦ Photosystem 1 (PSI): ▪ P700 reaciton center ▪ high amounts of chlorophylls a and b ▪ reaction center transfers electrons to Fd ▪ electrons from Ferredoxin are used to reduce NADP+ Reaction centers act in tandem to move electrons from H2O to NADP+ using sunlight ◦ Plastocyanin (Cu) moves electrons between PSII and PSI (one electron at a time) ◦ H2O is oxidized to O2 → replaces electrons transferred from PSII to PSI → this is why H2O is needed in photosynthesis ◦ Plants: oxygenic photosynthesis . which becomes positively charged Reaction centers of higher plants ◦ chloroplast thylakoids: two distinct reaction center types. 88 Energy transfer from antennas to reaction centers: exciton transfer ◦ one pigment absorbs a photon and is excited ◦ energy is randomly transferred to a neighboring light-harvesting molecule. exciting it ◦ first one returns to the ground state ◦ exciton transfer continues until it reaches a specialized pair of chlorphyll a at reaction center ◦ energy passed to chlorophyll a in reaction center causes one electron to be promoted to next orbital ◦ this electron is passed to an electron acceptor molecule → initiates plant electron transport ◦ leaves an electron hole (+) in the donor chlorophyll a ◦ Electron acceptor gains a negative charge (-) ◦ electron is replaced through transfer from a neighboring electron donor. 1000-fold difference in [H+] .are then used to replace the electrons that were excited by photons in P680. PSI and PSII are physically separated ◦ PSII is located in grana stacks ◦ PSI and ATP synthase are located in unstacked stromal thylakoids → access to stroma ◦ Cytochrome b6f distribution is more uniform ◦ Association of PS I and PS II with LSCHII is regulated by ▪ sunlight ▪ protein phosphorylation cytochrome b6f complex ◦ function = proton pumping as electrons are transported: moves 4 H+ per pair of electrons from stroma into thylakoid lumen. i. Establishes electrochemical gradient (proton motive force) ◦ volume of thylakoid lumen in chloroplasts is small → moving a small number of protons has large effect ◦ result: 3 unit pH difference.e. ◦ The 4 e. ▪ Note that for this reason photosynthesis is non-cyclic electron flow! ◦ The 4H+ are used to create the electrochemical gradient for ATP synthesis. 89 ◦ Bacteria: anoxygenic photosynthesis Oxygen evolving complex ◦ Oxygen evolving complex breaks down 2 H2O molecules into 4 H+ ions and 4 e-. the electrons used in the process are recycled. To re-generate electrons for photophosphorylation. The steps described above are for non-cyclic photophosphorylation. ◦ In cyclic photophosphorylation. oxygen is evolved as a byproduct. ▪ Both photosystems (I and II) are involved ▪ The active reaction center is P680 ▪ Electron from Photosystem I is accepted by NADP ▪ Both ATP and NAPDH are produced ▪ This system is predominant in green plants. non-cyclic photophosphorylation ◦ Non-cyclic photophosphorylation is when the electrons used in photophosphorylation are not recycled. 90 ◦ Proton motive force (PMF) drives ATP synthesis Cyclic vs. ▪ The active reaction center is P700 ▪ Electrons travel in a cyclic manner. ▪ Only photosystem I is involved. This sytem is predominant in bacteria. traveling back to photosystem I . ◦ The products of photorespiration are useless and are broken down by the peroxisome. ▪ This feature of rubsico probably arose because in the early earth atmosphere. there was not much O2 so it didn't matter. per O2 formed) ▪ 4 H+ by oxygen-evolving complex ▪ up to 8 H+ by cytochrome b6f complex ◦ electrochemical potential: change in pH = 3 across thylakoid membrane ◦ but: most of electrical potential is lost due to counterion movement unlike mitochondria where little is lost ◦ Energy stored in proton gradient per pole of proton: G = -17 kJ/mol ◦ 12 moles of protons translates to ~200 kJ ◦ enough free energy to drive synthesis of several ATP ◦ ATP yield is about 3 per mole of O2 (experimental value) Photorespiration ◦ Photorespiration is fixation of oxygen by rubisco instead of carbon dioxide. C4 photosynthesis ◦ Purpose is to move CO2 from the mesophyll to the bundle sheath cell to maximize photosynthesis and minimize photorespiration and water loss from stomata.e. . which becomes AMP → This is like using up “2 ATP” ◦ Structure of a C4 leaf is called the kranz anatomy (shown below). ◦ Found in hot dry. dry climates (think of corn and sugar cane!!!!) ◦ Requires one additional ATP. This is a problem because rubsico will fix both CO2 and O2 at the same time if both are present. ◦ Mechanism is called the hatch-slack pathway (shown below). 91 Photolysis of water splitting is absentATP synthesis in photophosphorylation: overview ◦ mechanism for ATP synthesis is analogous to that in mitochondria ◦ ATP synthesis is catalyzed by CF1/Cfo ATPase on outer surface of thylakoid membranes ◦ ATP is produced by rotational catalysis Balance sheet for photophosphorylation: we have a model but all is not known ◦ About 12 H+ move from stroma to thylakoid lumen per 4 electrons (i. Usually. Note that Malic acid is created and stored in the vacuole at night. 92 CAM photosynthesis ◦ Function is to allow the calvin cycle to proceed during the day when the stomata are closed. the stomata opens during the day! ◦ Mechanism shown below. ◦ Found in hot. malic acid is transported back into the vacuoule and broken down to release CO2. During the day. This in turns reduces H2O loss. dry climates (think of cactus and pineapple!!!) ◦ Special feature is that the stomata open during the night. . ◦ Unsaturated fatty acids are catabolyzed by the beta oxidation pathway but they require two additional enzymes to handle the double bonds. The liberated carnitine is shuttled back to the cytosol so this process can be repeated. This then must be chained to succinyl-CoA to enter the citric acid cycle. Acyl- carnitine then can move into the mitochondria through a special membrane protein. and acetone) that are produced by the liver from fatty acids during periods of low food intake. starvation. ▪ Therefore. instead of acetyl-CoA is propionyl-CoA which as 3 carbons. ◦ Fatty acids with an odd number of carbon atoms are common in plants and marine organisms. carbohydrate restrictive diets. fatty acids bind to coenzyme A to form acyl-CoA. ▪ (2) Oxidation of the beta carbon to a carbonyl group and cleavage of two-carbon segments resulting in acetyl-CoA • If you are interested in the exact mechanism of this pathway. they travel through transport proteins to enter the cytosol.org/wiki/Beta_oxidation. acyl-carnitine is converted back into acyl-CoA. each of which can be used in the citric acid cycle and then eventually oxidative phosphorylation. or untreated type I diabetes. . the end product. humans and animals that include these things in their diets must metabolize them in the beta oxidation pathway. • Ketone bodies ◦ Ketone bodies are one of three water-soluble molecules (acetoacetate. The acyl group is transferred from coenzyme A to carnitine to form acyl-carnitine. this is not the body's preferred fuel source. • Amino acids ◦ Amino acids can be oxidized for energy. beta- hydroxybutyrate. I don't think its necessary to know for the DAT. even carbon fatty acids: ▪ (1) Activation and membrane transport of free fatty acids by binding to coenzyme A. Once inside the mitochondria. ▪ They are the body's last resort fuel source. Therefore. • Fatty acids cannot penetrate through the plasma membrane because of their negative charge. • Once in the cytosol. and NADH and FADH2. Therefore. and then moves to the mitochondria for beta-oxidation. ◦ After removal of one or more amino groups. the remainder of the molecule can be used for energy by entering glycolysis or the citric acid cycle. 93 • Fatty acids can be metabolized for energy through beta oxidation ◦ Beta-oxidation is the catabolic process by which fatty acid molecules are broken down in the cytosol in prokaryotes and in the mitochondria in eukaryotes to generate acteyl-CoA. ◦ Overview of beta-oxidation for saturated. ◦ Fatty acids are a major source of energy because beta-oxidation can create many acetyl-CoA molecules. by moving its amino group to alpha-ketoglutarate (a citric acid cycle intermediate) forming glutamate (an amino acid). ◦ Degradation of an amino acid usually occurs in the liver and kidneys and involves deamination. which enters the citric acid cycle.wikipedia. • If the fatty acyl-CoA has a long chain. however. then the carnitine shuttle must be utilized because acyl-CoA is too big to pass through the mitochondrial membrane. ▪ (3) Oxidation of acetyl-CoA to carbon dioxide in the citric acid cycle ▪ (4) Electron transfer from electron carriers to the electron transport chain in oxidative phosphorylation. go to this link https://en. which are co-enzymes used in the electron transport chain. ▪ When the amount of ketone bodies rise in the blood. 94 ▪ These ketone bodies are readily picked up by tissues and converted into acetyl-CoA which enters the citric acid cycle and is oxidized in the mitochondria for energy. the pH of the blood changes. ◦ Ketosis is a metabolic state in which most of the body's energy supply comes from ketone bodies in the blood. leading to serious illness. . the next phase will be temporarily suspended. Longest phase ▪ S = synthesis of DNA (DNA replication) a duplication of the centrosome (2 x 2n) ▪ G2 = preparation for mitosis (2x2n) ◦ Meitotic phase (M) is the part of the cell cycle when the cell actually divides. it will move on to the S phase. 95 4 main phases of the cell cycle ◦ Cell cycle is the ordered sequence of events that extends from a time a cell is first formed from a dividing parent cell until its own division into two cells. the nucleus and its contents—most importantly the duplicated chromosomes —divide and are evenly distributed. forming two daughter nuclei that are identical. ▪ Around 10% of cycle. ▪ In mitosis. which usually begins before mitosis ends. ▪ During cytokinesis. G0 phase ◦ Many times a cell will leave the cell cycle. if the cell is not ready to divide. or wait until it is ready. ▪ 2x2n → 2n if mitosis. At the end of G1 phase. They are busy carrying out their other functions (secretion. temporarily or permanently. ▪ Two main stages: (1) a growing stage called interphase and (2) the actual cell division called the mitotic phase. The cell could possibly arrest in the G0 phase and never proceed. 3 subphases: ▪ G1 = growth and preparation of chromosomes for replication (2n). etc. It evaluates the accuracy of DNA replication and . the cytoplasm is divided into two. ◦ G2 Checkpoint is at the end of G2 phase. Checkpoints: quality control of the cell cycle ◦ G1 checkpoint is the most important checkpoint. ◦ It exits at the G1 and enters a stage called G0. ◦ Interphase is the time when a cell's metabolic activity is very high and the cell performs its various functions within the organism. attacking pathogens. When the cell is ready to divide.). Functional limitations of cell cycle ◦ Surface area-to-volume ratio: volume gets much large when cells grow vs SA. . When S/V is large. as cell grows. It checks to see if the microtubules are properly attached to kinetochores. ◦ Cyclin dependent kinases (CDKs) are enzymes that activate proteins that regulate the cell cycle via phosphorylation. ◦ Anchorage dependence: Most cells only divide when they are attached to an external surface such as a neighboring cell. G/V will be small and thus exceed the ability of its genome to produce sufficient amounts of regulator of activities. If not. or cell division to increase SA. anaphase is suspended. ◦ Density-dependent inhibition: Cells stop dividing when the surrounding density becomes too high. Some large cells are multinucleated to deal with this. 96 determines whether the cell is ready to begin mitosis. leads to cell death. exchange becomes much easier. ◦ Genome-to-volume ratio: genome size remains constant throughout life. They stimulate the cell for division. CDKs are activated by the protein cyclin. When S/V is small. exchange is hard. ◦ M checkpoint is at the end of metaphase. Other features of cell cycle control ◦ Growth factors attach to plasma membrane receptors. only volume increases. ” ▪ The gametophyte generation begins with a spore produced by meiosis. ◦ The gametophyte is an inconspicuous structure in angiospersm and other “higher” plants. Eventually through. . ▪ The sporophyte generation begins with a zygote. The spore is haploid. forming spores and starting a new gametophyte generation. meiosis and fertilization divide the life of an organism into two distinct phases or “generations. Cells will divide and grow. In due course. Cells contain diploid number of chromosomes. certain cells will undergo mitosis. and all the cells derived from it (by mitosis) are also haploid. 97 Alternation of generations ◦ In most plants. this multicellular structure produces gametes—by mitosis—and sexual reproduction then produces the sporophyte generation. ◦ Humans are diploid (we have 2 copies of each chromosome. In meiosis. are called leukemias and lymphomas. Meiosis occurs in 2 parts: The first division. ▪ A cancerous cell will exhibit defective cell differentiation. ▪ Gametes divide through the process of meiosis. the lump is called a benign tumor. ◦ The egg and sperm cells are collectively known as gametes. 2n). ▪ Usually. meiosis I. ▪ If the abnormal cells remain at the original site. is a key factor in the life cycle of humans and all other humans that reproduce sexually. that is. each inherited from one parent. The spread of cancer cells beyond their original site is called metastasis. it may proliferate to form a tumor. ▪ In contrast. The four gamete cells are not identical to one another. packaging them in separate (haploid) daughter cells but each chromosome is still doubled. displacing normal tissue and interrupting organ function as it goes. cell division reduces the number of chromosomes in the parent cell by half and produces four gamete cells. if the cell evades destruction. a malignant tumor can spread to neighboring tissues and other parts of the body. Our diploid number is 46. ▪ Having two sets of chromosomes. ▪ Each gamete has a single set of chromosomes and are said to be haploid (a cell with a single chromosome set. 2n = 46. However. spleen. 98 Cancer ◦ Cancer refers to uncontrollable cell division as a result of cell cycle regulatory mechanisms become inactive. segregates the two chromosomes of the homologous pair. n = 23 for humans). the sequence of stages leading from the adults of one generation to the adults of the next. an abnormally growing mass of body cells. . the immune system will be able to destroy a cancerous cell. and lymph nodes. Human life cycle ◦ The development of a fertilized egg into a new adult organism is one phase aof a multicellular organism's life cycle. ◦ A cancerous cell known as myeloma may be cultured indefinitely ◦ a lymphocyte may be fused with myeloma cell to produce a hybridoma ◦ sarcoma only occurs in connective tissue ◦ carcinoma occurs in epithelial tissue ◦ cancers of blood-forming tissues such as bone marrow. . 99 Meiosis II separates the sister chromatids. called a zygote. ▪ The resulting fertilized egg. Each of the four daughter cells is haploid and contains only a single chromosome from the homologous pair. involve an alternation of diploid and haploid stages. ▪ Producing haploid gametes prevents the chromosome number from doubling in every generation. ◦ All sexual life cycles. a haploid sperm cell from the father fuses with a haploid egg cell from the mother in the process of fertilization. including our own. ◦ In the human life cycle. has two sets of homologous chromosomes and is said to be diploid (one set comes from each parent) ▪ The life cycle is completed as a sexually mature adult develops from the zygote via mitosis. and asexual reproduction. ▪ The two liberated daughter chromosomes begin moving toward opposite ends of the cell as their kinetochore microtubules shorten. ◦ Prometaphase ▪ Nuclear envelop fragments ▪ Microtubules extending from each centrosome can now invade the nuclear area ▪ Each two of the chromatids of each chromosome now has a kinetochore. Each chromatid becomes a full-fledged chromosome. ▪ Mitotic spindle begins to form. ▪ Some of the microtubules attach to the kinetochores. cell replacement. The radial arrays of shorter microtubules that extend from the centrosomes are called asters. ▪ Nonkinetochore microtubules interact with those from the opposite pole of the spindle. the two ends to he cell have equivalent—and complete— collections of chromosomes. ▪ Mitosis is now complete. a specialized protein structure at the centromere. ▪ For each chromosome. ▪ Each chromatid in anaphase is its own chromosome. ◦ Prophase ▪ chromatin fibers become more tightly coiled. ◦ Cytokinesis . 100 Mitosis ◦ Why is mitosis important? ▪ Mitosis provides for growth. ▪ Begins when the cohesin proteins are cleaved. ◦ Telophase ▪ Two daughter nuclei form in the cell. the kinetochores of the sister chromatids are attached to kinetochore microtubules coming from opposite poles. Centrosomes are regions in the animal cells that organize the microtubule of the spindle. The chromosomes' centromeres lie at the metaphase plate. Nuclear envelops re-arise. ▪ By the end of anaphase. It is composed of two centrosomes and the microtubules that extend from them. Each centrosome contains two centrioles. ◦ Metaphase ▪ The centrosomes are now at opposite poles of the cell ▪ The chromosomes have all arrived at the metaphase plate. which jerk the chromosomes back and forth. ◦ Anaphase ▪ Anaphase is the shortest stage of mitosis. condensing into discrete chromosomes ▪ Each duplicated chromosome appears as two identical sister chromatids joined at their centromeres. ▪ Chromosomes become less condensed. ◦ Karyokinesis is nuclear division (occurs first) ◦ Cytokinesis is cell division (occurs second) ◦ G2 of interphase ▪ Nuclear envelope encloses the nucleus ▪ The nucleus contains DNA ▪ Two centrosomes have formed by duplication of a single centrosome. a plane that is equidistant between the spindle's two poles. Allows the sister chromatids of each pair to part suddenly. therefore the chromosome number during anaphase is equal to 4n. so the two daughter cells appear shortly after the end of mitosis. which pinches the cell in two. . ▪ In animal cells. a cell plate forms. ▪ In plants. cytokinesis involves the formation of a cleavage furrow. 101 ▪ Division of the cytoplasm is well under way by late telophase. The two chromosomes of such a matching pair are called homologous chromosomes because they both carry genes controlling the same inherited characteristics. The two chromosomes of a homologous pair may have different versions of the same gene. called a somatic cell. a typical body cell. XY = male) ▪ Autosomes = the 22 remaining pairs of autosomes ◦ Prophase I ▪ Centromere movement. spindle formation. ▪ Sex chromosomes – the chromsomes that determine a human's sex (the 23rd pair of chromsomes in humans. . has 46 chromosomes. 102 Meiosis ◦ Chromosomes are matched in homologous pairs ▪ In humans. can be arranged in matching pairs. ▪ We see that the chromosomes. and nuclear breakdown occur as in mitosis. each consisting of two sister chromatids. XX = female. In plants. ▪ Cytokinesis usually occurs simultaneously with telophase I. ▪ Both chromatids of one homolog are attached to kintochore microtubules from one pole. 103 Chromosomes condense progressively throughout prophase I ▪ Homologous pairs of chromosomes line up (synapsis). ▪ Synaptonemal complex is a protein structure that temporarily forms between homologous chromosomes. It gives rise to the tetrad with chiasmata and crossing over. ◦ Anaphase II ▪ Breakdown of proteins holding the sister chromatids together at the centromere allows the cromatids to separate. . and tetrads are ready for metaphase ◦ Metaphase I ▪ Pairs of homologous chromosomes are now arranged at the metaphase plate. ▪ Crossing over occurs between sister chromatids here. a cell plate forms. guided by the spindle apparatus. with one chromosomes in each pair facing each pole. ▪ Sister chromatid cohesion persists at the centromere. Each chromosome is composed of two sister chromatids. chromosomes. ▪ In animal cells. microtubules from one pole or the other will attach to the two kinetochores. ◦ Telphase I and cytokinesis ▪ When telophase I begins. ◦ Telophase II and cytokinesis ▪ Nuclei form. causing chromatids to move as a unit toward the same pole. Each homologous pair has one or more X-shaped regions called chiasmata. each with a haploid set of chromosomes. the chromosomes begin decondensing and cytokinesis occurs ▪ Meiotic division of parent cell produces 4 daughter cells. one at each centromere. forming two haploid daughter cells. ◦ Prophase II ▪ Spindle apparatus forms. The chromatids move toward the opposite poles as individual chromosomes. chromosomes complete condensing. ▪ In late prophase II. one or both chromatids chormatids include regions of nonsister chromatid DNA. each still composed of two chromatids. where crossovers have occurred. forming tetrads (4 chromatids). ▪ Homologs move toward opposite poles. ◦ Anaphase I ▪ Breakdown of the proteins that are responsible for sister chromatid cohesion along chromatid arms. associated at the centromere. ◦ Metaphase II ▪ Chromosomes are positioned at the metaphase plate as in mitosis. each half of the cell has a complete haploid set of duplicated chromosomes. move toward the metaphase II plate. ▪ 5 steps: leptotene – chromosomes start condensing zygotene – synapsis begins and the synaptonemal complex begins to form pachytene – synapsis is complete and crossing over occurs diplotene – synaptonemal complex disappears but the chiasmata still present diakinesis – nuclear envelope fragments. a cleavage furrow forms. ▪ Later in prophase I. ▪ (3) Immediately. the two broken chromatids join together in a new way. ▪ (2) The DNA molecules of two nonsister chromatids—one maternal and one paternal— break at the same place. chiasmata) is a place where two homologous (nonsister) chromatids are attached to each other. ◦ Steps of crossing over: ▪ (1) Crossing over begins very early in prophase I of meiosis. Sources of genetic Variation FROM MEIOSIS (NO genetic variation is created from mitosis) ◦ Crossing over during prophase I ◦ Independent assortment of homologues during metaphase 1 (which chromosome goes to which cell). homologous chromosomes are paired all along their lengths. ▪ (4) When the homologous chromosomes separate in anaphase I. ◦ Chromosomes with a combination of genes from crossing over are called recombinant because they result from genetic recombination. an average of one to three crossover events occur per chromosome pair. producing hybrid chromosomes with new combinations of maternal and paternal genes. or cross over. with a precise gene-by-gene alignment. each contains a new segment originating from its homolog. each is called a chiasma (plural. How crossing over works ◦ Crossing over is an exchange of corresponding segments between nonsister chromatids of homologous chromosomes. in meiosis II. the sister chromatids separate. ◦ The sites of crossing over appear as X-shaped regions. ◦ Random joining of gametes during fertilizations . In effect. ◦ In meiosis in humans. Law of independent assortment is explained in the genetics unit. At that time. the production of gene combinations different from those carried by the original paternal chromosomes. 104 ▪ The 4 daughter cells are genetically distinct from one another. ▪ (5) Finally. each going to a different gamete. the homologous segments trade places. Crossing over creates tremendous diversity in gametes. 105 . 106 . Is there really a LUCA? ▪ LUCA is by far the most probable theory than the closest competing hypothesis even when counting for exchanging material between organisms (horizontal gene transfer) ◦ There was probably more than one self-replicating early life form.45 billion years ago ◦ Sulfur isotopes of organic matter preserved in 3. All living things today are descended from this one lineage. 107 We know there was life by 3. One population was successful enough to establish itself .45-billion-year-old stromatolites reveal microbial metabolism ◦ Stromatolite: layered calcareous structures formed by bio-films (microorganisms adhered together) binding sedimentary gains LUCA ◦ Last universal common ancestor (LUCA): the population of organisms at the base of the tree of life. ammonium chloride. 108 What are the properties of life? ◦ Organization: maintenance of parts (whether cells or more complex) ◦ metabolism: control of chemical reactions to sustain life ◦ Growth and reproduction: creation of offspring ◦ homeostasis: the ability to regulate one's internal environment ◦ external response: response to external environment and stimuli What are some critical steps required for life? ◦ Generation of simple organic molecules from inorganic molecules ◦ origin of self replication ◦ genotype and phenotype linkage and natural selection ◦ moving from RNA to DNA ◦ creation of cells (compartmentalization) Prebiotic soup hypothesis ◦ Prebiotic soup hypothesis: the idea that the earliest life emerged in a “soup-like” liquid environment. The original Earth environment was very reducing (allowing chemical parts to turn into more complex ones) ▪ Miller-Urey experiments simulated ocean and atmosphere interface methane. ammonia. drawing energy from the cosmic rays. This may not be accurate. and the Earth's internal heat Organic from Inorganic ◦ Many experiments have shown that life related molecules can be synthesized from simple inorganic components ▪ 1828 urea (organic) created from inorganic salts. volcanic eruptions. and hydrogen mixed with boiling water and simulated lighning reactions produced amino acids these were done in reducing environments (without compounds with oxygen). no organic molecules would have formed. and cilver cyanate helped disprove that the chemistry of living systems were fundamentally different from nonliving systems ▪ Oparin and Haldane's organic soup theory If there was oxygen. . The discovery of chemosynthesis at vents in 1977 gave some credence to deep sea origins.6 billion year old meteorite . 109 ▪ Reducing environments exist in hydrothermal sites. Amino acids were found on a 4. ▪ Reducing environments exist in space as well. might be coopted by other organisms ◦ Metabolism ▪ Primitive heterotrophic prokaryotes: obtained materials by consuming other organic substances (pathogenic bacteria) ▪ Primitive autotrophic prokaryotes: mutation. heterotroph gained ability to produce its own food → cyanobacteria. fulfilling both an information role and a catalytic role. ◦ Microspheres. ◦ Problems with organic from inorganic ▪ some compounds have still never been produced (nucleotides) ▪ low quantities are produced Origin of self replication ◦ chicken egg problem: DNA encodes information for proteins. a self replicating system. 2010 suggests glancing strikes would allow survival. ◦ Reproduction ▪ Reproduction may have resulted from overproduction. ◦ Minimal gene sets ▪ Minimal gene set is the hypothetical minimal number of genes thought necessary to . ▪ They can be more complex and diverse than RNA ◦ Molecular bridge from RNA to DNA still unknown ▪ Reverse transcriptase can convert from RNA to DNA today Precursors to first organisms ◦ Protobionts are precursors of cells. proteins can't replicate' proteins are required for replication of DNA ◦ Solution: RNA world ▪ RNA was the information carrier and catalyst ▪ RNA has diverse roles that include catalyst and temporary information carrier ▪ Ribozymes = RNA enzymes ▪ RNA world: a hypothetical early stage in the history of life in which RNA was the fundamental unit upon which life was based. you need to contain the parts ▪ Also. 110 ▪ Could extreme pressure and heat of impact destroy amino acids? Goldman et al. error correction) lower mutation rates – better storage ◦ proteins were used for catalytic functions (phenotype). are experimentally produced protobionts that have some selective permeable qualities. the cell expands so large that splitting is more stable. DNA replaces RNA ◦ RNA was replaced by DNA around 3. They are like cells and metabolically active but are unable to reproduce. What were the first organisms like? ◦ The first single celled life was prokaryotic (they have no nucleus or organelles) ◦ Organisms were compartmentalized ▪ If functions are delegated.5 billion years ago as the genotype ▪ DNA is more stable whereas RNA is more reactive ▪ DNA have repair mechanisms (proofreading. spontaneously formed lipid or protein bilayer bubbles. if not compartmentalized. Also suggested that heat could encourage more complex amino acid complexes. Around 206 genes (done by comparing genomes) ◦ Early population of these organisms exchanged material most likely ▪ Horizontal gene transfer: the transfer of genetic material from one organisms to another that is not its offspring. ◦ Ozone layer formed. blocking energy for abiotic synthesis of organic materials. often within the cell. early cells may have swapped DNA frequently. ◦ This terminated primitive cells. Where do viruses fit in here? ◦ Hypotheses ▪ Escaped gene hypothesis: escaped selfish genes that have evolved protein coatings and self replication ▪ Reduction hypothesis: extremely reduced cellular organisms ▪ Remnants of the RNA world ▪ viruses may have predated or coexisted with LUCA Oxygen and ozone layer ended abiotic chemical evolution ◦ O2 and O3 formed by production of photosynthetic activity of autotrophs (cyanobacteria). Formation of the first eukaryotes ◦ Endosymbiosis: a mutually beneficial relationship in which one organism lives within the body. which absorbs UV light. Basically. ◦ It has been shown that mitochondria and chloroplasts formed through this process ◦ Evidence for symbiosis (commonly asked on DAT): ▪ Membranes – mitochondria have their own cell membranes. 111 allow for cellular based life. This was more prevalent in the early tree of life. of another. just like a prokaryotic cell does . but much smaller. . it can't build new ones from scratch. 112 ▪ DNA – each mitochondrion has its own circular DNA genome. ▪ Reproduction – Mitochondria multiply by pinching in half — the same process used by bacteria. Every new mitochondrion must be produced from a parent mitochondrion in this way. like a bacteria's genome. if a cell's mitochondria are removed. This DNA is passed from a mitochondrion to its offspring and is separate from the host cell's genome in the nucleus. ◦ Phase-contrast: Uses light phases and contrast to allow for detailed observation of living organisms if thin. Can’t use on living samples. can look at specific parts of cell via fluorescent tagging. ◦ Scanning elctron microscope (SEM): Look at surface of (3D) objects with high resolution. lysosomes. Can look at living cells. ◦ Compound microscope: Uses visible light to view a thin section of sample. 113 Studying cells ◦ Stereomicroscope: Uses visible light to view surface of sample. ▪ Fastest to pellet out = nucleus ▪ then mitochondria. but can’t be used on living things. Can’t use on living specimens as sample needs to be dried and coated. vesicles ▪ then ribosomes. ◦ Cell fractionalization (centrifugion): cells whose membranes have been centrifuged at various speeds for varying lengths to separate components of different sizes. and shapes. Can look at internal structures. larger macromolecules . viruses. chloroplats. ◦ CryoSEM: Like SEM but no dehydration so you can look at samples in more “natural” form. ◦ Transmission electron microscope (TEM): look at very thin cross-sections in high detail. ◦ Confocal laser scanning + fluorescence: Can look at thin slices while keeping sample intact. May require staining for increased viability. peroxisomes ▪ then ER. densities. very high resolution. but only fluorescently tagged parts. Due to differences in density. Used to observe chromosomes during mitosis. but only at low resolutions. ◦ Electron tomography: 3D-Electron tomography: 3D model buildup using TEM data. 114 ◦ Freeze fracture: split lipid bilayer of a frozen specimen. Used to study cell membranes and organelles. ◦ Gram straining: common technique used to distinguish gram positive from gram negative bacteria. ▪ Gram positive bacteria strain violet due to the presence of a thick layer of peptidoglycan. ▪ Gram negative bacteria strain red because of the thinner peptidoglycan wall. 115 Introduction ◦ DNA contains 4 special abilities: ▪ Diversity of structure ▪ Ability to replicate ▪ Mutability ▪ Regulated expression ◦ Central dogma: ▪ DNA gets transcribed into RNA which will get translated into a polypeptide ◦ ◦ Genes and organisms ▪ The number of genes varies greatly between organisms ▪ Having more genes doesn't mean the organism is higher order or more complex ◦ Organization of DNA ▪ In viruses: DNA or RNA is surrounded by a protein coat ▪ In prokaryotes: DNA is organized into a circular chromosome or potentially a plasmid ▪ In eukrayotes: Most of the DNA is in the nucleus. Some of the DNA is located in the mitochondria and the chloroplast. The nucleus contains multiple linear chromosomes. Each chromosome contains one double stranded DNA molecule. ◦ Human karyotype ▪ Diploid = 2 copies of each chromosome. Humans are diploid; we inherit one copy of each chromosome from each of our parents. Nomenclature: 2n = _____ ▪ Haploid = 1 copy of each chromosome. Examples are sperm and egg cells. Nomenclature: n = ______ ▪ 22 pairs of autosomes (homologous chromosomes) Just because you have the same genes doesn't mean you have the same alleles! ▪ 1 pair of sex chromosomes (XX – homologous, XY – not homologous) ▪ All somatic cells in the body have the same DNA ◦ Gene regulation ▪ Determines when and where a given gene is expressed ▪ non-coding DNA also encodes regulatory functions ▪ Most human-chimp differences due to gene regulation-not genes 116 ◦ Genetics and variations ▪ Differences among individuals are called polymorphisms. ▪ They can result from: 1) mutations 2) environment 3) mixture of both ▪ Environmental polymorphisms are usually not heritable ◦ Mutations vs mutants ▪ Mutations are changes in the DNA sequence that may or may not affect phenotype. Arise from natural processes as well as environmental factors. ▪ Mutants are individuals that have change sin their DNA that alter the “wild-type” phenotype ◦ How can we find mutants ▪ From natural populations: Spontaneously find them Survey the population for mutants ▪ Lab populations: mutagenesis – controllable introduction of mutations selection – kill what you don't want screen – look for what you want ◦ Forward vs reverse genetics ▪ Forward genetics: begin with a change in phenotype and then look to see how changes in genotype cause the observed effects. ▪ Reverse genetics: begin with a change in genotype and then look to see how this causes a change in phenotype. ◦ Model organisms ▪ Model organisms are used in genetics research frequently because they are small, easy to culture, have short generation times have small genomes, and are easy to transport. ◦ Nature vs. nurture ▪ Genotype: The genetic makeup of an organism. It describes an organism's complete set 117 of genes. ▪ Phenotype: The observable physical and/or biochemical characteristics of the expression of a gene; the clinical presentation of an individual with a particular genotype. ▪ The phrase nature and nurture relates to the relative importance of an individual's genes as compared to an individual's environment on phenotype. Genes x Environment = Phenotype. The relative contributions of genes and the environment on phenotype differ per phenotype. Mendel's laws and classical genetics ◦ Mendel's law of segregation and independent assortment ▪ Mendel's law of segregation: During gamete formation, the alleles for the same gene segregate from each other so that each gamete carries only one allele for each gene. ▪ Law of independent assortment: Alleles for different traits segregate independently during the formation of gametes. 118 ▪ Mendel's law of segregation allows us to predict outcomes. ◦ Alleles ▪ Since human cells carry two copies of each chromosome, they have two versions of each gene. The different versions of a gene are called alleles. ▪ Alleles can be either dominant or recessive. Dominant alleles show their effect even if the individual only has one copy of the allele. A dominant allele is the stronger version of a pair of alleles. Dominant alleles are depicted as capital letters (i.e. “A”). Recessive alleles only show their effect if the individual has two copies of the allele. Recessive alleles are depicted as lowercase letters (i.e. “a”). ▪ Heterozygous refers to an individual who carries two different alleles for a particular gene. ▪ Homozygous refers to an individual who carries two of the same alleles for a certain gene. ◦ Loci ▪ A locus in genetics is the specific location or position of a gene, DNA sequence, on a chromosome. ◦ Monohybrid cross ▪ A monohybrid cross is a mating between two individuals with different alleles (two heterozygotes) at one genetic locus of interest. ▪ Genotypes predicted = 1 homozygous dominant, 2 heterozygous, 1 homozygous recessive (1:2:1) 119 ◦ Dihybrid cross ▪ A dihybrid cross is a cross between two different organisms that differ in two observed traits. They tend to result in a 9:3:3:1 ratio. ◦ Probability stuff ▪ Use multiplication when you see the word AND ▪ Use addition when you see the word OR ◦ Common crosses ▪ True-breeding: homozygous for the trait (either dominant or recessive) ▪ Parental cross: parental strains are crossed with one another to form the F1 generation. P x P = F1 Parental strains are usually true-breeding ▪ Intercross: crosses between genetically identical individuals (selfing, sibling mating) F1 x F1 = F2 F2 x F2 = F3 etc. ▪ Backcross: F1 progeny mated back to one of the parents F1 x P = backcross ▪ Testcross: Dominant phenotype x recessive phenotype. “A_ x aa” A testcross allows you to determine the genotype of the organism with the dominant phenotype (dominant homozygous or dominant heterozygous). If all of the offspring of a testcross have dominant phenotypes, the parent organism with the dominant phenotype has a homozygous dominant genotype (“AA”). If some of the offspring of a testcross have recessive phenotypes, the parent organism with the dominant phenotype has a heterozygous dominant genotype (“Aa”). A testcross also can be used for dihybrids (A_B_ x aabb) ◦ Finding mutants with mutagenesis ▪ Mutagenesis – treatment with conditions that cause mutations: chemical mutagens (carcinogens), radiation, mobile genetic elements. Screen = look for what you want selection = kill what you don't want Sex-linked traits and nondisjunction ◦ X and Y chromosome gene content 120 ▪ X chromosome contains 2000-3000 genes. Nearly all genes are required in both males and females. ▪ Y chromosome contains ~100 genes. ~5% of gene numbers on X made up the SRY gene. This is the master control gene for making male embryos. ▪ X and Y genes have sequence similarity at the tip of their shorter arms. This is the region where they pair up in meiosis. Recombination happens only in regions that pair. Therefore, the Y chromosome has little recombination. ◦ X-linked inheritance ▪ A gene located on either sex chromosome is called a sex-linked gene. ▪ Because the human X chromosome contains many more genes tan the Y, the term has historically referred to genes on the X chromosome. ◦ Y-linked inheritance ▪ Y linked traits are very rare Y-linked traits are neither dominant nor recessive because there is only one copy. ▪ In a pedigree, you'd expect a Y-linked trait to be transmitted from fathers to sons only, with no affected females observed. ◦ Three common sex-linked disorders ▪ Hemophilia is an X-linked recessive trait that causes excessive bleeding upon injury because the person lacks one or more of the proteins required for blood clotting. ▪ Colorblindness is a malfunction of light-sensitive cells in the eyes. It is a disorder that involves several X-linked genes. ▪ Duchenne muscular dystrophy is a condition characterized by a progressive weakening of the muscles and loss of coordination. The symptoms appear in very early childhood and becomes progressively worse as the child ages. Most affected individuals don't live past their early 20s. ◦ Nondisjunction: meiosis mistakes ▪ Nondisjunction is when homologous chromosomes do not assort correctly during mitosis. One daughter cell would get too many chromosomes, while the other daughter cell would be getting too few chromosomes. Causes Aneuploidy, a genome with a wrong chromosome number (either too many or too few). ▪ Nondisjunction during meiosis I generates a daughter cell with n + 1 chromosomes and . Note that wild-type traits aren't necessarily specified by dominant alleles. In genetics. ◦ Genetic traits in humans can be tracked through family pedigrees ▪ Mendel's laws apply to the inheritance of many human traits. the word “dominant” does not imply that a phenotype is either normal or more common than a recessive phenotype. ▪ Partial monosomy is the partial chromosomal deletion of 1 homologous chromosome. ▪ Non-disjunction diseases XYY = Jacobs syndrome XXY = Kleinfelter syndrome XO = Turner Syndrome XXX = Triple X ▪ Mosaicism in cells that undergo nondisjunction in mitosis during embryonic development. ▪ Polyploidy: all chromosomes undergo meiotic nondisjunction and produce gametes with twice the number of chromosomes. we use the word wild-type trait to describe traits that are prevailing in nature. Therefore. fraction of body cells have extra or missing chromosome. We determine the inheritance pattern of a particular human trait by assembling this information into a family tree called a pedigree. and 2 normal daughter cells. ▪ Nondisjunction during meiosis II generates 1 daughter cell with n + 1 chromosomes. 1 daughter cell with n – 1 chromosomes. 2 daughter cells will be n + 1 and 2 daughter cells will be n-1. Common in plants. 121 another daughter cell with n – 1 chromosomes. After meiosis II. cytoplasmic inheritance. whereas a female needs to inherit two recessive alleles to have a recessive phenotype. ▪ Autosomal recessive diseases tends to “skip” generations whereas autosomal dominant diseases tends to be present in every generation. a male only needs to inherit one recessive allele to have a recessive phenotype. genes controlling quantitative traits will fall in a bell-shaped distribution. You can't identify all alleles for all individuals usually. Therefore. height. Cytoplasmic inheritance . Males only have one X-chromosome. whereas Females have two x-chromosomes. ▪ Fill out genotypes. Thus. ▪ Human sex-linked disorders affect mostly males. ▪ Therefore. 122 ◦ Inferring the mode of inheritance on pedigrees ▪ Make an educated guess and see whether it is consistent with the available information. it is the behavior of chromosomes during meiosis and fertilization that accounts for inheritance patterns. albinism) ▪ Continuous or quantitative traits: distribution of phenotypes varies along a continuum (i.e. ◦ Chromosomal theory of inheritance ▪ The chromosomal theory of inheritance states that genes occupy specific loci (positions) on chromosomes.e. each with a similar and additive effect on the trait. Polygenic inheritance. and maternal effects ◦ Discrete vs continuous traits ▪ Discrete or discontinuous phenotypes fall into distinct classes (i. and it is the chromosomes that undergo segregation and independent assortment during meiosis. blood pressure) ◦ Polygenic model for quantitative traits ▪ The polygenic model assumes that phenotype is affected by many gene loci. The sperm just carries over DNA. every chromosome is expected to have at least 1 chiasmata. Maternal effects ◦ Maternal effects ▪ Maternal effect is when genotype of the mother determines phenotype of the child. ▪ We only inherit our mtDNA from our mother. ▪ The production of recombinant phenotypes depends on: The location of genes on the chromosome the location of crossing over . ▪ The location of the crossovers within each germ cell is random and different in each meiosis. any mutation seen in the mother's mtDNA will affect the progeny. ◦ Molecular basis of cytoplasmic inheritance ▪ Mitochondria and chloroplasts have their own genomes. Therefore. The egg contains all of the cytoplasm organelles when fertilized with a sperm. Genetic recombination ◦ Recombination ▪ The formation of chiasmata (which determine the location of recombination events) are necessary for proper chromosome segregation during meiosis. ▪ Mediated by RNAs and proteins produced by the mother. like bacteria. and their genomes are circular. ▪ We know that mitochondria contains its own set of DNA (mtDNA). ▪ Not caused by organelles. ▪ Mitochondria and chloroplasts replicate themselves. ▪ Cytoplasmic inheritance is uniparental and the genes are NOT located in the nucleus. 123 ▪ The egg is much larger than the sperm. ▪ In each cell. ▪ Typically controlled by nuclear genes. ▪ We can estimate the number of parental and recombinant gametes by looking at the phenotypes produced by particular genetic crosses. ▪ The maximum genetic distance that can be measured between 2 genes in one cross is 50 cM. null allele ▪ Dominance: complete. dominance series ◦ Genetics of sickle-cell anemia ▪ example of pleiotropy: where one gene has effects on multiple phenotypes . temperature sensitive) ▪ Multiple alleles: codominance. Extensions to mendelism ◦ Extensions to Mendelism: alleleism (relating genotypes to phenotypes) ▪ Types of alleles: loss of function. gain of function. neofunctional. incomplete. In other words. 124 ◦ Genetic distance ▪ Genetic distance determines the proportions of recombinant gametes produced during meiosis.g. the two genes are linked. ▪ If over 50% of your progeny are “recombinant. codominant ▪ Lethals: recessive. ▪ Haplotype is a set of DNA variations. conditional (e.” then the two genes are not linked. or polymorphisms that tend to be inherited together. ▪ Genetic distance (cM) is proportional to physical distance (bp). ▪ Two genes affecting the trait can show: independence (no interaction) redundancy complementarity (mutual epistasis) epistasis suppression (another specialized case of epistasis) ◦ Two genes: Additive effects ▪ Additive effects are when the contribution of each gene adds up to create the phenotype. ▪ Different alleles are favored under different conditions: A allele is better if no malaria-carrying mosquitoes present S allele better if malara-carrying mosquitoes present ◦ Multifactorial inheritance ▪ Most traits are controlled by multiple genes. ▪ This is basic dihybrid cross (9:3:3:1) . 125 ▪ Sicke-cell anemia has pleiotropic effects: hemoglobin protein function cell shape cell density malaria resistance → heterozygote (AS) confers malaria resistance because the malaria toxin cannot effect sicke cells. both the A and S alleles of the beta-globin gene are found in human populations at high frequency. Heterozygote gives malaria resistance so it gives higher fitness effects. ▪ Because of the pleiotropic functions (namely malaria resistance). ▪ The polymorphism is maintained by balancing selection. Mutations in two different genes can give the same phenotype. ▪ When both genes creates the correct proteins. a protein complex will form and each protein will only be functional then. 7 because 3 + 3 + 1. ▪ F2 generation would see a 9:7 dominant:recessive frequency. ◦ Complementary gene interaction – mutual epistasis ▪ Mutual epistasis results when the protein each individual gene creates is not functional alone. . 126 ◦ Two genes: Gene interactions ▪ The phenotypic effect of an allelic combination at one gene is influenced by the allelic combination at another gene. ▪ Any mutation in either gene will automatically cause a recessive phenotype. ▪ The only way a recessive phenotype can be seen is if the genotypes of both individual genes are homozygous recessive. 127 ◦ Redundancy ▪ Redundancy results when two genes have the same function and only one gene is necessary for a normal phenotype. ▪ F2 generation would see a 9:4:3 frequency. then aaBB. If A is epistatic over B. . aaBb. then the phenotype will be the same. ▪ F2 generation would produce a 15:1 dominant:recessive frequency. regardless of the genotype of the other gene. ◦ Epistasis ▪ Epistasis is when mutation at one gene masks phenotypic effects of mutation at another gene ▪ If the epistatic gene is recessive. aabb will all produce the same phenotype. . or O. ▪ Produces an F2 generation ratio of 13:3 if the recessive allele was the suppressor. the heterozygous genotype would produce a phenotype that is equivalent to “mixing” the other two phenotypes together. the dominant and recessive phenotype are seen equally throughout the heterozygous phenotype. an example of codominance ◦ The ABO blood group phenotype in humans involves three alleles of a single gene. pink ◦ codominance ▪ In codominance. ◦ Incomplete dominance ▪ In incomplete dominance. B. white. The gene that does the suppression can do it through the dominant or recessive genotype. white. 128 ◦ Suppression ▪ suppression results when the mutant phenotype of one gene can be suppressed (or “hidden”) by another gene. AB. ▪ Various combinations of three alleles for the ABO blood type produce four phenotypes: A person's blood type may be A. red + white spots Inhertance of blood type. If the dominant allele was the suppressor the F2 generation would produce a 15:1 ratio. Red. Red. known as Rh+ (produces the Rh surface protein) and Rh. auxotrophs ▪ Auxotrophs – mutant that requires a specific supplement in the environment in order for it to grow (cannot synthesize that supplement) .” ◦ Another level of specificity is added to blood type by examining the presence or absence of the Rh surface protein. pathways ◦ Prototrophs vs. ▪ There are 2 different alleles for the Rh factor. ▪ If a donor's blood cells have an agglutinogen that is foreign to the recipient. Each blood type is either positive “+” (has the Rh protein) or negative “-” (no Rh protein). 129 ▪ These letters refer to two agglutinogens (a type of antigen) that are attached to the surface of red blood cells. ◦ The A and B antigen molecules on the surface of red blood cells are made by two different enzymes. ▪ The Rh factor genetic information is inherited independently of the ABO blood type alleles. Gene/enzyme hypotheses. making those with type O blood “universal donors.(does not produce the Rh surface protein. ◦ Matching compatible blood types is critical for safe blood transfusions. metabolic mutants. making them “universal recipients” while donated type O blood never causes clumping. then the recipient's immune system produces blood proteins called antibodies that bind specifically to the foreign agglutinogens and cause the donor blood cells to clump together. ◦ AB individuals can receive blood from anyone without fear of clumping. type A and type B. potentially killing the recipient. each of which are encoded by different alleles of the same gene. If one gene mutates. This tends to lead to accumulation of an intermediate. ◦ Assumptions of hardy-weinberg ▪ No natural selection ▪ No mate preference (random mating) ▪ No mutations ▪ No migrations ▪ Population size is infinite ◦ Hardy-weinberg equilibrium ▪ If populations are in hardy-weinberg equilibrium: the frequencies of alleles (A and B) do not change over time without an evolutionary force loci that are not in equilibrium will be after one generation with allele frequencies (say A and B). ▪ Two types of biochemical pathways: Convergent: two intermediates come together to create a product Divergent: one intermediate splits into two products Evolutionary genetics ◦ Hardy-weinberg model ▪ Hardy-weinberg model is a null hypothesis for population genetics ▪ By rejecting hardy-weinberg. protein hypotheses ▪ One-gene-one-enzyme hypothesis: all enzymes are composed of a single gene product ▪ One-gene-one-polypeptide hypothesis: enzymes can be composed of more than one gene products This is more accurate because some enzymes require multiple subunits. we can predict genotype frequencies. we can conclude that one or more of the 5 assumptions of hardy-weinberg have been violated and are present in the population. assuming no evolutionary forces. which are different polypeptides from different genes ◦ Biochemical pathways and genes ▪ Some genes code for enzymes which help catalyze reactions in biochemical pathways. Q = recessive allele frequency ▪ P2 + 2PQ + Q2 = 1 ▪ P2 = homozygous dominant genotype frequency . Can synthesize all nutrients normally. Wild-type. 130 ▪ Prototrophs – can grow on minimal media. the enzyme that gene coded for will be synthesized incorrectly which will prevent it from catalyzing the necessary reaction. ◦ Hardy-weinberg equations ▪ P = dominant allele frequency. ◦ Gene. Guanine. uracil ▪ DNA backbone = alternating phosphates and deoxyriboses bonded together by phosphodiester linkages (5' phosphate group bound to 3'-OH) Deoxyribonucleotide (structural unit of DNA) = N base + phosphate + deoxyribose ▪ RNA backbone = alternating phosphates and riboses Ribonculeotide (structural unit of RNA) = N base + phosphate + ribose ▪ Directionality of DNA = 5' to 3' 5' end is the end with the free 5' phosphate-group 3' end is the end with the free 3' OH group on the sugar . 131 ▪ Q2 = homozygous recessive genotype frequency ▪ 2(PQ) = heterozygous genotype frequency Structure of DNA and RNA (also covered in cellular and molecular bio unit – know all info from both sections) ◦ Building blocks of DNA ▪ 4 nitrogenous bases: Adenine. Thymine Purines = adenine and guanine Pyrimidines = cytosine. Cytosine. thyamine. Many sequence specific DNA binding proteins bind here. ▪ Minor groove: small grove created by double helix. C = G ▪ A + T doesn't always equal C + G ◦ Grooves on DNA ▪ Major groove: big groove created by double helix. Many non-specific DNA binding proteins bind to the backbone. ▪ 10. 132 ▪ The bases hydrogen bond with one another: one of the most important mode of interaction between 2 complementary strands of nucleic acid A bonds to T = 2 hydrogen bonds C bonds to G = 3 hydrogen bonds ▪ Hydrophilic backbones are on outside of the helix.5 base pairs per helical turn when in aqueous solution ◦ Chargaff's rules ▪ A = T. These strands are antiparallel to each other – one strand goes in 5' to 3' direction whereas the other strand goes from 3' to 5'. facing the surrounding water. . . Occurs over BOTH strands. ◦ Special DNA sequences ▪ Palindromes are sequences of bases that reads the same forwards and backwards. 133 ◦ Major forms of DNA ▪ B-form DNA is the most stable structure for DNA molecule under physiological conditions. ▪ A-form DNA is favored in solutions devoid of water. Barely a minor groove. May play a role in regulating the expression of genes. ▪ Z-form DNA has 12 bps per helical turn and is left handed. Occurs over ONE strand in BOTH strands. Right-handed double helix. ▪ Inverted repeats are sequences of bases that reads the same forwards and backwards. but the helix is wider and its 11 base pairs per turn. Been found in bacteria and eukaryotes. not deoxyribose ▪ Uses uracil. Composite DNA molecules comprising covalently linked segments form two or more sources are called recombinant DNAs. The enzyme DNA ligase links the cloning vector and the DNA to be cloned. The result is selective amplification of a particular gene or DNA segment. 134 ◦ RNA information ▪ Single stranded RNA tends to create complex 3D conformations ▪ Can base-pair with complementary DNA or RNA ▪ Double stranded RNA usually found in the A-form ▪ Uses ribose in the backbone. These DNAs are called cloning vectors (a vector is a delivery agent). not thymine ▪ Uses ribose. attaching it to a much smaller piece of carrier DNA. (2) Selecting a small carrier molecule of DNA capable of self-replication. (3) Joining two DNA fragments covalently. Steps: ◦ 1) run protein on gel ◦ 2) transfer to membrane ◦ 3) probe blot with antibody ◦ Approaches to introducing DNA into organisms ▪ 1) take obtained DNA ▪ 2) add additional sequences ▪ 3) transfer it into the organism ◦ DNA cloning ▪ DNA cloning: The process of cutting the gene out of the larger chromosome. not deoxyribose Genetic technology ◦ Southern blots ▪ Southern blots are used to analyze the length of restriction fragments of DNA. They are typically plasmids or viral DNAs. Steps: ◦ 1) Run RNA on gel ◦ 2) transfer to membrane ◦ 3) hybridize with radioactive probe ◦ Western blot ▪ Western blots are used to analyze lengths of protein fragments. and allow microorganisms to make many copies of it. There are five general procedures: (1) cutting target DNA at precise locations: sequence-specific endonucleases (restriction endonucleases) provide the necessary molecular scissors. (4) Moving recombinant DNA from the test tube to a host cell that will provide the . ▪ Steps: 1) cut DNA with restriction enzyme 2) run on gel 3) Transfer DNA to membrane 4) hybridize with radioactive probe ◦ Northern blots ▪ Northern blots are used to analyze length of RNA fragments. ◦ They are found in a wide range of bacterial species. (5) Selecting or identifying host cells that contain recombinant DNA. 135 enzymatic machinery for DNA replication. a particular fragment of known size can be partially purified by gel electrophoresis. They are introduced into vectors to make cloning easier by providing sites that allow cloning DNA. ◦ The classic E. multisubunit complexes containing both the endonuclease and methylase activities. ▪ Blunt ends are when there are no unpaired bases on the ends. Once the DNA molecule has been cleaved. ▪ Several unique recognition sequences in pBR322 are targets for restriction endonulceases. into a single plasmid. Both types can cleave DNA at 25bp-1000bp from t he recognition sequence ▪ Type II restriction endonucleases are simpler. This sequence is required to propagate the plasmid. Coli plasmid pBR322 is a good example of a plasmid with features useful in all cloning vectors: ▪ The plasmid pBR322 has an origin of replication. ◦ A polylinker is a short DNA sequence containing 2 or more different sites for cleavage by restriction enzymes. ▪ Restriction endonucleases and DNA ligases yield recombinant DNA Two classes of enzymes that cut DNA are restriction endonucleases and DNA ligases ◦ Restriction endonucleases (also called restriction enzymes) recognize and cleave DNA at specific sequences (restriction sequences or restriction sites) to generate a set of smaller fragments. II. allowing the selection of cells that contain the intact plasmid or a recombinant version of the plasmid. or ori. Both require ATP to function. cut with any of a number of different restriction enzymes. require no ATP. a vector digested by the same restriction endonuclease. ▪ Cloning vectors allow amplification of inserted DNA sequences Plasmids ◦ A plasmid is a circular DNA molecule that replicates separately from the host chromosome. . and cleaves the DNA within the recognition sequence itself. it is called an episome. and III. ▪ The small size of the plasmid facilitates its entry into cells and the biochemical manipulation of the DNA. ◦ If a plasmid becomes incorporated into a chromosome. After the target DNA fragment is isolated. They can base-pair with each other or with complementary sticky ends of other DNA fragments. a sequence where replication is initiated by cellular enzymes. ◦ Restriction endonucleases make either sticky ends or blunt ends. ▪ The plasmid contains genes that confer resistance to the antibiotics tetracycline and ampicillin. DNA ligase can be used to join it to a similarly digested cloning vector— that is. providing sites where the plasmid can be cut to insert foreign DNA. ▪ Sticky ends are when there are unpaired nucleotides left on one side of each strand after cleavage. they are used originally to cleave foreign DNA (self = methylated DNA) ◦ There are 3 types of restriction endonulceases: designated I. ▪ Types I and III are generally large. Sticky ends are easier than blunt ends to paste into a vector because of the overhang. Bacterial artificial chromosomes ◦ Bacterial artificial chromosomes. The rate of . ▪ Cloned genes can be expressed to amplify protein production Frequently. small plasmids can be introduced into bacterial cells by a process called transformation and plasmid DNA are incubated together at at 0 degrees Celsius in calcium chloride solution. ◦ Only a few cells uptake the plasmid DNA. or BACs. ◦ Cloning vectors with the transcription and translation signals needed for regulated expression of a cloned gene are called expression vectors. cells incubated with the plasmid DNA are subjected to a high voltage pulse. often at very high levels to make purification easier. referred to as selectable and screenable markers. are artificial vectors large enough to be thought of as chromosomes that can hold much larger DNA segments than plasmids. The calcium ions are believed to neutralize charges on phosphates and membrane. so a method is needed to identify those that do. transiently renders the bacterial membrane permeable to large molecules. YAC vectors can be used to clone very long segments of DNA. is of interest. Plasmid vectors have been constructed for yeast. called electroporation. the product of a cloned gene. 136 ◦ In the laboratory. Investigators can manipulate cells to express cloned genes in order to study their protein products. ◦ Yeast artificial chromosomes (YACs) contain all the elements needed to maintain a eukaryotic chromosome in the yeast nucleus needed for stability and proper segregation of the chromosome ant cell division. ◦ Some of these plasmids have multiple ori sites so it can be used in more than one species—these are called shuttle vectors. ▪ One strategy is to utilize one of two types of genes in the plasmid. this approach. A screenable marker is a gene encoding a protein that causes the cell to produce a colored or fluorescent molecule. then subjected to heat shock by rapidly shifting the temperature between 37-43 degrees Celsius. ▪ To accommodate very long segments of cloned DNA. rather than the gene itself. BAC vectors have very stable ori sites that maintain the plasmid. ◦ The goal is to alter the sequences around a cloned gene to trick the host organism into producing the protein product of the gene. ◦ Pulsed field gel electrophoresis are used to separate the fragments of YAC when cut up by restriction endonucleases. ▪ In an alternative method. The heat shock causes the cells to uptake the plasmid DNA. Selectable markers either permit the growth of a cell (positive selection) or kill the cell (negative selection) under a defined set of conditions. It is a variation of gel electrophoresis that can separate very large DNA segments. Yeast Artifical Chromosomes ◦ Yeast is very easy to maintain and grow on a large scale in the laboratory. ▪ The BAC vector includes both selectable and screenable markers. ▪ BAC also include genes that encode proteins that direct reliable distribution of the recombinant chromosomes to ensure equal division. ◦ They are easy to store and grow in the laboratory. ▪ Many different systems are used to express recombinant proteins Bacteria ◦ Bacteria remains the most common host for protein expression because the regulatory sequences that govern gene expression in many bacteria are well understood and can be harnessed to express cloned proteins at high levels. ◦ DNA microarray ▪ DNA microarray is a method to determine which genes are expressed and which genes are not expressed in a given sample. ◦ Yeast have tough cell walls that are difficult to breach in order to introduce DNA vectors. Requires knowledge of the DNA sequence in the region of interest (need primers) no host cells are involved requires very little starting material PCR primers: you need primers (sequences of DNA that are complementary to a sequence on a DNA strand) that flank both sides of the target region. the solution is cooled to allow the DNA primer to bind to the original DNA for amplification. With enough heat. You are now left with a cDNA strand. 3) use cDNA as template in a PCR reaction. 137 expression of the cloned gene is controlled by replacing the gene's normal promoter and regulatory sequences with more efficient and convenient versions supplied by the vector. ▪ Steps: 1) use “intron free” mRNA and then reverse transcribe it to create cDNA. so taq polymerase (a heat resistant DNA polymerase) can replicate the DNA. It can provide a snapshot of all the genes in an . ◦ Problems: many intrinsically disordered regions. 2) Annealing (60 C): Once the DNA strands are separated. ▪ Steps: 1) reverse-transcribe the mRNA into a mRNA/cDNA hybrid 2) use RNAse to degrade the RNA. on inexpensive growth media. the hydrogen bonds can be broken and the two strands will separate. Number of DNA strands after “n” cycles of PCR = 2n * 2 ▪ Steps in one cycle (there are usually many): 1) Denaturation (95 C): Two strands of DNA are held together by hydrogen bonds. ◦ cDNA ▪ Complementary DNA (cDNA) is DNA that consists of only the npart of the gene that gets translated. proteins may not fold correctly Yeast ◦ Yeast is probably the best understood eukaryotic organism and one of the easiest to grow and manipulate in the laboratory. ◦ RT-PCR ▪ Reverse-transcriptase PCR: amplify mRNA sequence into many DNA sequences with the help of reverse transcriptase. ◦ PCR ▪ Polymerase chain reaction amplifies DNA sequences in vitro. 3) Elongation (72 C): The solution is raised in temperature again. then they will only be separated by size. informing the researcher about the genes that are expressed at a given stage in the organism’s development or under a particular set of environmental conditions. Replication begins in multiple different ori spots along the chromosome and extends to the end of the chromosome. ◦ DNA replication basics DNA replication is semiconservative. DNA replication ◦ Replication of DNA occurs differently in prokaryotes and eukaryotes ▪ A bacterial chromosome is a circular double stranded DNA complexes with nucleoid proteins. ▪ Smallest proteins travel the longest. indicating that a specific antigen exists. and if they bind to their specific antigen there will be a color change in the microtiter plate. largest proteins travel the shortest. . they will light up with florescence. ◦ Gel electrophoresis ▪ Gel electrophoresis is a method to separate sequences of DNA. Antibodies are placed on a microtiter plate. so negatively charged molecules will move faster down the plate. This is because DNA polymerase can only add new nucleotides to the 3'-OH end. ▪ Eukaryotic chromosomes are linear and there are more than one chromosome. DNA replication occurs in a 5' to 3' direction. RNA. meaning that a replicated DNA molecule contains one old and one new strand. Useful in diagnosing chromsomal disorders such as down's syndrome. ◦ Karyotyping ▪ Karyotyping is a method to count the number of chromosomes. When the proteins are ran through gel electrophoresis. without having to worry about charge. ◦ SDS Page ▪ SDS page is a detergent used to denature proteins into their primary form and to “de- charge” the proteins. or proteins by their size and charge. When they do. Attach thousands of copies of DNA for the genes you want to test for. ▪ Steps: 1) Begin with a glass slide or chip. the telomere. Replication begins in a specific spot called the origin of replication region (ori) and ends at the termination region (ter). 138 organism. ◦ ELISA ▪ ELISA is a technology to determine if a specific antigen exists. the more you know that gene is being transcribed. which will have a tougher time to move. The brighter the signal. The cDNA will hybridize (bond) to the complementary strands if they match. ▪ Smaller fragments will travel further down the gel towards the positive side than the larger fragments. 3) Use the cDNA as a probe and wash it over your chip. 2) take all mRNA being transcribe and convert it to cDNA. ▪ The plate is positively charged. replication does not take place in discrete steps. A sliding clamp tethers the DNA pol II to the template to allow the enzyme to catalyze consecutive additions without releasing the DNA strand it is attached to. The replication machinery allows all these steps to take place at the same time (concerted). It adds new dNTPs to the 3'-OH end. DNA pol III extends the RNA with DNA. it is ahead of the replication fork. forming an okazaki fragment. ▪ 2) In leading strand synthesis.fas. ▪ Bacteria have 3 different DNA polymerases: DNA pol I is used for primer removal and gap filling of okazaki fragments. DNA primase synthesizes a short RNA primer. DNA ligase joins the DNA fragments. DNA gyrase relieves strain while double- strand DNA is being unwound by helicase.swf for an excellent animation of DNA replication!!!!!! ◦ Replication of prokaryotic chromosomes ▪ Replication proceeds bidirectionally from ori to ter. DNA pol II is used for DNA repair. ▪ In actuality. . 139 ◦ Eukaryotic DNA synthesis ▪ 1) DNA helicase unwinds the DNA helix.edu/~biotext/animations/replication1. ▪ 4) As the replicating form move son. ▪ 3) Lagging strand synthesis occurs discontinuously because the DNA is exposed in the 5' to 3' direction. ▪ http://sites. As the fork extends. Single-stranded DNA binding proteins (SSBs) attach to the unwound DNA strands to prevent re-annealing of the DNA strands. the process repeats. DNA topoisomerase removes the supercoils. replacing it with DNA. the leading and lagging strands twist into helical forms. ▪ Replicon is the length of DNA that is replicated following one initiation event at a single region. DNA polymerase I removes it with RNA. DNA polymerse III synthesizes DNA in a 5' to 3' direction. forming a continuous leading strand and multiple okazaki fragments.harvard. . meaning that multiple polypeptides can be synthesized from the same mRNA. the tips of chromosomes. This process counteracts the tendency for the teolmere to shorten at replication. called telomeres. the lagging strand reaches a point where its system of RNA priming cannot work. At the tip. have adjacent repeats of simple DNA sequences (i. ▪ Proteins are polycistronic. These repeats do not code for an RNA or a protein but nevertheless are important. meaning that only one polypeptide can be synthesized from the same mRNA. ▪ An enzyme called telemorase adds these simple repeat units to the chromosome ends. ▪ To solve this problem. ▪ Eukaryotes are monocistronic. part of which acts as a template for the polymerization of the telomeric repeat unit that is added to the 3' end. 140 DNA pol III is used for DNA synthesis. and an unpolymerized section remains and a shortened chromosome would be the result. in humans the repeat sequence is TTAGGG).e. The telemorase carries a small RNA molecule. DNA Transcription ◦ Transcription ▪ Transcription is the creation of RNA molecules from DNA template. ◦ Completing DNA replication: Eukaryotes ▪ The ends of the chromosomes present a special problem for the replication process. The telemorase protein is a member of a class of enzymes called reverse transcriptases (recall this from the chapter on viruses). A promoter region is a sequence. For prokaryotes. the pribnow box is the most common sequence of nucleotides at the promoter. the TATA box is the most common sequence of nucleotides a the promoter. Transcription is occurring in the 3' to 5' direction of the DNA-template strand. In eukaryotes. For eukaryotes and archaea. 141 ▪ RNA synthesis occurs in the 5' to 3' direction. ◦ Steps of transcription ▪ Initiation: RNA polymerase attaches to the promoter region on DNA and unzip the DNA into two strands. usually found upstream of the gene region. variations from it causes . that RNA polymerase and transcription factors bind to. The most common sequence of nucleotides at the promoter region is called the consensus sequence. RNA polymerase requires the assistance of proteins called transcription factors. which bind to DNA control sequences called enhancers. Termination in prokaryotes: ◦ Intrinsic (rho-independent): The mRNA contains a sequence that can base pair with itself to form a stem-loop structure that is rich in GC content. only one strand is transcribed. . The DNA strand not used for transcription is called the anti-sense DNA strand. ▪ Termination: RNA polymerase reaches special sequences that signals for the end of transcription. it stalls and eventually detaches from the DNA template strand. ▪ Elongation: RNA polymerase unzips the DNA and assembles RNA nucleotides using one strand of DNA as a template. The DNA strand used for transcription is called the coding strand. Following the stem-loop structure is a chain of uracils. 142 less tight RNA pol binding → lower transcription rate. Used for protection against degradation. RNA polymerase will then release the DNA strand from itself. When RNA polymerase reaches the uracil area. When RNA pol hits this region. a rho protein binds to the forming RNA transcript.. 143 ◦ Rho-dependent: When a certain mRNA sequence is transcribed. (poly-A) signal. .. When Rho binds. Termination in Eukaryotes: ◦ The termination sequence is usually AAAAAAAAAAA. it causes RNA polymerase to stall and detach from the DNA. it stalls and detaches from the DNA template. ▪ Small subunit is the initial binding of mRNA. ◦ Poly-A tail: This sequence is attached to the 3' end of the mRNA. It is a ribozyme: the catalytic function is performed by rRNA. Therefore. the primary RNA transcript is the mature mRNA. Peptidyl site = P site. In eukaryotes. ◦ Ribosomes ▪ Ribosomes are sites of protein synthesis. ▪ 50S + 30S = 70S (prokaryotic ribosome) ▪ 60S + 40S = 80S (eukaryotic ribosome) ▪ Large subunit is the site of peptidyl transferase activity (tRNA binds here). providing stability for the mRNA and point of attachment for ribosomes. Different splicing combinations yield different polypeptides when translated. ▪ Exit site = E site. Provides stability and control movement of mRNA across the nuclear envelope. Transcription occurs first in the nucleus. DNA Translation ◦ Transcription and translation ▪ Prokaryotes: transcription and translation occur simultaneously ▪ Eukaryotes: transcription and translation are spatially and temporally separate. a combination of genes can yield many different polypeptides. ◦ RNA Splicing: Removes introns (non-coding sequences) from the RNA transcript. Aminoacyl site = A site. ◦ Alternative splicing allows different mRNA to be generated from same RNA transcript by selectively removing differences of an RNA transcript into different combinations. 144 ▪ mRNA processing In prokaryotes. Done by small nuclear ribonculeoproteins (snRNPs). Each combination codes for a different protein product. and translation occurs second in the cytoplasm. the primary RNA transcript undergoes modification: ◦ 5' cap: A special sequence is added to the 5' end of the mRNA. . 145 ◦ tRNA ▪ tRNA is a special RNA molecule that serves as the intermediate between RNA and amino acids. Another site has a special 3 letter sequence called an anticodon: this sequence binds to a complementary sequence on the mRNA. Contains 2 sites: One site is attached to a specific amino acid. . One enzyme for each amino acid. ▪ Aminoacyl-tRNA synthetase binds an amino acid to a specific tRNA. All tRNAs shift down one site. 4) Repeat steps 1-3 to grow the polypeptide chain. A dipeptide is formed. The growing polypeptide remains in the P site. When the tRNA moves from the P to the E site. ◦ Features of the genetic code ▪ No overlaps. ▪ Prokaryotes: 1) Small subunit binds to one of the many shine-dalgarno (AUG + few other nucleotides) sequences on the mRNA transcript. scans mRNA for first AUG. the tRNA in the E site gets released. the large ribosomal subunit and the charged initiator tRNA (carrying n-formylmethionine) binds. 146 ◦ Translation initiation ▪ Eukaryotes: 1) Small subunit binds 5'-cap. There is only one AUG sequence per mRNA transcript. ◦ Translation termination ▪ 1) Ribosome hits stop codon (UAG). 3) Ribosome moves down 3 more nucleotides. ◦ Translation elongation ▪ Prokaryotes and Eukaryotes 1) Entry of second tRNA into A site. . the large ribosomal subunit and the charged initiator tRNA (carrying methionine) binds. ▪ 2) Polypeptide dissociates from the tRNA. 2) Amino acid bound to tRNA in P site bonds to amino acid bound to tRNA in A site. Release factor binds to the A site instead of another tRNA. 2) Once found. There are multiple translation initiation sites. A polysome is a single mRNA molecule bound by multiple ribosomes. no gaps between codons. tRNA and mRNA separates from the ribosome. 2) Once found. Ribosome dissociates into large and small subunits. ▪ Triplet nature: three nucleotides per amino acid. this position can vary yet still produce the same amino acid (wobble effect). ▪ Frameshift: change in length of DNA sequence alters the reading frame of the mRNA. and resumes DNA synthesis. DNA error-correction and mutations ◦ Correction mechanisms ▪ DNA polymerase makes mistakes during DNA replication. replaces it with right one. negative effects on protein function. causing a totally different polypeptide to be produced. . Have varying effects – depends on how important the amino acid is to the protein structure and function. 147 ▪ Degenerate: more than one codon per amino acid. ▪ The third nucleotide in the codon is the least important. Creates wrong base. natural selection. ▪ Excision repair: enzymes remove nucleotides damaged by mutagens. ▪ Mismatch repair: enzyme repair things DNA polymerase missed. Usually. Possible causes: mutations (some mutations are favored over others). Depurination: Purine spontaneously leaves the deoxyribose sugar it was bound to. Removes wrong base by 3'-5' exonuclease activity. ◦ Types of Mutations ▪ Substitution: one nucleotide is switched with another nucleotide. Due to wobble effect. Have large. Oxidative damage Base analogs (structures that are similar to bases) are attached by accident. Missense mutation: Change in a single base of DNA sequence yields a different amino acid. Backbone breaks from UV ray can break DNA molecule in half. No change in protein function. Intercalating agents insert themselves between nitrogenous bases and causes indel mutations. Silent mutation: A change in a single base of the DNA sequence yields the same protein. Deamination: Amine groups on nucleotide react with water to form a ketone. Nonsense mutation: Change in a single base of DNA sequence yields a premature STOP codon. ◦ Mutagens ▪ A mutagen is an agent/process that catalyzes mutations in the DNA sequence. ▪ Codon bias: different species prefer different codons that code for the same amino acid. accuracy of translation. DNA polymerase has a built in proofreader. ◦ Nucleosome: DNA is supercoiled around bundles of 8/9 histone proteins (beads on a string). This exists when the cell is not dividing. DNA organization ◦ Chromatin is a complex of DNA and proteins that forms chromosomes within the nucleus of eukaryotic cells. ▪ Regulatory mutations: Mutations in regulatory sites affecting splicing or expression. Reciprocal Translocation: the attachment of a chromosomal fragment to a nonhomologous chromosome and vice versa. 148 Insertion: Insertion of one or more base pairs. One of two types: ▪ Euchromatin: loosely bound to nucleosomes. actively being transcribed. . ▪ Chromosomal mutations: Deletion: A segment of the chromosome is removed Inversion: A segment of the chromosome is removed and then reinserted “backward” to its original orientation Duplication: A segment of a chromosome is copied and inserted into the homologous chromosome. Deletion: Deletion of one or more base pairs. ◦ Transposons: DNA segments that can move to a new location on the same or a different chromosome. . Retrotransposon (copy and paste): nonconservative transposons are transposable elements that creates duplicate copies of themselves to be inserted elsewhere in the genome. 149 ▪ Heterochromatin: areas of tightly packed nucleosomes where DNA is inactive. etc. replication. Contains a lot of junk DNA. ◦ Long interspaced elements (LINE) are a class of autonomous transposable elements that code for reverse transcriptase ◦ Short interspaced elements (SINE) are a class of nonautonomous elements that do not code for reverse transcriptase. 2 types: ▪ Insertion sequences that consist of only one gene that codes for enzymes that transports it (transposase) ▪ Insertion sequences that code for transposase and extra genes (antibiotic resistance. ▪ Two general methods of transposition (look in the picture below): DNA transposon (cut and paste): conservative transposon is a transposable element that excises itself and moves to a new location.) ▪ Insertions of transposons into another region could cause mutation. lac Z --. With no glucose available. and thus a change in activity. then the stem and loop structure does not form and transcription continues through the operon normally. the repressor is released and transcription proceeds. B. Lac Y. If domain 3 pairs with domain 4. If domain 3 pairs with domain 2. there won't be transcription of the lac operon (even if there is lactose present as well). meaning that binding of the effector molecule to the repressor greatly reduces the affinity of the repressor for the operator. a stem and loop structure form on the mRNA and transcription stops. the stem and loop structure cannot form and transcription will occur even in the presence of tryptophan. This structure forms when the level of tryptophan is high in the cell. Domain 4 is called the attenuator because its presence is required to reduce mRNA transcription in the presence of high levels of tryptophan. ◦ Structure of the trp (tryptophan) operon ▪ -------P/O-------trp L--------trp E-----trpD------trpC------trpB-----trpA------------ P/O = promoter (operator sequence is found in the promoter) L = Leader sequence (attenuator sequence is found in the leader) trp E. Lac Z.operator –. The leader sequence has 4 domains (1-4): Domain 3 of the mRNA can base pair with either domain 2 or domain 4. . lactose binds to the allosteric site of the repressor protein. D. ◦ How the lac operon works ▪ The lac operon is an example of an inducible system. Promoter: site where RNA polymerase binds. If there is glucose present in the cell. ▪ 3) When lactose is present in the cell and there are no glucose molecules available. ▪ 2) When there is no lactose present in the cell. and transcription won't occur. 150 Prokaryotic transcription regulation ◦ Structure of the Lac (lactose) operon: ▪ -------lac I–----------------------promoter --. ▪ 1) Lac I gene gets transcribed and translated to create the repressor protein.lac Y ---. The repressor now cannot bind to the operator and RNA polymerase can proceed to transcribe the structural genes. Lac Z = structural genes. cAMP will bind to the promoter and help RNA polymerase more efficiently transcribe the structural genes. meaning that binding of the effector molecule to the repress greatly increases the affinity of the repressor for the operator and thus the repressor binds and stops transcription. This binding will cause a conformational change in the protein.lac A---- lac I gene: encodes for the Lac operon repressor protein. C. This leader sequence controls the expression of the operon through a process called attenuation. A = structural genes ◦ How the trp operon works ▪ The trp operon is a repressible system. there will be high cAMP levels. The activator (cAMP) will not bind to the promoter. the repressor binds to the operator and prevents RNA polymerase from transcribing the structural genes. If domain 4 is deleted. ▪ A key element of the trp operon is the leader sequence. Operator: site where Lac operon repressor protein binds. ▪ MicroRNAs (miRNAs): forms a complex with a protein. ◦ Nucleosome packing: methylation of histones cause tighter packing and thus preventing transcription. ▪ Silencers bind to DNA sequences and inhibit the start of translation. ▪ Modifications to the histones can be inherited by offspring. . ◦ Short interfering RNAs block mRNA translation by altering the mRNA conformation or configuration before it gets to the ribosome. then the protein-miRNA complex can bind to any complementary mRNA sequence. Eukaryotic transcription regulation ◦ Regulatory proteins: repressors and activators influence RNA pol's attachment to the promoter region. The process of miRNAs blocking translation is called RNA interference. Binding can either degrade the target mRNA or block its translation. ▪ Activators are transcription factors that help RNA polymerase binding to the correct DNA sequence. Methylation of histones keeps the DNA tightly coiled and further prevents transcription. Acetylation of histones catalyzes uncoiling and promotes transcription. 151 ◦ Repressible enzymes ▪ Repressible enzymes are when structural genes stop producing enzymes only in the presence of an active repressor. Inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence is called epigenetic inheritance. 152 Later stages of gene expression are also subject to regulation ◦ Breakdown of mRNA ▪ Molecules of mRNA do not remain intact forever. Prokaryotic mRNAs tend to have much shorter lifetimes than eukaryotic mRNAs. ◦ Initiation to translation ▪ Many proteins control the start of translation (polypeptide synthesis). Enzymes in the cytoplasm break them down. ▪ It also enables the cell to maintain its proteins in prime working order. cells can avoid wasting energy if the needed components are currently unavailable. ▪ By controlling the start of protein synthesis. some polypeptides require alterations before they become functional. ◦ Protein breakdown ▪ The final control mechanism operating after translation is the selective breakdown of proteins. and the timing of this event is an important factor regulating the amounts of various proteins that are produced in the cell. ▪ By controlling the timing of such protein modifications. the rate of reactions can be further fine-tuned. ▪ This regulation allows a cell to adjust the kinds and amounts of proteins in response to changes in its environment. ◦ Protein activation ▪ After translation is complete. ▪ Post-translational control mechanisms in eukaryotes often involve the cleavage of a polypeptide to yield a smaller final product that is the active protein. . Long-lived mRNAs can be translated into many more protein molecules than short-lived ones. one of the two X chromosomes does not uncoil into chromatin. only the genes on the X chromosome will be expressed. . ▪ It remains a dark and coiled chromosome called a Barr body. 153 ◦ Putting regulation all together (look at the picture below) X-inactivation ◦ During embryonic development in female mammals. ◦ Thus. ◦ Either X chromosome can be inactivated. meaning genes in the female will not be expressed similarly. Barr bodies cannot be expressed. so all calls in a female mammals are not necessarily functional identical. . cells contain genes whose normal products inhibit cell division. can become a cancer- causing oncogene. Examples of how proto-oncogenes can turn into oncogenes are shown in the picture below: ◦ Tumor-suppressor genes ▪ In addition to genes whose products normally promote cell division. ▪ A proto-oncogene is a normal. in effect stimulating growth through the absence of suppression. ▪ Many proto-oncogenes code for growth factors. if changed. ▪ Any mutation that decreases the normal activity of a tumor-suppressor protein may contribute to the onset of cancer. 154 The genetic basis of cancer ◦ Oncogenes and proto-oncogenes ▪ Genes that can cause cancer when present in a single copy in the cell are called oncogenes. healthy gene that. Such genes are called tumor-suppressor genes because the proteins they encode prevent uncontrolled cell growth. proteins that stimulate cell division. or for other proteins that somehow affect growth factor function or some other aspect of the cell cycle. Very little is intergenic. ◦ Genome size does not correlate with the total number of genes Features of viral genomes ◦ Viral genomes are very small because there is high selection for smaller genomes ◦ In many cases. ▪ Made up of regulatory sequences. ◦ Genome size correlates highly with the total number of genes Features of the eukaryotic genome ◦ Contains multiple linear chromosomes that are condensed via histones ◦ Contain at least two copies of each gene (diploid or polyploid) ◦ Extrachromosomal plasmids are not common ◦ 97% of human DNA is non-coding. genes can overlap . introns. repetitive sequences. etc. non-coding regions ◦ Have pseudogenes: nonfunctional and typically untranslated segment of DNA that arises from a previously functional gene. they have similar genomic architecture to bacteria ◦ Mostly haploid ◦ Both generally have a singular circular chromosome ◦ Both can potentially contain plasmids: circular extrachromosomal genetic elements (often encode for resistance to antibiotics or toxins) ◦ Most of the genome is coding (85-95%). 155 Contents of Bacteria and Archaea genomes ◦ Though archaea are more closely related to eukaryotes. ◦ Contains trandem repeats – abnormally long stretches of back to back repetitive sequences within an effected gene. . green beetles tend to get eaten by birds and survive to reproduce less often than brown beetles do. the present is the key to understanding the past. some beetles are green and some are brown. • Continuing on the example. • For example. New life forms move din from other areas. the fossil record for a region shows abrupt changes in species. ▪ Believed in inheritance of acquired characteristics: body features acquired during the lifetime can be passed down to offspring. ◦ Carolus Linnaeus developed a logical classification system for all living things (binomial nomenclature). As a result. Plants and animals living in those parts of the world were often killed off. ◦ Jean-Baptiste Lamarck's theory of evolution: ▪ Proposed the idea of use and disuse: body parts can develop with increased usage and unused parts were weakened. In other words. ▪ There is differential reproduction. • Darwin's theory of natural selection ◦ 3 key components that lead to an end result: ▪ There is variation in traits. ◦ Uniformitarianism (proposed by Charles Lyell): Held that natural forces now changing the shape of the earth's surface have been operating in the past for much of the same way. He described plants and animals on the basis of physical appearance and their method of reproduction and classified them relative to each other according to the degree of their similarities. Since the environment can't support unlimited population growth (there are limited resources) and individuals compete for survival. not all individuals get to reproduce to their full potential. 156 • Theories of evolution before Charles Darwin ◦ Catastrophism (proposed by George Cuvier): Held that there were violent and sudden natural catastrophes such as great floods and the rapid formation of of major mountain chains. 157 ▪ There is heredity. • The surviving brown beetles have brown baby beetles because this trait has a genetic basis. The molecular biology . not common ancestry. all beetles that make up the population will be brown. all individuals in the population have the advantageous trait. eventually. ▪ Fitness is usually in reference to a particular trait or allele. • Modern Evolutionary Synthesis ◦ Do we study evolution just as first described by Darwin? No. ▪ Analogous structures are structures of different species having similar or corresponding function but not from the same evolutionary origin (not from being related). • The trait for brown colored exoskeleton becomes more common in the beetle population. ▪ End result: The more advantageous trait. If this process continues. If this process continues. you will have evolution by natural selection as an outcome. which allows the organism to have more offspring. differential reproduction. becomes more common in the population. • Comparative anatomy ◦ Characteristics that results from common ancestry is known as homology. ◦ If you have variation. ◦ Analogy are similar traits that are due to convergent evolution. ▪ Biologists call anatomical similarities in different organisms homologous structures— features that often have different functions but are structurally similar because of common ancestry. and heredity. ◦ Natural selection is responsible for producing adaptations (heritable modifications that allow organisms to better survive in their environment) that increase an individual's fitness (a differential effect on the reproductive success of an individual in comparison with other individuals in the population). ▪ Convergent evolution is the process whereby organisms not closely related independently evolve similar traits as a result of having to adapt to similar environments or ecological niches. eventually. we look at fluctuations in allele frequencies at a single locus in a large population over time. ◦ Neutral variation: variation without selective value (e. However. we don't see Mendelian ratios in populations. ▪ Post-translational modifications of proteins can cause variation in phenotypic traits. ▪ We can calculate what alleles and genotypes would be (expected) if the assumptions of . genotype/phenotype distinction. ◦ Molecular biology has given us new methods. change regulation of the gene (expression and regulatory elements). ▪ Molecular biology is integral to modern evolutionary biology studies. silence a gene (mutations influencing microRNAs). ▪ Alternative splicing increases the variation of proteins that can be translated. change how a gene is spliced • Many mutations are lethal. • Sources of genetic variations in individuals ◦ Mendelian genetics (review topics in genetics unit) ▪ Chromosomal crossover and segregation help produce novel allele combinations in gametes. ▪ The random joining of gametes (fertilization in sexual reproduction) produce novel zygote combinations. ▪ The revolution in molecular biology gave us sources of variation. mechanism of inheritance. where a recessive allele can remain in the gene pool and be “stored” for later generations. ▪ Mutations influence organism evolution in multiple ways: • change the structure of the protein produced (coding region mutations). deleterious. • Microevolution typically refers to short term evolution (populations and species) • Macroevolution typically refers to long term evolution (species and longer term) ▪ Modern synthesis states that gradual evolution results from small genetic changes that are acted upon by natural selection. ◦ To study variation in populations. or where these frequencies will not change anymore? ◦ The Hardy-Weinberg model (review topics in genetics unit) is used as a null hypothesis for population genetics. and theory for evolutionary biology. fingerprints in humans) • Sources of variation in populations ◦ Unlike individuals. The origin and diversification of species can be explained by natural selection acting on individuals (so macroevolution can be explained by microevolution). and data. equilibria. or approximately neutral. data. recessive traits and even those without selective advantage can remain in populations.g. 158 revolution has led to the theory of modern synthesis. ▪ Modern synthesis specifically synthesized evolution and natural selection with genetics. if a mutation is beneficial (increases fitness). paleontology. Molecular data (DNA sequences) is now the primary data source. ▪ For example. and botany. systematics. ▪ Modern synthesis joined together micro and macroevolution. ◦ Molecular biology (review topics in genetics unit) ▪ Differential gene expression lead to variations in phenotype. ▪ Presence of two or more chromosomes (diploidy/polyploidy) permits the presence of a heterozygous condition. then it can be selected for through natural selection. ecology. We often ask two numerical questions: ▪ How do allele and genotype frequencies change over time? ▪ When is there a steady state. selection drives in one direction. but its pace slows once it is common in the population. but once common. This is an example of underdominance (heterozygote disadvantage). then the allele will reach fixation (frequency of the allele reaches 100% for that population). 159 Hardy-weinberg were met. ▪ If the values we count in nature are different. ◦ Relaxing assumptions of Hardy-weinberg: (1) natural selection is occurring ▪ Directional selection: when one allele is favored over another. If that allele is consistently being favored over a long period of time. will go to fixation quickly. • Occurs because of heterozygote advantage (overdominance): The heterozygous allele combination confers the highest fitness increase. Three scenarios: • (1) The favored allele is the dominant allele—its initial increase in frequency is the most rapid. ▪ Frequency independence is when there is no feedback on selection based on the frequency of the allele in the population (what we have been looking at so far). Two types: . • (2) The favored allele is a codominant allele—it will reach fixation most rapidly. then one of the assumptions is not met. ▪ Balancing selection is a type of selection that favors an intermediate phenotype (heterozyote) and leads to a balanced polymorphism. Frequency dependence is when the fitness of an allele is influenced by the frequency of that allele in the population. • (3) The favored allele is a recessive allele—it will take much longer to increase in frequency. • Balanced polymorphism is the condition where multiple alleles are present in the population. • The picture below depicts what the frequency of two alleles. p and q. the positive influence increases (fitness of the allele increases). ▪ As previously stated. natural selection will cause these alleles to be eliminated from the population. ◦ Relaxing assumptions of Hardy-weinberg: (3) there is mate preference . • Negative frequency dependence: means that as a trait increases in the population. and vice versa. ▪ Mutation-selection balance is an equilibrium in the number of deleterious alleles in a population that occurs when the rate at which deleterious alleles are created by mutation equals the rate at which deleterious alleles are being eliminated by selection. and some are deleterious. some mutations are beneficial. will look like over successive generations when the alleles are in mutation-selection balance. the negative influence increases (fitness of the allele decreases). Although mutations will cause the number of deleterious alleles to increase in frequency. 160 • Positive frequency dependence: as the allele increases in the population. ◦ Relaxing assumptions of Hardy-weinberg: (2) there are mutations and selection ▪ Mutations are going to randomly cause the recessive allele to turn into the dominant allele in some individuals. Inbreeding depression is the reduced biological fitness in a given population as a result of inbreeding. ◦ Relaxing assumptions of Hardy-weinberg: (5) population size is not infinite ▪ Wright-fisher model is essentially a small population version of the hardy-weinberg model. Inbreeding causes the loss of heterozygotes. Migration can introduce new alleles to the population. meaning they will have identical alleles because of a shared ancestor. then some offspring will be identical by descent to their ancestor. populations will equilibrate. ▪ Wright's F quantifies the degree of inbreeding. and increases the probability of individuals for being homozygous for deleterious alleles. ◦ Relaxing assumptions of Hardy-weinberg: (4) there is migration ▪ Migration is simply the flow of individuals from one population to another. • Inbreeding decreases the overall genetic variation within the gene pool. • The larger F. the higher homozygosity (the higher probability of identity by descent and inbreeding) ▪ Inbreeding does not positively affect fitness. meaning that variation will eventually decrease. • The assumptions of the wright-fisher model are the same as the hardy-weinberg . It is the inbreeding coefficient. Over time. ▪ With inbreeding. 161 ▪ If inbreeding (breeding of related individuals) exists in the population. the allele frequencies stay the same (p and q). the probability that two alleles at any locus in an individual will be identical as a result of inheritance (not mutation). ◦ Genetic drift. • Effective population size (Ne) is the number of individuals in an ideal population (where every individual reproduces. 162 model except the wright-fisher model assumes that the population size is not infinite. ◦ The smaller the Ne. and selection ▪ Drift and selection are important in two major ways: • Beneficial mutations may not always go to fixation because initial mutations will be so infrequent at first. mutation. mutation. • The probability that an allele will be fixed is dependent on (1) the population size (N) and (2) the number of allele copies in the population (k). ▪ Genetic drift is the process of random fluctuation in allele frequencies due to sampling effects. ▪ Two important elements that determine if selection or drift will dominate are effective population size and the strength of selection (measured by selection coefficient. no migration. s). • Genetic drift may overpower selection in very small populations (even if they are frequent at first. and populations may diverge in which alleles are present without migration. • Because of genetic drift. . selection has to be strong enough to overcome genetic drift. allele frequencies vary over time without selection. alleles may be fixed or lost (meaning you can lose heterozygotes). the less variation exists in the population.) in which the rate of genetic drift (measured by the decline in heterozygosity) would be the same as it is in the actual population. This is only seen in finite populations. etc. ▪ Why this matters: If genes are close enough together on the same chromosome.e. etc.) or human activities (i. • founder effects: subsample of a population move to a new area ◦ Neutral evolution ▪ Some mutations have little to no effect: redundancy in the genetic code. ▪ Assuming the neutral theory is true. a phenomenon where over time a location in a gene region has had more than one nucleotide substitution but we only see one. ▪ Compensatory mutations: certain advantageous mutations (i. then we can estimate the timing of events by how many substitutions there are between lineages. ◦ Haplotype is a set of alleles at different loci on the same chromosome. • Molecular clock: The assumption that molecular substitutions at neutral loci occur at a constant (clocklike rate). ▪ Neutral theory: Most molecular variation in populations is selectively neutral and most mutations in DNA. floods. mutations in introns. we need to look at multiple loci to understand evolutionary processes. 163 ◦ Founders and bottlenecks ▪ Two phenomena that cause short periods of small Ne are: • population bottlenecks: sharp reduction in the size of a population due to environmental effects (i. pseudogenes (resemble functional genes but have lost their function). ▪ Some traits are affected by many genes interacting with each other simultaneously (review polygenic inheritance and types of gene interactions in genetics unit). earthquakes. substitution rates (mutation rates) should be the same across populations and lineages. genocide). ▪ Nearly neutral theory attempts to accommodate for slightly deleterious or advantageous substitutions that might get fixed due to drift (as a result of differences in population size and other effects). • Moving from single genes to multiple genes ◦ Sometimes. underestimating the substitution rate. resistance to a toxin) can come at a fitness cost.e. loci that are physically linked segregate in the production of gametes. In the absence of recombination. . genetic drift is the most important process in DNA sequence change (not selection).e. This allows us to apply time to phylogenies. they will not independently segregate. and RNA are selectively neutral. synonymous mutations. This cost may be negated by additional compensatory mutations. ◦ Physical linkage: two or more loci on the same chromosome. ▪ A complicating factor to neutral theory is saturation. If mutation rates are constant. Therefore. then there is linkage disequilibrium. many other loci go to fixation. • Genetic hitchhiking: the process by which an allele is able to “ride along” with a nearby favorable allele to which hit is physically linked and thus increase in frequency • Background selection: The process by which an allele is lost because it is physically linked to a nearby deleterious allele. or beneficial. • Chromosome evolution (i. 164 ◦ Linkage disequilibrium: statistical association of alleles at different loci due to linkage.g. ▪ For example. ▪ Genes closely related to other genes that confer fitness effects (positive or negative) can change in frequency in a population over time: • Selective sweep: beneficial allele arises and goes to fixation. . height. Tends to randomize genotypes at a locus. thus eliminating linkage disequilibrium from a population. or background selection can be deleterious.e. neutral. They study genotype-phenotype starting from the phenotype and go down. ◦ Quantitative genetics is the study of quantitative traits and the genotype-phenotype connection. if A is more likely to be with B than b. selective sweep. and because of tight linkage. weight) ▪ Tries to answer the question: how much of the phenotypic variation (in a trait) we see in a population is due to genetic variation and not other things (like environment). chromosomal mutations – look this up in genetics unit) ◦ Why does linkage disequilibrium matter? ▪ We can look at linkage disequilibrium in populations for the signal of things like migration and selection. ▪ A quantitative trait is a measurable phenotype that depends on the cumulative actions of many genes and the environment (e. • Fitness landscapes and quantitative genetics ◦ Fitness landscape: a heuristic representation of fitness as a function of genotype or phenotype. ◦ The hitchhiker in genetic hitchhiking. ▪ Sources of linkage disequilibrium: • mutations • natural selection • migration • genetic drift • mating preference ▪ How does linkage disequilibrium go away? • Recombination: the creation of new combination of alleles at a locus. It is also a property within a population. species is an independently evolving lineage (or the smallest unit of independent evolving lineage. Cryptic species complicate taxonomic . and disruptive selection (occurs when environment favors extreme or unusual traits while selecting against common traits) • (3) Look for a reaction norm. taxonomists identified an individual to be a species if they sufficiently looked like a type specimen. not between populations. If we want to identify loci that are important for a quantitative trait we can do QTL mapping. variation has and continues to complicate this notion. and VP = observed variation in the phenotype. which explains why there is a species problem. Heritability is a property of a population. (1) Evolutionary species concept is not helpful for identification. stabilizing selection (bell curve. Favors an intermediate (heterozygote advantage). VE = variation due to environment. ◦ Traditionally. ◦ The so-called species problem is the problem of agreeing on a definition of species that is both clear and useful. (2) there are misunderstandings about identifying and defining species. ▪ In simple terms. • Species and speciation ◦ Why are species important? ▪ Species are important because many species are the basic biological unit and the study of speciation is essential for biology. and (4) determine the genetic location of quantitative trait loci • (1) VG is quantified as heritability. (2) determine the response to selection. (3) examine the effect of environment. ▪ There are problems with both definitions up above. Evolutionary species concept is a lineage that maintains a unique identity over time. not something general about a trait. 165 ▪ V P =V G +V E Where VG = variation due to genes. ▪ Quantitative genetics sees the evolution traits as four tasks: (1) estimate heritability. • (2) One of three responses can occur to selection: directional selection (previously explained). ▪ Cryptic species: groups of organisms that are genetically distinct and do not interbreed. but are morphologically almost indistinguishable. • (4) Quantitative trait loci (QTL): the genetic loci that contribute to a quantitative trait. the distribution of phenotypes for one genotype over a range of environmental conditions. However. e. Hybrid inviability and sterility. and can lead to embryos that do not develop fully. They can disappear as a result of selection against hybrids. ▪ Allopatric speciation: speciation between populations that are geographically separated. . • Cline: a spatial gradient in genotypes and phenotypes that exists because of different selective conditions • Hybrid zone: an area where diverging populations encounter. usually a result of diffusion of the same species to a different and isolated environments which blocks the gene flow among the distinct populations allowing differentiated fixation of characteristics. outcrossing (not selfing) organisms • doesn't have a concept of time (i. ▪ Biological species concept: species are composed of actually or potentially interbreeding individuals that are reproductively isolated. and form hybrid offspring. ▪ Parapatric speciation: process of speciation that occurs when diverging populations have distributions that abut one another. • Hybrid inviability: zygote fails to develop properly and dies before reaching maturity • Hybrid sterility: hybrids become functional adults but cannot produce • Hybrid breakdown: hybrids produce offspring that have reduced viability/fertility (hybrid's children cannot produce) ◦ Modes of speciation ▪ Divergent evolution is the accumulation of differences between groups which can lead to the formation of new species. 166 sorting. ▪ Sympatric speciation: process of speciation where diverging populations are not geographically separated. can't say whether today's sunflower could interbreed with a sunflower fossil) • there is no way to practically test reproductive isolation • hybrids ▪ Phylogenetic species concept: species are defined as the smallest monophyletic group ◦ What causes isolation? ▪ Prezygotic isolating mechanisms: isolating mechanisms that prevent mating from occurring or prevent fertilization from occurring (if mating has occurred) • Habitat isolation: species do not encounter • Behavior isolation: does not perform correct courtship rituals • temporal isolation: species mate at different seasons/time • Mechanical isolation: male/female genitalia are not compatible • Gametic isolation: male gametes do not survive in environment of female gametes (gametes do not recognize each other) ▪ Postzygotic isolating mechanisms: reproductive isolating mechanisms that occur after fertilization. ▪ Peripatric speciation: also known as peripheral isolation is a type of allopatric speciation where a small part of a population becomes isolated on the edges and forms a new species. reproduce. ◦ Biologists have developed four ideas of species concepts: ▪ Evolutionary species concept ▪ Phenetic species concept: an approach to determining species boundaries in which species are identified as clusters of phenotypically similar individuals or populations. Problems: • restricted to sexual. A tetraploid would be reproductively isolated from a diploid (instant speciation). rates of speciation and extinction are pretty close ◦ What might cause increases in speciation? ▪ Key innovation: phenotypic or genotypic trait that is associated with an increase in diversification. body size) ▪ In general. ◦ How do traits evolve and do these trends influence speciation? ▪ Cope's rule: observation that clades tend to increase in body size over time (classic example is the horse – look at picture below for the evolution of the horse vs. ▪ More specifically. we can look at broader scales and ask about general trends. ◦ Net diversification = speciation – extinction ▪ if speciation >> extinction = speciation explosion ▪ if extinction > speciation = total extinction of the group ▪ Often times. Not uncommon in plants. they look at the rate of speciation (rate that new species form) and rate of extinction (rate at which species go extinct). 167 ▪ Polyploid speciation: A polyploid is an organism with more than two copies of chromosomes. • Macroevolution ◦ Macroevolution looks at speciation and extinction to explain the evolution of individual species and groups of species. ▪ colonization of a new area (or niche) or expansion into area (or niche) ▪ Adaptive radiation: evolutionary lineages that have undergone rapid diversification into a variety of lifestyles or ecological niches. Three types of trends (the picture below describes this in terms of the trait of body size. but it can apply to any trait) . ◦ Extinctions ▪ Background extinction: normal rate of extinction for a clade or taxon ▪ Mass extinction: a statistically significant departure from background extinction that result in a substantial loss of diversity. • Stasis: a period of little to no evolutionary change ▪ Realistically. ▪ Sex (recombination) scrambles genotypes. all the pattens are probably present in some form between the two extremes of phyletic gradualism and punctuated equilibrium. Five mass extinctions have been traditionally recognized: • Ordivician-Sularian (440 mya) • Denovian (360 mya) • Permian-Triassic (250 mya) • Triassic-Jurassic (200 mya) • Cretaceous-Tertiary (65 mya) • Sexual selection ◦ What are the costs of sex? ▪ Twofold cost of sex: asexual lineages multiply faster than sexual lineages because all asexual individuals can reproduce. asexual reproduction preserves advantageous genotypes. 168 ◦ Two general ideas about the rate of speciation ▪ Phyletic gradualism: new species arise by a gradual transformation of an ancestral species through slow and continual change. ▪ Search cost: males and females must locate each other which costs time and energy and risk of predation. Sexual populations are reliant on the number of females. ▪ Risk of sexually transmitted disease ◦ Benefits of sex? ▪ Fisher-muller hypothesis: sexual reproduction can combine beneficial mutations from . ▪ Punctuated equilibrium: predicts that a lot of evolutionary change takes place in short periods of time tied to speciation events. disrupting favorable combinations. males compete for males and there is sexual selection. accelerating adaptive evolution ▪ Generates novel phenotypes ▪ Clearance of deleterious mutations ◦ What causes mate choice? ▪ Females often invest more than males. body size. sperm from multiple males compete for fertilization ▪ Sexual conflict: evolution of phenotypic characteristics that confer a fitness benefit to one sex but a fitness cost to the other. enhanced defense. • Sensory bias: females choose males that have a characteristic that is similar in nature to a preference unrelated to reproduction. • Conflict and cooperation ◦ Types of conflict ▪ Intragenomic conflict: conflict within the genome (transposable elements. 169 different individuals. • Males are ready to mate after mating and have selection for parental care when they are certain of paternity. decreased certainty of paternity. parasitism) ◦ Costs and benefits of cooperation ▪ Benefits: vigilance (increased awareness of danger). protection) • Indirect benefits: benefits that affect the genetic quality of a particular female's offspring. structures) • sperm competition: sexual selection after mating. ▪ Interspecific conflict: conflict between species (predation. replication of genes to the detriment of the organism) ▪ Intraspecific conflict: conflict within a species (can be for resources. cooperative hunting/foraging. limited resources. ▪ Intersexual selection: • Direct benefits: benefits that affect a particular female directly (food. ▪ Intrasexual selection • sexual dimorphism: difference between males and females of the same species (color. but the number of females ready to mate is lower. • When OSR is male biased. sexual selection) • Intraspecific interactions between members of the same species are influenced by disruptive (competition) and cohesive (reproduction and protection from predators and weather) forces. nest. ◦ Sexual selection: differential reproductive success resulting from competition for fertilization can occur through competition among the same sex (intrasexual) or attraction to the opposite sex (intersexual). Their investment results in better outlook for their own offspring. increased disease transmission . selfish genetic elements. ▪ Certainty of paternity: probability that a male is the genetic sire of the offspring his mate produces. dilution effect (if a predator attacks. ▪ Operational sex ratio (OSR): ratio of male to female individuals who are available for reproducing at any given time • Often the ratio of male and females in the population are close. less chance you will be attacked because you are with many other organisms that the predator can attack). increased competition for food. defense of resources ▪ Costs: increased visibility to predators. increased competition for mates. • Life history . ▪ Guild (diffuse): several species involved and the responses are not independent ▪ Escape and radiate: a species evolves a defense against enemies and is thereby enabled to proliferate into a diverse clade. ▪ Antagonistic coevolution: when the effect of interaction is negative. Geographic mosaic theory of evolution: geographic structure of populations is central to coevolution. The prey will evolve to gain defense from the predator. ▪ Diversifying coevolution: an increase in genetic diversity caused by the heterogeneity of processes across the range of ecological settings. owing to the natural selection imposed by each on the other ▪ Reciprocal selection: selection that occurs in two species due to their interactions with one another ▪ Pattern of coevolution doesn't have to be the same everywhere. ▪ Cospeciation: speciation in one species leads to speciation in another. ▪ Specific: two species evolve in response to each other. 170 ◦ Cooperation ▪ Kinship cooperation: cooperation among close relatives • inclusive fitness: sum of direct and indirect fitness • direct fitness: number of viable offspring • indirect fitness: increase in reproduction of relatives due to individual's behavior ▪ Reciprocity: exchanging actions of altruism ▪ Altruism: behavior by an individual that increases the fitness of another individual while decreasing the fitness of the actor. • Example would be in predation and herbivory interactions. ▪ Kin selection: natural selection that increases inclusive fitness ◦ How does cooperation evolve? Why should natural selection favor altruism in unrelated individuals? ▪ Reciprocal altruism: altruistic behavior can be maintained evolutionarily if individuals sequentially exchange acts of altruism • it may be beneficial to help an individual (even if they aren't your relative) if the favor will be returned • Coevolution ◦ What is the pattern of evolution of species interactions? ▪ Coevolution: reciprocal genetic change in interacting species. ▪ Evolutionary arms race: species interact antagonistically in a way that result in each species exerting reciprocal directional selection on the other. Then the predator will evolve in response to the prey's adaptation so they can continue eating the prey. taste bad. Both predator and prey can use camouflage. all with some special defense mechanism. ▪ Pollination of many kinds of flowers occur as the result of coevolution of finely-turned traits between flower and pollinators. ▪ Lack clutch: the clutch size (number of eggs laid in a single brood by a nesting pair of birds) that maximizes the number of surviving offspring. bite. ◦ Adaptations that have evolved as a result of coevolution: ▪ Secondary compounds: toxic chemicals produced in plants that discourage would-be herbivores ▪ Camouflage (cryptic coloration): any color. . or behavior that enables an animal to blend in with its surroundings. • Trade-off between clutch size and offspring survival. • Mullerian mimicry occurs when several animals. ◦ Dispersal: process by which a population or species moves individuals or propagules from one area to another. shape. ▪ Mimicry occurs when two or more species resemble one another in appearance. 171 ◦ Life history is the investment an organism makes in growth in reproduction. • Batesian mimicry occurs when an animal without any special defense mechanism mimics the coloration of an animal that does posses a defense. ▪ trade-offs: advantage of a change in a character is correlated with a disadvantage in other characters. pattern. ▪ Aposematic coloration: conspicuous pattern or coloration of animals that warns predators that they sting. ◦ Why do some species have many offspring and others have one? ▪ The probability of an offspring surviving past a week affects the number of offspring produced as shown in the picture on the next page. ▪ Optimallity theory: speechifying the state of a character (or reproductive strategy) that would maximize fitness. share the same coloration. poisonous. or other wise to be avoided. • Biogeography ◦ Vicariance: process by which the geographical range of a population or species is split by the formation of a physical or biotic barrier. . 172 ◦ Biogeography: the study of the distribution of species in space and time ▪ biomes: geographically and climatically defined regions with similar climatic conditions ▪ ancestral range reconstruction: reconstruction of ancestral ranges based on dispersal and vicariance analysis ◦ disjunct distributions: non-contiguous distributions of one or more species ▪ timing and availability of land bridges can explain disjunct distributions ◦ Phylogeography: the study of the processes that govern the geographical distribution of genes within species and populations. includes the biotic and abiotic factors present in its surroundings.e. ◦ Ecologists study the environment on several levels. arrays of ecosystems. ▪ At the organism level ▪ Populations. 173 • General ideas ◦ Ecology is the scientific study of the interactions of organisms with the environment. and organisms may be exchanged within a landscape. ▪ Landscapes. . These variables are grouped into two major types: ▪ Biotic factors: all of the organisms in the area. a group of individuals of the same species living in a particular geographic area. the living component of the environment. the physical and chemical factors (i. ▪ The biosphere. materials. Usually visible from the air as distinctive patches. is all of Earth that is inhabited by life. ◦ An organism's habitat is the specific environment it lives in. ◦ Organisms can be affected by many different variables in the environment. A landscape perspective emphasizes the absence of clearly defined ecosystem boundaries. which extends from the atmosphere several kilometers above the Earth to the depths of the oceans. ▪ Community. energy. includes both the biotic and abiotic components of the environments. an assemblage of all the populations of organisms living close enough together for potential interaction—all the biotic factors in the environment. temperature). ▪ Abiotic factors: The environment's nonliving components. ▪ Ecosystem. ▪ In aquatic environments. drying out in the air is a major danger. ◦ Inorganic nutrients ▪ The distribution and abundance of photosynthetic organisms depend on the availability of inorganic nutrients such as nitrogen and phosphorus. Most photosynthesis occurs near the surface. Thus any particular area of land or ocean near the equator absorbs more heat than comparable areas in the more northern or southern latitudes. their problem is maintaining adequate internal solute concentrations. ◦ Water ▪ Water is essential to life. The sun's rays strike the equatorial areas most directly (perpendicularly) whereas away from the equator. ▪ In dark environments. the rays strike Earth's surface at a slant. ▪ Aquatic organisms are surrounded by water. ▪ Few organisms can maintain a sufficiently active metabolism at temperatures close to 0 degrees Celsius. captured during photosynthesis. As a result. 174 • Physical and chemical factors influence life in the biosphere ◦ Energy sources ▪ All organisms require a source of energy to live. Thus. and temperatures above 45 degrees Celsius destroy the enzymes of most organisms. . for terrestrial organisms. ▪ Because of earth's curvature. light is not uniformly available. powers most ecosystems. ▪ Solar energy from sunlight. Earth receives an uneven distribution of solar energy. • Regional climate influences the distribution of terrestrial communities ◦ Earth's global climate patterns are largely determined by the input of radiant energy from the sun and the planet's movement in space. ◦ Temperature ▪ Temperature is an important abiotic factor because of its effect on metabolism. bacteria that extract energy from inorganic chemicals power ecosystems. ◦ The seasons of the year result from the permanent tilt of the planet on its axis as it orbits the sun. Lack of sunlight is the most important factor limiting plant growth for terrestrial ecosystems. the same amount of solar energy is spread over a larger area. As the dry air descends. ◦ After losing their moisture over equatorial zones. ◦ The latitudes between the tropics and the Arctic Circle in the north and the Antarctic circle in the south are called temperate zones. some of it spreads back to the equator. This creates seasonal change. . As the air moves back toward the equator. ▪ This descending dry air absorbs moisture from the land. This movement creates the cooling trade winds which dominate the tropics. ◦ Doldrums: an area of very calm or very light winds at areas near the equator because the high temperatures cause water to evaporate and the most air rises. ▪ As warm equatorial air rises. these regions have seasonal variations in climate and more moderate temperatures than the tropics or the polar zones. ▪ Generally. creating the abundant precipitation typical of most tropical regions. high altitude air masses spread away from the equator until they cool and descend again at latitudes of about 30 degrees north and south. ▪ The northern hemisphere and southern hemisphere is tipped most toward the sun for a few months and tipped furthest away from the sun for a few months. the region surrounding the equator between latitudes 23. 175 ▪ The globe's position relative to the sun changes through the year. it warms and picks up moisture until it ascends again.5 degrees north and 23. ▪ The tropics. ◦ Notice in the picture below that some of the descending air heads into the latitudes above 30 degrees.5 degrees south experience the least seasonal variation in solar radiation. it cools and releases much of its water content. and drops a large amount of water. Earth's rapidly moving surface deflects vertically circulating air. ▪ Prevailing winds (pink arrows) result from the combined effects of the rising and falling of air masses (blue and brown arrows) and Earth's rotation (gray arrows). cools at higher altitudes. 176 ▪ At first these air masses pick up moisture. and the dry descending air also absorbs moisture. making the trade winds blow from east to west. This is why the north and south temperate zones. especially around 60 degrees. the planet's rotation. precipitation increases again as the air moves up and over higher mountains. ◦ Landforms can also affect local climate. ◦ The figure below shows the major global air movements. ◦ A combination of the prevailing. ▪ Air temperature declines about 6 degrees Celsius with every 1. called the prevailing winds. winds that blow from west to east. tend to be moist. • In the tropics. there is little precipitation. As moist air moves in off the Ocean and encounters the westernmost mountains (we are assuming the air is moving west to east for this scenario). the slower-moving surface produces the westerlies. but they tend to drop it as they cool at higher latitudes. ▪ Because Earth is spherical. ◦ Climate and other abiotic factors of the environment control the global distribution of . Further inland. its surface moves faster at the equator (where the diameter is greatest) than at other latitudes. river-like flow patterns in the oceans. unequal heating of surface waters.000-m increase in elevation. • In temperate zones. ▪ Mountains affect rainfall. On the eastern side of the high mountain. and the location and shapes of the continents creates ocean currents. ▪ Ocean currents have profound effects on regional climates. it flows upwards. This effect is called a rain shadow. a maximum of 200m. ▪ Below the photic zone lies the aphotic zone. The influence of these abiotic factors results in biomes. marine animals. some light does reach these depths. where the ocean meets land. ▪ In the intertidal zone. and the substrate—the seafloor —is known as the benthic realm. marks the photic zone. 177 organisms. • The rocky intertidal zone is home to many sedentary organisms which attach to rocks and are thus prevented from being washed away when the tide comes in. major types of ecological associations that occupy broad geographic regions of land or water. • Coral reefs support a huge variety of invertebrates and fishes. drifting animals). called continental shelves. ▪ Terrestrial biomes are determined primarily by temperature and precipitation. • Zooplankton (small. is dominated by a fascinating variety of small fishes and crustaceans. sometimes called the twilight zone. • This dimly lit world. • Aquatic biomes ◦ Marine biomes ▪ The pelagic realm of the oceans includes all open water. the photic zone includes both the pelagic and benthic realms. ▪ Coral reefs are scattered around the globe in the photic zone of warm tropical waters above continental shelves. ▪ The depth of light penetration. . • In shallow areas such as the submerged parts of continents. • In these sunlit regions. fish. and many other types of animals are abundant in the pelagic photic zone. Although there is not enough light for photosynthesis in the aphotic zone. photosynthesis by phytoplankton (microscopic algae and cyanobacteria) and multicellular algae provides energy and organic carbon for a diverse community of animals. ▪ Aquatic biomes are determined primarily on salinity. the shore is pounded by waves during the high tide and exposed to the sun and drying winds during low tide. • A reef is built up slowly by successive generations of coral animals and by multicellular algae crusted with limestone. Very rich in species diversity. cooler water. 178 ▪ An estuary is a biome that occurs where a freshwater stream or river merges with the ocean. Algae blooms reduce light penetration and then the algae decomposes. low in nutrients. • If the lake or pond is deep enough. • Near the source. the communities of organisms are distributed according to depth of water and its distance from shore. a river or stream generally widens and slows.01% of its water but they harbor a disproportionate share of biodiversity—an estimated 6% of all described species. The water is usually warmer and murkier because of sediments and phytoplankton suspended in it. ◦ Freshwater biomes ▪ Freshwater biomes cover less than 1% of Earth's surface and contain a mere 0. it may produce a heavy growth of algae. large population of microorganisms decompose dead organisms that sink to the bottom. • Temperature plays an important role in these biomes: during the summer. as in the oceans. deep lakes have a distinct upper layer of water that has been warmed by the sun and does not mix with the underlying. • In the benthic realm. ▪ Freshwater wetlands • Range from marshes to swamps and bogs. the water is usually cold. ▪ Wetlands constitute a biome that is transitional between an aquatic ecosystem—either marine or freshwater—and a terrestrial one. killing organisms that need the oxygen. and clear. . ▪ Three major categories: (1) lakes and ponds. a pond or lake can suffer severe oxygen depletion. ▪ Lakes and ponds • In lakes and large ponds. known as an algae bloom. ◦ If there is an over-supply of nitrogen and phosphorus. (2) rivers and streams. • Downstream. Respiration by these microbes remove oxygen from water. • The mineral nutrients nitrogen and phosphorus typically determine the amount of phytoplankton growth in a lake or pond. and (3) freshwater wetlands. ▪ Rivers and streams • A river or stream changes greatly between its source and the point at which it empties into the lake or ocean. with a swift current that does not allow much to accumulate on the bottom. there is a photic and aphotic zone. The channel is often narrow. • Rainfall in these areas is quite variable. with dramatic seasonal variation. Rainfall is low. ▪ The temperature is warm year around. It is the most diverse of all biomes. ▪ Many of the world's large herbivores and their predators inhabit savannas. ◦ Savannas ▪ A savanna is a biome dominated by grasses and scattered trees. • The forest contains different layers that provide many habitats: a closed upper canopy. it averages 30-50 cm per year. harboring enormous numbers of different species. • Because of the closed canopy. 179 • Terrestrial biomes ◦ Tropical forests ▪ Tropical forests occur in equatorial areas where the temperature is warm and days are 11-12 hours long year-round. and this variability generally determines the vegetation that grows in a particular tropical forest. ▪ Tropical rain forests are found in very humid equatorial areas where rainfall is abundant (200-400 cm per year). and a sparse ground layer of plants. ▪ Poor soils and a lack of moisture inhibit the establishment of most trees. little sunlight reaches the forest floor. • Epiphytes are plants that grow commensally on other plants (like vines). ▪ Subject to frequent fires caused by lighting or human activity. 1-2 layers of lower trees. . a shrub understory. including California. ▪ Chaparral vegetation is adapted to periodic fires. ▪ Limited to small coastal areas. ▪ Deserts experience large daily temperature fluctuations. which produce mild. characterized by low and unpredictable rainfall (less than 30 cm per year). ▪ The cycles of growth and reproduction of plants in the desert are keyed to rainfall. rainy winters and hot. is a significant environmental problem. large deserts may occur in the rain shadows of mountains. ◦ Chaparrals ▪ Chaparral is characterized by dense. ▪ Perennial shrubs and annual plants are commonly seen. • At higher latitudes. • Large tracts of desert occur in two regions of descending dry air centered around 30 degrees north and 30 degrees south latitudes. . with the temperature being very hot during the day and then dropping to low temperatures at night. ▪ Plants and animals adapt to conserve as much water as possible. ▪ The process of desertification. evergreen leaves. the conversion of semi-arid regions to desert. dry summers. 180 ◦ Deserts ▪ Deserts are the driest of all terrestrial biomes. spiny shrubs with tough. ▪ The climate that supports chaparral vegetation results mainly from cool ocean currents circulating offshore. most common by lightnings. ▪ Precipitation. low branches. . ▪ Large grazing animals are characteristics of grasslands. Many mammals hibernate through cold winter. except along rivers or streams. but they are mostly treeless. ▪ The amount of annual precipitation influences the height of the grassland vegetation. ▪ Fires and grazing by large animals also inhibit growth of woody plants but do not harm the belowground grass shoots. ▪ Temperatures in temperate broadleaf forests range form very cold in the winter (-30 degrees Celsius) to very hot in the summer (30 degrees Celsius). ◦ Temperate broadleaf forests ▪ Temperate broadleaf forests grow throughout midlatitude regions. ▪ The soil is rich in organic and organic nutrients due to leaf shed. with periodic severe droughts. ▪ Vertical stratification: plants and animals live on ground. where there is sufficient moisture to support the growth of large trees. and are found in regions of relatively cold winter temperatures. 181 ◦ Temperate grasslands ▪ Temperate grasslands have some characteristics of tropical savannas. Trees drop their leaves and become dormant in late autumn. is too low to support forest growth. ▪ Annual precipitation is relatively high—75 – 150 cm and usually evenly distributed throughout the year as rain or snow. and treetops. deciduous trees characterize temperate broadleaf forests. averaging between 25 and 75 cm per year. preventing water loss and then produce leaves in the spring. • These forests typically have a growing season of 5 to 6 months and a distinct annual rhythm. • In the Northern hemisphere. moist air from the Pacific Ocean supports this unique biome. • Taiga is found across North America and Asia south of the Arctic Circle and is also found at cool. • The soil is thin and acidic. ▪ Permafrost prevents the roots of plants from penetrating very far in the soil. 182 ◦ Coniferous forests ▪ Cone-bearing evergreen trees. pine. • Most of the precipitation is in the form of snow. ▪ The arctic tundra may receive as little precipitation as some deserts. unlike most coniferous forests. ▪ High winds and colt temperatures create plant communities called alpine tundra on very high mountaintops at all latitudes. plants grow quickly and flower in a rapid burst. fir. or taiga. ◦ Tundra ▪ Tundra covers expansive areas of the Arctic between the taiga and polar ice. wet summers. which is one factor that explains the absence of trees (extremely cold temperatures and high winds are other factors that contribute to this) ▪ During the brief. high elevations in more temperate latitudes. when there is nearly constant daylight. • Warm. is the largest terrestrial biome on Earth. ▪ The climate is often extremely cold. • The conical shape of many conifers prevents too much snow from accumulating on their branches and breaking them. ▪ The temperate rain forests of coastal North America (from Alaska to Oregon) are also coniferous forests. which are sometimes warm. which. But poor drainage. warm summers. with little light for much of the autumn or winter. due to the permafrost. and the slow decomposition of conifer needles make few nutrients available for plant growth. continuously frozen subsoil—only the upper part of the soil thaws in the summer. ▪ Animals of the tundra withstand the cold by having good insulation that retains heat. is dominated by a few tree species. dominate coniferous forests. such as spruce. The northern coniferous forest. There is no permafrost beneath alpine tundra. cold winters and short. and slow evaporation keep the soil continually saturated. . and hemlock. • Taiga is characterized by long. including the tropics. ▪ The arctic tundra is characterized by permafrost. . 183 ◦ Polar ice ▪ In the Northern Hemisphere. • Only a small portion of these landmasses is free of ice or snow. small plants and invertebrates and wingless insects inhabit the frigid soil. ▪ Nevertheless. ▪ The terrestrial polar biome is closely interconnected with the neighboring marine biome. and precipitation is very low. polar ice covers land north of the tundra and in the southern hemisphere. even during the summer. polar ice covers the continent of Antarctica. ▪ The temperature in these regions is extremely cold year-round. ▪ Questions investigated by behavioral ecologists fall into two broad categories: • Proximate questions concern the immediate reason for a behavior—how it is triggered by stimuli (environmental cues that cause a response). it is called a reflex. and what underlying genetic factors are at work. ▪ Simple reflex: automatic 2 nerve (afferent/efferent) response to a stimulus controlled at the spinal cord. The answers to ultimate questions. uses a side-to-side motion to nudge the egg back with its back. Once initiated. are evolutionary explanations—they lie in the adaptive value of the behavior. This allows reflex actions to occur relatively quickly. Doing this is called homeostasis. • The specific stimulus is called a sign stimulus. there are big changes going on outside your body. ▪ You need to detect a change in the environment (a stimulus) and react to the change (a response) in a way that maintains homeostasis. In higher animals. Proximate causes are answers to such questions about the immediate mechanism for a behavior. Yet. evolve. ◦ Fixed action patterns are innate behaviors ▪ Innate behavior (instinct) is behavior that is under strong genetic control and is performed in virtually the same way by all individuals of a species. ▪ A reflex arc is a neural pathway that controls a reflex action. and contribute to the animal's survival and reproductive success. regardless of any changes in circumstances. ▪ A fixed action pattern is an unchangeable series of actions triggered by a specific stimulus. or ultimate causes. ▪ Small changes inside your body can cause its cells to be damaged or destroyed. • Ultimate questions address why a particular behavior occurs. ▪ A graylag goose retrieving an egg (sign stimulus) is an example of a fixed action pattern. and then sits down on the nest again. Will involve an intermediary interneuron or even the brain for 'processing' before synapsing with an efferent neuron and target tissue. The goose extends its neck. ◦ Simple and complex reflexes ▪ You need to keep the conditions inside your body constant. Collectively. When you do this without thinking. what mechanisms play a role. 184 • The scientific study of behavior ◦ Behavioral ecology ▪ Behavior is an action carried out by muscles or gland sunder the control of the nervous system in response to an environmental cue. but synapse in the spinal cord. . behavior is the sum of an animal's responses to internal and external environmental cues. As a component of the animal's phenotype. ▪ Complex reflex: Automatic response to a significant stimulus (controlled at brainstem or even cerebrum). most sensory neurons do not pass directly into the brain. Tries to describe the details of animal behavior and investigate how they develop. behaviors are adaptations that have been shaped by natural selection. the sequence is performed in its entirety. ▪ Behavioral ecology is the study of behavior in an evolutionary context. in which an animal learns not to respond to a repeated stimulus that conveys little to no information. but the animal's performance of most innate behaviors improve with experience. And despite the genetic component. Learning enables animals to change their behaviors in a response to changing environmental conditions. ▪ In terms of ultimate causation. ◦ Imprinting ▪ Imprinting is learning that is limited to a specific time period in an animal's life and that is generally irreversible. Lorenz showed that the most important imprinting stimulus for graylag geese was the movement of an object away from the hatchlings. habituation may increase fitness by allowing an animal's nervous system to focus on stimuli that signal food. including diet and social interactions. ▪ The limited phase in an animal's development when it can learn certain behaviors is called the sensitive period. the Hydra contracts when disturbed by a slight touch. input from the environment is required to trigger the behavior. if disturbed repeatedly by such a stimulus. Although a fixed action pattern is a simple behavior. ◦ Behavior is the result of both genetic and environmental factors ▪ Just like phenotype. ▪ Innate behaviors are under strong genetic control. can modify how genetic instructions are carried out. rather than their mother. • For example. complex behaviors can result from several fixed action patterns performed sequentially. ▪ Many environmental factors. behavior is the result of the environment as well as genes. or real danger and not waste time or energy on a vast number of other stimuli that are irrelevant to survival and reproduction. they steadfastly followed Lorenz and showed no recognition of their mother or other adults of their species. • Learning ◦ Learning is a modification of behavior as a result of specific experiences. it stops responding. 185 ▪ In its simplest form. a fixed action pattern is an innate response to a certain stimulus. . however. mates. The table below summaries the types of learning that will be discussed next. ◦ Habituation ▪ One of the simplest forms of learning is habituation. ▪ A classic example done by Konrad Lorenz: when the incubator-hatched graylag goslings spent their first few hours with Lorenz. ▪ In one type of associative learning. ▪ The simplest movement do not involve learning. The . phototaxis it he movement toward or away from light and chemotaxis is the movement toward or away from a chemical. migrate to a more favorable environment. birds navigate at night by the stars).e. or gesture (stimulus) with a specific punishment or reward (outcome). is the ability to associate one environmental feature with another. changing speed. word. • Researchers have found that migrating animals stay on course by using a variety of cues (i. ◦ Movements of animals may depend on cognitive maps ▪ An animal can move around its environment using landmarks alone. obtain food. nest sites. the regular back-and-forth movement of animals between two geographic areas. and potential hazards. An even more powerful mechanism is a cognitive map. of the spatial relationships among objects in an animal's surroundings. ▪ Studies of cognitive maps have involved animals that exhibit migration. or turning more or less frequently. ▪ In another type of associative learning. ▪ A random movement in response to a stimulus is called a kinesis. an animal learns to associate one of its own behaviors with a positive or negative effect. an internal representation. ▪ In contrast to kinesis. ▪ In spatial learning. 186 ◦ Animal movement may be a response to stimuli or require spatial learning ▪ Moving in a directed way enables animals to avoid predators. • For example. • A kinesis may merely be starting or stopping. prospective mates. Migration allows many species to access food resources throughout the year and to breed or winter in areas that favor survival. • For example. or code. or classical conditioning. ◦ Associative learning ▪ Associative learning. and find mates and nest sites. called trial-and-error learning. a taxis is a response directed toward (positive taxis) or away from (negative taxis) a stimulus. gray whales use the coastline to pilot their way north and south. a dog or a cat will learn to associate a particular sound. animals establish memories of landmarks in their environment that indicate the locations of food. an animal learns to link a particular stimulus with a particular outcome. and capture food. ▪ Whenever an animal has food choices. • Survival and Reproductive Success ◦ Foraging ▪ Foraging includes not only eating. we should expect natural selection to refine behaviors that enhance the efficiency of foraging. smell. The amount of energy required to capture the prey for the consumption. • For example. predators quickly learn to associate certain kinds of prey with painful experiences. but also any mechanism an animal uses to search for. and the nutritional value of the prey varies. ▪ The mechanism that enables an animal to find particular foods efficiently is called a search image. especially dolphins and primates. many predators seem to learn some of their basic hunting tactics by observing and imitating others. recognize. . and use information gathered by the senses. • Predation is one of the most significant potential costs for foraging. It is the set of key characteristics that will lead an animal to the desired object. ▪ Because adequate nutrition is essential to survival.” ▪ Some animals have complex cognitive abilities that include problem solving—the process of applying past experience to overcome obstacles in novel situations. ◦ Communication ▪ Interactions between animals depend on some form of signaling between the participating individuals. 187 animal then tends to repeat the response if it is awarded or avoid the response if it is harmed. • For example. The brain must form a memory that connects the environmental feature or behavior with the outcome or else associative learning won't occur. an animal's feeding behavior should provide maximal energy gain with minimal energy expense and minimal risk of being eaten by foraging.) and is “switched on” for that type. integrate. ◦ Problem-solving behavior relies on cognition ▪ A broad definition of cognition is the process carried out by an animal's nervous system to perceive. ▪ Animals forage in a great many ways. etc. store. ◦ Social learning ▪ Another form of learning is social learning—learning by observing the behavior of others. ▪ According to the optimal foraging theory. • One area of research in the study of animal cognition is how an animal's brain represents physical objects in the environment. the danger of being eaten by a predator. Some researchers have discovered that many animals are capable of categorizing objects in their environment according to concepts such as “same” and “different. • Problem solving behavior is highly developed in some mammals. ▪ Memory is the key to all associative learning. performs a behavior that generates a positive outcome. looks. there are trade-offs involved in the selection. Studies show that foraging in groups reduces the individual's risk of predation.e. • A predator develops a knowledge of a prey type (i. • Also has been observed in some bird species. ▪ Insight: When animal exposed to new situation without prior experience. the more complex signaling will be required to sustain it. A territory is an area. ◦ Chemicals that trigger reversible behavioral changes are called releaser pheromones. ▪ Examples of communication: • Chemical – chemicals used for communication are called pheromones. • The sending of. physically primed for mating. with shared parental care • Polygamous: An individual of one sex mating with several of the other ◦ Polygamous relationships often involve a single male and many females ▪ Parental care involves significant costs. Animal mating systems fall into one of three categories: • Promiscuous: no strong pair-bonds or lasting relationships between males and females • Monogamous: a bond between one male and one female. grooming. ◦ Mating behaviors ▪ Animals of many species tend to view members of their own species as competitors to be driven away. reception of. aggression. the entire routine is a chain of FAPs that must be performed flawlessly if mating is to occur. • Social behavior and Sociobiology ◦ Sociobiology ▪ Biologists define social behavior as any kind of interaction between two or more animals. ◦ Territorial behavior ▪ Many animals exhibit territorial behavior. and mating ▪ Animals use more than one type of signal simultaneously. • The size of the territories varies with the species. 188 • A signal is a stimulus transmitted by one animal to another animal. prospective mates must perform an elaborate courtship ritual. and not threats to each other. and .e. the function of the territory. • In general. of the opposite sex. ◦ Chemicals that trigger long term physiological and behavior changes are called primer pheromones • Visual – occur during displays of aggression or during courtship • Auditory • Tactile: common in social bonding. cooperation) ▪ The discipline of sociobiology applies evolutionary theory to the study and interpretation of social behavior—the study of how social behaviors are adaptive and how they could have evolved by natural selection. an essential element of interactions between individuals. May be smelled or eaten. usually fixed in location. • This is common among vertebrates and some groups of invertebrates. usually of the same species (i. and response to signals constitute animal communication. the more complex the social organization of the species. infant care. • Movements in courtship rituals are FAPs. ▪ Careful communication is an essential prerequisite for mating. Thus. including energy expenditure and the loss of mating opportunities. ▪ In many species. ◦ Mating systems and parental care ▪ The needs of the young are an important factor in the evolution of mating systems. Certainty of paternity (discussed in evolution unit) plays a big role in the mating relationships of females and males. which confirms that individuals are of the same species. that individuals defend and from which other members of the same species are usually excluded. often for several months or even years. rearing young. or lowest. including threats. And this is what usually happen sin nature. The beta. The alpha hen has first access to resources. each animal's status in the group is fixed. hen in the pecking order is dominant. and sometimes combat that determine which competitor gains access to the resource. rituals. animal. intruders will avoid marked territory and a potentially confrontation with its proprietors. 189 the resources available. • Not all species are territorial. . mates. ◦ Agnostic behavior ▪ In many species. ▪ Hens establish a clear pecking order: the alpha. conflicts that arise over limited resources such as food. hen similarly subdues all the others except the alpha. • Once a hierarchy is established. or territories. are settled by agnostic behavior. mating. ▪ Because violent combat may injure the victor as well as the vanquished in a way that reduces reproductive fitness. ◦ Dominance hierarchies ▪ Many animals live in social groups maintained by agnostic behavior. and so on down the line to the omega. or second-ranked. and so this form of social behavior can directly affect an individual's evolutionary fitness. ▪ Individuals that have established a territory usually proclaim their territorial rights continually. or top-ranked. we would predict that natural selection would favor ritualized contests. ▪ Often the victor of an agnostic ritual gains first or exclusive access to mates. a ranking of individuals based on social interactions. ▪ Pecking order in chickens is an example of a dominance hierarchy. • Territories are typically used for feeding. • Usually. she is not pecked by any other hens and can usually drive off all the others by threats rather than actual pecking. or combinations of these activities. the chance of an individual in a population surviving to various ages. Clumping often results from an unequal distribution of resources in the environment. without a pattern. individuals are placed in an unpredictable way. varying habitat conditions and social interactions make random dispersion rare. ▪ Examine population dynamics. ▪ In a random dispersion pattern. the interactions between biotic and abiotic factors that cause variation in population sizes. ◦ Within a population's geographic range. ▪ A uniform dispersion pattern (an even one) often results from interactions between the individuals of a population. Animals may exhibit uniform dispersion as a result of territorial behavior. However. ◦ Population ecology is concerned with changes in population size and factors that regulate populations over time. ▪ Use statistics to describe a population. 190 • What is population ecology? ◦ Ecologists usually define a population as a group of individuals of a single species that occupy the same general area. ◦ Estimates of population density and dispersion patterns enable researchers to monitor changes in a population and to compare and contrast the growth and stability of populations in different areas. local densities may vary greatly. The dispersion pattern of a population refers the way individuals are spaced within their area. Three types: ▪ A clumped dispersion pattern is one in which individuals are grouped in patches (most common in nature). . and are likely to interact and breed with one another. • Density and dispersion patterns are important population variables ◦ Population density is the number of individuals of a species per unit area or volume. ▪ Because it is impractical or impossible to count all individuals in a population in most cases. are influenced by the same environmental factors. ecologists use a variety of sampling techniques to estimate population densities. ▪ These individuals rely on the same resources. • Life tables track survivorship in populations ◦ Life tables track survivorship. Clumping may reduce the risk of predation or be associated with social behavior. which plot survivorship as the proportion of individuals from an initial population that are alive at each age. lizards. but give them good care. ▪ By using a percentage scale instead of actual ages on the x-axis. • Idealized models predict patterns of population growth ◦ Population size fluctuates as new individuals are born or immigrate into an area and others die or emigrate.. That is. ◦ The exponential growth model ▪ The rate of population increase under ideal conditions. ▪ Type II curve (e.g. increasing the likelihood that they will survive to maturity. called exponential growth. we can compare species with widely varying life spans on the same graph. individuals are no more vulnerable at one stage of the life cycle than at another. followed by a period when survivorship is high for those few individuals who live to a certain age. Most individuals survive to the older age intervals. Thus. ▪ When a population is expanding without limits. ▪ Type III curve indicates low survivorship for the very young. Species with this type of survivorship typically produce very large numbers of offspring but provide little or no care for them. can be calculated using the simple equation G = rN where G stands for the growth rate of the population (number of new individuals added per time interval). 191 ◦ Life tables can be used to construct survivorship curves. the value of r depends on the kind of organism. humans and mammals) usually produce very few offspring. r is the maximum capacity of members of that population to reproduce. number of births • Per capita rate of increase = total number of people ▪ In a population growing in an ideal environment with unlimited space and resources. and r stands for the per capita rate of increase (the average contribution of each individual to population growth). ◦ Three types of survivorship curves: ▪ Type I curve (e. population ecologists can predict how the size of a particular population will change over time under different conditions.. and rodents) is intermediate.g. ▪ Biotic potential: Maximum growth rate under ideal conditions (unlimited resources and no restrictions). ◦ Using idealized models. with survivorship constant over the lifespan. . r remains constant and the rate of population growth depends on the number of individuals already in the population (N). invertebrates. even explosively. N is the population size (the number of individuals in the population at a particular time). Other populations change rapidly. 192 • intrinsic rate of growth is when reproductive rate (r) is maximum (biotic potential) ▪ The exponential growth model is unrealistic because any population will eventually be limited by the resources available. ◦ Limiting factors and the Logistic Growth Model ▪ Environmental factors that restrict population growth are called limiting factors. ▪ The logistic growth model is a description of an idealized population growth that is slowed by limiting factors as the population size increases. The formula for logistic ( K −N) growth is G=rN K • The only new symbol in this equation is K, which stands for carrying capacity (the maximum population size that a particular environment can sustain). Changes in abiotic or biotic factors might increase or decrease carrying capacity. ▪ With the logistic growth model, the rate increases until around N = 1/2K. Beyond 1/2K, population growth rate decreases until N = K. At N = K, the growth rate is equal to zero. ▪ The model predicts that a population’s growth will be small when the population is either small or large, and highest when the population is at an intermediate level relative to carrying capacity. • When population is small, growth rate is small because N is small. • When population is high, limiting factors cause the growth rate to be small. • Multiple factors may limit population growth ◦ Density-dependent factors—limiting factors whose intensity is related to population density—appear to limit growth in natural populations. ▪ The most obvious is intraspecific competition. ▪ Density-dependent factors often depress a population's growth by increasing death rate. ◦ A population-limiting factor whose intensity is unrelated to population density is called a density independent factor. 193 ◦ Over the long term, most populations are probably regulated by a mixture of factors. • Population cycles ◦ Population cycle: predictable fluctuations in population over a period of time. ▪ When population grows over carrying capacity, it may be limited (lower) than the initial K due to the damage caused to the habitat → lower new carrying capacity K or it may crash to extinction. ◦ “boom-and-bust” cycle: characterized by rapid exponential growth (boom) followed by time which population falls back to a minimal level (bust). ▪ May be caused by winter food shortages. ▪ May be due to predator-prey interactions. ▪ Could be affected by a combination of limited food resources and excessive predation. • R-selection vs. K-selection ◦ K-selected population – members have low reproductive rates and are roughly constant in size (at K). Have a carrying capacity that the population levels out at. Carrying capacity is a density dependent factor. (like humans) ◦ R-selected population – Rapid exponential population growth, numerous offspring, fast maturation, little postnatal care. Generally found in rapid changing environments affected by density independent factors. Characterized by opportunistic species. (i.e. bacteria) 194 • The human population ◦ The human population continues to increase, but the growth rate is slowing. ◦ The world population is undergoing a change known as a demographic transition, a shift from zero population growth in which birth rates and death rates are high but roughly equal, to zero population growth characterized by low but roughly equal birth and death rates. ▪ Demographic transition comes with economic development. ▪ Reduced family size is the key to demographic transition. ◦ A demographic tool called an age-structure diagram is helpful for predicting a population's future growth. The age structure of a population is the number of individuals in different age-groups. ◦ Population momentum refers to population growth that would occur even if levels of childbearing immediately declined to replacement level (number of births = number of deaths). ▪ For countries with above-replacement fertility, population momentum represents natural increase to the population. ▪ For below-replacement countries, momentum corresponds to continued population decline. ◦ Ecological footprint: estimate of the amount of land required to provide the raw materials an individual or nation consumes, including food, fuel, water, housing, and waste disposal. 195 • Community Structure and Dynamics ◦ What is a community? ▪ A biological community is an assemblage of all the populations of organisms living close enough together for potential interaction. ▪ Ecosystems define the boundaries of the community according to the research questions they want to investigate. ▪ A community can be described by its species competition. Community ecologists seek to understand how abiotic factors and interactions between populations affect the composition and distribution of communities. ◦ Interspecific interactions are fundamental to community structure ▪ Organisms engage in interspecific interactions—relationships with individuals of other species in the community—that greatly affect population structure and dynamics. • Interspecific interactions are classified according to the effect on the populations concerned, which may be helpful (+) or harmful (-) or neutral (o). ▪ Types: • Interspecific competition occurs when populations of two different species compete for the same limited resource. ◦ In general, the effect of interspecific competition is negative for both populations (-/-). ◦ However, it may be far more harmful for one population than the other. • Commensalism: one species benefits while the other one is unaffected (+/o). • In mutualism, both populations benefit (+/+). ◦ Plants and mycorrhizae, herbivores and the cellulose-digesting microbes that inhabit their digestive tracts, lichens, nitrogen fixing bacteria and legumes, and reef-building corals and photosynthetic dinoflagellates are important examples of mutualism. ◦ obligate mutualism: each partner can only survive and reproduce successfully in the presence of the other ◦ facultative mutualism: mutualism is beneficial but not essential for the survival of each ◦ symbiosis is a long term interaction between two or more species. • In parasitism, a parasite lives in a host with minimum expenditure of energy and benefit at the expense of the host (+/-). ◦ Parasites can be ectoparasites (cling to the exterior of the host) or endoparasites (live within the host). ◦ Examples of ectoparasites are ticks, lice, mites and mosquitoes, which attach temporarily to feed on blood or other body fluids. ◦ Bacteria and viruses are examples of endoparasites. ◦ All viruses are parasites. • In predation, one species (the predator) kills and eats another species (the prey) (+/-). • Herbivory is the consumption of plant parts or algae by an animal (+/-). ◦ Types of predation and herbivory ▪ A true predator kills and eats other animals. ▪ Parasites spend most of their life cycles living on or in the host. The host doesn't usually die (if at all) until the parasite completes one life cycle. 196 ▪ A parasitoid is an inset that lays eggs on its host. After the eggs hatch, the larvae obtain nourishment by consuming host tissues. The host eventually dies, but not until the larvae complete development and have begun pupation. ▪ Carnivores are animals that eat animals. ▪ Omnivores are animals that eat plants and animals. ▪ A herbivore is an animal that eats plant. • Granivores are seed eaters • Grazers are animals that eat grasses • Browsers eat leaves ▪ Saprophytism: protists and fungi that decompose dead matter externally and absorb the decomposed nutrients. ◦ Competition may occur when a shared resource is limited ▪ Each species in a community has an ecological niche, defined as the sum of its use of the biotic and abiotic resources in its environment. ▪ Reminder about competition: • Interspecific competition is competition among members of different species. • Intraspecific competition is competition among members of the same species. ▪ Release from competitive exclusion – two species compete for the exactly the same resource (or occupy the same niche). One is likely to be more successful (no two species can sustain coexistence if they occupy the same niche). No two species can occupy the same niche. ▪ Interspecific competition occurs when the niches of two populations overlap and both populations need a resource that is in short supply. • In general, competition lowers the carrying capacity for the competing populations because the resources used by one population are not available to the other population. ▪ What else can happen if the niches of two populations overlap? • Resource partitioning – two species occupy the same niche but pursue slightly different resources or securing their resources in different ways, individuals minimize competition to maximize success (SLIGHTLY DIFFERENT niches • Character displacement (niche shift) – As a result of resource partitioning, certain traits allow for more success in obtaining resources in their partitions. This reduces competition and causes a divergence of features between the two species. ▪ Fundamental niche: The potential area and resources an organism is capable of using. The presence of limiting factors prevent species from occupying the fundamental niche. ▪ Realized niche: niche that an organism occupies in absence of competing species in its fundamental niche. • Even in the presence of a competing species, both species may be able to occupy their respective realized niches if there is no overlap between both species' realized niches. ◦ Trophic structure is a key factor in community dynamics ▪ Every community has a trophic structure, a pattern of feeding relationships consisting of several different levels. • The sequence of food transfer up the trophic levels is known as a food chain. • The transfer of food moves chemical nutrients and energy from organism to organism up through the trophic levels in a community. ▪ Starting at the bottom, the trophic level that supports all others consists of autotrophs 197 (“self-feeders”), which ecologists call producers. • Photosynthetic producers use light energy to power the synthesis of organic compounds. • Plants are the main producers on land whereas in water, the producers are mainly photosynthetic unicellular protists and cyanobacteria (collectively called phytoplankton). ▪ All organisms in the trophic levels above the producers are heterotrophs (“other- feeders”), or consumers, and all consumers are directly or indirectly dependent on the output of producers. ▪ Herbivores, which eat plant, algae, or phytoplankton, are primary consumers. • Herbivores have a long digestive tract with greater surface area and time for more digestion. • Have symbiotic bacteria in digestive tract to help break down cellulose which the herbivore itself cannot. ▪ Above primary consumers, the trophic levels are made up of carnivores and insectivores, which eat the consumers form the level below. ▪ Secondary consumers prey on primary consumers. • On land, they include many small mammals such as a mouse eating a herbivorous insect. • In aquatic environment, secondary consumers are mainly small fishes that eat zooplankton. ▪ Higher trophic levels include tertiary (third-level) consumers, such as snakes that eat mice and other secondary consumers. • Most ecosystems have secondary and tertiary consumers. ▪ Some ecosystems have a higher level, quaternary (fourth-level) consumers. • These include hawks in terrestrial ecosystems and killer whales in the marine environment. ▪ In another trophic level, consumers that derive their energy from detritus, the dead material produced at all the trophic levels. By breaking down detritus, decomposers link all trophic levels. Different organisms consume detritus in different stages of decay. • Scavengers, which are large animals, such as crows and vultures, feast on dead carcasses. 198 • The diet of detritivores is made up primarily of decaying organic material. • Decomposers, mainly prokaryotes and fungi, secrete enzymes that digest molecules in organic material and convert them to inorganic form. The breakdown of organic materials into inorganic ones is called decomposition. ◦ Food chains interconnect, forming food webs ▪ A more realistic view of the trophic structure of a community is a food web, a network of interconnecting food chains. • Greater number of pathways in a community food web, the more stable the community is. ▪ Notice that a consumer may eat more than one type of producer, and several species of primary consumers may feed on the same species of producer. ▪ Food webs, like food chains, do not typically show detritivores and decomposers, which obtain energy from dead organic material from all trophic levels. ◦ Species diversity includes relative abundance and species richness ▪ A community's species diversity is defined by two components: species richness, or the number of different species in a community, and relative abundance, the proportional representation of a species in a community. ▪ In the pictures above, the species diversity in woodlot B is greater than in A. Although there are four species in each lot, woodlot A mostly has the first species whereas each species is relatively equal in abundance in woodlot B. ▪ Plant species diversity in a community often has consequences for the species diversity of animals in the community. • Certain herbivores eat certain plants. Therefore, if there are a wider variety of plants, there will be a wider variety of herbivores (primary producers), and so on. ▪ Species diversity also has consequences for pathogens. • When many potential hosts are living close together, it is easy for a pathogen to spread from one to another. In woodlot A, a pathogen that infects the most abundant tree would be rapidly transmitted across the entire forest. ◦ Keystone species have a disproportionate impact on diversity ▪ Less abundant species may exert control over community composition. A keystone species is a species whose impact on its community is much larger than its biomass or abundance would indicate. • A keystone species occupies a niche that holds the rest of its community in place. ◦ As environment changes. the mussel. or human activities that damage biological communities and alter the availability of resources. floods. • The number of different organisms present in experimental areas dropped from more than 15 species to fewer than 5 species. • The type of disturbances and their frequency and severity vary from community to community. . 199 ▪ Example: • Experimenter removed a predator. can tolerate harsh conditions (lichens and mosses). The disturbed area may be colonized by a variety of species. • When ecological succession begins in a virtually lifeless area with no soil. ◦ Disturbance is a prominent feature of most communities ▪ Disturbances (blowouts) are events such as storms. r-selected species). r-selected will be replaced by stable k-selected species (live longer. slow succession) and reach climax where it remains for hundreds of years. ▪ Communities change drastically following a severe disturbance that strips away vegetation and even soil. diversity and total biomass increase. As it progresses. from experimental areas within the intertidal zone along the Washington coast. fires. A final successional stage of constant species composition is called a climax community (this usually never occurs). Pioneer species are plants and animals that are the first to colonize a newly exposed habitat (usually opportunistic. it is called primary succession. in a process called ecological succession. outcompeted many of the other shoreline organisms for the important resource of space on the rocks. • Secondary succession occurs where a disturbance has cleared away an existing community but left the soil in tact. droughts. • The result was that the sea star's main prey. Succession has a factor of randomness that makes it hard to predict. a sea star (a keystone species). which are gradually replaced by a succession of other species. • Chemical elements such as carbon and nitrogen are cycled between the abiotic and biotic components of the ecosystem. ▪ General chemical cycling in an ecosystem: • In ecosystems the supply of chemical elements used to construct molecules is limited. • Decomposers obtain chemical energy when they decompose the dead remains of plants and animals. There is no single explanation for why any non-native species turns into a destructive pest. spreading far beyond the original point of introduction and causing environmental or economic damage by colonizing and dominating wherever they find a suitable habitat. sometimes intentionally and sometimes by accident. the passage of energy through the components of the ecosystem. • Subject to a coveolutionary arms race by the prey (invasive species) and the predator. ▪ Ecosystem ecologists are especially interested in energy flow. and not every species that is able to survive in its new habitat becomes invasive. ▪ Many of these non-native species have established themselves firmly in their new locations. and chemical cycling. • Ecosystem structure and dynamics ◦ Ecosystem ecology emphasizes energy flow and chemical cycling ▪ An ecosystem consists of all the organisms in a community as well as the abiotic environment with which the organisms interact. . • Every use of chemical energy by organisms involves a loss of some energy to the surroundings in the form of heat. • Plants acquire the chemical elements and use them to build organic molecules. 200 ◦ Invasive species can devastate communities ▪ For long as people have traveled from one region to another. the transfer of materials within the ecosystem. • Plants (producers) convert the light energy into chemical energy through the process of photosynthesis. many have become invasive species. the intentional release of a natural enemy to attack and decrease the invasive species population. they have carried organisms along. decomposers return most of the elements to the soil and air in inorganic form. ▪ Humans fight invasive species with biological control. • When the plants and animals become detritus. • Animals consume the organic molecules. • Not every organism introduced to a new habitat is successful. ▪ Furthermore. • Animals (consumers) take in some of this chemical energy in the form of organic compounds when they eat the plants. ▪ General energy flow in an ecosystem: • Energy typically enters the ecosystem in the form of sunlight. ▪ Net primary production refers to the amount of biomass produced minus the amount used by producers as fuel for their own cellular respiration. . of living organic material in the ecosystem the biomass. Only about 1% of this is converted to chemical energy by photosynthesis. ▪ The amount of solar energy converted to chemical energy (in organic compounds) by an ecosystem's producers for a given area and for a given time period is called primary production. Earth receives 1019 kcal of solar energy. ◦ Energy supply limits the length of food chains ▪ When energy flows as organic matter through the trophic levels of an ecosystem. • The width of each tier indicates how much of the chemical energy of the tier below is actually incorporated into the organic matter of that trophic level. or mass. • This also explains why the population of top- level consumers is most sensitive to population fluctuations of lower levels. much of it is lost at each link in a food chain. it takes a lot of vegetation to support trophic levels so many steps removed from photosynthetic production. • Ideally. ▪ Different ecosystems vary considerably in their primary production as well as in their contribution to the total production of the biosphere. ▪ Ecologists call the amount. 10% of the energy available at each trophic level becomes incorporated into the next higher level (usually ranges from 5% to 20%). ▪ A pyramid of production illustrates the cumulative loss of energy with each transfer in a good chain. 201 ◦ Primary production sets the energy budget for ecosystems ▪ Each day. • Producers convert only 1% of the energy in the sunlight available to them to primary production. • This explains why top-level consumers such as lions and hawks require so much geographic territory. ▪ An important implication of this stepwise decline of energy in a trophic structure is that the amount of energy available to top-level consumers is small compared with that available to lower-level consumers. • Each tier of the pyramid represents the chemical energy present in all of the organisms at one trophic level of a food chain. ▪ Biogeochemical cycles can be local or global. phosphorus) • Chemicals that exist primarily in gaseous form (i. 202 ◦ Chemicals are cycled between organic matter and abiotic reservoirs ▪ Because chemical cycles in an ecosystem include both biotic and abiotic (geologic and atmospheric) components. ▪ Enter food chain: plants absorb water from soil. where chemicals accumulate or stockpiled outside of living organisms.e. carbon and nitrogen).e. ▪ Abiotic reservoir: surface and atmospheric water. • Soil is the main reservoir for nutrients in a local cycle (i. incorporating some of the chemicals into their own bodies. ◦ The water cycle ▪ All parts of the biomes are linked by the global water cycle. they are called biogeochemical cycles. • (3) Both producers and consumers release some chemicals back into the environment in waste products. Organisms on earth need water for almost all metabolic processes. • (4) Decomposers break down the complex organic molecules in detritus. ▪ The figure to the right is a general scheme for the cycling of a nutrient within an ecosystem. The products of decomposition are inorganic compounds. which replenish the abiotic reservoirs. ▪ Note that the cycle has abiotic reservoirs. animals drink and eat other organisms ▪ Recycling: transpiration ▪ Return to abiotic: evaporation and runoff . ▪ Steps of a general biogeochemical cycle: • (1) Producers incorporate chemicals from the abiotic reservoirs into organic compounds • (2) Consumers feed on the producers. the cycling is essentially global. where it may settle and eventually become part of new rocks. and as dissolved carbon compounds in the oceans. ▪ Return to abiotic: decomposers release phosphate to the soil by decomposing animal waste and the remains of dead plants and animals. phospholipids. decomposition of detritus ◦ The phosphorus cycle ▪ Organisms require phosphorus as an ingredient of nucleic acids. combustion of wood and fossil fuels. has an atmospheric reservoir and cycles globally. 203 ◦ The carbon cycle ▪ Carbon. ATP. which will then get eaten up by consumers. ▪ Return to abiotic: cellular respiration. Consumers obtain phosphorus in organic form by eating plants. the major ingredient of all organic molecules. minerals soil ▪ Enter food chain: weathering (break down) of rock release soluble phosphate to the soil. fossil fuels. ▪ Enter food chain: Photosynthesis (carbon fixation in Calvin cycle) by primary producers. Some phosphate drains from terrestrial ecosystems into the sea. ▪ Unlike the carbon cycle and other major biogeochemical cycles. This phosphorus will not cycle back into living organisms until geologic processes uplift and expose them . ▪ Abiotic reservoir: rocks. and as a mineral component of bones and teeth. peat. the phosphorus cycle does not have an atmospheric component (only rocks). Plants then uptake the soluble phosphate through the soil and build them into organic compounds. sedimentary rocks. ▪ Abiotic reservoir: CO2 in atmosphere. are made in the atmosphere by chemical reactions involving N2 and ammonia gas. ▪ Although not shown in the figure. Higher order consumers gain nitrogen from their prey. releasing N2 back into the atmosphere (this occurs in low-oxygen conditions). ▪ Return to abiotic: Consumers excrete waste nitrogen. and/or ammonium and then synthesize organic molecules. which can be then used as nitrogen sources for organisms. nitrogen is essential to the structure and functioning of all organisms. Nitrates and nitrites are more readily absorbed by plants. the phosphate availability is often quite low and commonly a limiting factor for population growth. it is a crucial and often limiting plant nutrient.(nitrate) by nitrifying bacteria. As a result. • Fixation occurs in lightning strikes and is done by free-living bacteria in the soil or bacteria living symbiotically in the roots of certain species of plants (most commonly legumes) • N2 is converted into ammonia (NH3). The process of nitrogen fixation converts N2 to compounds of nitrogen that can be used by plants. denitrifying bacteria strips oxygens from nitrites and nitrates. ◦ The nitrogen cycle ▪ As an ingredient of proteins and nucleic acids. . a process that takes millions of years. which then picks up another H+ to become ammonium (NH4+). some NH4+ and NO3. nitrates. ▪ Because phosphates are transferred from terrestrial to aquatic ecosystems much more rapidly than they are replaced. the amount in terrestrial ecosystems gradually diminishes over time. The ions produced by these chemical reactions reach the soil in precipitation and dust. In particular. aerobic denitrification produces N2O. ▪ Abiotic reservoir: Atmospheric N2 (makes up 80% of the atmosphere) and nitrogen in the soil • Atmospheric N2 cannot be absorbed by plants. decomposition of detritus releases ammonium from organic compounds back into the soil (nitrifying bacteria can convert this ammonium back into nitrites or nitrates). ▪ Enter food chain: Plants uptake nitrites. 204 to weathering. • NH4+ is then converted into NO2.(nitrite)and NO3. and changes in water patterns. regional. • Eutrophication is the process of nutrient enhancement in lakes and subsequent increase in biomass. mining. so. many toxins produced by industrial waste or applied as pesticides become concentrated as they pas through the food chain. . Lakes polluted with nutrients (i. Agriculture. • Deforestation: clear-cutting of forests. an irreversible situation.e.. species and genes ▪ Biodiversity encompasses more than in individual species—it includes ecosystem diversity. such as oil spills. from fertilizer runoff) stimulate algal blooms (massive algae/phytoplankton growth) which respire and deplete oxygen. contaminate local areas. The ozone layer protects Earth from the harmful UV rays in sunlight. and environmental pollution have brought about massive destruction and fragmentation of habitats. or biological magnification. As natural ecosystems are lost. ▪ Ecosystem diversity • The world's natural ecosystems are rapidly disappearing. • Desertification: overgrazing of grasslands that border deserts transform the grasslands into deserts. so are essential services (e. • If local populations are lost and the total number of individuals of a species declines. ▪ Genetic diversity • The genetic diversity within and between populations is the raw material that makes microevolution and adaptation to the environment possible—a hedge against future environmental changes. • Ecologists refer to the loss of a single population of a species as extirpation. ◦ Major causes of threats to biodiversity loss ▪ Habitat loss: Human alteration of habitats poses the single greatest threat to biodiversity. or parasitizing native species. do the genetic resources for that species. This concentration. too. which disrupt communities by competing with. urban development. • In addition to being transported to areas far away from where they originate. ▪ Overharvesting: The third major threat to biodiversity is over-exploitation of wildlife of harvesting at rates that exceed the ability of populations to rebound. occurs because the biomass at any given trophic level is produced from a larger toxin-containing biomass ingested from the level below. • Ozone depletion in the upper atmosphere is another example of global impact of pollution. populations of the species that make up their biological communities are also lost. and global effects. Although extirpation and declining population size are strong signals that a species is in trouble. 205 • The loss of biodiversity ◦ The loss of biodiversity includes the loss of ecosystems. it is still possible to save it. ▪ Invasive species: Ranking section behind major habitat loss is invasive species. flooding. Many animals die of oxygen starvation.g. • Severe reduction in genetic variation threatens the survival of a species. ▪ Pollution: Pollutants released by human activities can have local. • Small pollutants. water purification) ▪ Species diversity • When ecosystems are lost. preying on. Causes erosion. Breakdown of the dead algae and phytoplankton by decomposers deplete even more oxygen. species diversity. forestry. • Extinction means that all populations of a species have disappeared. and genetic diversity. allowing less heat to escape back into space. an increase in global temperatures. When they react with water vapor. but they are protected from extensive alteration. • Phenotypic plasticity is itself a trait that has a genetic basis and can evolve. ▪ Global climate change: burning of fossil fuels and forests increase CO2 in atmosphere. Thus. The increase of greenhouse gases in the atmosphere leads to the greenhouse effect. can be a deciding factor in conserving biodiversity. ◦ Restoration ecology is a developing science ▪ The expanding field of restoration ecology uses ecological principles of returning . they turn into sulfuric acid and nitric acid. • Ecologically. a narrow strip or series of small clumps of high-quality habitat connecting otherwise isolated patches. CO2 is part of a class of molecules called greenhouse gases. • Landscape ecology is the application of ecological principles to the study of the structure and dynamics of a collection of ecosystems. ◦ Sustaining ecosystems and landscapes is a conservation priority ▪ One of the most harmful effects of habitat loss is population fragmentation. Choosing locations for protection often focuses on biodiversity hot spots. or shield. The increase in global temperature leads to a rise in sea level by melting ice (affecting weather patterns). against further intrusion into the undistributed areas. ▪ To counteract the effects of fragmentation. they serve as a buffer zone. • These relatively small areas have a large number of endangered and threatened species and an exceptional concentration of endemic species. • Because endemic species are limited to specific areas. ▪ The lands surrounding these areas continue to be used to support the human population. ▪ Where habitats have been severely fragmented. biodiversity hots spots can also be hot spots of extinction. a landscape is a regional assemblage of interacting ecosystems. ◦ Climate change is an agent of natural selection ▪ Why do some species appear to be adapting to global climate change while others are endangered by them? ▪ Most of the adaptations can be attributed to phenotypic plasticity. a movement corridor. ◦ Zoned reserves are an attempt to reverse ecosystem disruption ▪ One type of protection is called a zoned reserve. gases that can absorb heat. • Phenotypic plasticity allows organisms to cope with short-term environmental changes. conservation biology often aims to sustain the biodiversity of entire ecosystems and landscapes. those that are found nowhere else. the ability to change phenotype in response to local environmental conditions. they are highly sensitive to habitat degradation. • Conservation biology and restoration ecology ◦ Protecting endangered populations is one goal of conservation biology ▪ Conservation biology is a goal-oriented science that seeks to understand and counter the loss of biodiversity. 206 • Acid rain: Burning of fossil fuels release SO2 and NO2 in the air. the splitting and consequent isolation of portions of populations. ▪ As a result. Both acids kill plants and animals when they rain to earth. an extensive region of land that includes one or more areas undisturbed by humans. ◦ Establishing protected areas slows the loss of biodiversity ▪ Conservation biologists tend to protect certain areas to maintain biodiversity. . the use of living organisms to detoxify polluted ecosystems. ▪ One of the major strategies in restoration ecology is bioremediation. 207 degraded areas to their natural state. a discipline called taxonomy. ▪ The terms used to describe how an organism obtains energy and carbon are combined to describe its modes of nutrition: • Photoautotrophs harness sunlight for energy and use CO2 for carbon. prokaryotic phototrophs capture energy from sunlight. and are by far the largest and most diverse group of prokaryotes. or binomial. Carolus Linnaeus introduced a system of naming and classifying species. ◦ In addition to naming species. including in and on the bodies of multicellular organisms. meaning they obtain their carbon atoms from the organic compounds of other organisms. Linnaeus also grouped them into a hierarchy of categories. ◦ In the 18th century. ▪ There are two major domains of prokaryotes. ▪ Biologists assign each species a two-part scientific name. • Photoheterotrophs obtain energy from sunlight but get their carbon atoms from organic sources. ▪ It places similar genera in the same family. but some have thylakoid membranes where photosynthesis takes place. 208 • Systematics connects classification with evolutionary history ◦ Systematics is a discipline of biology that focuses on classifying organisms and determining their evolutionary relationships. ▪ Sources of carbon: • Autotrophs. obtain their carbon atoms from carbon dioxide (CO2). orders into classes. • Prokaryotes called chemotrophs harness the energy stored in chemicals. including plants and some prokaryotes and protists. as well as animals. classes into phyla. ▪ The second part of the binomial is unique for each species within the genus. • Chemoheterotrophs acquire both energy and carbon from organic molecules. But benign or beneficial prokaryotes are far more common than harmful prokaryotes. and some protists. They are found wherever there is life. prokaryotes have an immense impact on our world. chemoautotrophs can thrive in conditions that seem totally inhospitable to life. ◦ Biologists typically use phylogenetic trees to depict hypotheses about the evolutionary history of a species. ▪ When we discuss prokaryotes. phyla into kingdoms. fungi. either organic molecules or inorganic molecules. we tend to focus on bacterial pathogens. ▪ Prokaryotes are essential to the health of the environment. making them indispensable components of the chemical cycle. Prokaryotic cells do not have chloroplasts. • Prokaryotes ◦ Prokaryotes are diverse and widespread ▪ Despite their small size. puts families into orders. . • Most prokaryotes. ▪ The first par is the genus to which ha species belongs. are heterotrophs. ◦ The evolutionary history of a species or group of species is called phylogeny. They function as decomposers. Because they don't depend on sunlight. • Chemoautotrophs harvest energy from inorganic chemicals and use carbon and CO2 to make organic molecules. Archarea and Bacteria. disease-causing agents. and kingdoms into domains. ◦ Prokaryotes have unparalleled nutritional diversity ▪ Two sources of energy are used by prokaryotes: • Like plants. plastic. • You have biofilm on your teeth—dental plaque is a biofilm that can cause tooth decay. organic material. • Similarity with eukaryotes (Archaea is more similar to eukaryotes than bacteria): ◦ DNA of both archaea and eukaryotes are associated with histones. • Phospholipid components (different from eukaryotes and bacteria): glycerol is different and the hydrocarbon chains are branched with ether-linkages instead of ester-linkages. and TEETH. • Biofilms are common among bacteria that cause disease in humans. metal. soil. ▪ Bacteria: • Distinct from archaea and eukaryotes by these features: ◦ cell wall made up peptidoglycan ◦ bacterial DNA not associated with histones ◦ ribosome activity is inhibited by streptomycin and chloramphenicol • How bacteria are classified ◦ Mode of nutrition/how they metabolize resources . • Archael cell walls (different from bacteria) contain various polysaccharides and proteins. but not peptidoglycan. ◦ Ribosome activity is not inhibited by certain antibiotics such as streptomycin and chloramphenicol unlike bacteria. but bacterial DNA is not. 209 ◦ Biofilms are complex associations of microbes ▪ In many natural environments. including rocks. ◦ Bacteria and archaea are the two main branches of prokaryotic evolutionarily ▪ Archaea: • Archaea are prokaryotes but differ from bacteria. prokaryotes attach to surfaces in highly organized colonies called biofilms. ▪ Biofilms form on almost any support. the metahnogens. the extreme thermophiles (“heat lovers). or gliding through slime material ◦ Shapes: cocci (spherical). • A second major group of bacteria. Include species that live symbiotically with other species. some are nitrifying bacteria • Nitrogen-fixing: heterotrophs that fix nitrogen. Most often. are helical bacteria that spiral through their environment by means of rotating. They are obligate anaerobes. Aklaliphile is an organism with optimal growth at pH levels 9 or above. ▪ Another group of archaea. corckscrew motion. Provide an enormous amount of food for freshwater and marine ecosystems. • Chemosynthetic: autotrophs. a pathogen establishes itself in the body and causes illness. ▪ A third group of archaea. • Spirochetes. Symbiosis is a close association of two or more species. have gram-positive cell walls (review prokaryote structure chapter). bacilli (rod-shaped). live in anaerobic (oxygen-lacking) environments and give off methane as a waste product. ▪ Acidophile is an organism with an optimal growth at pH levels 3 or below. Occasionally. which live in eukaryotic host cells. spirilla/spirochetes (spiral) ◦ Thick peptidoglycan cell wall (gram-positive). ◦ Bacteria include a diverse assemblage of prokaryotes ▪ Domain bacteria is currently divided into multiple groups based on comparisons of genetic sequences: • Proteobacteria are all gram-negative and share a particular rRNA sequence. however. • Cyanobacteria are the only groups of prokaryotes with plantlike. thrive in very hot temperatures. . ◦ Contain accessory pigment phycobillins ◦ Some are specialized cells called heterocysts that produce nitrogen-fixing enzymes ◦ Known as blue-green algae. the fifth group. however. our body's defenses prevent pathogens from affecting us. • Most are aerobic and heterotrophic whereas others are anaerobic and photosynthetic with the pigment bacteriorhodopsin. Typically sulfur-based. Some are notorious pathogens. lives in nodules of plants (mutualism) ◦ Some bacteria cause disease ▪ All organisms are almost constantly exposed to pathogenic bacteria. internal filaments. With regard to other characteristics. thin peptidoglcyan cell wall covered with lipopolysaccharides (gram-negative). • The chlamydias. 210 ◦ Ability to produce endospores (resistant bodies that contain DNA and a small amount of cytoplasm surrounded by a durable wall) ◦ Means of motility: flagella. ◦ Archaea thrive in extreme environments—and in other habitats ▪ A group of archaea called the extreme halophiles (“salt lovers”) thrive in very salty places. ◦ Include species that live symbiotically with other species. • Extremely salty environments may turn various colors as a result of the dense growth and colorful pigments of halophilic bacteria. oxygen-generating photosynthesis. live inside eukaryotic host cells (the sexually transmitted disease Chlamydia is part of this group). gram-positive bacteria. this large group encompasses enormous diversity. ▪ Protists are a diverse collection of mostly unicellular eukaryotes. its photosynthesis would have provided a steady source of food for the heterotrophic host and thus given it a significant selective advantage. ▪ Most protists are aquatic but others inhabit the bodies of various host organisms. ◦ Secondary endosymbiosis is the key to much of protist diversity ▪ Why are protists so diverse? ▪ Scientists think that heterotrophic eukaryotes evolved first. these had mitochondria but not chloroplasts. ▪ As shown in the figure below. they are considered the simplest eukaryotes. ◦ Parasites derive their nutrition from a living host. eating bacteria and other protists. For a human disease. green algae and red algae . • Protists ◦ Protists are an extremely diverse assortment of eukaryotes. • If the cyanobacterium continued to function within its host cell. capable of both photosynthesis and heterotrophy. • Still other protists are mixotrophs. producing their food by photosynthesis. ▪ Koch's postulates are used to prove that a bacterium causes a disease. autotrophic eukaryotes are though to have arisen later from a lineage of heterotrophic eukaryotes descended from an individual that engulfed an autotrophic cyanobacterium through primary endosymbiosis. 211 ▪ Most bacteria that cause illness do so by producing a poison—either an exotoxin or an endotoxin. ▪ The chloroplast-bearing lineage of eukaryotes later diversified into the autotrophs green algae and red algae. and their flagella and cilia have 9+2 pattern of microtubules. ▪ Protists are more complicated than any prokaryotes because their cells have a membrane-enclosed nucleus (containing multiple chromosomes). ▪ Over time. informally called protozoans. They are difficult to characterize because of this. the researcher must be able to: • (1) find the candidate bacterium in every case of the disease • (2) isolate the bacterium from a person who has the disease and grow it in pure culture • (3) show that the cultured bacterium causes the disease when transferred to a healthy subject • (4) isolate the bacterium from the experimentally infected subject. However. • Other protists. the descendants of the original cyanobacterium evolved into chloroplasts. • And because the cyanobacterium had its own DNA. depending on the availability of light and nutrients. these are called algae (another useful term that is not taxonomically meaningful). which is harmed by the interaction. have organelles. are heterotrophs. ▪ Over subsequent occasions during eukaryotic evolution. ▪ Protists obtain their nutrition in a variety of ways: • Some protists are autotrophs. it could reproduce to make multiple copies of itself within the host cell. Some are fungus-like and some are parasitic. • Endotoxins are lipid components of the outer membrane of gram-negative bacteria that are released when the cell dies or is digested by a defensive cell. Most are unicellular. • Exotoxins are proteins that bacteria cells secrete into their environment. • Some produce nerve toxins that concentrate in filter-feeding shellfish. and mixotrophs. unicellular algae that have a unique glassy cell wall called a test which is made up of silicon dioxide. ◦ Chromoalveolates represent the range of protist diversity ▪ Chromalveolata is a large. and are also very common components of marine and freshwater plankton (communities of microorganisms that live near the water's surface). extremely diverse group that includes autotrophic. while the second is transverse (across the body) and rests in an encircling mid groove perpendicular to the first flagellum. • Are an important food source in all aquatic environments. ▪ Heterotrophic host cells enclosed the algal cells in food vacuoles but the algae—or parts of them—survived and became cellular organelles. 212 themselves became endosymbionts following ingestion by heterotrophic eukaryotes. in which an autotrophic eukaryotic protist became endosymbiotic in a heterotrophic eukaryotic protist. and mixotrophic species and multicellular as well as unicellular species. • Blooms—population explosions—of autotrophic dinoflagellates sometimes warm coastal waters to turn pinkish orange. is called secondary endosymbiosis. which can cause illness in humans . • Have two flagella: one is posterior. a phenomenon known as “red tide. ▪ Autotrophic chromalveolates include diatoms. This is a major key in protist diversity.” Toxins produced by red-tide dinoflagellates have killed large numbers of fish. heterotrophic. ▪ This process. • The cell wall of a diatom consists of two halves that fit together like the bottom and the lid of a shoe box. heterotrophs. ▪ Dinoflagellates are a group that includes unicellular autotrophs. which are temporary extensions of the cell. ◦ Rhizarians include a variety of amoebas ▪ The clade Rhizaria was recently proposed based on similarities in DNA. complex. and other features. Form “kelp forests” which many marine animals use as their feeding grounds. ▪ Water molds are heterotrophic. They owe their brownish color to some of the pigments in their chloroplasts. ▪ Amoebas move and feed by means of pseudopodia. • Perhaps the most complex of all cell. • Have flagellated sperm cells. and most are marines. contractile vacuoules. • Paramecium is the prime example of ciliates. • All are multicellular. 213 ▪ Brown algae are large. composed of organic material hardened by calcium carbonate. ▪ Foraminiferans are found both in the ocean and cell water. • Because many species resemble fungi. . Kelp are anchored to the seafloor by their root-like structures. ▪ Ciliates are a group of unicellular protists that includes heterotrophs and mixotrophs. • They have porous shells. water molds were classified as fungi until molecular comparisons revealed they were protists. • Pseudopodia encircle food and absorb it by phagocytosis. • Have specialized features such as mouths. anal pores. called tests. unicellular chromalveolates that typically decompose dead plants and animals in freshwater habitats. • Most amoebas in Rhizaria are distinguished from other amoebas by their threadlike (rather than lobe-shaped pseudopodia). which allow them to grow very tall. autotrophic chromalveolates. • Seaweed and kelp are brown algae. two kinds of nuclei (one large and one small). The largest two groups are the foraminiferans and the radiolarians. • Named for their use of cilia to move and to sweep food into their mouth. although some believe that the rhizarians should be placed in Chromalveolata. • Parasitic water molds sometimes grow on the skin or gills of fish. known as radiolarian ooze. which function in feeding and locomotion. • 90% of forams that have been identified are fossils. • Some excavates are parasites. • When they die. ▪ Like forams. • The cell is also surrounded by a test composed of organic materials. are hundreds of meters thick. which are a component of sedimentary rock. ◦ Some excavates have modified mitochondria ▪ Excavata (the excavates) have recently been proposed as a clade on the basis of their molecular and morphological characteristics. their hard parts settle to the bottom of the ocean and become part of the sediments. Many excavates have modified mitochondria that lack functional electron transport chains and use anaerobic pathways to extract energy. radiolarians are so abundant that sediments. are excellent markers for correlating the ages of rocks in different parts of the world. 214 • The pseudopodia. in this case an internal skeleton made up of silica dioxide. extend through small pores in the test. The fossilized tests. radiolarians produce a mineralized support structure. • Most species of radiolarians are marine. In some areas. . • The name revers to an '”excavated” feeding groove possessed by some members of the groups. Within the fine channels of the plasmodium. multinucleate mass of cytoplasm undivided by plasma membranes. have lobe-shaped pseudopodia. a complex of organelles located at each end (apex) of the cell. which migrates as a slug. Despite growing as a plasmodium. and the slime molds. 215 ◦ Other Protozoans ▪ Protozoa are animal-like protists. which are protists. the amoebas aggregate into a single unit. Plasmodium is a single. ◦ Unikonts include protists that are closely related to fungi and animals ▪ Unikonta is a controversial grouping that joins two well established clades: amoeboazoans. stalks bearing more capsules form. ▪ Cellular slime molds are also common on rotting logs and decaying organic matter. cytoplasm streams first one way and then the other in pulsing flows that probably help with nutrient distribution. • Its pseudopodia arch around the prey and will inclose in a food vacuoule. some parasitic amoebas. which repeat the cycle. • No physical means of motility • Form spores that are dispersed by one or more hosts. • When food becomes unavailable or when the environment desiccates (dries up). • The plasmodium extends pseudopodia through soil and rotting logs. plasmodial slime molds are unicellular organisms. • Grow as a plasmodium feeding on decaying vegetation. including many species of free-living amoebas. • Other fungi-like protists . • Exhibit both funguslike and protozoalike characteristics during their life cycle. ▪ The yellow. • The diploid cell grows into the spreading plasmodium. The individual cells of the slug mobilize to form a stalk with a capsule at the top similar to the spore-bearing bodies of many fungi. They are heterotrophs that consume either living cells or dead organic matter. and a second clade that includes animals and fungi. ▪ Amoebozoans. branching growth on a dead log is an amoebozoan called a plasmodial slime mold. Spores are then released. • The stimulus for aggression is cyclic AMP. ▪ Apicomplexans • Parasites of animals • Characterized by apical complex. • Haploid spores released from the capsule germinate into haploid amoeboid or flagellated cells. • Spores germinate into amoebas which feed on bacteria • When food sources are depleted. engulfing food by phagocytosis as it grows. which fuse to form a diploid cell. which is secreted by the amoebas that experience food deprivation first. include unicellular and colonial species as well as multicellular seaweeds. unikonts (fungi and animals). ▪ According to one hypothesis. • Because they lack septa. where both sperm and egg are motile and equal in size • Some species have ansiogamous. where the sperm and egg differ in size • Some species are oogamous. • They form filaments (hyphae) which secret enzymes that digest the surrounding substances. motile sperm. where a large egg cell remains with the parent and is fertilized by a small. or cross walls. • Have chlorophyll a and b. • Evidence suggests that a group of unikonts called choanoflagellates are the closest . and archaeplastids (red algae and green algae). containing many nuclei within a single cell. • Have cellulose cell walls • Store carbohydrates as starch • Some species have isogamous gametes. not chitin like fungi ◦ Archaeplastids include red algae. the charophytes. green algae. • The filaments of Oomycota lack septa. It is estimated that the ancestors of animals and fungi diverged more than 1 billion years ago. and land plants ▪ Almost all of the members of the supergroup Archaeplastida are autotrophic. but some have cell walls encrusted with hard. • Contain red accessory pigments called phycobilins that masks the green of chlorophyll. ▪ The warm costal waters of the tropics are home to the majority of species of red algae. The breakdown products are then absorbed. • Gametes do not have flagella. chalky deposits. are believed to be the ancestors of plants. • Cell walls made up of cellulose. ▪ Green algae. ◦ Multicellularity evolved several times in eukaryotes ▪ Multicellular organisms have evolved from three different ancestral lineages: chromalveolates (brown algae). which in many of the true fungi have. while some are unicellular. • Multicellular red-algae are typically soft-bodied. 216 ▪ Oomycota are either parasites or saprobes. • Saprobes are organisms that gets nutrition from nonliving/decaying organic matter. • A lineage of Chlorophytes. two separate unikont lineages led to fungi and animals. • Most are multicellular. which are named for their grass-green chloroplasts. they are coenocytic. 217 living protist relatives of animals. amoebas that feed on algae and bacteria. . are the closest living relatives of fungi. ▪ A group of green algae called charophytes are the closest living relatives of of land pants. • Evidence suggests that a group of single-celled protists called nucleariids. ▪ A different group of unikont protists is thought to have given rise to fungi. A diploid structure is more apt to survive genetic damage because two copies of each chromosome allow recessive mutations to be masked. and leaves help meet this resource challenge. flagellated sperm require water to swim to eggs. In the more advanced divisions (Coniferophyta and Anthophyta). Gas exchange cannot occur directly through the cuticle. the sperm. The elongation and branching of plant's stems and roots maximize exposure to the resources in the soil and the air. ▪ A plant must be able to connect its subterranean and aerial parts. the Anthophyta. including xylem. ▪ In the most advanced divisions. the dominant generation of all plants is the diploid sporophyte generation. are thickened and reinforced by a chemical called lignin. plants must be able to hold themselves up against the pull of gravity. they shed their leaves to minimize water loss during slow-growing seasons. This multicellular. conducting water and minerals upward from its roots to its leaves and distributing sugars produced in the leaves throughout its body. ▪ Because air provides much less support than water. are adapted for delivery by wind or animals. ▪ Plants must obtain nutrients from both soil and air. ▪ Plants of the Coniferophyta and Anthophyta have developed adaptations to seasonal variations in the availability of water and light. ▪ In the more primitive plant divisions. that is. a waxy covering on aerial parts that reduces desiccation (prevents water loss). two very different media. Roots. the gametophytes are enclosed (and thus protected) inside an ovary. distinguishing them from algae. some trees are deciduous. . Roots developed to obtain water and minerals from the soil and to anchor the plant. but through tiny pores called stomata that are regulated. Leaves developed as centers for photosynthesis. packaged as pollen. • For example. the fertilized egg (zygote) develops into an embryo while attached to and nourished by the parent plant. In all plants. Development of a vascular system allows the plant to distribute water and nutrients throughout all parts. stems. Stems developed to provide a framework to support leaves. ▪ All plants are covered a waxy cuticle. The cell walls of some plant cells. 218 • Plant Evolution and Diversity ◦ Plants have adaptations for life on land ▪ Except for primitive bryophytes. dependent embryo is the basis for designating plants as embryophytes. g. • Lycophytes (e. Two clades of vascular plants are informally called seedless vascular plants: the lycophytes and the pterophytes. • Must remain small and water must be readily available for absorption through surface tissues and as a transport medium for sperm. ▪ 3) The first vascular plants with seeds evolved about 360 million years ago. but they lack true roots and leaves. • Cell walls are not made up of lignin. and hornworts.. and they disperse their offspring as spores that are carried by air currents. these structures were lost as whisk ferns diverged from their ancestors. branches. • Three important pterophytes are ferns. • They resemble other plants in having apical meristems and embryos that are retained on the parent plant. club mosses. Stems. branches. quillworts) produce clusters of spore- bearing sporangia in conelike structures called strobili. meaning that bryophytes with an upright growth habit lack support. ▪ 2) The origin of vascular plants (tracheophytes) occurred about 425 million years ago. 219 ◦ Plant diversity reflects the evolutionary history of the plant kingdom ▪ 1) After plants originated from an algal ancestor approximately 475 million years ago. Sporangia are called strobili. Seeds and . produce small leaves and. enabling stems to stand upright and grow tall on land. liverworts. ribbed stems that are joined at nodes. in some species. ◦ Ferns produce clusters of sporangia called sori that develop on the under-surface of fern fronds (leaves). Bryophytes have flagellated sperm. and leaves are green and photosynthetic and have a rough texture to the presence of silicon dioxide. and whisk ferns. nonvascular plants. ◦ Whisk ferns have branching stems without roots. The absence of roots and leaves is considered a secondary loss—that is. Leaves are very small or absent. spike mosses. including mosses. Nodes occur at intervals along the stem. early diversification gave rise to bryophytes: seedless. • Both lycophytes and pterophytes require moist conditions for fertilization. Their lignin-hardened vascular tissues provide strong support. ◦ Horsetails have hollow. horsetails. or Anthophyta. haploid spores are released from the sporangium. argegonia). • Alternation of Generations and Plant Life Cycles ◦ Review alternation of generations in life cycles and cancer chapter in cell/molec bio unit ◦ The life cycle of a moss is dominated by the gametophyte (Bryophyte life cycle) ▪ (1) Haploid gametes are produced in protective structures called gametangia. Coniferophyta (conifers) + other minor divisions make up the gymnosperms. Male and female reproductive structures are borne in pollen-bearing male cones and ovule-bearing female cones. After meiosis. • Two major clades: Gymnosperms and Angiosperms. are the flowering plants. ▪ Note: The haploid gametophyte stage is the dominant stage of the life cycle of bryophytes . This survival packet facilitates wide dispersal of plant embryos. The male gametangium. or archegonium (plural. Numerous variations in habitat in growth. the zygote remains in the gametangium. • A seed consists of an embryo packaged with a food supply within a protective outer covering. • Gymnosperms were among the earliest seed plants. ▪ (4) Meiosis occurs in the sporangia at the tips of the sporophyte stalks. ◦ Coniferophyta are the cone bearing plants. produces flagellated sperm that swim through water to fertilize eggs produced by the female gametangium. A vast majority do not have flagellated sperm. ▪ (2) After fertilization. No flagellated sperm. Fertilization and seed development are lengthy: 1-3 years. or antheridium (plural. 220 pollen are key adaptations that improved the ability of plants to diversify in terrestrial habitats. antheridia). • Angiosperms. which remains attached to the gametophyte. Can survive in a variety of environmental conditions. ▪ (5) The spores undergo mitosis and develop into the gametophyte plants. developing into a sporophyte embryo and then a mature sporophyte. They have seeds produced in unprotected megaspores (“naked” seeds) near the surface of the reproductive structure. ▪ (3) There it divides by mitosis. Zygote is diploid. More specialized vascular tissues. The spores are released and develop into gametophytes by mitosis. ▪ (3) The zygote remains on the gametophyte as it develops into a new sporophyte. ▪ Unlike seedless plants. Tracheophytes have flagellated sperm that require moisture to reach an egg. which unite to form a new sporophyte. ▪ (4) Unlike Bryophytes. In gymnosperms. the spores are not released. however. producing haploid spores. Rather. including spores. Like Bryophytes. and embryos. Although eggs and sperm are usually produced in separate locations on the same gametophyte a variety of mechanisms promote cross-fertilization between gametophytes. like most plants. The gametophytes later produce gametes. ▪ (5) The black dots in the photograph are clusters of sporangia. the gametophyte dies and the sporophyte becomes an independent plant. ▪ A Gymnosperm bears two types of cones. sperm. Tracheophyte gametophytes produce antheridium and archegonium. eggs. ◦ A pine tree is a sporophyte with gametophytes in its cones (Gymnosperm life cycle) ▪ In seed plants.” or scale. • Each “leaf. a specialized structure within the sporophyte houses all reproductive stages. in which cells undergo meiosis. of the cone contains sporangia that produce spores by meiosis. which produces spores that develop into the . unlike Bryophytes (gametophyte dominated). ▪ (2) Like Bryophytes. 221 ◦ Ferns. such as pines and other conifers. have a life cycle dominated by the sporophyte (Tracheophyte life cycle) ▪ (1) Fern gametophytes often have a distinctive heart-like shape. this structure is called a cone. but they are quite small and inconspicuous. spores give rise to gametophytes within the shelter of the cone. zygotes. ▪ Note: Tracheophytes (and all other vascular plants) have a dominant sporophyte generation in their life cycle. near an egg. In a typical Gymnosperm. and eventually releases sperm. Pollen grains are released by the cones and are carried by the wind to another cone that contains a female gametophyte ▪ (2) An ovulate cone. seeds are shed about two years after pollination. or pollen grains. and its embryo grows into a pine seedling. ▪ (4) Over the course of many months. a tiny tube grows out of each pollen grain. • Male gametophytes. ▪ (5) Meanwhile. Each of its stiff scales bears a pair of ovules. ▪ The smaller ones. the scales of the cone grow together. which make eggs. which produces the female gametophyte. is larger than a pollen cone. but ordinarily only one zygote develops fully into a sporophyte embryo. vascular plants in the chapters on plant structure and function) ▪ (6) Usually. each of which makes numerous haploid spores by meiosis. ▪ (7) The ovule matures into a seed. Fertilization typically occurs more than a year after pollination. which contains the embryo's food supply and has a tough seed coat. Meiosis then occurs in a spore “mother cell” within the ovule. ▪ (3) Pollination occurs when a pollen grain lands on an ovulate scale and enters the ovule. . Pollen cones contain many sporangia. sealing it until the seeds are mature. After pollination. all eggs in an ovule are fertilized. which are simply nuclei rather than independent cells. develop from the spores. called pollen cones (1 in the figure below). produce the male gametophytes). ▪ (8) The seed is dispersed by the wind. 222 male and female gametophytes. one surviving haploid spore cell develops into the female gametophyte. digests its way through the ovule. it germinates. (More on how fertilization works in seed. and when conditions are favorable. or pollen grains. flowers are the sites of pollination and fertilization. ▪ (4) As in gymnosperms. And like cones. and the mechanisms of sexual reproduction. including pollination and fertilization. vascular plants in the chapters on plant structure and function) . a tube grows from the pollen grain to the ovule. lands on the stigma. • Plucking off a flower's petals reveals the filaments of the stamens (male reproductive structure). are similar to Gymnosperms. flowers are also short stems bearing modified leaves. Clusters of flowers are called inflorescences. • When the sepals are peeled away. The anther. Flowers house separate male and female sporangia and gametophytes. one of which becomes an egg. which are conspicuous and attract animal pollinators. The ovary matures into a fruit. a sac at the top of each filament. Incomplete flowers lack one or more floral organs. carried by the wind or an animal. • At the center of the flower is the carpel (pistil). the female reproductive structure. for example stamens or carpels. ▪ Parts of a flower: • The structures of the flower are attached in a circle to a receptacle at the base of the flower. which are usually green. The filament holds the anther. contains male sporangia and will eventually release pollen. which aids seed dispersal. ◦ The angiosperm plant is a sporophyte with gametophytes in its flowers (Angiosperm life cycle) ▪ (1) Meiosis in the anthers of the flower produces haploid spores that undergo mitosis and form the male gametophytes. The style is a tube on top of the ovary that connects it to the stigma. ▪ (3) Pollination occurs when a pollen grain. 223 ◦ The flower is the centerpiece of angiosperm reproduction ▪ Like pine cones. It holds the ovary. a unique angiosperm adaptation that encloses the ovules. ▪ Complete flowers contain all four floral organs. ▪ (2) Meiosis in the ovule produces a haploid spores that undergoes mitosis and forms the few cells of the female gametophyte. a structure that receives pollen during fertilization. • The outer layer of the circle consists of the sepals. (More on how fertilization works in seed. and a sperm fertilizes the egg. They enclose the flower before it opens. the next layer is the petals. forming a zygote. When ripe. • While the seeds are developing. 224 ▪ (5) A seed develops from each ovule. these fruits are green and effectively camouflaged against green foliage. Each seed consists of an embryo (a new sporophyte) surrounded by a food supply and a seed coat. ▪ When an animal digests a fruit. (fruit formation is discussed in more detail in the chapters on plant structure and function) ▪ (7) When conditions are favorable. completing the life cycle. advertising its presence to animals. the fruit turns a bright color. most of the tough seeds pass unharmed through its digestive tract. the ripened ovary of a flower. (seed formation is discussed more in depth in the chapters on plant structure and function) ▪ (6) While the seeds develop. forming the fruit that encloses the seeds. it develops into a mature sporophyte plant. edible fruits that are attractive to animals as food. is an adaptation that helps disperse seeds. . As the embryo begins to grow. Eventually. ◦ The structure of a fruit reflect its function in seed dispersal ▪ A fruit. The animal may deposit the seeds some distance away from where it ate the fruit. it uses the food supply from the seed until it can begin to photosynthesize. a seed germinates. the ovary’s wall thickens. ▪ Many angiosperms produce fleshy. If the algae is nitrogen-fixing. and even nuclei to flow from cell to cell. ▪ Fungi cannot run or fly in search of food. • Of special significance is the symbiosis between fungi and plant roots called a mycorrhiza. ▪ Fungi are essential decomposers in most ecosystems. ▪ Fungal hyphae are surrounded by a cell wall. • A popular human fungal infection is athlete's foot. making the relationship mutually beneficial. • The general term for a fungal infection is called mycosis. have cell walls made up of chitin. ▪ The feeding structures of a fungus are a network of threadlike filaments called hyphae. Hyphae branch repeatedly as they grow. unlike plants. then nitrogen is also provided. The reproductive structures are made up of hyphae. ▪ Some fungi are parasites. 225 • Diversity of Fungi ◦ Fungi absorb food after digesting it outside their bodies ▪ All fungi are heterotrophs that acquire their nutrients by absorption. which is usually a chlorophyta or cyanobacteria. Sugars produced by the plant through photosynthesis nourish the fungus. ▪ Fungi are more similar to human cells than bacterial cells. ▪ Because a fungus's hyphae grow longer without getting thicker. They secrete powerful enzymes that digest macromolecules into monomers and then absorb the small nutrient molecules into their cells. identical to the chitin found on the exoskeletons of many arthropods. ▪ Some fungi lack cross-walls entirely (coencytic) and have many nuclei within a single mass of cytoplasm. obtaining nutrients at the expense of living plants or animals. Some fungi produce pigments that shield algae from UV radiation or excess light. flexible nitrogen-containing polysaccharide. • Lichens is a mutualistic association between fungi and algae. but their mycelium makes up for the lack of mobility by being able to grow at a phenomenal rate. Most fungi. the hyphae consist of chains of cells separated by cross-walls (septum) that have pores large enough to allow ribosomes. the fungus develops a huge surface area from which it can secrete digestive enzymes and through which it can absorb food. • Plants are more susceptible to fungal infections than animals. • Many parasitic fungi have hyphae called haustoria that penetrate their host. . which is most often an ascomycete. The fungus. forming a mass called a mycelium ▪ The “umbrellas” that many recognize as fungi are reproductive structures. ▪ Some fungi live symbiotically with other organisms. the algae. branching throughout a food source and extending its hyphae into new territory. Mycorrhizae absorb phosphorus and other essential minerals from the soil and make them available to the plant. provides sugar from photosynthesis. a strong. provides water and protection from the environment. ▪ In most fungi. mitochondria. • (1) When the hyphae meet. ▪ Spores can be produced sexually or asexually. This stage is called karyogamy. forming the usually short-lived diploid phase. or even centuries may pass before the parental nuclei fuse. not enclosed inside sacks. • (3) Zygotes undergo meiosis. their cytoplasms fuse. which are transported over great distances by wind or water. often at the tips of specialized hyphae. many fungi have what is called a heterokaryotic stage. There are two types of asexual spores: ◦ Sporangiospores are produced in sack-like capsules called sporangia that are born on a stalk called a sporangiophore. Hyphae bearing conidia are called conidiophores. producing haploid spores. A spores that lands in a most place where food is available germinates and produces a new haploid fungus. A pair of haploid nuclei one from each strain. is called a dikaryon. • Asexual reproduction is the only known means of spore production in some fungi. No sexual reproduction takes place. But this fusion of cytoplasm is often not followed immediately by the fusion of “parental” nuclei. ◦ Conidia are formed at the tips of specialized hyphae. . ▪ Sexual reproduction: • In many fungi. Thus. sexual reproduction involves mycelia of different mating types. spore-producing structures arise from haploid mycelia that have undergone neither a heterokaryotic stage nor meiosis. 226 ◦ Fungi produce spores in both asexual and sexual life cycles ▪ Fungal reproduction typically involves the release of vast numbers of haploid spores. in which cells contain two genetically distinct haploid nuclei. • The term mold refers to any rapidly growing fungus that reproduces asexually by producing spores. Hyphae from each mycelium release signaling molecules that grow toward eachother. This stage is called plasmogamy. • The term yeast refers to any single-celled fungus. ▪ Asexual reproduction: • (4) In asexual reproduction. days. Yeast typically reproduces asexually by budding. • Two general types of asexual reproduction: ◦ fragmentation of the hyphae and regeneration ◦ budding – the pinching off a small hyphal outgrowth • Many fungi that reproduce sexually can also produce asexually. • (2) Hours. informally known as imperfect fungi. formally known as Duteromycota. • Common in lakes. are thought to represent the earliest lineage of fungi. are characterized by their protective zygosporangium. but do not produce zygospores. . ponds. ▪ Basidiomycetes. or sac fungi. ▪ The ascomycetes. ▪ The zygomycetes. • After plasmogamy of hyphae from unlike strains. a dikaryotic hypha produces more • filaments by mitosis. or zygote fungi. • These 4 cells divide by mitosis to produce 8 haploid ascospores in a sac called an ascus. • Plasmogamy between two unlike hyphae is followed by mitosis and the growth of dikaryotic hyphae to form a fruiting body is called a basidiocarp. • Example: bread mold • Lack septa. except when filaments border reproductive filaments. 8 ascospores grouped together into fruiting bodies called ascocarps. the only fungi with flagellated spores. • Lack septa. or club fungi are named after their club-shaped. • Occur only in mutualistic associations with roots of plants • About 90% of all plants have symbiotic partnerships with glomeromycetes as mycorrhizae. are named for sack-like structures called asci (plural: ascus) that produce spores in sexual reproduction. • Karyogamy and meiosis subsequently occur in terminal hyphal cells producing 4 • haploid cells. spore-producing structure called a basidium. and soil. • Example: yeast • Have septa and reproduce sexually by producing haploid ascospores. • Example: mushrooms • Many species excel at breaking down the lignin found in wood and thus play key roles as decomposers. 227 ◦ Fungi are classified into five groups ▪ The chytrids. ▪ The glomeromycetes form a distinct type of mycorrhiza in which hyphae invade plant roots branch into tiny treelike structures known as arbuscules. where zygotes produce haploid spores by meiosis. the fungus reproduces asexually • (1) Hyphae from mycelia of different mating types fuse • (2) Produce a cell containing multiple nuclei from two parents • (3) This young zygosporangium develops into a thick-walled structure that can tolerate dry or harsh environments • (4) When conditions are favorable. producing haploid spores called zygospores. forming spores in sporangia at the tips of upright hyphae. the haploid nuclei fuse. they germinate and grow into haploid mycelia. • (3) In the club shaped cells called basidia. 228 ◦ Fungal groups differ in their life cycles and reproductive stages ▪ Life cycle of Zygomycetes • As hyphae grow with food. • (4) A mushroom can release as many as a billion spores. ▪ Life cycle of Basidiocarps • (1) The heterokaryotic stage begins when hyphae of two different mating types fuse • (2) The fusion creates a heterokaryotic mycelium. . the parental nuclei fuse to form diploid zygotes. Each diploid then undergoes meiosis. When the food is depleted. the fungus produces asexually. • (5) If spores land on moist matter that can serve as food. forming diploid nuclei. forming haploid spores called basidiospores. which undergo meiosis. which line the gills of a mushroom. which grows and produces the mushroom. Animals digest food within their body after ingesting other organisms. . and mesoderm to form. They are held together by extracellular structural proteins. • Animal cells lack cell walls that provide strong support in the bodies of plants and fungi. many animals develop directly into adults. • (8) The larva undergoes a major change of body form. and by unique types of intercellular junctions. all animals undergo a period of embryonic development during which 2-3 layers of tissue form. the most abundant of which is collagen. forming a gastrula • (6) Gastrulation causes the endoderm. heterotrophic eukaryotes that (with a few exceptions) obtain nutrients by ingestion. • All but the simplest animals have muscle cells for movement and nerve cells for conducting impulses. one side of the blastula folds inward. producing a zygote • (3) the zygote divides by mitosis • (4) division of the zygote forms an early embryonic stage called a blastula • (5) in the sea star and most other animals. Lastly. Others (such as the sea star shown in the picture) develop into one or more larval stages at first. in becoming and adult capable of reproducing sexually. ▪ General life cycle of an animal: • (1) male and female adults make haploid gametes by meiosis • (2) an egg and sperm fuse. Most animals are diploid and reproduce sexually. 229 • Animal evolution and diversity ◦ What is an animal? ▪ Animals are multicellular. This mode of nutrition contrasts animals with fungi. • (7) After the gastrula stage. ◦ A larva is an immature individual that looks different from the adult animal. Most are motile during at least some point in the life cycle. • Other unique features are seen in animal reproduction and development. ectoderm. eggs and sperms are the only haploid cells. Animals' dominant generation in the life cycle is the diploid generation. • Ingestion means eating food. called metamorphosis. have closely functioning cells organized into tissues. but not front. Because many animal body plans and new phyla appear in the fossils from such an evolutionarily short time span. back. ▪ Scientists are not sure what caused the Cambrian explosion. A body cavity is a fluid-filled space between the digestive tract and outer body wall cushions the internal organs and enables them to grow and move independently of the body wall. Have 2 axes of orientation: front to back and top to bottom. a noncompressible fluid in the body forms a hydrostatic skeleton that provides a rigid structure against which muscles contract. while pseudocoelomate animals have a . In bilaterally symmetric animals. Invertebrates lack a vertebral column (backbone). • The symmetry of an animal reflects its lifestyle. sense organs. moving the animal. ▪ During embryonic development in more advanced animals. a left and a right side. during the Cambrian period. collectively called the eumetazoa. the type of symmetry found in a shovel. the parazoa. In soft-bodied animals. A radial animal is typically sedentary or passively drifting. In another group of animals. The fluid-filled coelom cushions the internal organs and allows for their expansion and contraction. biologists call this episode the Cambrian explosion. a body cavity called a coelom develops from tissue derived from the mesoderm. Other animals have bilateral symmetry. cells are not organized into true tissues. and organs do not develop. Have a dorsal (top) side and a ventral (bottom) side. 230 ◦ Animal diversification began more than half a billion years ago ▪ The lineage that gave rise to animals is thought to have diverged from a flagellated unikont ancestor more than 1 billion years ago. and mouth are usually located in the head. Acoelomate animals lack a coelom. Most animals. meeting its environment equally on all sides. • The animal phyla that have bilateral symmetry belong to the clade called bilaterians. the brain. ▪ Of the 35 or so animal phyla. There is a top and bottom side. ▪ Animal diversification appears to have accelerated rapidly from 535-525 million years ago. left. They have two (diplopblastic) or three (triploblastic) layers of tissue called germ layers. the type of symmetry found in a flowerpot. ▪ Animals arising from embryos may be characterized by the presence or absence of a body cavity. ◦ Animals can be characterized by basic features of their “body plan” ▪ Symmetry: Animals can have radial symmetry. or right sides. This arrangement facilitates mobility. ▪ Body plans also vary in the organization of tissues. an anterior (front) end and a posterior (back) end. all of the animals in all but one phylum are invertebrates. Alimentary canals are also organized into specialized compartments that carry out digestion and nutrient absorption stepwise. ▪ Many animals have segmented body parts. The picture to the right represents a morphology-based phylogenetic tree of the major phyla of the animal kingdom. Folds of the archentron form the coelom. ◦ The body plans of animals can be used to build phylogenetic trees ▪ Because animals diversified so rapidly on the scale of geologic time. . determinate cleavages. becomes concentrated toward one end of an organism. ▪ The digestive systems of animals vary. • Duterostomes have radial and indeterminate cleavages. while in other cases the body parts are modified and adopt specialized functions. over many generations. • Protostomes have spiral. there is a progressively greater increase in nerve tissue concentration at the anterior end as organism increase in complexity. This process eventually produces a head with sensory organs. In animals with bilateral symmetry. which is found in more developed clades. the body parts are the same and repeat. Simpler clades have a gastrovascular cavity: a central body cavity in the sacklike body of certain animals that functions in both the digestion and distribution of nutrients. the protostomes and duterostomes. The blastopore turns into the mouth. ▪ Cephalization is a trend whereby nervous tissue. An alimentary canal. and it probably evolved as an adaptation facilitating movement. ▪ Two markedly different cleavage patterns occur to produce two groups of animals. In some cases. A segmented boy allows for greater flexibility and mobility. it is difficult to sort out the evolutionary relationships among the various phyla using only the fossil record. 231 cavity that is not completely lined by mesoderm- derived tissue. is a digestive tract consisting of a tube running between a mouth and an anus (food goes in the mouth and out of the anus). Solid masses of the mesoderm split and form the coelom. The anus develops from the blastopore. . which help to sweep water through the sponge's body. • Sponges produce defensive compounds such as toxins and antibiotics to deter pathogens. though their individual cells can sense and react to changes in the environment. They have no nerves or muscles. • Reproduce asexually (budding) or sexually (sponges are hermaphrodites). • Does not have coelom. • Sponges have no respiratory system. ▪ The body of a sponge consists of two layers of cells separated by a gelatinous region. and predators. ▪ Adult sponges are sessile. Water enters through the pores into a central cavity. meaning they are anchored in place—they cannot escape from predators. • Amoebocytes. • Choanocytes trap food particles in mucus on the membranous collars that surround the base of their flagella and then engulf the food by phagocytosis. parasites. they are not considered true tissues and are classified with parazoa. Since the cell layers of sponges are loose associations of cells. • Most sponges lack body symmetry. animals that collect food particles from water passed through some type of food-trapping equipment. digest it. produce supportive skeletal fibers composed of a flexible protein called spongin and mineralized particles called spicules made up of CaCO3 or SiO2. • The inner cell layer consists of flagellated “collar” cells called choanocytes. ▪ Sponges are examples of suspension feeders. 232 • Invertebrate Diversity ◦ Sponges have a relatively simple. excretory system. circulatory system. porous body ▪ Sponges (phylum Porifera) are the simplest of all animals. ▪ A simple sponge resembles a thick-walled sac perforated with holes. although some are radially symmetric. Amoebocytes pick up food packaged in food vacuoules from choanocytes. then flows out through a larger opening called the osculum. and carry the nutrients to other cells. which wander through the middle body region. ▪ Have no respiratory system. that function in defense and capturing prey. Does not have coelom.. • Cnidarians have a gastrovascular cavity for digestion and absorption of nutrients. • A polyp (found in Hydras) is a sessile. hydras.g. ▪ Cnidarians are carnivores that use their tentacles to capture small animals and protists and to push the prey into their mouths. corals. called cnidocytes. sea anemones. . ▪ Undergoes asexual or sexual reproduction. supporting the body and helping to give cnidarians its typical shape. • A medusa (found in jellyfish) is a floating. the thread can sting or entangle prey. A jelly-filled middle region may contained scattered amoeboid cells. When it is discharged. ▪ The fluid of the gastrovascular cavity also acts as a hydrostatic skeleton. or circulatory system. ▪ Phylum Cnidaria is named for its unique stinging cells. umbrella-shaped body with dangling tentacles. ▪ Cnidarians exhibit two kinds of radially symmetric body forms. cylinder-shaped body with rising tentacles. ▪ The simple body of most cnidarians has an outer epidermis and an inner cell layer that lines the digestive cavity. and jellies) are characterized by radial symmetry and bodies arising from two tissue layers (diploblastic). • Each cnidocyte contains a fine thread coiled within a capsule. The stinging organelle is called a nematocyst. 233 ◦ Cnidarians are radial animals with tentacles and stinging cells ▪ Cnidarians (e. excretory system. ▪ Contractile tissues and a nerve net occur in their simplest forms in cnidarians. phylum Platyhelminthes. When a planarian feeds. tapeworms have a complex life cycle. anterior centralized ganglia (brain) • No circulatory system and no respiratory system • Excretory system consists of protonephridia and flame cells. • Reproduction: asexual (fragmentation and regeneration) or sexual (hemaphroditism) ▪ Three major groups of flatworms: • Free-living flatworms (planatians) has a head with a pair of light-sensitive eyecups and a flap at each side that detects chemicals. Larvae develop in an intermediate host. are the simplest of the bilaterians with cephalization. Like flukes. Crawl using cilia. • Most Flatworms have a gastrovascular cavity with only one opening. Fine branches of the gastrovascular cavity distribute food throughout the animal. They inhabit the digestive tract of vertebrates. They absorb nutrients across their body surface and have no digestive tract. • Tapeworms are another parasitic group of flatworms. Have “segments” called proglottids but are not considered true segments because they only develop secondarily for reproduction. usually involving one or more hosts. eumetazoa • Nervous system: two nerve cords. Many flukes have suckers that attach to their host and a tough protective opening. Dense clusters of nerve cells form a simple brain. 234 ◦ Flatworms are the simplest bilateral animals ▪ Flatworms. • Flukes live as parasites in other animals. They take advantage of predator-prey relationships of their hosts. • Triploblastic. acoelomates. The larvae then infect the final host in which they live as adults. Many flukes have complex life cycles that facilitate dispersal of offspring to new hosts. elongated invertebrate. tapeworms are an exception to the original definitions of animal. • The term worm is commonly applied to any slender. Because of this adaptation to their parasitic lifestyle. it sucks food through the mouth at the tip of a muscular tube that projects from the mid-ventral surface of the body. and a pair of nerve cords connect with small nerves that branch throughout the body. other animals ingest nutrients. . these animals have bilateral symmetry and as an embryo with three layers (triploblastic. Several layers of tough. ▪ When the worm grows. • Free-living or parasitic. not completely lined with mesoderm) and a digestive tract with two openings (alimentary canal). • Nervous system: nerve chord and ring • No respiratory and excretory systems • Not segmented • As bilaterians. The fluid in the pseudocoelom helps distribute nutrients absorbed by the digestive system throughout the body. • Roundworms have a fluid-filled body cavity (a pseudocoelom. . eumetazoa). the cuticle protects the nematode from the host's digestive system. make up the phylum Nematoda. It also functions as a hydrostatic skeleton. it periodically sheds it cuticle (molts) and secretes a new. ▪ Nematodes are cylindrical with a blunt head and a tapered tail. when ingested via incompletely cooked meat. also called roundworms. ◦ Free living soil dwellers help decompose and recycle nutrients ◦ Nematodes are responsible for trichinosis in humans. nonliving material called a cuticle cover the body and prevent the nematode from drying out. larger one. In parasitic species. 235 ◦ Nematodes have a pseudocoelom and a complete digestive tract ▪ Nematodes. Rotifers are filter-feeders. the corona or wheel organ. Some are benthic (living at the bottom) but most are free-living in fresh water. complete digestive system. . 236 ◦ Phylum Rotifera ▪ Rotifers are aquatic organisms. meaning there are distinct male and female individual organisms. ▪ Body cavity is a pseudocoelom. ▪ Parthenogenesis is common. ▪ Bilateral. The male is generally smaller than the female. ▪ Excretory system consists of protonephridia and flame cells. ▪ The pharynx is armed with jaws (the mastax). eumetazoa ▪ No circulatory and respiratory systems ▪ Digestive system: alimentary canal with mouth and anus ▪ Nervous system: cerebral ganglia (brain) with some nerves extending through the body ▪ Their body is spherical or cylindrical. ▪ The anterior part is modified to a ciliary organ. ending in a bifurcate foot. ▪ Sexes are dioecious. triploblasts. • A mantle. oysters. a fold of tissue that drapes over the visceral mass and secretes a shell in molluscs such as clams and snail. They have shells divided into two halves that are hinged together. Cephalopods use break-like jaws and a radula to crush or rip prey apart. ▪ Nervous system: ventral nerve chords and brain ▪ Respiratory system: gills ▪ Digestive system: alimentary canal with mouth. anus. and scallops. living in sand or mud. 237 ◦ Diverse molluscs are variations on a common body plan ▪ Slugs. • A visceral mass containing most of the internal organs. which houses the gills. with reproductive organs located in the visceral mass. • The main body cavity is a hemocoel. Made up of CaCO3. clams. the mantle extends beyond the visceral mass. Most bivalves are sedentary. • A radula is a unique rasping organ that is used to scrape up food. through which blood circulates. ▪ Basic body plan of a mollusc: • A muscular foot which functions in locomotion. • Molluscs are soft-bodied animals. • In many molluscs. ▪ Molluscs have a true coelom and a mainly open circulatory system. agile predators. snails. ▪ The life cycle of many marine molluscs includes a ciliated larva called a trochophore. Most bivalves are suspension feeders. octopuses. . and squids are just a few of the great variety of animals known as molluscs. mussels. Most gastropods are protected by a single. and terrestrial environments. ▪ Most molluscs have separate sexes. and radula ▪ Excretory system: Nephridia ▪ Embryonic development: Protostome ▪ Three diverse groups of molluscs: • The largest group of molluscs is called the gastropods. • The cephalopods differ from gastropods and bivalves in being adapted to the lifestyle of fast. • The bivalves include numerous species of clams. but most are protected by a hard shell. All cephalopods have large brains and sophisticated sense organs that contribute to their success as mobile predators. oysters. which his drawn out into several long tentacles for catching and holding prey. Many gastropods have a distinct head with eyes at the tips of tentacles. found in fresh water. The mouth is at the base of the foot. salt water. producing a water-filled chamber called the mantle cavity. The mantle cavity contains gills that are used for feeding as well as gas exchange. spiraled shell into which the animal can retreat when threatened. ◦ The digestive tract (alimentary canal) is not segmented. 238 ◦ Annelids are segmented worms ▪ A segmented body resembling a series of fused rings is the hallmark of phylum Annelida. The “heart” is simply an enlarged region of the dorsal blood vessel plus five pairs of segmental vessels on the anterior end. ◦ Are hermaphrodites but they don't fertilize their own eggs. which are mostly marine. form the largest group of annelids. . ◦ Internally. the coelom is partitioned by membrane walls. An earthworm. Most are bottom-dwelling scavengers that burrow in the sand and mud. Free- swimming polychaetes travel in the open ocean by moving their paddle-like appendages on each segment. eumetazoa. segmented body to crawl and burrow rapidly into the soil. ◦ Earthworms move by coordinating the contraction of longitudinal and circular muscles. in the sea. • Triploblasts. ◦ They live in tubes and extend feathery appendages coated with mucus that trap suspended food particles. protostome. The picture below shows the segmented anatomy of an earthworm. The main vessels of the earthworm circulatory system—a dorsal blood vessel and a ventral blood vessel—are connected by segmental vessels. • Polychaetes ◦ The polychaetes. which acts as a hydrostatic skeleton. • They are found in damp soil. ◦ Have a closed circulatory system. it passes through the segment walls from the mouth to anus. and in most freshwater habitats. ◦ Have metanephridia as excretory organs. ◦ The nervous system includes a simple brain and a ventral nerve cord with a cluster of nerve cells in each segment. These muscles work against the coelomic fluid in each segment. a typical annelid. no respiratory system ▪ Three main groups of annelids: • Earthworms and their relatives. uses its flexible. ◦ Many of the internal body structures are retreated within each segment. the appendages are richly supplied with blood vessels and are either associated with the gills or function as gills themselves. stiff bristles on the appendages help the worm wriggle about in the search of small invertebrates to eat. which hare notorious for their bloodsucking habits. • The third main group of annelids is the leeches. Most species are free-living carnivores that eat small invertebrates such as snails and insets. In many polychaetes. 239 ◦ In polychaetes. . eumetazoa. . ▪ The arthropod body. a nonliving covering in arthropods that is hardened by layers of protein and chitin. is covered by an exoskeleton. the thorax. • The appendages are variously adapted for sensory reception. protostome. Each segment group is specialized for a different function. In some arthropods (i. and their jointed appendages. 240 ◦ Arthropods are segmented animals with joined appendages and an exoskeleton ▪ Over a million species of arthropods have been identified. their hard exoskeleton. Living chelicerates include the scorpions. the exoskeleton of the head and the thorax is partly fused. Use trachea or book lungs for respiration. The diversity and success of arthropods are largely related to their segmentation. feeding. the lobster). The exoskeletons in arthropods is a cuticle. an external skeleton that protects the animals and provides points of attachment for the muscles that move appendages. book lungs. including the appendages. ▪ Nervous system: fused ganglia. Most arachnids live on land. ventral nerve cord ▪ Bilateral. coelomate ▪ Excretory system: malphagian tubules ▪ Respiratory system: varies between spiracles and tracheal tubes. defense. a complex process called molting. ▪ Arthropods have an open circulatory system. triploblastic. ▪ The body of most arthropods arises from several distinct groups of segments that fuse during develop: the head.e. and swimming. forming a body region called the cephalothorax. and the abdomen. collectively called arachnids. walking. ticks. • As it grows. and gills ▪ Four major groups of arthropods: • Chelicerates are marine organisms that were abundant in the sea some 300 million years ago. a polysaccharide. and mites. an arthropod must periodically shed its old exoskeleton and secrete a larger one. spiders. in which the transition from larva to adult is achieved through multiple molts. then exists as an encased. and large numbers of offspring. • Insects are the most diverse group of animals on the planet. Each of their body segment bears a single pair of long legs. Other inspect species undergo incomplete metamorphosis. exoskeleton. ◦ Life cycles: More than 80% of insect species undergo complete metamorphosis. They are distributed worldwide and have a remarkable ability to survive challenging environments. 241 • Millipedes are wormlike terrestrial creatures that eat decaying plant matter. They have two pairs of short legs per body segment. The larval stage is specialized for eating and growing. but without forming a pupa. joined appendages). Lobsters. a complex life cycle. comprising over 70% of all animal species. Use gills to breathe. flight. nonfeeding pupa while its body grows. short generation times. . and shrimps are part of this group. • Crustaceans are nearly all aquatic. ◦ What characteristics account for the success of insects? They have shared features with other arthropods (segmented body. Centipedes are terrestrial carnivores with a pair of poison claws used in defense and to paralyze prey. crayfish. crabs. barnacles. a waterproof coating on the cuticle. The inset emerges as an adult that is specialized for reproduction and dispersal. ◦ Use spiracles and tracheal tubes to breathe. A larva typically molts several times as it grows. 242 ◦ Modular body plan: like other arthropods. and an abdomen. These regions arise from the fusion of embryonic segments during development. insects have specialized body regions —a head. ◦ Protective color patterns: In many groups of insects. The insect body plan is essentially modular: each embryonic segment is a separate building block that develops independently of other segments. aposematic coloring). Most adult insects have three pairs of legs. thorax. mimicry. which may be adapted for any type of locomotion basically. Head typically bears a pair of sensory antennae. Insects learned to fly without sacrificing any legs because wings are extensions of the cuticle. This explains much of the extraordinary diversification that is observed in insects. As a result. adaptations of body structures have been coupled with protective coloration (camouflage. and several pairs of mouthparts. As a result of the variety in mouthparts. insects have adaptations that exploit almost any conceivable food source. a mutation that changes homeotic gene expression can change the structure of one segment or its appendages without affecting any of the others. The mouthparts are adapted for particular kinds of eating. a pair of eyes. . or internal skeleton. under the thin skin of the animal. 243 ◦ Echinoderms have spiny skin. and gas exchange. ▪ Unique to echinoderms is the water vascular system. we see evidence of their relation to other animals in their embryonic developments. ▪ Though echinoderms have many unique features. • Exhibit bilateral symmetry as larvae but then radial symmetry as an adult. sand dollars. • Triploblast. • When it encounters prey. meaning that they are more closely related to humans than any other protostome phylum. which function in locomotion. and sea urchins. . a network of water-filled canals that branch into extensions called tube feet. an endoskeleton. ▪ Some echinoderms such as sea stars are capable of regeneration. feeding. coelomate • open circulatory system with no heart • nervous system: nerve ring and radial nerves • no respiratory system and no excretory system • digestive: alimentary canal with mouth and anus ▪ Have prickly bumps or spines. are slow-moving or sessile marine animals. They are extensions of the hard calcium-containing plates that form the endoskeleton. eumetazoa. • A sea star pulls itself slowly over the seafloor using its suction-cup-like tube feet. and a water vascular system for movement ▪ Echinoderms. They are duterostomes. such as sea stars. it grips the prey with its tube feet. nerve cord. or tail. They are suspension feeders. and are common on coral reefs. supportive. They are small. hollow nerve cord • (2) a notochord. is a swimming. Chordata. blakelike chordates that live in marine sands. • Lancelets. Has no trace of a notochord. ▪ Two main groups of invertebrate chordates (have been extensively studied to examine the origin of vertebrates): • Adult tunicates are stationary and look more like small sacs. however. 244 ◦ Our own phylum. Tunicates likely represent the earliest branch of the chordate lineage. ▪ Vertebrate chordates will be discussed in the next chapter. tadpole-like organism that exhibits all four distinctive chordate features. another group of marine invertebrate chordates. They often adhere to rocks and boats. a flexible. longitudinal rod located between the digestive tract and the nerve cord • (3) pharyngeal slits located in the pharynx. unlike tunicates. The tunicate larva. They clearly illustrate all four chordate features throughout their lives. the region just behind the mouth • (4) a muscular post-anal tail (a tail posterior to the anus) ▪ Body segmentation is also a chordate characteristic. but it does have prominent pharyngeal slits that function in feeding. is distinguished by four features ▪ 4 unique features of chordates: • (1) a dorsal. . also feed on suspended particles. coelomate. The notochord also persists in the adult lamprey. All chordates with a head are called craniates. ◦ The next major transition was the origin of jaws. ◦ Unlike tunicates. followed by muscular lobed fins with skeletal support. ◦ The origin of a backbone came next. The vertebrates are distinguished by a more extensive skull and a backbone. ◦ In hagfishes. composed of a series of bones called vertebrae. were the first vertebrates on land. ◦ Tetrapods. but rudimentary vertebral structures are also present. ◦ The next transition was the development of a head that consists of a brain at the anterior end of the dorsal nerve cord. or vertebral column. ◦ The evolution of lungs or lung derivatives. ◦ The evolution of amniotes. These innovations opened up completely new way of feeding for chordates: active predation. jawed vertebrates with two pairs of limbs. albeit a small one in the lancelets (only a swollen tip of the nerve cord). two chambered heart circulatory system. 245 • Derived characters define the major clades of chordates ◦ Here is the proposed phylogeny for phylum Chordata: ◦ The tunicates are thought to be the first group to branch from the chordate lineage. They have bilateral symmetry. . eyes and other sensory organs. complete brain. eumetazoa. completed the transition to land. and alimentary canal. opened the possibility of life on land. and a skull. tetrapods with a terrestrially adapted egg. triploblasts. which opened up new feeding opportunities. • Hagfishes and lampreys lack hinged jaws ◦ The two most primitive surviving craniates are hagfishes and lampreys. the notochord is the body's main support in the adult. gills for breathing. The vertebrae encloses the nerve cord. all other chordates have a brain. as well as to their jaws. Most species of lamprey are parasites. ◦ Hagfishes scavenge dead or dying vertebrates on the cold. ◦ Hinged jaws are thought to have evolved by modification of skeletal supports of the anterior pharyngeal (gill) slits. ◦ Lamprey larvae resemble lancelets. ray-finned fishes. dark seafloor. which allowed them to swim after prey. but hagfishes are not. they have excellent senses of smell and touch. Most lampreys migrate to the sea or lakes as they mature into adults. They are suspension feeders that live in freshwater streams. and lobe-finned fishes ◦ Jawed vertebrates' success probably relates to their paired fins and tail. ◦ Three lineages of jawed vertebrates with gills and paired fins are commonly called fishes. They feed by entering the animal through an existing opening or by creating a hole using sharp. Although nearly blind. • Jawed vertebrates with gills and paired fins include sharks. which enabled them to catch and eat a wide variety of prey. 246 Consequently. . lampreys are considered vertebrates. where they are buried in sediment. tooth-like structures on the tongue that grasp and tear flesh. a protective flap called an operculum covers a chamber housing the gills. ▪ Their fins are supported by thin. trout. ▪ Most have flattened scales covering their skin that secrete a coating of mucus that reduces drag during swimming. eumetazoa. ▪ A lineage of the lobed-finned fish. with eyes on the top of the head. have two chambered hearts. Their bodies are dorsoventrally flattened. ◦ Class Sarcopterygii (lobe-finned fish) ▪ The key derived character of the lobe-fins is a series of rod-shaped bones in their muscular pectoral and pelvic fins. Sharks and most other aquatic vertebrates have a lateral line system. ▪ Ray-finned fishes also have a lung derivative that helps keep them buoyant—the swim bladder. Movement of the operculum allows the fish to breathe without swimming. which include tuna. ▪ On each side of the head. flexible skeletal rays. ◦ Class Actinopterygii (ray-finned fish) ▪ In ray-finned fishes. Bodies of sharks are streamlined for swimming in the open ocean. 247 ▪ All are triploblasts. gills. the skeleton is made of bone—cartilage reinforced with a hard matrix of calcium phosphate. the tetrapods. and alimentary canals. ◦ Class Chondrichthyes (sharks and rays) ▪ Have a flexible skeleton made of cartilage. were the first to adapt to life on land. . ▪ Some sharks are suspension feeders while others are adept predators. complete brains. and goldfish. ▪ Rays are adapted for life on the bottom of the ocean. The tails of stingrays bear sharp spines with venom and glands at the base. a row of sensory organs running along each side that are sensitive to changes in water pressure and can detect minor vibrations caused by animals swimming nearby. coelomates. aquatic algae-eater with gills. ◦ Not all amphibians live such a double life. and a long. called a tadpole. frogs. In changing into a frog. a lateral line system. some are strictly terrestrial and some are strictly aquatic. the distribution of amphibians was limited by their vulnerability to dehydration. ◦ The larval stage. is a legless. . Eggs are encapsulated in a jellylike material so they must be surrounded by moisture to prevent them from drying out. have three chambered hearts. ◦ The term toad is a term generally used to refer to frogs that have rough skin and live entirely in terrestrial habitats. gills. However. ◦ Amphibians were the first vertebrates to colonize the land. but lay their eggs in water. ◦ Many amphibians “live a double life. the tadpole undergoes a radical metamorphosis. triploblasts. and caecilians. finned tail. coelomates.” For example. where their most skin supplements their lungs for gas exchange. ◦ Most amphibians are found in damp habitats. frogs spend much of its time on land. ◦ Amphibian skin usually has poison glands that may play a role in defense. eumetazoa. and alimentary canals. They are bilateral. 248 • Amphibians are tetrapods—vertebrates with two pairs of limbs ◦ Amphibians include salamanders. complete brains. 249 • Reptiles are amniotes—tetrapods with a terrestrially adapted egg ◦ Reptiles. . coelomates. using their rib cage to help ventilate lungs. birds. have three chambered hearts. ▪ Reptiles cannot breathe through their dry skin and obtain most of their oxygen with their lungs. meaning they absorb external heat rather than generating much of their own. keeps the body from drying out. and alimentary canals. ▪ Reptilian skin. turtles. birds. They are bilateral. ▪ Many reptiles are “cold-blooded” because they do not use their metabolism to produce body heat. The amnion is a fluid-filled sac surrounding the embryo. crocodilians. ◦ Reptiles have several other adaptations other than the amniotic egg for terrestrial living not found in amphibians. The amniotic egg contains specialized extraembryonic membranes. ▪ Lizards are the most numerous and diverse reptiles other than birds. lungs. They regulate temperature through their behavior. snakes. so called because they are not part of the embryo's body. The major derived character of this clade is the amniotic egg. and mammals are amniotes. ◦ The clade of amniotes called reptiles includes lizards. A better term than “cold- blooded” is ectothermic. triploblasts. covered with scales waterproofed with the tough protein keratin. and dinosaurs. complete brains. providing lift and maneuverability in the air. have four chambered hearts. Large flight muscles anchored to a central ridge along the breastbone provide power. particularly during breeding seasons. using heat generated by metabolism to maintain a warm. ◦ Many features help reduce weight for flight: ▪ birds lack teeth ▪ their tail is supported by only a few small vertebrae ▪ their feathers have hollow shafts ▪ their bones have a honeycombed structure ◦ Flying requires a great amount of energy and birds have a high rate of metabolism. coelomates. They are endothermic. triploblasts. ◦ Birds have excellent eyesight to aid flight. ▪ They are bilateral. Highly efficient circulatory systems help support the high metabolic rate. and alimentary canals. ◦ Strong evidence indicates that birds evolved from a lineage of small. steady body temperature.e. 250 • Birds are feathered reptiles with adaptations for flight ◦ Almost all birds can fly. two-legged dinosaurs called theropods. eumetazoa. ◦ Birds typically display very complex behaviors. The forelimbs have been remodeled as feather-covered wings that act as airfoils. and nearly every part of a bird's body reflects adaptations that enhance flight. ostrich). . Few birds are flightless (i. Insulating feathers help to maintain their warm body temperature. Courtship often involves elaborate rituals. complete brains. lungs. coelomates. and eutherians—differ in reproductive patterns. Hair provides insulation that helps maintain a warm body temperature. eumetazoa. and the young complete their embryonic development in the mother's uterus attached to the placenta. known as monotremes. mammals are endothermic. 251 • Mammals are amniotes that have hair and produce milk ◦ Two features—hair and mammary glands that produce milk—are the distinguishing traits of mammals. ▪ Marsupials have a brief gestation and give birth to tiny. ◦ Other than the platypus. ▪ Eutherians are mammals that bear fully developed live young. ◦ Like birds. and alimentary canals. ▪ The only existing egg-laying mammals. embryonic offspring that complete development while attached to the mother's nipples. complete brains. the embryos remain inside the mother and receive their nourishment directly from her blood. all mammals are born rather than hatched. lungs. are echidnas (spiny anteaters) and the duck-billed platypus. triploblasts. have four chambered hearts. a structure in which nutrients from the mother's blood diffuse into the embryo's blood. ◦ Three major lineages of mammals: monotremes. Membranes from the embryo join with the lining of the uterus to form a placenta. Mammalian embryos produce extraembryonic membranes that are homologous to those found in the amniotic egg. ◦ Efficient respiratory and circulatory systems (including a four-chambered heart) support the high rate of metabolism characteristic of endotherms. They are bilateral. They are commonly called placental mammals because their placentas are more complex than those of marsupials. . marsupials. ◦ Differentiation of teeth adapted for eating many kinds of foods is also characteristic of mammals. During development. The nursing young are usually housed in an external pouch. • Vascular bundles – arrangement of bundles of vascular tissue (xylem and phloem) in stems. single root). stamens. • Each root hair is an extension of an epidermal cell (a cell in the outer layer of the . a dicot embryo has two seed leaves (two cotyledons). and other flower parts. like most animals have organs comprised of different tissues. or cotyledons. branching. Eudicots have taproots (a large. and stores food. ▪ Monocots and eudicots vary over four other characteristics: • Leaf venation – the pattern of veins in leaves. In this unit. ▪ The great majority of dicots. venation pattern whereas monocots have a parallel venation pattern. having diverged from a common ancestor about 125 million years ago. An organ consists of several types of tissues that together carry out a particular function. ▪ A plant's root system anchors it in the soil. 252 • Plant structure and function ◦ The two major groups of angiosperms are the monocots and eudicots ▪ Plant biologists have traditionally placed most angiosperms into two groups. The names monocot and eudicot refer to the first leaves on the plant embryo. which in turn are composed of one or more cell types. are evolutionarily related. sepals. Eudicots are organized in a circle whereas monocots are scattered. a few smaller groups of dicots have evolved independently. Cotyledons provide nutrition • A monocot embryo has one seed leaf (one cotyledon). we will focus on monocots and eudicots. 5s. or multiples thereof whereas monocots are in 3s or multiples thereof. and leaves ▪ Plants. • Flower parts – numbers of petals. called monocots and eudicots. • Root – form of root. • Near the root tips. Eudicots have a netted. absorbs and transports minerals and water. called the eudicots (“true” dicots). stems. These embryonic leaves are called seed leaves. a vast number of tiny tubular projections called root hairs enormously increase the root surface area for absorption of water and minerals. Eudicots are in 4s. whereas monocots have a fibrous system (A cluster of many fine roots) ◦ A typical plant body contains three basic organs: roots. the points at which leaves are attached. • When a plant stem is growing in length. ▪ The two types of buds are undeveloped shoots. and under certain conditions. leaves. roots must constantly grow to provide new root hairs for the absorption of water. • The axillary buds. the portions of the stem between nodes. the axillary buds begin growing. The older epidermal cells protect the root. at the apex (tip) of the stem has developing leaves and a compact series of nodes and internodes. root hairs die. and internodes. . the terminal bud produces hormones that inhibit the growth of axillary buds. Most leaves consist of a flattened blade and a stalk. Therefore. • The leaves are the main photosynthetic organs in most plants. the terminal bud (also called the apical bud). branching is also important for increasing the exposure of the shoot system to the environment. • In many plants. A stem has nodes. New epidermal cells form. which in angiosperms are the flowers. ▪ The shoot system of a plant is made up of stems. • By concentrating resources on growing taller. are usually dormant. a phenomenon called apical dominance (more on this later). • The stems are the parts of the plant that are generally above ground and support and separate the leaves (thereby promoting photosynthesis) and flowers. which joins the leaf to a node of the stem. one in each of the angles formed by a leaf and the stem. which will form new root hairs. and adaptations for reproduction. apical dominance is an evolutionary adaptation that increases the plant's exposure to light. or petiole. 253 root). although green stems also perform photosynthesis. However. As the plant gets older. having buds. . • Cacti have modified leaves that protect the plant from being eaten by animals. stems. The main part of the cactus is the stem. such as celery. Stolons enable a plant to reproduce asexually. stems. • A potato plant has rhizomes that end in enlarged structures specialized for storage called tubers. have enormous petioles. ▪ Certain plants (monocots) have unusually large taproots that store food in the form of carbohydrates such as starch. with its tips coiled around a support structure. and leaves ▪ The plant's three basic organs—roots. can also form new plants. 254 ◦ Many plants have modified roots. Tendrils help plants climb. • Some plants have a modified leaf called a tendril. which is adapted for photosynthesis and water ▪ Examples of modified leaves: • Grasses and many other monocots have long leaves without petioles. and leaves—have become adapted for a variety of functions. ▪ Examples of modified stems: • The strawberry plant has a horizontal stem called a stolon that grows along the ground. • Rhizomes are horizontal stems that grow near the soil surface. as plantlets form at nodes along their length. • Some eudicots. The plants consume the stored sugars during flowering and fruit production. They store food and. • Roots do not have a cuticle because having a cuticle would prevent them from absorbing water. stems. • Primary tissue in the stem contain many of the same characteristics as that in the . It is a selective barrier. The cuticle is made up of a waxy material called cutin. • In many plants. the dermal tissue system consists of a single layer of tightly packed cells called the epidermis. the vascular tissue system forms a vascular cylinder. with the cross sections of xylem cells radiating from the center like the spokes of a wheel and phloem cells filling in the wedges between the spokes. It forms the first line of defense against physical damage and infectious organisms like our skin. the young stem of a eudicot looks quite different from a young stem of a monocot. The outer part of the vascular cylinder consists of one to several layers of cells called the pericycle. ▪ The views at the bottom left shows in cross section the three tissue systems in a young eudicot root. with a vascular cylinder (vascular tissue) at the center surrounded by the pericycle. • Water and minerals that are absorbed from the soil must enter through the epidermis. ▪ The second tissue system is the vascular tissue system. • Ground tissue internal to vascular tissue is called pith. filling the spaces between the epidermis and vascular tissue system. and ground tissue external to the vascular tissue is called cortex. • The ground tissue system of the root. the vascular tissue consists of a central core of cells (pith) surrounded by a ring of xylem and a ring of phloem. The cortex cells store food as starch and take up minerals that have entered the root through the epidermis. consists entirely of cortex. 255 ◦ Three tissue systems make up the plant body ▪ Organs of plants contain tissues. ▪ Tissues that are neither dermal nor vascular make up the ground tissue system. ▪ As the center of the picture indicates. storage. surrounding a large cortex (ground tissue). which helps prevent water loss. ▪ The bottom right of the picture shows a cross section of a young monocot root. • But in a monocot root. including photosynthesis. determining which substances pass between the rest of the cortex and the vascular tissue. the monocot root has an outer layer of epidermis (dermal tissue). the region between the vascular cylinder and the epidermis. from which lateral roots arise. It accounts for most of the bulk of a young plant. The innermost layer of the cortex is the endodermis. The epidermis of leaves and most stems has a waxy coating called the cuticle. • In the center of the root. a cylinder one cell thick. and support. and leaves. • Like eudicots. • Ground tissue has diverse functions. Made up of of the xylem and phloem. ▪ The picture on the next page shows how the three tissue systems are organized in typical plant roots. • Xylem tissue contains water-conducting cells that convey water and dissolved minerals upward from roots. ▪ The dermal tissue system is the plant's outer protective covering. • Phloem tissue contains cells that transport sugars and other organic nutrients from leaves or storage tissues to other parts of the plant. a tissue is a group of cells that perform a specialized function. • This ring separates the ground tissue into cortex and pith regions. The pith fills the center of the stem and is often important in food storage. However. However. in monocots stems the bundles are scattered. whereas in eudicots they are arranged in a ring. the endodermis and the casparian strips are lacking. . • Both stems have their vascular tissue system arranged in numerous vascular bundles. the ground tissue is not separated into these regions because the vascular bundles do not form a ring. 256 root. In a monocot stem. • The spongy mesophyll consists of parenchyma loosely arranged below the palisade mesophyll. • Plasmodesmata are open channels in adjacent cell walls through which cytoplasm and various molecules can flow from cell to cell. The numerous intercellular spaces provide air chambers that provide carbon dioxide to photosynthesizing cells and oxygen to respiring cells. air bubbles cannot enter vessels where they could impede the movement of water. • The palisade mesophyll consists of parenchyma cells equipped with numerous chloroplasts and large surface areas. In this way. a central vacuoule (contains fluid that helps the cell maintain turgor) and a protective cell wall made up of cellulose surrounding the plasma membrane. especially that provide structural support. Stomata are openings in the epidermis that allow gas exchange between the inside of the leaf and the external environment. and then a more rigid secondary cell wall forms between the plasma membrane and the primary wall. or the loss of water through evaporation. a protective layer of the waxy material cutin. specializations for photosynthesis. ◦ Bundle sheath cells surround the veins in such a way that no vascular tissue is exposed to inter-cellular space. The epidermis is covered by the cuticle. . Photosynthesis in leaves occurs primarily in this tissue. • The leaf's vascular tissue system is made up of a network of veins. • The epidermis is the protective covering of one or more layers of cells. Many plant cells. A vein is a vascular bundle composed of xylem and phloem tissues surrounded by a protective sheath of cells called bundle sheath cells. The vein also functions as a skeleton that reinforces the shape of the leaf. 257 ▪ The picture below illustrates the arrangement of a typical plant leaf. allow migration of water between plant cells. • Guard cells are specialized epidermal cells that control the opening and closing of stomata. ▪ The picture on the next page highlights the adjoining cell walls of two cells. The cuticle reduces transpiration. have a two-part cell wall: • A primary cell wall is laid down first. ◦ Plant cells are diverse in structure and function ▪ Plant cells have three unique features: chloroplasts (the sites of photosynthesis). • Pits. • The primary cell walls in adjacent cells in plant tissues are held together by a sticky layer called the middle lamella. where the cell wall is relatively thin. They perform most of the metabolic functions of a plant and food storage. but they have unevenly thickened primary walls. They provide flexible support in actively growing parts of the plants. such as during the repair of an injury. ◦ Sclereids. • Collenchyma cells also lack secondary walls. When mature. Two types of scherenchyma cells: ◦ One. called a fiber. is long and slender and is usually arrange din bundles. which are thin and flexible. Their cell walls form a rigid “skeleton” that supports the plant. . Most parenchyma cells can divide and differentiate into other types of plant cells under certain conditions. and very hard secondary walls. young stems and petioles often have collenchyma cells just below their surface • Scherenchyma cells have thick secondary cell walls usually strengthened with lignin. have thick. which are shorter than fiber cells. They usually only have primary cell walls. irregular. most scherenchyma cells are dead. 258 ▪ 5 types of cells in plants: • Parenchyma cells are the most abundant type of cell in most plants. the main chemical component of wood. They cannot elongate and are thus found only in regions of the plant that have stopped actively growing in length. This reduction in cell contents enables nutrients to pass more easily through the cell. • The end walls between sieve-tube members. These areas are called perforations and are literally holes between cells. shorter. have pores that allow fluid to flow from cell to cell along the sieve tube. vessel elements are considered a more evolutionarily advanced feature. One companion cell may serve multiple sieve-tube elements by producing and transporting proteins to all of them. • Vessel elements are more efficient at moving water than tracheids. 259 ▪ Xylem tissue includes two types of water-conducting cells: tracheids and vessel elements. • Alongside each sieve-tube element is at least one companion cell. Water passes from one vessel member to another through areas devoid of both primary and secondary cell walls. they are essentially cell wall. • Vessel elements are wider. and less tapered. which is connected to the sieve-tube element by numerous plasmodesmata. although they lose most organelles. that is. ▪ Phloem tissue is made up of cells called sieve-tube elements arranged end to end to form fluid-conducting columns called sieve tubes. • Tracheids are long. A column of vessel members is called a vessel. lignin-containing secondary cell walls. Both have rigid. • Sieve-tube elements remain alive at maturity. They are found most predominantly among the flowering plants. thin cells with tapered ends. and contain only the material being transported. called sieve plates. including the nucleus and ribosomes. therefore. completely lacking cellular components. Most xylem cells are dead at maturity. . The root tip is covered by a thimble-like root cap that protects the delicate. Indeterminate growth allows a plant to continuously increase its exposure to sunlight. • Annuals complete their life cycle in a single year or less (i. while others differentiate and are incorporated into tissues and organs of the growing plant.e. and soil. or perennials. Differentiation of cells results from differential gene expression. somewhat like an expanding accordion. legumes). actively dividing cells of the apical meristems. generating additional cells. where the three zones of cells at successive stages of primary growth are located (each zone overlaps). they cease growing after reaching a certain size. based on the length of their life cycle. The zone of cell division includes the root apical meristem and the cells that derive from it. ▪ Mechanisms of primary growth: • The picture to the right illustrates primary growth in a root. with flowering and seed production usually occurring during the second year (i. biennials. the cellulose fibers separate.e. It is cell elongation that pushes the root tip farther in into the soil. • Meristems at the tips of roots and in the buds of shoots are called apical meristems. trees. that is. ▪ Flowering plants are characterized as annuals. Tissues produced by primary growth are called primary tissues. Most species of plants. Cells of the vascular system differentiate into primary xylem and primary phloem. root cells elongate. however. grains. beets. turnips) • Perennials are plants that live and reproduce for many years (i. • Biennials complete their life cycle in two years. Growth in length occurs just behind the root tip. Primary growth enables roots to push through the soil and allows shoots to grow upward.e. rather than expand equally in all directions. The three tissue systems of a mature plant complete their development in the zone of differentiation. because of the circular arrangement of cellulose fibers in parallel bands in their cell walls. air. Cell division in the apical meristem produces the new cells that enable a plant to grow in length. The cells elongate by taking up water and as they do. including cells of the root cap. a process called primary growth. shrubs) ▪ Growth in all plants is made possible by tissues called meristems. In the zone of elongation. continue to grow as long as they live. parsley. A meristem consists of undifferentiated cells that divide when conditions permit. The cells lengthen. . 260 • Plant growth ◦ Primary growth lengthens roots and shoots ▪ The growth of a plant differs from that of an animal in a fundamental way. • Some products of this division remain in the meristem and produce still more cells. the time of germination through flowering and seed production to death. a condition called indeterminate growth. New root cells are produced in this region. Most animals are characterized by determinate growth. ▪ The vascular cambrium is a cylinder of meristem cells one cell thick between the primary xylem and primary phloem. called secondary growth. You can see the apical meristem. as its vascular cambrium produces layer upon layer of secondary xylem. which increases root and stem thickness. giving wood its characteristic hardness and strength. thickening older regions where primary growth has ceased. Gives rise two two new tissues: secondary xylem to its interior and secondary phloem to its exterior. Over the years. As the apical meristem advances upward. and these become new axillary bud meristems at the base of the leaves. known as the vascular cambium and the cork cambium. the apical meristem has been pushed upward by elongating cells underneath. These diving cells are arranged into two cylinders. is caused by the activity of dividing cells that are called lateral meristems. This increase in thickness of stems and roots. that extend along the length of roots and stems. Secondary growth adds layers of vascular tissue on either side of the vascular cambium. ◦ Secondary growth increases the diameter of woody plants ▪ Woody plants (such as trees) grow in diameter in addition to length. 261 • The micrograph to the right shows a section through the end of a growing shoot that was cut lengthwise from its tip to just below its uppermost pair of axillary buds. . • Secondary xylem makes up the wood of a plant. Two stages in the growth of a shoot: Stage (1) is like the micrograph and in stage (2). some of its cells remain behind. Tissues produced by secondary growth are called secondary tissues. The cells of the secondary xylem have thick walls rich of lignin. a woody stem gets thicker and thicker. and the elongating cells push the apical meristem upward. which is a dome-shaped mass of dividing cells at the tip of the terminal bud. Elongation occurs just below this meristem. creating seasons during which plants alternate growth with dormancy. The youngest secondary phloem (next to the vascular cambium) functions in sugar transport. These cells no longer transport water. consists of the older layers of secondary xylem. Mature cork cells are dead and have thick. The main components of bark are the secondary phloem. the vascular cambrium begins dividing again The layers are visible as rings because of uneven activity of the vascular cambrium during the year as previously explained. and aid in wound repair. the cork cambium. • The heartwood. the vascular cambrium is actively dividing. ▪ The epidermis and the cortex. the cork cambrium and the phelloderm is called the periderm. the phelloderm may be produced. 262 • Annual growth rings result from the layering of secondary xylem. A new cork cambium forms to the inside. During periods of growth. On the inside. which first forms from parenchyma cells in the cortex. and cells in the wood rays. When no cortex is left. too. physical damage. it forms from parenchyma cells in the phloem. When the next season begins. divisions and growth gradually come to a halt. waxy walls that protect the underlying tissues of the stem from water loss. Together. The living tissue sin it are the vascular cambium. the epidermis is sloughed off and replaced with a new outer layer called cork. conditions vary during the year. make up the young stem's external covering. the youngest secondary phloem. • The wood rays consist of parenchyma cells that transport water and nutrients. Keeping pace with secondary growth. The cork cambrium produces new cells on the outside and sometimes on the inside. they are clogged with resins and other compounds that make heartwood resistant to rotting. • The lighter-colored sapwood is a younger secondary xylem that does conduct xylem fluid (sap). are sloughed off as part of the bark. • Everything external to the vascular cambrium is called bark. as does the cork cambium you see here. . store organic nutrients. • Cork is produced by meristem tissue called the cork cambium. in the center of the trunk. the cork cambium. When secondary growth begins. In many environments. The older secondary phloem dies. these tissues and cork produced by the cork cambium help protect the stem until they. and pathogens. and when the season draws to an end. • As the stem thickens and the secondary xylem expands. ▪ The bulk of a tree trunk log is dead tissue. Pushed outward. both the result of primary growth. and cork. cork cambium keeps regenerating from the younger secondary phloem and keeps producing a steady supply of cork. the original cork and cork cambium are pushed outward and fall off. • The pollen grain further divides into three cells (in flowering plants) or four cells (in conifers). A pollen grain represents the male gametophyte generation. • Other accessory cells. in addition to the egg may be produced: one of two tissue layers called integuments surround the megasporangium. which divides by meiosis to produce 4 haploid cells. • An opening through the integuments for pollen access to the egg is called the micropyle. • The integuments. ▪ When a pollen grain lands on the sticky sigma (pollination). the microspores. and megaspore daughter cells are collectively called the ovule. nucellus. or tube. grows down the style toward an ovule. called the nucellus. an elongating cell that contains the vegetative nucleus. ▪ The megasporangium. Summary of reproduction in seed plants: ▪ Microsporangium produces numerous microspore mother cells. One of these cells survives to become the megaspore and represents the female gametophyte generation. 263 • Reproduction of flowering plants ◦ The development and pollen and ovules culminates in fertilization ▪ Microsporangia produce the microspores (male spores). The megaspore mother cell divides by meiosis to form 4 . Other cells become the sperm cells. produces a macrospore mother cell. • Ovules within the ovary consist of a megaspore mother cell surrounded by the nucellus and integuments. a pollen tube. and the macrosporangia produce the macrospores (female spores). • Microspores mature into pollen grains. There are two sperm cells inside the pollen tube. One of these cells is a vegetative. cell that controls the growth of the pollen tube. • Megaspore divides by mitosis to produce one egg (in flowering plants) or two eggs (n conifers). which divide by meiosis to produce 4 haploid cells. ▪ The dormant embryo contains a miniature root and shoot. • The other cell divides to form a thread of cells that pushes the embryo into the endosperm. After the seed germinates. because they contain the endosperm to feed the embryo plant. ▪ Embryonic development begins when the zygote divides by mitosis into two cells (basal and terminal cells). • The major storage material is the endosperm (a nutritious package of food for the embryo). Dicots have two seed leaves inside the seed coat. In the middle are the two haploid nuclei. it will not develop further until the seed germinates. the polar nuclei. • Monocots have only one seed leaf inside the seed coat. the megaspores. and some kind of storage material. The fertilization of the egg and the polar nuclei each by a separate sperm nucleus is called double fertilization. At the micropyle end of the embryo sac are the three cells. Dormancy is a key adaptation because it allows time for a plant to disperse its seeds and increases the chance that a new generation of plants will begin growing only when environmental conditions favor survival. The nucleus of the second sperm fuses with both polar nuclei. ▪ Endosperm development usually precedes embryo development. The result is an embryo sac. forming a triploid nucleus. the epicotyl. They are usually rounded and fat. the ovule. The embryo. One surviving megaspore divides 3 times by mitosis to produce 8 nuclei. . resistant seed coat (formed from the integuments). • When the pollen tube enters the embryo sac through the micropyle. an egg cell and two synergids. 6 of the nuclei undergo cytokinesis and form plasma membranes. ▪ The result of embryonic development is a mature seed. It is often only a thin leaf. ▪ The seed consists of an embryo. surrounded by its endosperm food supply. becomes the shoot tip. The triploid nucleus divides by mitosis to produce the endosperm. containing the triploid central cell and the diploid zygote. one sperm fertilizes the egg. the apical meristem will sustain primary growth as long as the plant lives. ▪ The embryo consists of the following parts: • The top portion of the embryo (above the cotyledons). ◦ The ovule develops into a seed ▪ After fertilization. because the endosperm to feed the new plant is not inside the seed leaf. • Repeated division of one of the cells then produces a ball of cells that becomes the embryo. At the opposite end of the micropyle are the three antipodal cells (play a part in embryo nutrition). The bulges seen on the embryo are the developing cotyledons. begins developing the seed. which provides the nourishment for subsequent development of the embryo and seedling. becomes dormant. a hard. 264 haploid cells. forming a diploid zygote. each equipped with an apical meristem. and the ovary starts to grow. have a special cotyledon called a scutellum. • In many monocots. ▪ Enzymes begin digesting stored nutrients in the endosperm or cotyledons. (2) the flower drops its petals. Two sheathes enclose the embryo of a grass seed: a coleopitle and a coleorhiza (covers the young root). rupturing its coat. and its wall thickens. • Grasses. and these nutrients are transported to the growing regions of the embryo. the coleopitle emerges first. however. ▪ In many eudicots (garden bean). ▪ The radicle (embryonic root) emerges first. The ovary expands tremendously. emerge from the plumule within the coleopitle. a sheath called the coleopitle surrounds and protects the epicotyl. ◦ Seed germination continues the life cycle ▪ At germination. ▪ In many monocots (maize). It becomes the young shoot. such as maize and wheat. the shoot tip breaks through the soil surface. 265 • Often attached to the epicotyl are young leaves usually called the plumule. In a developing young plant. ▪ Germination depends on imbibition. ▪ An accessory fruit contains other floral parts in addition to ovaries. ▪ Fruits are classified by their development: • simple: a single or several fused carpels • aggregate: a single flower with multiple separate carpels • multiple: a group of flowers called an inflorescence ▪ Steps of fruit formation: (1) soon after pollination. a radicle develops below the hypocotyl. ◦ The ovary develops into a fruit ▪ A fruit is a specialized vessel that houses and protects seeds and helps disperse them from the parent plant. The radicle develops into the root. . • In some embryos. The first true leaves. the uptake of water due to low water potential of the dry seed. The hydrated seed expands. ▪ Next. the coleopitle pushes up through the soil. a hook forms the hypocotyl. (sometimes the plumule refers to the epicotyl and the leaves) • Below the epicotyl and attached to the cotyledons is the hypocotyl. (3) forming the fruit. appearing as a leaf. the plant does not begin life but rather resumes the growth and development that were temporarily suspended during seed dormancy. The hook straightens and pulls the cotyledons up. and growth pushes the hook above ground. The inflow of water triggers metabolic changes in the embryo that makes it start growing again. water. a plant's ability to reject its own pollen. is specific to each species. • Asexual reproduction results in a clone of genetically identical organisms. ▪ Advantages and disadvantages of asexual vs. 266 ◦ Asexual reproduction produces plant clones ▪ Many angiosperm species reproduce both asexually and sexually. ▪ Mechanisms of Asexual Reproduction • Fragmentation. However. The angle between leaves is 137. the arrangement of leaves on a stem.5o and likely minimizes shading of lower leaves. ▪ Stems serve as conduits for water and nutrients and as supporting structures for leaves. and soil ▪ The success of plants depend son their ability to gather and conserve resources from their environment (air. It can be beneficial to a successful plant in a stable environment. • In some species. ◦ Adaptations for acquiring resources were key steps in the evolution of vascular plants ▪ Adaptations in each species represent compromises between enhancing photosynthesis and minimizing water loss. • Sexual reproduction generates genetic variation that makes evolutionary adaptation possible. separation of a parent plant into parts that develop into whole plants. Most angiosperms have alternate phyllotaxy with leaves arranged in a spiral. There is a generally a positive correlation between water availability and leaf size. and soil). is a very common type of asexual reproduction. • Apomixis is the asexual production of seeds from a diploid cell. • Phyllotaxy. ▪ The transport of materials is central to the integrated functioning of the whole plant. • Sexual reproduction results in offspring that are genetically different from their parents. a clone of plants is vulnerable to local extinction if there is an environmental change. • Dioecious species have staminate and carpellate flowers on separate plants. • Others have stamens and carpels that mature at different times or are arranged to prevent selfing. water. a parent plant's root system gives rise to adventitious shoots that become separate root systems. • The uptake and transport of plant nutrients ◦ Plants acquire nutrients from air. Recognition of a self pollen triggers a signal transduction pathway leading to a block in growth of a pollen tube. • The most common is self-incompatibility. only a fraction of seedlings survive ▪ Mechanisms that prevent self-fertilization • Many angiosperms have mechanisms that make it difficult for a flower to self- fertilize. However. . sexual reproduction • Asexual reproduction is also called vegetative reproduction. In low-light conditions. • The symplastic route. across cell walls. • The symplast consists of the cytosol of the living cells in a plant. In sunny conditions. Taproot systems anchor plants and are characteristic of gymnosperms and eudicots. through the cytosol.e. 267 ▪ Light absorption is affected by the leaf area index. Root growth can adjust to local conditions (i. ▪ Three transport routes for water and solutes are: • The apoplastic route. horizontal leaves capture more sunlight. Roots are less competitive with other roots from the same plant than with roots from different plants. the ratio of total upper leaf surface of a plant divided by the surface area of land on which it grows. and the interior of vessel elements and tracheids. ▪ Self-pruning is the shedding of lower shaded leaves when they respire more than they photosynthesize. through cell walls and extracellular spaces. There is a trade-off between growing tall and branching. ▪ Review diffusion and osmosis chapter in cellular and molecular bio unit. These affect the rate of water movement across the membrane. ▪ Leaf orientation affects light absorption. vertical leaves are less damaged by sun and allow light to reach lower leaves. extracellular spaces. ▪ Shoot height and branching pattern also affect light capture. ◦ Different mechanisms transport substances over long or short distances ▪ There are two major pathways through plants: apoplast and symplast. • The transmembrane route. as well as the plasmodesmata. ▪ The root system mines soil. • The apoplast consists of everything external to the plasma membrane. roots branch more in a pocket of high nitrate than low nitrate). . It includes cell walls. ▪ Aquaporins are transport proteins in the cell membrane that allow the passage of water. • The endodermis regulates and transports needed minerals from the soil into the xylem. • Water and minerals now enter the tracheids and vessel elements. ◦ Transpiration drives the transport of water and minerals from roots to shoots via xylem ▪ Plants can move a large volume of water from their roots to shoots. ▪ Moving water and minerals into the roots • Most water and mineral absorption occurs near root tips. where root hairs are located and the epidermis is permeable to water. Water and minerals move from the protoplasts of endodermal cells into their cell walls. the movement of fluid driven by pressure. . ▪ Transport of water and minerals into the xylem • The endodermis is the innermost layer of cells in the root cortex. and sieve-tube elements have few organelles in their cytoplasm. It surrounds the vascular cylinder and is the last checkpoint of selective passage of minerals from the cortex into the vascular tissue. the extensive surface area of cortical cell membranes enhances the uptake of water and selected minerals. Diffusion and active transport are involved in this movement from symplast to apoplast. After soil solution enters the roots. Water can cross the cortex via the symplast or apoplast. 268 ▪ Efficient long distance transport of fluid requires bulk flow. Efficient movement is also achieved in the fact that tracheids and vessel elements have no cytoplasm. Water and minerals in the apoplast must cross the plasma membrane of an endodermal cell to enter the vascular cylinder. • The concentration of essential minerals is greater in the roots than in the soil because of active transport. ◦ The waxy casparian strip of the endodermal wall blocks the apoplastic transfer of minerals from the cortex to the vascular cylinder. ◦ At night. Adhesion of water molecules to xylem cell walls helps offset the force of gravity. This negative pressure pulls water in the xylem into the leaf. ◦ Water molecules are attracted to cellulose in xylem cell walls through adhesion. or tension. ◦ Water vapor in airspaces of a leaf diffuses down its water potential gradient and exits the leaf via stomata. Transpired water is replaced as water travels up from the roots. The transpirational pull on xylem sap is transmitted from leaves to roots. ◦ Water molecules are attracted to each other through cohesion. 269 ▪ Bulk flow transport via the xylem • Xylem sap. transpiration and water cohesion pull water from shoots to roots. generating root pressure. water and dissolved minerals. • The transport of xylem sap involves transpiration. Cohesion make sit possible to pull a column of xylem sap. ▪ Thick secondary cell walls prevent vessel elements and tracheids from collapsing under negative pressure. the air-water interface retreats further into the mesophyll cell walls. is transported from roots to leaves by bulk flow. the evaporation of water from a plant's surface. root cells continue pumping mineral ions into the xylem of the vascular cylinder. . the exudation of water droplets on the tips or edges of leaves. • According to the cohesion-tension hypothesis. Water flows in from the root cortex. As water evaporates. The surface tension of water creates a negative pressure potential. Xylem sap is normally under negative pressure. lowering the water potential. Root pressure sometimes results in guttation. Positive root pressure is relatively week and is a minor mechanism of xylem flow. 270 ▪ Bulk flow differs from diffusion. It is driven by differences in pressure potential, not solute potential. It occurs in hollow dead cells, not across the membranes of living cells. It moves the entire solution, not just water or solutes. It is much faster than diffusion. ◦ The rate of transpiration is regulated by stomata ▪ Leaves generally have broad surface areas and high surface-to-volume ratios. These characteristics help increase photosynthesis and increase water loss through stomata (this is a trade-off). ▪ Guard cells help balance water conservation with gas exchange for photosynthesis. ▪ About 95% of the water a plant loses escapes through stomata. Each stoma is flanked by a pair of guard cells, which control the diameter of the stoma by changing shape. Stomatal density is under genetic and environmental control. ▪ Mechanisms of stomatal opening and closing: • Changes in turgor pressure open and close stomata. When turgid, guard cells bow outward and the pore between them opens. When flaccid, guard cells become less bowed and the pore closes. • This results primarily from the reversible uptake and loss of potassium ions by guard cells. When potassium ions enter the guard cell, the osmolarity of the internal surroundings of the guard cell is increased compared to the extracellular space. As a result, water moves into the guard cells. When water flows into the guard cells, the stomata opens. • Because ions are flowing into the cell, a charge gradient is created. To relieve this gradient, chloride ions are pumped into the cell along with potassium ions in some plants. In other plants, hydronium ions are pumped out. 271 ▪ Stimuli for stomatal opening and closing: • Stomata close when temperatures are high. This reduces loss of water but shuts down photosynthesis. • Stomata opens when carbon dioxide concentrations are low inside the leaf. Allows photosynthesis but risks water loss. • Stomata close during the night and opens during the day. May be due to carbon dioxide levels: CO2 levels are low during the day because the plant is actively doing photosynthesis but at night, CO2 levels are high because the plant is only respiring. • The hormone abscisic acid is produced in response to water deficiency and causes the closure of stomata. ◦ Effects of transpiration on wilting and leaf temperature ▪ Plants lose a large amount of water by transpiration. If the lost water is not replaced by sufficient transport of water, the plant will lose water and wilt. ▪ Transpiration also results in evaporative cooling, which can lower the temperature of a leaf and prevent denaturation of various enzymes involved in photosynthesis and other metabolic processes. ▪ Xerophytes are plants adapted to arid climates. • Some desert plants complete their life cycle during the rainy season. • Others have leaf modifications that reduce the rate of transpiration. • Some plants use a specialized form of photosynthesis called crassulacean acid metabolism (CAM). ◦ Sugars are transported from sources to sinks via the phloem ▪ The products of photosynthesis are transported to the phloem by a process of translocation. In angiosperms, sieve-tube elements are the conduits for translocation. ▪ Phloem sap is an aqueous solution that is high in sucrose. It travels from sugar source to sink. • A sugar source is an organ that is a net producer of sugar, such as mature leaves. • A sugar sink is an organ that is a net consumer or storer of sugar, such as a tuber or bulb. • Starch is an important player, since it is essentially insoluble in water. Any cell that converts extracellular soluble sugars into starch acts as a sink. Oppositely, any cell can act as a source if it breaks down starch into soluble sugars. • A storage organ can be both a sugar sink in summer and sugar source in winter. ▪ Sugar must be loaded into sieve-tube elements before being exposed to sinks. Depending on the species, sugars may move by symplastic or both symplastic and apoplastic pathways. ▪ Companion cells enhance solute movement between the apoplast and symplast. ▪ In many plants, phloem loading requires active transport. Proton pumping and cotransport of sucrose and H+ enable the cell to accumulate sucrose. At the sink, sugar molecules diffuse from the phloem to sink tissues and are followed by water. 272 ▪ Phloem sap moves through a sieve tube by bulk flow driven by positive pressure called the pressure flow mechanism. Steps: • (1) sugar is loaded from a photosynthetic cell into a phloem tube by active transport. Sugar loading at the source end raises the solute (sugar) concentration inside the phloem tube. • (2) The high solute concentration draws water into the tube by osmosis, usually from the xylem. The inward flow of water raises the water pressure at the source end of the phloem tube. • (3) At the sugar sink, both sugar and water leave the phloem tube. As the sugar departs the phloem, lowering the solute concentration at the sink end, (4) water flows by osmosis back into the xylem. The exit of water lowers the water pressure in the tube. • The building of water pressure at the source end of the phloem tube and the reduction of that pressure at the sink cause phloem sap to flow from source to sink— down a gradient of water pressure. Sieve plates allow free movement of solutes as well as water. Thus, sugar is carried along from the source to sink a the same rate as the water. • Plant nutrients and the soil ◦ Soil contains a living, complex ecosystem ▪ Plants obtain most of their water and minerals from the upper layers of soil. Living organisms play an important role in these soil layers. This complex ecosystem is fragile. ▪ The basic properties of soil are texture and composition. • Soil texture: soil particles are classified by size; from smallest to larges they are called sand, silt, and clay. Soil is stratified into layers called soil horizons. Topsoil consists of mineral particles, living organisms, and humus, the decaying organic material. Soil solution consists of water and dissolved minerals in the pores between soil particles. Loams are the most fertile topsoils and contain equal amounts of sand, silt, and clay. • Soil composition: A soil's composition 273 refers to its inorganic and organic chemical components. Cations adhere to negatively charged soil particles; this prevents them from leaching out of the soil through percolating groundwater. Topsoil contains organic components such as bacteria, fungi, algae, other protists, insects, earthworms, nematodes, and plant roots. These organisms help to decompose organic material and mix the soil ▪ Cation exchange is a mechanisms by which the root hairs take up certain positively charged ions (cations). • Inorganic cations such as calcium, magnesium, and potassium adhere by chemical attraction to the negatively charged surfaces of clay particles. This adhesion helps prevent these positively charged nutrients from draining away during heavy rain or irrigation. • In cation exchange, root hairs release hydrogen ions into the soil solution. The hydrogen ions help displace cations on the clay particle surfaces, and root hairs can then absorb them. ▪ In contrast to cations, anions are not usually bound tightly to soil particles. Unbound ions are readily available to plants, but they tend to drain out of the soil quickly due to irrigation or rainfall. ◦ Plants require essential elements to complete their life cycle ▪ More than 50 chemical elements have been identified among the inorganic substances in plants, but not all of these are essential to plants. There are 17 essential elements, chemical elements required for a plant to complete its life cycle. ▪ Nine of the essential elements are called macronutrients because plants require them in large amounts. The remaining eight are called micronutrients because plants need them in very small amounts. ◦ Plant nutrition often involves relationships with other organisms ▪ Plants and soil microbes have a mutualistic relationships. Dead plants provide energy needed by soil-dwelling microorganisms. Secretions from living roots support a wide 274 variety of microbes in the near-root environment. ▪ The layer of soil bound to the plant's roots is the rhizosphere. The rhizosphere contains bacteria that act as decomposers and nitrogen-fixers. ▪ Free-living rhizobacteria thrive in the rhizosphere, and some can enter roots. • They can play several roles: produce hormones that influence plant growth, produce antibiotics that protect roots from disease, and absorb toxic materials or make nutrients more available to roots. ▪ Mycorrhizae are mutualistic associations of fungi and roots (previously discussed in other chapters). ▪ Some plants have nutritional adaptations that use other organisms in nonmutualistic ways. Three unusual adaptations are: • Epiphytes: grows on another plant and obtains water and minerals from rain • Parasitic plants: absorb sugars and minerals from their living host plant • Carnivorous plants • Plant responses to internal and external signals ◦ Signal transduction pathways link signal reception to response ▪ Review cell signaling chapter in cellular and molecular bio unit. ▪ Morphological adaptions for growing in darkness is called etiolation. After being exposed to light, a plant undergoes changes called de-etiolation, in which shoots and roots grow normally. • A plant's response to a stimuli is an example of cell-signal processing. Therefore, it will follow a signal- transduction pathway. ▪ De-etiolation activates enzymes that function in photosynthesis directly, supply the chemical precursors for chlorophyll production, and affect the levels of plant hormones that regulate growth. ◦ Plant hormones help coordinate growth, development, and responses to stimuli ▪ Plant hormones are chemical signals that modify or control one or more specific physiological processes within a plant. ▪ Plant hormones are produced in very low concentration, but a minute amount can greatly affect growth and development of a plant organ. In general, they control plant growth and development by affecting the division, elongation, and differentiation of cells. ◦ Auxin ▪ The term auxin refers to any chemical that promotes elongation of coleoptiles. Indoleacetic acid (IAA) is a common auxin in plants; in this chapter the term auxin refers specifically to IAA. Auxin is a modified tryptophan amino acid. ▪ Auxin is produced in shoot tips and is transported down the stem. Auxin transporter proteins move the hormone from the basal end of one cell to the apical end of a neighboring cell. Auxin is actively transported (using ATP) from cell to cell in a specific 275 direction (polar transport). ▪ Auxin plays a major role in cell elongation. According to the acid growth hypothesis, auxin stimulates proton pumps in the plasma membrane. • (1) The proton pumps lower the pH in the cell wall, (2) activating expansins, enzymes that loosen the cell wall. (3) The cross-linking molecules are now more exposed to enzymes that loosen the cell wall. (4) The cell then swells with water and elongates because its weakened wall no longer resists the cell's tendency to take up water via osmosis. ▪ Auxin promotes cell elongation only within a certain concentration range. Above a certain level, it usually inhibits cell elongation in stems, probably by inducing the production of ethylene; a hormone that generally counters the effects of auxin. ▪ Auxin influences plant responses to light (phototropism) and gravity (geotropism). ▪ Auxin's role in plant development: • Polar transport of auxin plays a role in pattern formation of the developing plant • Reduced auxin flow from the shoot of a branch stimulates growth in lower branches • Auxin transport plays a role in phyllotaxy, the arrangement of leaves on the stem • Polar transport of auxin from leaf margins directs leaf venation pattern • The activity of the vascular cambium is under control of auxin transport ◦ Cytokinins ▪ Cytokinins are so named because they stimulate cytokinesis (cell division). Structurally, they are variations of the nitrogen base adenine. Two types: naturally occurring zeatin and artificially produced kinetin. ▪ Cytokinins are produced in actively growing tissues such as roots, embryos, and fruits. ▪ Cytokinins work together with auxin to control cell division and differentiation. ▪ Cytokinins, auxin, and strigolactone interact in the control of apical dominance, a terminal bud's ability to suppress development of axillary buds. If the terminal bud is removed, plants become bushier. ▪ Cytokinins slow aging of some plant organs by inhibiting protein breakdown, stimulating RNA and protein synthesis, and mobilizing nutrients from 276 surrounding tissues. ▪ Cytokinins influence the direction of organ development (organogensis). ◦ Gibberellins ▪ Gibberellins have a variety of effects, such as stem elongation, fruit growth, and seed germination. ▪ Gibberellins are produced in young roots and leaves. ▪ They stimulate growth of leaves in stems. In stems, gibberellins stimulate cell elongation and cell division. High concentrations of gibberellins cause the rapid elongation of stems called bolting. ▪ In many plants, both auxin and gibberellins must be present for fruit development. ▪ After water is imbibed, release of gibberellins from the embryo signals seeds to germinate. ◦ Brassinosteroids ▪ Brassinosteroids are chemically similar to the sex hormones of animals. ▪ They induce cell elongation and division in stem segments. ▪ They slow leaf abscission and promote xylem differentiation. ◦ Abscisic acid ▪ Abscisic acid (ABA) slows growth. ▪ In buds, it delays growth and causes the formation of scales in preparation for overwintering. ▪ Two of the many effects of ABA: seed dormancy and drought tolerance. • Seed dormancy ensures that the seed will germinate only in optimal conditions. In some seeds, dormancy is broken when ABA is removed by heavy rain, light, or prolonged cold. Precocious (early) germination can be caused by inactive or low levels of ABA. • ABA is the primary internal signal that enables plants to withstand drought. ABA accumulation causes stomata to close rapidly. ◦ Strigolactones ▪ Hormones called strigolactones stimulate seed germination, help establish mycorrhizal associations, and help control apical dominance. ◦ Ethylene ▪ Plants produce ethylene in response to stresses such as drought, flooding, mechanical pressure, injury, and infection. ▪ Ethylene induces the triple response to mechanical stress, which allows a growing shoot to avoid obstacles. It consists of a slowing of stem elongation, thickening of stem, and horizontal growth. ▪ Senescence is the programmed death of cells or organs. A burst of ethylene is associated with apoptosis. ▪ A change in the balance of auxin and ethylene controls leaf abscission, the process that occurs in auto when a leaf falls off the plant. • The base of the leaf stalk separates from the stem. The separation region is called the abscission layer. The abscission layer consists of a narrow band of cells with thin walls that are further weakens when enzymes digest the cell walls. The leaf drops off when its weight splits the abscission layer apart. • Plant responses to stimuli ◦ Tropisms and phototropism ▪ Any growth response that results in plant organs curving toward or away from stimuli s called a tropism. growth of the stem is uniform and the stem grows strength. ◦ The higher concentration of auxin in the shady side of the stem causes differential growth. Ethylene triggers ripening. ▪ Also involved in stimulating the production of flowers. It is achieved by the action of the hormone auxin. ▪ Mechanism of action: • Auxin is produced in the apical meristem. auxin moves downward into the zone of elongation but concentrates on the shady side of the stem. and generates growth by stimulating elongation. • When the stem is unequally illuminated. that is. moves downward by active transport into the zone of elongation. and ripening triggers release of more ethylene. ▪ The growth of a shoot in response to light is called phototropism. the shady side grows more than the sunny side. • When all sides of the apical meristem are equally illuminated. When this happens. 277 ▪ A burst of ethylene production in a fruit triggers the ripening process. the stem bends toward the light . Ethylene gas fills the intercellular spaces within the fruit and stimulates its ripening by enzymatic breakdown of cell walls. Thus. the relative lengths of day and night. it requires daily signals from the environment to remain tuned to a period of exactly 24 hours. ▪ Plants whose flowering is triggered by photoperiod fall into one of two groups: • One group. The short-day plant will not blossom if the nighttime part of the photoperiod is interrupted (3) even by a brief flash of light. generally flower in late summer. when light periods shorten. ▪ Circadian rhythms are controlled by internal timekeepers known as biological clocks. There is no effect if the daytime portion of the photoperiod is broken by a brief exposure to darkness. Effects on light on plant morphology are called photomorphogenesis. • In contrast. . but may also influence seasonal events that are important in a plant's life cycle. ▪ Action spectra are useful in studying any process that depends on light. ◦ Plants mark the seasons by measuring photoperiod ▪ A biological clock does not only time a plant's everyday activities. intensity. when light periods lengthen. Photoperiodism is a physiological response to photoperiod. ▪ A short day-plant will not flower (1) until it is exposed to a continuous dark period (2) exceeding a critical length. not the length of continuous daylight. long-day plants usually flower in late spring or early summer. circadian rhythms occur with or without external stimuli. ▪ The environmental stimulus plants most often use to detect the time of year is called photoperiod. fall. • Day-neutral plants do not flower in response to daylight changes. and wavelength (color) ▪ A graph called an action spectrum depicts relative response of a process to different wavelengths. or winter. • Short-day plants will only flower if it stays dark long enough and long-day plants will flower if the dark period is short enough. ▪ Plants detect not only the present of light but also its direction. ◦ Plants have internal clocks ▪ An innate biological cycle of about 24 hours is called a circadian rhythm. 278 ◦ Action spectrums ▪ Light cues many key events in plant growth and development. ▪ Circadian rhythms can be entrained to exactly 24 hours by the day-night cycle. It persists even when an organism is sheltered from environmental cues. ▪ Flowering and other responses to photoperiod are actually controlled by the length of continuous darkness. ▪ Although a biological clock continues to mark time in the absence of environmental cues. the short-day plants. cues responses such as seed germination. flowering occurs when the night length is shorter (4) than the critical length. • Each night. flowering. When the Pr form absorbs red light (660 nm). ▪ There are two major classes of light receptors: blue-light photoreceptors and phytochromes. the clock monitors photoperiod and. new phytochrome molecules are synthesized only in the Pr form. shade avoidance). Sunlight contains both red light and far-red light. • After sunrise. R stands for red light. Thus. A dark interval that is too long will prevent flowering. and when Pfr absorbs far-red light (730 nm). ▪ Various blue-light photoreceptors control hypocotyl elongation. • It is the sudden increase in Pfr each day at dawn that resets a plant's biological clock. In doing so. but the conversion to Pfr is faster than the conversion to Pr. Additionally. the red wavelengths of sunlight cause much of the phytochrome to be rapidly converted from the Pr form to Pfr. FR stands for far-red light. ▪ Phytochromes are pigments that regulate many of a plant's responses throughout its life (e. 279 ▪ In long-day plants.g. Both types of plants behave as though there is no interruption in the night length. . • Bar (1) shows the results we saw for both short-day and long-day plants that receive a flash of light during their critical dark period. and phototropism. when detecting seasonal changes in day and night length. only the wavelength of the last flash of light affects the plant's measurement of night length. and the beginning and end of bud dormancy. seed germination. flowering can be induced in a long-day plant by a flash of light (6) during the night. ▪ The consequences of the phytochrome switch are shown in the picture below. molecules of Pr slowly accumulate in the continuous darkness that follows sunset. • Bar (2) reveals that the effect of a flash of red light that interrupts a period of darkness can be reversed by a subsequent flash of far-red light. • Phytochromes change back and forth between two forms that differ slightly in structure: Pr (absorbs red light). it is quickly converted to Pfr. ▪ Interactions between phytochrome and the biological clock enable plants to measure the passage of night and day.. • Bars (3) and (4) indicate that now matter how many flashes of red or far-red light a plant receives. stomatal opening. and Pfr (absorbs far-red light). it is slowly converted back to Pr. ◦ Photoreceptors include light detectors that may help set the biological clock ▪ Different plant responses can be mediated by the same or different photoreceptors. The flowering hormone is called florigen. in roots. . ◦ Other tropisms ▪ Gravity • Response to gravity is known as gravitropism. auxin produced at the apical meristem moves down the stem and concentrates on its lower side. ◦ A flowering hormone? ▪ Photoperiod is detected by leaves. • When vines and other climbing plants contact some object. production of gibberellins or destruction of ABA occurs and germination follows. When the critical exposure is exceeded. It is produced in leaves and travels to shoot tips. • Both auxins and gibberellins are involved but their action depends on their relative concentrations and the target organ. which cue buds to develop as flowers. ▪ Drought • During drought. • Plants may detect gravity by the settling of statoliths. as in stems. and the stem bends upward as it grows. auxin inhibits growth. Mechanism of action for auxin: ◦ If a stem is horizontal. dense cytoplasmic components. 280 ◦ Phytochromes control more than just the biological clock ▪ Phytochrome can detect if enough light has been exposed to a seed before it germinates. Shaded plants receive more far-red than red light. ▪ The phytochrome system also provides the plant with information about the quality of light. ◦ If a root is horizontal. Since auxin stimulates cell elongation. In the shade avoidance response. It can determine shade from the sun. the phytochrome ratio shifts in favor of Pr when a tree is shaded. plants reduce transpiration by closing stomata. concentrates on the lower side of the root. However. growth of the lower side is greater than that of the upper side. and. slowing leaf growth. auxin is produced at the apical meristem (root tip). ▪ Touch • Thigmotropism is a response to touch. • Mechanism is not well understood. they respond by wrapping around it. • Roots show positive gravitropism whereas shoots show negative gravitropism. . • Growth of shallow roots is inhibited. as well as other organisms. ▪ Heat stress and cold stress • Heat-shock proteins help protect other proteins from heat stress. while deeper roots continue to grow. ▪ Flooding • Enzymatic destruction of root cortex cells creates air tubes that help plants survive oxygen deprivation during flooding. • Many plants. ▪ Salt stress • Plants respond to salt stress by producing solutes tolerated at high concentrations. have antifreeze proteins that prevent ice crystals from growing and damaging cells. • This process keeps the water potential of cells more negative than that of the soil solution. 281 and reducing exposed surface area. Variation in patterns of sexual reproduction ◦ Hemaphroditisim is when an individual has both male and female reproductive systems. wasps. the separation of a parent organism into two individuals of approximately equal size (similar to mitosis). is much smaller and motile ◦ In asexual reproduction. ants. 282 Types of reproduction Asexual and sexual reproduction ◦ In sexual reproduction. new individuals are generated without the fusion of egg and sperm. ▪ Reproduction relies entirely on mitotic cell division Mechanisms of asexual reproduction ◦ Budding is when new individuals arise from outgrowths of existing ones (reef building coral) ◦ Common among invertebrates is fission. occurs at the midpoint of a cycle. global climate change can affect reproduction. often related to changing seasons. Secretion of hormones is regulated by environmental cues. ◦ In humans: ▪ The female gamete. ◦ Parthenogenesis is when an egg develops without being fertilized (bees. the egg. ▪ Because reproductive cycles are regulated by environmental cues. ▪ Eventually. the animal that develops from a zygote can give rise to gametes by meiosis. .) ▪ Progeny can be haploid or diploid ◦ Asexual reproduction can be a two-step process: ▪ fragmentation: breaking of the body into several pieces ▪ regeneration: regrowth of lost body parts ▪ If more than one piece grows and develops into a complete animal. ◦ Ovulation. ▪ Found in asexully and sexually reproducing animals ▪ Cycles controlled by hormones. is large and non-motile ▪ The male gamete. the effect is reproduction Reproductive cycles ◦ Most animals exhibit cycles in reproductive activity. the release of mature eggs. etc. the fusion of haploid gametes form a diploid cell. the sperm. the zygote. The young are hatched from eggs. marsupials. There is limited exchange of food and oxygen between mother and young. nourish. can be either internal or external. fertilization. ◦ Animals also employ a variety of reproductive systems ▪ Gonads are organs that produce gametes. ◦ monotremes are egg laying mammals (platypus) ◦ marsupials are mammals where the young is carried in a pouch ◦ a viviparous mammal is one in which the offspring develop within the uterus ◦ an oviparous mammal is one in which the parent lays eggs (birds. others only have a 1 chamber uterus.g. excretory. most repitles) ◦ oviviparous animal is a combination. and protect the gametes. and fertilization occurs within that tract. ▪ These precursor cells are created very early in life and remain inactive until later in life. to prevent gametes from dying out and allow the sperm to swim to the eggs ◦ Other species have internal fertilization. tropical fish) have no placenta. the cloaca. ▪ Moist habitat is almost always required for external fertilization. where they are amplified to increase production of gametes. where sperm is deposited in or near the female reproductive tract. ▪ It is an adaptation that enables sperm to reach en egg even when the environment is dry ▪ Usually requires copulation (sexual intercourse) and complex reproductive systems ▪ Non-placental internal development: certain animals (e. Male and female reproductive anatomy . ▪ In many nonmammalian vertebrates. ◦ In external fertilization. ▪ In many insect species. ◦ Vertebrate reproductive systems display limited but significant variations. ▪ More elaborate reproductive systems include sets of structures that carry. t he female releases eggs into the environment where the male fertilizes them. ◦ Animals often mate with more than one member of the other sex. the digestive. Ensuring the survival of offspring ◦ Internal fertilization is typically associated with the production of fewer gametes than external fertilization but results in the survival of a higher fraction of zygotes. Gamete production and delivery ◦ Sexual reproduction in animals relies on sets of cells that are precursors for eggs and sperm. ▪ This is because the environment of internal fertilization is shielded from predators and also contains mechanisms that provide greater protection and care of the embryos. some amphibians. ▪ Placental internal development: lots of exchange of food and oxygen between mother and young. and reproductive systems have a common opening to the outside. sacs in which sperm may be stored for extended periods. but the eggs are kept in the mother's body until they are ready to hatch. 283 Types of fertilization Introduction ◦ the union of sperm and egg. ▪ Some vertebrates have a 2 chamber uterus. the female reproductive system contains one or more spermathecae. the sperm pass into the coiled duct of an epidiymis. Takes 3 weeks for sperm to pass through this (enough time for it to grow and mature). the erectile tissue fills with blood from the arteries and the increased pressure blocks of the veins. the outlet tube for both the excretory system and the reproductive system. Each vas deferens. ▪ The main shaft of the penis is covered by relatively thick skin. or glans. Activated by follicle-stimulating hormone (FSH). During sexual arousal. of the penis has a much thinner outer layer and is more sensitive to stimulation ▪ the human glans is surrounded by a fold of skin called the prepuce. ▪ Sertoli cells are the “nurse” cells of the testes that helps in the process of spermatogenesis. . Neutralizes acidity of urine that may still be in urethra. The ejaculatory duct opens to the urethra. ◦ Ducts (path of sperm is SEVEnUP) ▪ From the seminiferous tubules of a testis. the prostate glands. or testes produce sperm in highly coiled tubes called seminiferous tubules. Provides mucus (liquid for sperm). ▪ Two seminal vesicles contribute about 60% of the volume of the semen. ▪ The scrotum is the small muscular sac that contains and protects the testicles. one from each epididymis (one for each testes). This causes an erection. ◦ Penis ▪ The human penis contains the urethra as well as three cylinders of spongy erectile tissue. ▪ Intersticial cells (leydig cells) produce male sex hormones (testosterone) in the presence of luteinizing hormone (LH). ◦ Accessory glands ▪ three sets of accessory glands—the seminal vesciles. the fluid that is ejaculated. forming a short ejaculatory duct. ▪ Bulbourethral glands secrete small amount of fluid of unknown function into the urethra. and prostaglandins ▪ The prostate gland secretes its products directly into the urethra through the small ducts. which is removed during circumcision. the vas deferens. fructose as ATP. Keeps the testes cooler than the rest of the body for proper production of sperm. and seminal fluid. vagina acidity. the sperm are propelled from each epidiymis through a muscular duct. 284 Male reproductive anatomy ◦ Testes ▪ The male gonads. where it joins a duct from the seminal vesicle. extends around and behind the urinary bladder. ▪ During ejaculation. ▪ The head. and the bulbourethral glands—produce secretions that combine with sperm to form semen. ▪ Support cells nourish and protect oocyte during development. surrounded by support cells. extends from the uterus to each ovary. ▪ The uterus is a thick. ▪ Outer layer is packed with follicles. muscular organ that can expand during pregnancy to accommodate a fetus. ▪ The cilia that lines the oviduct helps facilitate movement of the egg. . ▪ The inner lining of the uterus is the endometrum (richly supplied with blood vessels). ◦ Oviduct and uterus ▪ Oviduct. a partially developed egg. 285 Human Female reproductive anatomy ◦ Ovaries ▪ The female gonads are a pair of ovaries that flank the uterus and are held in place by ligaments. or fallopian tube. each consisting of an oocyte. Spermatogenesis ◦ Begins at puberty within the seminiferous tubules of testes . Mammary glands ◦ Mammary glands (only in mammals) are present in both sexes. Also serves as the birth canal where a baby is born. the cervix opens up to the vagina. ◦ Vagina ▪ Vagina is a muscular but elastic chamber that is the site of insertion of the penis. 286 ▪ The neck of the uterus. but they normally produce milk only in females. ▪ The clitoris consists of erectile tissue supporting a rounded glans. ▪ Acrosome is at the tip of the sperm head and contains enzymes which are used to penetrate the egg ◦ Midpiece: flagellum (9+2 microtubule array) and lots of mitochondria for ATP generation ◦ Tail: remainder of flagellum. Sperm ◦ Sperm are compact packages of DNA specialized for effective male genome delivery ◦ Sperm head: contains chromosomes and the acrosome. 287 ◦ The father cell of sperm is clalled the spermatogonia cells → primary spermatocytes (mitosis) → (meiosis I) 2 secondary spermatocytes → (meiosis II) 4 spermatids ◦ Sertoli cells nourish the newly formed sperm cells and help make them motile. sperm is propelled by whiplike motion of tail and midpiece . 288 Oogenesis ◦ Oogonia (fetal cells) → (mitosis) primary oocytes → (meisosis) and remain at prophase I until puberty → menstural cycle releases 1 egg per month → released egg continues development through remainder of meiosis I in a follicle (protects and nourishes oocyte) → (completion of meiosis I) secondary oocyte and polar body → (meiosis) and remains at metaphase II until sperm enters the egg → completion of meiosis II at fertilization . follicle stimulating hormone (FSH) and lutenizing hormones (LH). the follicle. ◦ After ovulation. ▪ LH causes leydig cells. The hypothalamus secretes gonadotropin-releasing hormone (GnRH). which then directs the anterior pituitary to secrete the gnoadotropins. Low levels of estrogen and progesterone lead to the secretion of GnRH. direct spermatogenesis by acting on different types of cells in the testis. ◦ Are called gonadotropins because they act on male and female gonads. ◦ FSH stimulates the development of the follicle and the oocyte. ◦ Hormonal upregulation: ▪ FSH stimulates sertoli cells. stimulates production of FSH and LH. to produce testosterone and other androgens. a process that occurs in a flow through the cervix and vagina. ▪ Inhibin. ◦ FSH also stimulates the secretion of estrogen from the follicle. Menstrual cycle ◦ menarche is a girl's first menstrual period ◦ Hypothalamus and anterior pituitary initiate the reproductive cycle. FSH. negative feedback from the high levels of estrogen and progesterone cause the anterior pituitary to crease production of FSH and LH through the . a hormone that in males is produced by sertoli cells. The surge of LH triggers ovulation. ◦ If no implantation occurs. 289 Hormonal control of reproductive cycles Hormones from multiple glands govern reproduction in males and females. among with other mechanisms. but they also have other actions. ◦ Menstrual cycle refers to the changes that occur about once a month in the uterus ◦ The cyclic changes in the uterus is called the ovarian cycle. now called the corpus luteum. Hormonal control of female reproductive cycles ◦ The cyclic shredding of the blood-rich endometrium from the uterus. continues to develop under the influence of LH and secretes both estrogen and progesterone. ◦ The rising levels of estrogen stimulate the anterior pituitary to create lots of LH. to nourish developing sperm. and they support gametogenesis by stimulating sex hormone production. is called menstruation. Hormonal control of the male reproductive system ◦ FSH and LH. located within the seminiferous tubules. ◦ Estrogen and progesterone stimulate the development of the endometrium. Estrogen thickens the endometrium whereas progesterone develops and maintains the endometrial wall. Sex hormones: ◦ androgens = testosterone ◦ estrogens = estradiol and progesterone ◦ gonads are major source of sex hormones ◦ Sex hormones regulate gametogenesis both directly and indirectly. which in turn. and LH. ◦ Negative feedback routes: ▪ Testosterone regulates blood levels of GnRH. released by the anterior pituitary in response to GnRH from the hypothalamus. which promote spermatogenesis. acts on the anterior pituitary gland to reduce FSH secretion. Estrogen and progesterone production will then be maintained by the placenta later on. Birth control pills contain synthetic estrogen and progestin. Estrogen and progestin stops pituitary gland from releasing FSH and LH. 290 hypothalamus. . the corpus luteum deteriorates. proliferative phase. the endometrium disintegrates. the corpus luteum will produce estrogen and progesterone to maintain the endometrium. ◦ If implantation of the embryo occurs. Progesterone levels are at the highest during this phase. In absence of FSH and LH. Ovarian cycle ◦ follicular phase: development of the egg and secretion of the estrogen from the follicle. As a result. The deterioration stops production of estrogen and progesterone. and secretory phase ◦ menstrual phase is when the endometrium is shed ◦ proliferative phase is when estrogens allow the endometrium to thicken as allow glands and arteries to grow during the secretory phase ◦ secretory phase is when the corpus luteum produces progestrone which allows the endometrium to be receptive to implantation of the blastocyst. the growth of the endometrium cannot be supported. the menstrual cycle consists of the menstrual flow phase. When estrogen and progesterone stop getting produced. As a result. the implanted embryo will secrete human chorionic gonadotropin (HCG) to sustain the corpus luteum. sloughing off during menstruation. ◦ Ovulation: the midcycle release of the egg ◦ Luteal phase: the secretion of estrogen and progesterone from the corpus luteum after ovulation. from the time of fertilization of the egg to the organism's mature form. Actin filaments extend from the sperm onto sperm-binding receptors (ZP3) on the plasma membrane (zona pellucida) of the egg. ◦ 3) contact and fusion of sperm and egg membranes: fusion triggers depolarization of the membrane. ▪ In non-mammals. it results in sterility of the second species due to immune response—fertilization cannot occur because antibodies have already bound the zona pellucida. The sperm then moves through the corona radiata (dense layer of granulosa cells surrounding the oocyte) and eventually reaches the zona pellucida. When the zona pellucida of one animal species is injected into the blood stream of another. Helps the sperm create a hole through the zona pellucida. ▪ Zona pellucida is commonly used to control wildlife populations by immunocontraception. 291 Four stages of growth and development in an animal: ◦ (1) Gametogenesis – spermatogenesis and oogenesis ◦ (2) Embryonic development – fertilization of egg until birth ◦ (3) Reproductive maturity – puberty ◦ (4) Aging until death ▪ Stages 2 and 3 can collectively be called ontogeny: the origination and development of an organism. making the head more fluid which helps it prepare for fertilization. The secreted contents clip off the sperm-binding receptors and cause the fertilization envelope to form. triggering exocytosis of the sperm's acrosome. This acts as a slow block to polyspermy. which acts as a fast block to polyspermy (prevents other sperm from fusing) ◦ 4) cortical reaction: cortical granules in the egg fuse with the plasma membrane. This triggers meiosis II ◦ 6) fusion of nuclei and replication of DNA: sperm and ovum nuclei fuse to create the zygote . The binding to the ZP3 receptors triggers the acrosome reaction during which the enzymatic contents of the acrosome are released. and makes the sperm hyperactive (Faster and wiggle more) ◦ 1b) Contact: The sperm contacts the egg's jelly coat. preventing sperm from binding. Fertilization ◦ 1a) Capacitation: Secretions from the uterus wall and uterine tube destabilize the plasma membrane surrounding the head of the sperm. ◦ 5) Entry of sperm nucleus. the zona pellucida plays an important role in preventing cross- breading of different species (especially in species that fertilize outside the body). ◦ 2) Acrosomal reaction: the hydrolytic enzymes make a hole in the jelly coat. ◦ As cell divisions continue. liquid fills the morula and pushes cells out to form a circular cavity surrounded by a single layer of cells. cells are in S and M phase. and a lower. forming cells that are shifted with respect to those below them. ▪ Pattern of cleavage divisions differs among species. Blastomeres produced by a determinate cleavage cannot develop into a complete embryo if separated from other blastomeres. The division can also be polar if the line is the same line connecting the poles. In protosomtes. pooling at the vegetal pole. the cells are totipotent). ▪ Polar and equatorial cleavages: The yolk begins to affec the relative size of cells produced in the two hemispheres. can individually complete normal development. ▪ during cell cleavage the nuclear to cytoplasmic ratio increases ▪ G1 and G2 phase of cell cycle basically skipped. if separated. forming cells at the animal and vegetal poles that are aligned together. The yolk (stored nutrients) will be distributed unequally. ▪ No increase in mass ▪ Cleavage partitions of the cytoplasm of the larged fertilized egg into many smaller cells called blastomeres. cleavages are spiral. The hollow sphere of cells is called the blastula . ▪ Holoblastic vs meroblastic: Holoblastic is when the cleavage furrow passes entirely through the egg whereas meroblastic means when the cleavage furrow does not pass entirely through the egg. vegetal pole. early cleavages are radial. ▪ Indeterminate and determinate cleaves: A cleavage is said to be indeterminate if it produces blastomeres that. 292 Cleavage ◦ The zygote undergoes a succession of rapid cell divisions that characterize the cleavage stage of early development. ◦ Successive cleavage divisions result in a solid ball of cells called a morula (8 cell stage. This division is equatorial if the line is perpentiduclar to the line connecting the poles. ◦ Common characteristics of early cleavage: ▪ Embryo polarity (asymmetric cleavage): Egg has an upper. animal pole. Radial cleavages in duterostomes are usually indeterminate. whereas spiral cleavages in protostomes are usually determinate. the top cells directly above the bottom cells. ▪ Radial and spiral cleavages: In duterostomes. forming a two layered embryo with an opening from the outside into a center cavity. mesoderm. middle. and parathryoid glands. thymus. jaws and teeth. ▪ Three germ layers: A third cell layer forms in between the outer and inner layers of the invaginated embryo. the ectoderm. germ cells Mesoderm: muscle. bone. Completely surrounded by endoderm cells. Ecotderm: forms epidermis skin. and the lungs . and inside layer. kidneys. thyroid. These three cell layers. pituitary gland. and connective tissues Endoderm: epithelial lining of most organs. Special features: ▪ Archentron: The center cavity formed by gastrulation. Becomes the mouth (in protostomes) or the anus (in duterostomes). respectively) are the three primary germ layers from which all subsequent tissues develop. nervous and sensory systems. 293 (128 cell stage) and the cavity is called the blastocel. ◦ Formation of the gastrula occurs when a group of cells invaginate (move inward) into the blastula. and endoderm (outside. blood. gonads. liver. Develops into the digestive tract of an animal. ▪ Blastopore: opening into the archentron. Yolk is a part of an egg that feeds the developing embryo. etc. ▪ Neutral tube: In the ecotderm layer directly above the notochord. In birds and reptiles. and together they act as one membrane for gas exchange. extraembryonic (outside the embryo) membranes develop. a more complex. and then rolls up into a cylinder. Eventually forms the umbilical cord. joined skeleton develops around the ancestral notochord. a yolk sack membrane digests enclosed yolk. the yolk sack is empty as the umbilical cord/placenta delivers nutrients. the chorion forms the placenta—a blaned of maternal and embryonic tissues across which gases. the neural tube. it acts as a membrane for gas exchange. Organogenesis ◦ The development of organs is called organogenesis. it encircles the embryo. The neural tube develops into the nervous system. a layer of cells form the neural plate. Later in development. ▪ In birds and reptiles. Eventually. . and wastes are exchanged. 294 Embryonic membrane development ◦ In birds. reptiles. nutrients. it initially stores waste products. and muscles of the skull. called the amniotes. Later. In placental mammals. Blood vessels transfer nutrients to the embryo. the allantois transports waste product to the placenta. the chorion implants into the endometrium. In most vertebrates. forming a layer below the chorion. In mammals. The plate indents. bone. as follows: ▪ Chorion: The chorion is the outer membrane that surrounds the embryo. and humans. Additional cells roll off the top of the developing neural tube and form the neural crest. a fluid-filled cavity that cushions the developing embryo. it fuses with the chorion. These cells form various tissues: including teeth. and the adult retains only remnants of the embryonic notochord. a stiff rod that provides support in lower order chordates. Features characteristic of chordates: ▪ Notochord: cells along the dorsal surface of the mesoderm germ layer form the notochord. In birds and reptiles. In mammals. ▪ Amnion: The amnion is a membrane encloses the amniotic cavity. forming the neural groove. ▪ Allantois: A sac that buds off from the archentron. is the site of initiation of gastrulation in the amphibian embryo. called the gray crescent. ▪ The dorsal lip. crescent-shaped region. The bottom and sides of the blastopore edge are called the ventral and lateral lips. which forms at the site of the grey crescent. 295 Important variations in other animals in development ◦ Frog (an amphibian) ▪ When the sperm penetrates a frog egg. a reorganization of the cytoplasm results in the appearance of a gray. ▪ Cells from the vegetal pole rich in yolk material form a yolk plug near the dorsal lip. . This is called a blastodisc. the crevice formed becomes an elongated blastopore. When gastrulation occurs. As cells migrate into the primitive streak. . Instead. invagination occurs along a line called the primitive streak. the cleavages occur in a blastula that consists of a flattened. disk-shaped region that sits on top of the yolk. 296 ◦ Bird ▪ Most of the yolk in the bird is not involved in cleavages. the trophoblast forms the chorion. it accomplishes implantation by embedding into the endometrium of the uterus. which maintains progesterone production of the corpus luteum (which. . 297 ◦ Humans ▪ At the end of cleavage. It produces human chorionic gonadotropin. First. Later. will maintain the endometrium). the embryo is a blastocyst. the mammalian version of a blastula. the extraembryonic membrane that will eventually turn into the placenta. 5 days after fertilization. in turn. ▪ The trophoblast have several functions. Clustered at one end of the blastocyst cavity is a group of cells called the inner cell mass (embryonic disk) and at the other end is another ring of cells called the trophoblast. the blastocyst performs zone hatching: the zona pellucida degenerates and is replaced by an underlying layer of trophoblastic cells so it can implant in the uterus. This is analogous to the blastodisk of birds and reptiles. The embryo is at the blastula stage by the time it reaches the uterus for implantation. A primitve streak develops. the individual digits separate after being fused. A homeobox is an 180 nucleotide sequence that is highly conserved between many species that are homeotic genes. ◦ Stem cells can be isolated from early embryos at the blastula stage.e. Cleavage occurs while the fertilized egg is still moving through the oviduct. and development of the embryo and the extraembryonic membranes ensues. a lineage map can be built (tells you which cells arose from which cells). influencing their development. cancer may develop. ▪ During embyronic development. This best illustrates apoptosis. they do this by secreting chemicals that diffuse to neighboring cells. ◦ Apoptosis. ▪ The dorsal lip functions as an organizer for the notochord. Cells are more likely to be determined later in the developmental sequence than earlier. ◦ The fate of a cell is said to be determined if its final form cannot be changed. Stem cells ◦ Many early animal embryos contain stem cells capable of giving rise to differentiated cells of any type (embryonic stem cells). Cells that exert this influence are called organizers. ◦ By tracing the fates of cells during development. 298 ▪ Within the trophoblast. ◦ Homeotic genes contribute to the control of development by turning on and off other genes that code for substances that directly affect development. When cleavages divide the egg. if not. Nonuniform distribution of the cytoplasm results in embryonic axes. a bundle of cells called the inner cell mass (embryonic disk) clusters at one end and flattens into the embryonic disk. Cytoplasmic material is distributed unequally in the egg and subsequent daughter cells during cleavage (i. the quality of cytoplamic substances will vary among daughter cells. is a normal part of development. yolk and gray crescent). ◦ Embyronic induction is the influence of one cell group or group of cells over neighboring cells. ▪ Fertilization (syngamy) takes place in the fallopian tubes (oviduct). gastrulation follows. ◦ Factors that influence development and differentiationInfluence of the egg cytoplasm. or the blastocyst stage in . Substances unique to certain daughter cells may influence their subsequent development. programmed cell death. Damaged cells undergo apoptosis. First few divisions in embryonic development produce totipotent cells. liver. Pregnancy and Labor ◦ Human oocytes can be fertilized most successfully by the use of micro-injection ◦ Fraternal twins result from more than one egg being fertilized. ▪ Ontogeny recapitulates phylogeny is an idea that suggests embryonic stages of development of an organism repeat the evolutionary history of the species. the embryo is called a fetus ◦ at 5 weeks. amniotic sac ruptures and releases fluids ▪ 2. This idea is not true. and limb buds have begun development ◦ Labor (three stages) – a series of strong uterine contractions ▪ 1. identical twins result from indeterminate cleavage ◦ Ectopic pregnancy results when the zygote makes contact and starts to grow in improper places. but they can only generate a few different types of cells. and the evolution of the regulation and expression of genetic networks. Uterus contracts and expels umbilical cord and placenta Evolution and development (evo-devo) ◦ Evolution and development is the combination of developmental biology and evolutionary biology. Can give rise to ANY and ALL human cells. the mother's immune system may launch an immune system against the baby's red blood cells. As a result. These cells can differentiate into many different types of cells. ◦ How do proteins take new functions? ▪ Subfunctionalization: gene duplication produces gene copies that diverge and divide the work initially undertaken by the gene before duplication. the evolution of function. ◦ Adult body has stem cells (adult stem cells). pancreas. ◦ Pluripotent stem cells can give rise to all tissue types. ▪ Promiscuous proteins: proteins capable of carrying out more than one function (usually sone strongly and one weakly) ▪ Gene recruitment: the co-option of a particular gene or network for a totally different function as a result of mutation. ◦ Multipotent stem cells give rise to a limited range of cells within a tissue type. Rh. eyes.mother ▪ ABO incompatibility disease ◦ first trimester of pregnancy is where organs are formed ◦ at approximately 8 weeks. Cervix thins out and dilates. Because of the incompatibility. heart. Two types: ▪ Rh incompatibility disease: Rh+ fetus. ◦ Totipotent stem cells are the most versatile of stem cell types. Rapid contractions followed by birth ▪ 3. Fertilization. ▪ Studies the evolution of the timing and rate of development. but is rather seen as an historical-side note. ▪ Tubal pregnancies are when the zygote implants itself into the fallopian tube ◦ Erythroblastosis fetalis = A fatal disease in pregnant women that is caused by incompatibility between a mother's blood and her unborn baby's blood. ▪ Gene duplication: any duplication of DNA that contains one or many genes . ▪ Neofunctionalization: duplicated genes diverge and one copy takes on a new function. 299 humans. the baby may die. but CANNOT give rise to an entire organism. Can give rise to an entire organism. .g. ◦ Complex adaptations: suites of coexpressed traits that together experience selection for a function ◦ What guides the development of organisms? ▪ Homeotic genes: genes associated with mapping body shape during development ▪ In insects. ▪ orthologs: homologous genes separated by a speciation event. 300 ◦ How do genes duplicate? ▪ Slippage during replication ▪ Ectopic recombination: error in recombination where unequal parts of the homologous chromosomes recombine ▪ Retrotransposition ▪ Whole genome duplication (e. molting and metamorphosis are regulated by the hormone ecdysone . polyploidy) ◦ Gene duplication ▪ homologs: genes that share common ancestry. ▪ paralogs: homologous genes within a genome separated by a gene duplication event. cartilage tissue is surrounded by a dense fibrous connective tissue called Perichondrium ◦ Muscle tissue is the tissue responsible for nearly all types of body movement. groups of cells with a similar appearance and a common function. 301 Body organization and types of tissues Hierarchical organization of body plans ◦ Cells are organized into tissues. ▪ They function as a barrier against mechanical injury. processing. providing an additional level of organization and coordination. Homeostasis Regulating and conforming . Types of animal tissues ◦ Epithelial cells or epithelia cover the outside of the body and line organs and cavities within the body. ▪ Organs are generally made up of 4 types of tissue: Nervous tissue Epithelial tissue Muscle Connective tissue ◦ Groups of organs that work together. It holds many tissues and organs together and in place. ▪ Skeletal muscle is responsible for voluntary movements. The opposite side of each epithelium is the basal surface. is responsible for involuntary body movements. ◦ Peritoneum is the tissue that covers all the digestive organs and lines in the body cavity. ▪ Bone generates the skeleton of animals. ▪ Different cell shape and arrangements correlate to distinct functions. ◦ Different types of tissues are further organized into functional units called organs. Very strong. ▪ Adipose tissue stores fat in adipose cells. meaning that they have two different sides. ▪ Three different types of connective tissue fibers: Collagenous fibers provide strength and flexibility Reticular fibers join connective tissue to form adjacent tissues Elastic fibers make tissues elastic ▪ Loose connective tissue is the most common tissue: binds epithelia to underlying tissues and holds organs in place. which transmits nerve impulses. ▪ Cardiac muscle forms the contractile wall of the heart and is involuntary. make up an organ system. which lacks striations. ▪ Also form active interfaces with the environment. pathogens. and fluid loss. ▪ Contains neurons. and transmission of information. and support cells called glial cells. ▪ Blood carry nutrients from one place to another. ◦ Nervous tissue functions in the receipt. ▪ They are polarized. The apical surface faces the lumen (cavity) or outside of the organ and is therefore exposed to fluid or air. ▪ Epithelial cells are closely packed. ▪ Cartilage contains collagenous fibers embedded in chondroitin sulfate. ▪ Fibrous connective tissues is dense with collagenous fibers. ◦ Connective tissue consists of a sparse population of cells scattered through an extracellular matrix. ▪ Smooth muscle. Specialized projections often cover this surface. often with tight junctions. you sweat to decrease the effects of heat (increase body temperature). a physiological activity that helps return the variable to the set point. animals maintain a relatively constant internal environment even when the external environment changes significantly. the stimulus. Variation in body temperature ◦ A poikilotherm is an animal whose body temperature varies with its environment. ◦ One way in which homeostasis may be altered is through acclimatization. ◦ Positive feedback (e. a control center generates an output that triggers a response. Feedback control in homeostasis ◦ Negative feedback is a control mechanism that reduces the stimulus.g.” referring to the maintenance of internal balance. ▪ Mainly adjust their body temperature by behavioral means. ◦ Ectothermic means that the organism gains heat from external sources. the gradual process by which an animal adjusts to changes in its external environment. ◦ An animal is a conformer for a particular variable if it allows its internal conditions to change in accordance with external changes in the variable. ◦ A fluctuation in the variable above or below the set point serves as the stimulus detected by a sensor. homeothermy. but helps drive processes to completion. poikilothermy. ◦ There is no fixed relationship between endothermy. ◦ Upon receiving a signal from the sensor. ◦ In achieving homeostasis. 302 ◦ An animal is a regulator for an environmental variable if it uses internal mechanisms to control internal change in the face of external fluctuation. Homeostasis ◦ Homeostasis means “steady state. ▪ Acclimatization is a temporary change during an animal's lifetime and does not bring about any changes within the genetic code. and ectothermy. Mechanisms of homeostasis ◦ An animal achieves homeostasis by maintaining a variable at a particular value. or set point. orgasm) is a control mechanism that amplifies. ◦ A homeotherm has a relatively constant body temperature. Alterations in homeostasis ◦ A circadian rhythm is a set of physiological changes that occur roughly every 24 hours. ▪ Can maintain a stable body temperature in the face of large fluctuations in the environmental temperature. Thermoregulation Endothermy and Ectothermy ◦ Endothermic means that the organism is warmed by internal mechanisms. ▪ Does not play a major role in homeostasis. rather than reduces. ◦ An animal may regulate some processes and conform to other processes. ▪ For example. ▪ Ectotherms generally need to consume much less food than endotherms of equivalent size. Balancing heat loss and gain ◦ The essence of thermoregulation is maintaining a rate of heat gain that equals the rate of . ◦ Organisms may be both ectothermic and endothermic in some way. the outer covering of the body. ◦ Conduction is the direct transfer of thermal motion (heat) between two molecules of objects in contact with each other. ▪ Insulation may include hair or feathers. Done in hot temperatures. Water absorbs considerable heat when it evaporates (high specific heat). and nails. ▪ Many of these mechanisms involve the integumentary system. Done in cold temperatures. ◦ Vasoconstriction reduces blood flow and heat transfer by decreasing the diameter of superficial vessels. the transfer of heat between fluids that are flowing in opposite directions. as well as layers of fat formed by adipose tissue. Circulatory adaptations ◦ Nerve signals that relax the muscles of vessel walls result in vasodilation. Cooling by evaporative heat loss ◦ Many terrestrial animals lose water by evaporation from their skin and respiratory surfaces. which reduces the flow of heat between an animal's body and its environment. ▪ Vasodilation warms the skin and increases the transfer of body heat to the environment. reducing heat loss from the body comes from countercurrent heat exchange. ◦ Convection is the transfer of heat by the movement of air or liquid past a surface. ◦ Radiation is the emission of electromagnetic waves by all objects warmer than absolute zero. a widening of superficial blood vessels. hair. it transfers heat to the colder blood returning from the extremities in the veins. ◦ Evaporation is the removal of heat from the surface of a liquid that is losing some of its molecules as gas. consisting of the skin. 303 heat loss. As warm blood moves from the body to the core in the arteries. As a result. ◦ In many birds and mammals. this heat is carried . ▪ Arteries and veins are located adjacent to each other. blood flow of the skin increases. Insulation ◦ A major thermoregulatory adaptation is insulation. they seek warm places. or turn in another direction. they bate. . orienting themselves toward heat sources and expanding their portion of body surface exposed to the heat source. This is evaporative heat loss. Adjusting metabolic heat production ◦ Endotherms can vary heat production. minimizing their absorption of heat form the sun. Physiological Thermostats ◦ The sensors for thermoregulation are concentrated in the hypothalamus ▪ within the hypothalamus. The breakdown of the adipose tissues eventually generates a proton gradient. Behavioral responses ◦ Many ectotherms maintain a nearly constant body temperature by engaging in relatively simple behaviors. responding to body temperatures outside the normal range by activating mechanisms that promote heat loss or gain. Instead of using the gradient to synthesize ATP. the gradient is used to generate heat. ◦ Nonshivering thermogenesis occurs in brown adipose tissues. ▪ When hot. thermogenesis. ▪ When cold. 304 away from the body surface with water vapor. moving to cool areas. ▪ It is increased by such muscle activity as moving or shivering. to match changing rates of heat loss. a group of nerve cells functions as a thermostat. every cell in the body is close enough to the external environment so that gases can diffuse quickly between any cell and the environment. Gills in aquatic animals ◦ Gills are outfoldings of the body surface that are suspended in the water. the two fluids are blood and water. The skin serves as the respiratory organ. ▪ As blood enters a gill capillary. ◦ In fishes. Respiratory media ◦ The conditions for gas exchange vary considerably. depending on whether the respiratory medium—the source of oxygen—is air or water. Even as the blood continues its passage. Respiratory surfaces are always moist. ◦ The movement of oxygen and carbon dioxide across respiratory surfaces takes place by diffusion. cnidarians. External vs internal respiration ◦ External respiration refers to the entrance of air into the lungs and the gas exchange between the alveoli and the blood ◦ Internal respiration includes the exchange of gas between blood and the cells and the intracellular processes of respiration. ◦ Aquatic animals that need to extract oxygen out of water have developed special adaptations to do this. the efficiency of gas exchange is maximized by countercurrent exchange. Do2 in air is higher than DO2 in water. ▪ In a fish gill. ◦ Gas exchange with air is much easier than gas exchange with water due to differing diffusional coefficients. ◦ In sponges. ◦ Respiratory surfaces tend to be large and thin to maximize surface area to maximize the flux of these gases. A gas always undergoes net diffusion from a region of higher partial pressure to a region of lower partial pressure. its partial pressure of oxygen steadily increases. and oxygen transfer takes place. . ◦ Movement of the respiratory medium over the respiratory. the exchange of a substance or heat between two fluids moving in opposite directions. The partial pressure of oxygen in the water is greater than that of the blood in the capillaries. the bulk of the body's cells lack immediate access to the environment. but so does that of the water it encounters. Respiratory surfaces ◦ The respiratory surface is the part of an animal's body where gas exchange occurs. since each successive position in the blood's travel corresponds to an earlier position in the water's passage over the gills. ◦ The cells that carry out gas exchange have a plasma membrane that must be in contact with an aqueous solution. ◦ In other animals. it encounters water that is completing its passage through the gill (almost depleted of oxygen). maintains the partial pressure gradients of oxygen and carbon dioxide across the gill that are necessary for gas exchange. at each point in its travel blood is less saturated with oxygen than the water it meets. They often have a total surface area much greater than that of the rest of the body's exterior. 305 Respiratory system Partial pressure gradients in gas exchange ◦ Partial pressure is the pressure exerted by a particular gas in a mixture of gasses. Because blood flows in the direction opposite to that of water passing over the gills. and flatworms. a process called ventillation. 306 Tracheal systems in insects ◦ The tracheal system is a network of airtubes that branch throughout the body. The right lung has 3 lobes whereas the left lung has 2 lobes. tracheoles. open tot he outside. extend close to the surface of nearly every cell. ◦ In humans. where gas is exchanged by diffusion across the moist epithelium that lines the tips of tracheal branches. They are an infold of the body surface that are typically subdivided into numerous pockets. Lungs ◦ Lungs are localized respiratory organs. the right lung is larger than the left lung. called tracheae. ▪ The largest tubes. . It is the largest internal organ. ▪ The finest branches. the epiglottis is covering the esophagus. if non-gas enters. ▪ Also controls action of the epiglottis. and sampled for odors through the nasal cavity. smooth membranous outer covering of the lungs. pollen. Mammalian respiratory systems ◦ Air enters through the nostrils. The air is then filtered by hairs. which is the opening of the trachea so food can move down through the esophagus. ▪ smoking can damage the cilia of the respiratory cells and allow toxins to remain in lungs ◦ The larynx is the upper part of the respiratory pathway. warmed. 307 ◦ Pleurae is the thin. ▪ All the contaminants and mucus are swept back here by cilia for disposal via spitting or swallowing. If air is moving through. ▪ Mucus secreted by goblet cells traps large dust particles. cough reflex activates. If food is moving down the pharynx. Called the mucus escalator. an intersection where the paths for air and food cross. humidified. and other particulate contaminants. . It is the voice-box. the larynx will tip the epiglottis over the glottis. the gap must be bridged by the circulatory system. ◦ Because the respiratory surface of a lung is not in direct contact with all other parts of the body. ◦ Book lungs are stacks of flattened membranes enclosed in an internal chamber. ◦ The nasal cavity leads to the pharynx. so air can travel down through the glottis. and into red blood cells. ▪ emphysema is a pathology marked by destruction of alveoli ▪ Oxygen diffuses through the alveolar wall through the pulmonary capillary wall. ◦ Instead of having alveoli. ▪ With the nostrils and the mouth closed. pushing air into the lungs ▪ Second inhalation: air passes through the lungs and fills the anterior air sacs ▪ Second exhalation: as anterior air sacs contract. the floor of the oral cavity rises. ▪ During exhalation. into blood. ▪ The air sacs do not function directly in gas exchange but acts as bellow that keep air flowing through the lungs. ▪ The walls of the trachea is reinforced by ringed cartilage that is C-shaped (for strength and to keep the airway open). ▪ White blood cells patrol the alveoli. drawing in air through its nostrils. inflating the lungs with forced airflow. the bronchi branch repeatedly into finer and finer tubes called bronchioles. which coats the alveoli and reduces surface tension which prevents collapse. engulfing foreign particles. ▪ Muscles lower the floor of an amphibian's oral cavity. Carbon dioxide moves in the opposite direction starting at the red blood cells and moving into the alveoli. How a bird breathes ◦ To bring fresh air into their lungs. air that entered the body at first inhalation is pushed out of the body. ▪ Covered by ciliated mucus cells. . air sacs clustered at the tips of the thinnest bronchioles. Breathing How an amphibian breathes ◦ An amphibian such as a frog ventilates its lungs by positive pressure breathing. birds use eight or nine air sacs situated on either side of the lungs. ◦ Two cycles of inhalation and exhalation are required to pass one breath through the system: ▪ First inhalation: air fills the posterior air sacs ▪ First exhalation: posterior air sacs contract. ◦ The trachea branches into two bronchi. forcing air down the trachea and into the lungs. sites of gas exchange in bird lungs are tiny channels called parabronchi. air is forced back out by the elastic recoil of the lungs and by compression of the muscular body wall. ◦ Gas exchange in mammals occur in alveoli. one leading to each lung. ▪ Alveoli produces a mixture of phospholipids and proteins called surfactant. ▪ Alveoli lack cilia or significant air currents to remove particles from the surface so they are highly susceptible to contamination. 308 ◦ The trachea is the windpipe. Within each lung. The pressure gradient causes air to flow into the lungs. 309 How a mammal breathes ◦ Tidal breathing is breathing in and out through the same tubing. ◦ During exhalation. some of it is re- breathed ▪ Much less efficient than birds as a result ◦ Mammals employ negative pressure breathing—pulling. inhibiting gas exchange during exhalation. rather than pushing. and the volume of the cavity is reduced. mammals use lower air pressure in their lungs below the air outside the body. ▪ Using muscle contraction to expand their thoracic cavity. ◦ Expanding the thoracic cavity during inhalation involves the animal's rib muscles and the . The increased air pressure in the alveoli forces air up into the breathing tubes and out of the body. ▪ Deoxygenated air is mixed with some fresh air during inhalation. air into their lungs. the muscles controlling the thoracic cavity relax. inhibiting further inhalation. near the base of the brain. sensors that detect stretching of the tissue send nerve impulses to control circuits in the medulla. ▪ In response to decreasing pH. residual volume increases while vital capacity decreases. the fluid surrounding the brain and the spinal cord. ▪ Carbon dioxide diffuses from the blood and into the cerebrospinal fluid. 310 diaphragm. The pressure gradient is created and there is a bulk flow of air into lungs. ▪ The diaphragm is a skeletal muscle and is controlled by the phrenic nerve It is also the only organ which only and all mammals have. Air then rushes out and the diaphragm relaxes and expands. ◦ The volume of air inhaled and exhaled with each breath is called tidal volume. and without which no mammal can live. This causes an increase in volume and a decrease in pressure in the lungs. ◦ In regulating breathing. ▪ The tidal volume during maximal inhalation and exhalation is called vital capacity. ▪ Inhalation is an active process – diaphragm and the intercostal muscles (between ribs) contract and flattens. the medulla uses the pH of the surrounding tissue fluid as in indicator as blood carbon dioxide concentration. ▪ The air that remains after a forced exhalation is called the residual volume. the medulla will increase the depth and rate of breathing . Carbonic acid then dissociates into bicarbonate anion and hydrogen ion. ◦ chemoreceptors located on the aorta and carotid arteries are involved in blood gas content monitoring. Neural circuits in the medulla form a pair of breathing control centers that establish the breathing rhythm. ◦ When you breathe deeply. where it reacts with water to form carbonic acid. a sheet of skeletal muscle that forms the bottom wall of the cavity. ▪ As you get older. ◦ The neurons mainly responsible for regulating breathing are in the medulla oblongata. ▪ Exhalation is a passive process – decrease in lung volume causes an increase in air pressure. ▪ Blood carbon dioxide is the main determinant of the pH of cerebrospinal fluid. a negative-feedback mechanism prevents the lungs from over expanding: during inhalation. Control of breathing in humans ◦ Most of the time your breathing is regulated by involuntary mechanisms. ▪ Hemolgobin binding to oxygen is reversible.3-DPG) is produced from an intermediate compound in glycolysis and decreases the affinity of hemoglobin for oxygen. ◦ By the time leaves the lungs in the pulmonary veins.3-DPG. ◦ Haldane effect: Deoxygenation of the blood increases hemoglobin's ability to carry carbon dioxide whereas oxygenated blood decreases hemoglobin's ability to carry carbon dioxide. 311 until the pH returns to a normal value. ◦ The resulting mixture formed in the alveoli has a higher Po2 and a lower PCO2 than the blood through the alveolar capillaries.3-diphosphoglycerate (2. During high levels of oxygen. ▪ Respiratory pigments greatly increase the amount of oxygen that can be carried within the circulatory fluid. oxyhemoglobin inhibits the enzyme that synthesizes 2. ▪ 2. the other subunits conformations change. ▪ CO2 does not dissolve in blood well. ▪ Chloride shift: carbonic anhydrase is in red blood cells so charge must be maintained when bicarbonate ions (negative charge) leaves the cell. meaning that when one oxygen molecule binds. Low pH decreases the affinity of hemoglobin for oxygen. ▪ At tissues we have high concentrations of carbon dioxide (from respiration). ▪ Binding for O2 is cooperative. ▪ As we have seen. each with a cofactor called a heme group with an iron atom at its center. it is return to the heart and pumped to the lungs again. Produced when there are low oxygen levels so that hemoglobin can be stimulated to release its bound oxygen molecules. so 1 hemoglobin molecule can carry 4 molecules of oxygen. ▪ In vertebrates. its Po2 and Pco2 match the values for those gases in the alveoli (because they are in equilibrium). Respiratory pigments ◦ Animals transport most of their oxygen bound to proteins called respiratory pigments. ◦ In the systemic capillaries. And the cycle re-begins. the partial pressure gradients favor oxygen to diffuse out of the blood and carbon dioxide to diffuse into the blood. ▪ Each heme binds one molecule of oxygen. ▪ As a result. so we need to convert it into H2CO3 to increase the dissolving ability. It will . there is a net diffusion of oxygen out of the alveoli and there is a net diffusion of carbon dioxide into the alveoli. allowing it to load O2 in one area and unload it elsewhere. an affect called the Bohr shift. it is contained in erythrocytes (RBCs) and has 4 subunits. Respiratory pigments coordination and circulation of gas exchange ◦ During inhalation. chloride anions enter. high amounts of carbon dioxide lowers the pH of its surroundings by reacting with water to form carbonic acid. This is to facilitate hemoglobin to release oxygen to offset the increased carbon dioxide concentrations. ◦ After the blood unloads oxygen and loads carbon dioxide. When bicarbonate diffuses out into the plasma. ◦ The main respiratory pigment of all most all vertebrates and many invertebrates is hemoglobin. fresh air mixes with air remaining in the lungs. increasing their affinities for oxygen. which then becomes bicarbonate and H+. ▪ At the lungs. the CO2 is in the bicarbonate form. ▪ Bigger picture: tissues are high [CO2] and [H+] and they are not getting a lot of oxygen so we want to oxygenate them. carbonic acid will be re-converted back into CO2. So in the presence of high [CO2] and [H+]. 312 diffuse into the blood cell. so it will have to re-enter the RBC where the carbonic anhydrase will reverse the reaction and turn it back into CO2. ◦ Factors that affect dissociation curve of hemoglobin: . the hemoglobin structure is altered to the alternative form that will release oxygen and will bind to CO2. This will raise the pH and cause the hemoglobin molecule to return back to its normal form with higher affinities for oxygen. At the lungs. When Hemoglobin binds to CO2. When hemoglobin arrives at these tissues. CO2 wants to leave the blood and into the alveoli while oxygen wants to leave the alveoli and into the blood cells. However. CO2 leaves to the alveoli while oxygen diffuses in and becomes bound to the hemoglobin. it prevents the CO2 from forming carbonic acid. hemoglobin is acting as a buffer by binding to CO2 molecules to prevent more CO2 molecules from turning into carbonic acid and decreasing the pH. the low pH causes Bohr shift which stimulates the hemoglobin to release its oxygen molecules to the tissues and will stimulate the hemoglobin to attach to CO2 molecules. It will then diffuse out of the lungs. where carbonic anhdyrase will turn it into H2CO3. ▪ Consider hemoglobin: hemoglobin is going to interact with H+ (Bohr shift) to form an alternative version of hemoglobin that doesn't bind to oxygen as well and therefore will end up binding to CO2 instead. This explains why high [CO2] lead sot low pH. In this sense. . ▪ It has a hyperbolic dissociation curve. CADET face right! ◦ Myoglobin is the oxygen binding pigment in muscles. and exercise. ▪ No cooperative binding ▪ single subunit ▪ Saturates very quickly and releases in very low oxygen “emergency muscle” situations ◦ Fetal hemoglobin has a dissociation curve shifted to the left compared to an adult. ▪ By shifting the curve to the left. ▪ Curve is shift right (oxygen is released easier. H+ concentrations. the fetal hemoglobin has a higher binding affinity to grab oxygen from maternal blood. lower oxygen affinity) increase of CO2 pressure. temperature. 313 ▪ the dissociation curve of hemoglobin is sigmodial. ▪ Heart contraction pumps hemolymph through the circulatory vessels into interconnected sinuses. However. ▪ Fluid bathes both the inner and outer tissue layers. ▪ In jellies and other cnidarians. called hemolymph is also the interstitial fluid that bathes body cells. chemical exchange occurs between the hemolymph and body cells. spaces surrounding the organs. ▪ Arthropods have open circulatory systems. the heart ◦ In an open circulatory system. ▪ In a hydra. Open and closed circulatory systems ◦ A circulatory system has 3 basic components: ▪ circulatory fluid ▪ set of interconnecting vessels ▪ a muscular pump. ▪ Flat body optimizes exchange with environment by increasing surface area and minimizing diffusion distances. the gastrovascular cavity has a much more elaborate branching pattern. the circulatory fluid. . facilitating exchange of gases and cellular waste. thin branches of the gastrovascular cavity extend into the animal's tentacles. Only the cells lining the cavity have direct access to nutrients released by digestion. the body wall is 2 cells thick so the diffusion distance is really small. 314 Circulatory systems in other animals Protozoans and other unicellular animals ◦ Movement of gas through simple diffusion within the cell Gastrovascular cavities ◦ Gastrovascular cavity is a digestion and circulatory system with only one opening – usually seen in Cnidarians. ◦ Flatworms and planarians survive without a circulatory system due to the combination of a gastrovascular cavity and a flat body. ▪ Within the sinuses. the vessels that carry blood back to the heart. ▪ Chemical exchange occurs between the blood and the interstitial fluid. a circulatory fluid called blood is confined to vessels and is distinct from the interstitial fluid. and venules converge into veins. ▪ Within organs. ▪ The chambers that receive blood entering to the heart are called atria (singular. ◦ The hearts of all vertebrates contain two or more muscular chambers. arteries branch into arterioles. atrium) and the chambers responsible for pumping blood out of the heart are called ventricles. ◦ Closed circulatory systems allows animals to be larger. Networks of capillaries. as well as between the interstitial fluid and the body cells. ◦ At their “downstream” end. Exchange of gases and nutrients occur between the interstitial fluid and capillary beds. and all vertebrates have closed circulatory systems. porous walls. ◦ Blood flow through blood vessels is unidirectional ◦ Blood vessels are only distinguished by the direction in which they carry blood ◦ Arteries carry blood from the heart to organs throughout the body. 315 ◦ In a closed circulatory system. ▪ Arterioles convey blood to capillaries. called capillary beds. microscopic vessels with very thin. capillaries converge into venules. . ▪ Portal veins (exception to the general rule) carry blood between pairs of capillary beds in the digestive system to capillary beds in the liver. ▪ One or more hearts pump blood into large vessels that branch off into smaller ones that infiltrate the organs. cephalopods. Organization of vertebrate circulatory systems ◦ The closed circulatory system of humans and other vertebrates is called the cardiovascular system. passing within a few cell diameters of every cell in the body. ▪ Annelids. infiltrate tissues. ◦ Open circulatory systems require less energy input than closed circulatory systems. ◦ Mammals and birds have 4 chambered hearts ◦ Repitles and amphibians have 3 chambered hearts ◦ Fish have 2 chambered hearts . ◦ The blood passes through the heart once in each complete circuit through the body. reptiles. ◦ After oxygen-enriched blood leaves the gas exchange tissues. delivers oxygen-poor blood to the capillary beds of the gas exchange tissues where oxygen/carbon dioxide exchange occurs. Deoxygenated blood then travels back to the heart. it enters the other pump. rays. the capillaries converge into a vessel that carries oxygen-rich blood to capillary beds throughout the body. ◦ Blood pumped out from the ventricles go to the capillary bed in the gills. the right side of the heart. the heart (allows for coordination of both circuits). It is called a pulmocutaneous circuit if it includes capillaries in both the lungs and the skin. This is called the pulmonary circuit if the capillary beds are all in the lungs. 316 Single circulation ◦ In bony fishes. ◦ As blood leaves the gills. an arrangement called double circulation. ▪ The pumps for the two circuits are combined into a single organ. Double circulation ◦ The circulatory systems of amphibians. ◦ Deoxygenated blood then travels back to the heart (atria). and sharks. ◦ One pump. completing the systemic circuit. as in many amphibians. the heart consists of two chambers: an atrium and a ventricle. the left side of the heart. and mammals have two circuits. an arrangement called single circulation. where oxygen diffuses into the blood and carbon dioxide diffuses out of the blood. The heart will propel the blood to capillary beds in organs and tissues throughout the body. where appropriate exchanges will occur between capillaries and the interstitial fluids. ◦ The aorta descends into the abdomen. The inferior vena cava drains blood form the bottom half of the body. where the appropriate exchanges occur. ◦ The two venae empty their blood into the right atrium. ◦ The first branches leading from the aorta are the coronary arteries. ◦ Oxygen-rich blood returns to the lungs via the pulmonary veins to the left atrium of the heart. it loads oxygen and unloads carbon dioxide. the superior vena cava. ◦ Then branches lead to capillary beds in the head and arms. ◦ Oxygen-rich blood flows into the left ventricle. which conveys blood to arteries leading throughout the body. 317 ◦ Crocodiles and alligators have 4 chambered hearts The heart Mammalian circulation ◦ Contraction of the right ventricle pumps blood to the lungs via pulmonary arteries. supplying oxygen-rich blood leading to capillary beds in the abdominal organs and legs. where the appropriate exchanges occur. ◦ As blood flows through capillary beds in the left and right lungs. Mammalian heart structure . which supply blood to the heart muscle itself. for which oxygen-poor blood flows into the right ventricle and restarts the cycle. ◦ Deoxygenated blood in the upper half of the body is channeled into a large vein. ◦ Blood leaves the left ventricle via the aorta. Made up of connective tissue. Valve on the right side of the heart has 3 cusps and is called the tricuspid valve The valve on the left side has 2 cusps and is called the mitral valve. ▪ The contraction phase is called systole. ◦ If blood squirts backward through a defective valve. ◦ When the atria contracts. meaning they can contract and relax repeatedly without any signal from the nervous system. preventing blood from flowing back into the atria. it pumps blood. ◦ The two ventricles have thicker walls and contract much more forcefully. Pressure generated by contraction of the ventricles closes the AV valves. ▪ Produces electrical impulses.1 seconds before spreading to the heart so that the atria can completely empty. causing both atria to contract in unison. The cells form a relay point called the atrioventricular (AV) node. ◦ The signals from the AV node are sent through the bundle of His. or heart rate (beats per minute) ▪ stroke volume. it may produce an abnormal sound called a heart murmur. ◦ Impulses from the SA node spread rapidly through the walls of the atria. ◦ The volume of the blood each ventricle pumps per minute is called the cardiac output (heart reat * stroke volume = cardiac output). and the relaxation phase is called diastole. ▪ It is autorhythmic and is located in the wall of the right atrium. the amount of blood pumped by a ventricle in a single contraction. ▪ Semilunar valves are located at the two exits of the heart: where the aorta leaves the left ventricle and where the pulmonary artery leaves the right ventricle. ◦ The sinoatrial (SA) node sets the rate and timing at which all cardiac muscle cells contract. Relaxation of ventricles closes the semilunar valves and prevents backflow. when it relaxes. valves open when pushed from one side and close when pushed from the other. Pushed open by pressure generated from contraction of ventricles. near where the superior vena cava enters the heart. Since cardiac muscle cells are electrically coupled through gap junctions. Stroke volume = end diastole volume – end systolic volume ◦ Four valves prevent backflow and keep blood moving in the right direction. ◦ The heart contracts and a rhythmic cycle called the cardiac cycle. Maintaining the heart's rhytmic beat ◦ Some cardiac muscle cells are autorhythmic. Papillary muscles are located in the ventricles and bind to the AV valve to prevent inversion of these valves during systole. The left ventricle contracts with more force than the right ventricle since it needs to pump blood to the entire body. impulses from the SA node spread rapidly throughout heart tissue. ▪ Atrioventricular (AV) valves lie between each atrium and ventricle. ▪ When the heart contracts. ▪ Some arthropods have SA nodes located in the nervous system. its chambers fill with blood. nodal tissue that passes . ▪ The impulses at the AV node are delayed by about 0. the impulses originating at the SA node reach other autorhythmic cells located in the wall between the left and right atria. outside the heart. Two factors: ▪ Rate of contraction. 318 ◦ The two atria have relatively thin walls and serve as collection chambers for blood returning to the heart from the lungs or other body tissues. ◦ The rhythmic bulging of the artery is the pulse. An increase in 1 degree Celsius increases heart rate by 10 beats per minute. ◦ During diastole. This is the diastolic pressure. ▪ Veins have a thinner wall than arteries. the arterioles narrow. an . ▪ The walls of arteries are thick and strong. This increases the artery blood pressure. ▪ As capillaries have the highest total cross sectional area. Blood flow velocity ◦ The velocity of blood slows as it moves from arteries to arterioles to the much narrower capillaries. velocity is lowest. ▪ The outer layer is connective tissue that contains elastic fibers. that provides strength. ▪ The layer next to the endothelium contains smooth muscle. ◦ Physiological cues can later heart tempo by regulating the SA node. Blood pressure ◦ Contraction of a heart ventricle generates blood pressure. and the parasympathetic nervous system slows down SA node and heartbeat. and the higher the velocity (arteries > arterioles and veins > venules) ◦ Note: the greatest resistance to blood flow is located in the arterioles. 319 down between both ventricles and then branches into the ventricles through the Purkinjie fibers. ▪ Body temperature affects SA node. ◦ TOTAL cross sectional area is inversely proportional to velocity. there is a lower but still substantial blood pressure when the ventricles are relaxed. ▪ The parasympathetic and sympathetic nervous systems are largely responsible for this. Sympathetic nervous system speeds up SA node and heartbeat. Blood Vessels Blood vessel structure ◦ Blood vessels contain a central lumen (cavity) lined with an endothelium. which exerts a force in all directions. ◦ When the smooth muscles in the arteriole relax. the arterioles undergo vasodilation. As a consequence. which consist of an endothelium and a surrounding extracellular layer called the basal lamina. ◦ Arterial blood pressure is highest when the heart contracts during ventricular systole. The pressure at this time is called systolic pressure. a single layer of flattened epithelial cells. This impulse results in the contraction of the ventricles. the lower the total cross sectional area. a process called vasoconstriction. Also contain valves which maintains a unidirectional flow of blood. ▪ Exchange of substances between blood and the interstitial fluid only occurs in capillaries because the walls are thin enough to permit this exchange. ◦ The walls of arteries and veins have more complex organization than those of capillaries. ▪ The larger the blood vessel. accommodating blood pumped at high pressure by the heart and are elastic. the elastic walls of the artery snap back. Regulation of blood pressure ◦ As the smooth muscles in the arteriole walls contract. ▪ The smooth surface of the endothelium minimizes resistance to the flow of blood ◦ Capillaries are the smallest blood vessels and have very thin walls. around the loop of henle. ◦ Double capillary beds occur in the glomerulus. which includes a tiny network of vessels intermingled among capillaries of the cardiovascular system. as well as larger vessels into which small vessels empty. ◦ Two opposing forces control the movement between the capillaries and the surrounding tissues: ▪ Blood pressure tends to drive fluid out of the capillaries ▪ the presence of blood proteins tend to pull fluid back. ▪ After entering the lymphatic system by diffusion. hypothalamus. ▪ A second mechanism involves precapillary sphincters. Capillary function ◦ Given that capillaries lack smooth muscle. how is blood flow in the capillary beds altered? ▪ One mechanism is constriction or dilation of the arterioles that supply capillary beds. where the blood pressure is highest. a peptide. is the major potent inducer of vasoconstriction. so this leads to a let loss of fluid from the capillaries. ◦ Nitric oxide is the major inducer of vasodilation and endothelin. 320 increase in diameter that causes blood pressure in the arteries to fall. liver. The net loss is generally greatest at the arterial end of these vessels. and anterior pituitary gland. small intestine. These sphincters regulate and redirect the passage of blood into particular sets of capillaries. the fluid lost by capillaries is called . rings of smooth muscle located at the entrance to each capillary bed. The dissolved proteins in the blood generates osmotic pressure ▪ Blood pressure > osmotic pressure. The capillary bed pools into another capillary bed without first going to the heart (transports products in high concentration without spreading to the rest of the body) ▪ Capillary bed 1 drains into the portal vein and capillary bed 2 drains into vein that returns to the heart Fluid return by the lymphatic system ◦ The lost fluid and proteins return to the blood via the lymphatic system. ▪ Contains phagocytic cells (leukocytes) that filter the lymph and serve as immune response centers. ◦ Vertebrate blood is a connective tissue of consisting of cells suspended in a liquid matrix called plasma. Lacks organelles and a nucleus to maximize hemoglobin content. are by far the most numerous blood cells. Blood components Blood composition and function ◦ Blood is 55% plasma and 45% other cellular components. which play an important role in the body's defense. respiratory gases. Derived from megakaryocytes. and destroys old blood cells. Maintenance of body pH . Some ions buffer the blood Some ions maintain the osmotic balance of blood Affects the composition of the intersitial fluid ▪ Plasma proteins acts as buffers against pH and helps maintain the osmotic balance ▪ Contains nutrients. ◦ Cellular elements ▪ Red blood cells. Do not contain a nucleus. stores blood cells. lymph-filtering organs called lymph nodes. metabolic wastes. The main function is oxygen transport. ▪ The lymphatic system drains into large veins of the cardiovascular system at the base of the neck. although the two fluids are otherwise similar. filters the blood. ▪ Has a much higher protein concentration than interstitial fluid. Contains hemoglobin. or erythrocytes. its composition is about the same as that of the interstitial fluid. and hormones. ▪ Lymph vessels have valves to prevent backflow ◦ Along a lymph vessel are small. an iron-containing protein that transports oxygen (up to 4 molecules per molecule). Functions in blood clotting. Diapedesis is the process by which white blood cells become part of the interstitial fluid (slip through endothelial lining) ▪ Platelets are pinched-off cytoplasmic fragments of specialized bone marrow cells. NOTE that erythrocytes derive their energy from glycolysis and not from the TCA cycle and oxidative phosphorylation! erythropoietin is a hormone released from the kidneys and will stimulate red blood cell formation in the bone marrow ▪ White blood cells are leukocytes. Their function is to fight infections. ◦ The spleen is an organ that makes lymphocytes. ▪ Many of the dissolved solutes are inorganic ions sometimes referred to as electrolytes. 321 lymph. nutrient-rich blood from placenta is carried to fetus via umbilical vein ◦ Blood bypasses the liver through the ductus venosus. ◦ Both the platelets and damaged tissue release clotting factor called thromboplastin. most blood will bypass the right ventricle and be shunted to the left atrium via the foramen ovale. However. 322 ◦ body fluid is relatively constant at 7. The ductus venosus provides a direct communication between the umbilical vein and the inferior vena cava. ◦ The placenta re-oxygenates blood returning from the umbilical arteries and repeats the . ▪ Because fetal lungs are not functional. Oxygenated blood from the ductus venosus combines with the deoxygenated blood in the inferior vena cava and continues to the heart. ◦ Thromboplastin converts inactive plasma protein prothombrin to thrombin ◦ Thrombin converts fribrinogen into fibrin ◦ Fibrin threads coat damaged area and trap blood cells to form a clot. ◦ Phosphate buffer system is the predominant buffer system that operates in the internal fluid of all cells. ◦ Blood travels to the fetus heart through the inferior vena cava and mixes with deoxygenated blood returning from the superior vena cava. Fetal circulation → important for the DAT ◦ oxygenated. Blood then enters the right atrium of the heart. These arteries are also carrying deoxygenated blood back to the placenta. ▪ Some blood will enter the right ventricle from the right atrium and proceed to the pulmonary trunk.4 – this consistency is attained by the removal of CO2 by the lungs and hydrogen ions by the kidneys and buffer systems (look in general chemistry notes for an explanation for buffers). ◦ Carbonic-acid-bicarbonate buffer system is by far. ◦ A thrombus is a blood clot that forms in a vessel abnormally. ◦ Blood circulates through the fetal body and returns to the placenta via the umbilical arteries. the most important buffer for maintaining acid-base balance in the blood. ◦ Disorders: ▪ Respiratory: affects the blood acidity by causing changes in PCO2 (high CO2 = acidic) ▪ Metabolic: affects the blood acidity by causing changes in HCO3. Serum is the fluid left after blood clotting.(High HCO3. most of this blood will be shunted away from the pulmonary arteries and into the aorta via the ductus arteriosus.= basic) Blood clotting ◦ Platelets adhere to exposed collagen of damaged vessel and cause neighboring platelets to form the platelet plug (temporary sealing the break in the vessel wall). Blood will then travel into the left ventricle and be distributed throughout the fetal body via the aorta. indiana. and select “fetal system” for an excellent animation to understand this! ▪ http://www. 323 fetal cardiovascular cycle by recycling the newly oxygenated blood to the fetus through the umbilical vein.html .edu/~anat550/cvanim/fetcirc/fetcirc. ◦ Click the link below. ▪ Essential nutrients include essential amino acids and fatty acids. which eat relatively large pieces of food. and phospholipids in foods. increasing the surface area available for chemical processes. are bulk feeders (humans). absorption. ◦ Vitamins are organic molecules that are required in the diet in very small amounts. ◦ These materials—pre-assembled organic molecules and minerals—are called essential nutrients. Dietary deficiencies ◦ A diet that lacks one or more essential nutrients or consistently supplied less chemical energy than the body requires results in malnutrition. ◦ In the third stage. ▪ Are either fat-soluble or water-soluble. ◦ Substrate feeders (caterpillar) are animals that live in or on their food source. Essential Nutrients ◦ Some cellular processes require materials that an animal cannot assemble from simpler organic precursors. It is the sum of all the energy used by biochemical reactions over a given time interval. is the act of eating or feeding. ◦ Most animals. nucleic acids. carbohydrates. and as cofactors in biosynthetic pathways. . ◦ Fluid feeders (mosquito) suck nutrient rich fluid from a living host. fats. ◦ Minerals are inorganic nutrients that are usually required in small amounts. ◦ Essential fatty acids are fatty acids that contain double bonds that cannot be normally synthesized within the body. ◦ Elimination completes the process as undigested material passes out of the digestive system. ▪ Essential nutrients serve key functions in cells such as serving as substrates of enzymes (as coenzymes). the second stage of food processing. food is broken down into molecules small enough for the body to absorb. ▪ Mechanical digestion breaks food into smaller pieces. ▪ Any activity will consume kilocalories in addition tot he BMR. the animal's cell take up (absorb) small molecules. which strain small organisms or food particles from the surrounding medium. ◦ A diet that fails to provide adequate sources of energy results in undernutrition.000 calories) ◦ The rate of energy consumption by an animal is called its metabolic rate. Digestion in other animals Main stages of food processing ◦ The first stage. failure to obtain adequate nutrition. ▪ Chemical digestion is necessary because animals cannot directly use the proteins. including humans. ◦ The number of kilocalories a resting animal requires to fuel essential biochemical processes for a given time is called the basal metabolic rate (BMR). vitamins and minerals. ◦ During digestion. ◦ Essential amino acids are the 8 amino acids that cannot be synthesized within the body. ingestion. ▪ Enzymatic hydrolysis – breaking macromolecules into smaller components through breaking bonds by adding water. 4 main feeding mechanisms of animals ◦ Many aquatic animals are filter feeders (whale). 324 Features of diet Chemcial energy and food ◦ The energy content of food is measured in kilocalories (1 kcal = 1. cellular organelles in which hydrolytic enzymes break down food. then secretes digestive enzymes that break the soft tissues of the prey into tiny pieces. A lysosome fuses with the food vacuoule. or more commonly. ◦ Many animals with relatively simple body plans have a digestive compartment with a single opening called a gastrovascular cavity. . The food vacuoule forms and moves toward the anterior of the cell. ◦ Amoeba captures food via phagocytosis. the f body. ▪ A hydra uses its tentacles to stuff captured prey through its mouth into its gastrovascular cavity. The engulfed food becomes a food vacuoule. hydrolysis occurs largely by extracellular digestion. Other cells of the gastrodermis engulf these food particles. a mouth and an anus. are the simplest digestive compartments. and its enzymes breakdown the food. where it will fuse with a lysosome and become degraded. ◦ The cilia of paramecium sweeps food into its cytopharynx. the tissue layer that lines the cavity. ◦ Most animals have a digestive tube extending between two openings. and most of the hydrolysis of macromolecules occur intracellularly. an alimentary canal. Extracellular digestion ◦ In most animal species. This is a complete digestive tract. The hydrolysis of food inside vacuoules is called intracellular digestion. ◦ This usually occurs after phagocytosis or pintocytosis. 325 Intracellular digestion ◦ Food vacuoules. It functions in digestion as well as in the distribution of nutrients throughout the body. Specialized gland cells of the hydra's gastrodermis. Further digestion and absorption occurs in the intestine. and a hindgut. Chemical digestion and absorption of nutrients occurs in the intestine. Food passes through the esophagus and is stored and moistened in the crop. Mechanical digestion occurs in the muscular gizzard. Pouches called gastric cecae extend from the beginning of the midgut and function in digestion and absorption. The intestine contains typholosole which helps increase surface area for absorption. ▪ Many birds have a crop for strong food and a stomach and gizzard for mechanically digesting it. with an esophagus and a crop. which pulverizes food with the aids of small bits of sand and gravel. 326 ▪ The alimentary canal of an earthworm includes a muscular pharynx that sucks food through the mouth. . a midgut. Food is stored and moistened in the crop. ▪ A grasshopper has several digestive chambers grouped into three main regions: a foregut. but most digestion occurs in the midgut. The protective effect of saliva is provided by mucus. pancreas. polymers are broken down into the appropriate monomers by enzymatic hydrolysis. or oral cavity. Human Digestive System Introduction ◦ In mammals. The enzyme amylase hydrolyzes starch into smaller polysaccharides and maltose. alternating waves of contraction and relaxation in the smooth muscles lining the canal. Saliva initiates chemical digestion while also protecting the oral cavity. liver. The oral cavity. They regulate passage of material between compartments. Most of digestion occurs intracellularly. and the gallbladder. ▪ Accessory glands are salivary galnds. pharnyx. and esophagus ◦ Ingestion and the initial steps of digestion occur in the mouth. ◦ At some junctions between specialized compartments. ▪ The salivary glands deliver saliva through ducts to the oral cavity. producing simple digestive products which are then absorbed by diffusion into rhizoid. The tongue aids digestive processes by evaluating ingested material to determine if . ▪ Fungi – rhizoids of bread mold secrete enzymes into bread. ◦ Some plants use extracellular digestion ▪ Venus flytrap – enzymes diggest trapped flies (serves as nitrate source). it is still autotrophic. and roots ▪ When nutrients are required. which protects the lining of the mouth from abrasion and lubricates food for easier swallowing. ◦ Food is pushed along the alimentary canal by peristalsis. The processes are similar to animals. 327 Digestion in plants and fungi ◦ Plants do not have a digestive system. the muscular layer forms ringlike valves called sphincters. However. stems. the digestive system consists of the alimentary canal and various accessory glands that secrete digestive juices through the ducts into the canal. ▪ Plants store starch primarily in seeds. ▪ Mechanical digestion occurs through chewing of food. or throat region. Only in the lumen the H+ and the Cl. Also pumps out chloride ions. Once food enters here. It also helps manipulate the mixture of saliva and food into a ball shape called a bolus. This mixture of ingested food and gastric juice is called chyme. stores foods and begins digestion of proteins. the larynx tips a flap of tissue called the epiglottis down. They release histamine which in turn stimulates parietal cells to produce hydrochloric acid. preventing food from entering the trachea. HCl converts pepsinogen into active pepsin. ▪ Pepsin. which lubricates and protects the cells lining the stomach. Also creates a low pH environment in the stomach (pH = 2). which is located just below the diaphragm. It stimulates parietal cells to secrete HCl. cleaves peptide bonds to turn proteins into smaller polypeptides. ▪ Mucous cells secrete mucus. ◦ Gastrin also stimulates ECL cells. a large polypeptide hormone which is absorbed into the blood. opens to two passageways: the trachea (windpipe) and the esophagus. Digestion in the stomach ◦ The stomach. ▪ Parietal cells use an ATP-driven pump to expel hydrogen ions into the lumen. allowing the bolus to pass through. . neuroendocrine cells in the digestive tract. ◦ papillae are projections on the tongue surface and are involved in the sensation of taste. Example of positive feedback. peristaltic contractions of smooth muscle move each bolus to the stomach. Then pepsin itself activates the remaining pepsinogens. ▪ Secretes a digestive fluid called gastric juice and mixes with the food. which kills most bacteria. Works best in a very acidic environment. a protease. The gastric glands have all three types of cells that secrete the different components of the gastric juice.ions combine to form HCl. and denatures proteins in food. ▪ Chief cells release pepsin into the lumen in an inactive form called pepsinogen. The upper esophageal sphincter (blocks esophagus) relaxes. ◦ The interior surface of the stomach wall is highly folded and dotted with pits leading into tubular gastric glands. When a food bolus arrives at the pharynx. ▪ The pharynx. The esophagus connects to the stomach. G cells secrete gastrin. 328 it should be ingested and then enabling its further passage if it is deemed okay. ◦ Components of gastric juice: ▪ Hydrochloric acid which disrupts the ECM that binds cells together. a backflow of chyme from the stomach into the lower end of the esophagus. ◦ The controlled release of chyme into the small intestine is controlled by the pyloric sphincter. pylori as well. ◦ Chemical digestion by gastric juice is facilitated by the churning action of the stomach. ◦ The lower esophageal sphincter. ▪ Churning is the coordinated series of muscle contractions and relaxations that mixes the stomach contents about every 20 seconds. or cardiac sphincter. a person experiences acid reflux. Can also be caused by excess stomach acid or H. ▪ Occasionally. . is the sphincter between the esophagus and the stomach that normally opens only when bolus arrives. 329 Peptic ulcers are caused by failure of mucosal lining to protect stomach. ▪ Large folds in the lining encircle the intestine and are studded with finger-like projections called villi. ◦ Peristalisis moves the mixture of chyme and digestive juices along the small intestine. 330 Digestion in the small intestine ◦ The small intestine is the alimentary canal's longest compartment and most of the enzymatic hydrolysis of macromolecules from food occurs here. each epithelial cell of a villus has on its apical surface many microscopic projections called microvilli. as well as gland cells of the intestinal wall itself. By channeling all nutrients through the liver. the jejunum and the ilenum. . and then it activates the other enzymes. ▪ The epithelial lining of the duodenum is a source of several digestive enzymes. Bile contains salts. Also allows liver to remove toxic substances. it allows it to regulate the distribution of nutrients to the rest of the body. a substance that helps digest fats and other lipids. Bile is stored and concentrated in the gallbaldder. Most of the digestion is completed in this section. transport across epithelial cells can be passive or active. This confers extremely high surface area. a blood vessel that leads directly to the liver. Pancreas also secretes lipases (digestion of fats) and pancreatic amylase (digestion of starch). Trypsin gets activated first by enteropeptidase (enzyme secreted from intestinal glands when food passes through duodenum). which greatly increases the rate of absorption. In turn. ◦ The remaining regions of the small intestine. Pancreatic enzymes secreted are trypsin and chemotrypsin. are the major sites for absorption of nutrients. Goblet cells secrete mucus to lubricate and protect epithelial cells from mechanical/chemical damage. liver. ▪ The capillaries and veins that carry nutrient-rich blood away from the villi converge into the hepatic portal vein. ▪ The pancreas aids chemical digestion by producing an alkaline solution rich in bicarbonate as well as several enzymes. The bicarbonate neutralizes the acidity of the chyme and acts as a buffer. which acts as emulsifiers. ◦ The first section of the small intestine forms the duodenum. proteases secreted into the duodenum in inactive forms. Absorption in the small intestine ◦ Most of the absorption occurs at highly folded surface of the small intestine. Some are secreted into the lumen of the duodenum. and gallbladder. ▪ Liver produces bile. whereas others are bound to the surface of epithelial cells. It is here that chyme from the stomach mixes with the digestive juices from the pancreas. Depending on the nutrient. . ▪ Hydrolysis of fats by lipase in the small intestine generates fatty acids and monoglycerides. forming globules called chylomicrons. The lacteal passes the chylomicrons to the heart. ▪ They are then coated with phospholipids. synthesizes plasma proteins. a lymph filled vessel at the core of each villus. ◦ Protein metabolism – liver deaminates amino acids. ▪ Chylomicrons are first transported from an epithelial cell in the intestine to a lacteal. cholesterol. ◦ Small intestine also absorbs water and ions. 331 ◦ Some products of fat digestion take a different path. forms urea from ammonia in blood. ▪ They are absorbed by epithelial cells and then recombined into triglycerides. Functions of the liver ◦ Blood storage ◦ Blood filtration – kupfer cells (macrophages) phagocytize bacteria picked up in intestines ◦ Carbohydrate metabolism – liver maintains normal blood glucose levels via gluconeogenesis (generation of glucose) and glycogenesis (generation of glycogen) ▪ All carbohydrates absorbed into the blood are carried by the hepatic portal vein into the liver. and proteins. synthesizes nonessential amino acids. secretin. cecum. high levels of secretin and cholecystrokinin released act on the stomach to inhibit peristalsis and secretion of gastric juices. ◦ Secretin is produced by cells lining duodenum when food enters. 332 ◦ Detoxification – detoxidifes chemicals. this stimulates the pancreas to deposit its mass of digestive enzymes into the duodenum. ◦ The terminal portion of the large intestine is the rectum. ◦ Gastric inhibitory peptide is produced in response to fat/protein digestates in the . What remain are the feces. ▪ If less water than normal is reabsorbed by the colon. Processing in the large intestine ◦ The alimentary canal ends with the large intestine. This suppression will decrease the rate of gastric emptying along with reducing blood flow within the intestines. thereby slowing down digestion. and rectum. ◦ Cholecystrokinin is produced by small intestine in response to fats. secreted by liver as part of bile ◦ Erythrocyte destruction – kupfer cells destroy irregular erythrocytes (most are done by spleen) ◦ Vitamin storage and iron storage ◦ if blood glucose levels are high → glycogenesis if blood glucose levels are low → glycogenolysis ◦ Produces bile ◦ Jaundice is yellowing of the skin due to excess bilirubin (typically liver failure). ▪ If the chyme is rich in fats. The small intestine connects to the large intestine at a T-shaped junction. Regulation of digestion Hormonal control of digestion ◦ A branch of the nervous system called the enteric division is dedicated to regulating digestive events and peristalisis in the small and large intestines. the result is diarrhea ▪ If too much water is reabsorbed by the colon. which includes the colon. which is important for fermenting ingested material. the result is constipation. the inner one being involuntary and the outer one being voluntary. and the effects have been discussed above. ◦ A rich community of mostly harmless bacteria lives on the unabsorbed organic material in the colon. ◦ Gastrin is produced by the stomach lining. It will suppress the release of gastrointestinal hormones such as gastrin. ◦ The appendix. and cholecystokinin. which leads to the rectum and anus. has a minor and dispensable role in immunity. the wastes of the digestive system. a finger-like extension of the human cecum. The main source of vitamin K and vitamin B come from these symbiotic bacteria. where the feces are stored until they can be eliminated. which becomes increasingly solid by the end. ▪ The other arm is a pouch called the cecum. stimulates gallbladder to release bile and pancreas to release its enzymes. ◦ Somatostatin is produced by delta cells of the pancreas. this stimulates pancreas to produce bicarbonate (neutralizes the chyme). ▪ Between the rectum and anus are two sphincters. ◦ The colon completes reabsorption of water that began in the small intestine. ▪ One long arm is the colon. ◦ Enteropeptidase is produced by cells lining the duodenum when food enters. 333 duodenum. . Glucose homeostasis ◦ When the blood glucose level rises above the normal range. When the amount of body fat decreases. and blood glucose levels remain elevated. ◦ Type 1 diabetes is when the immune system destroys the beta cells within the pancreas and thus destroys the person's ability to synthesize insulin. mild decrease of stomach motor activity. ▪ Insulin does not act on the brain. insulin suppresses appetite by acting on the brain. leptin levels fall. the secretion of insulin triggers the uptake of glucose from the blood into body cells. acts as an appetite suppressant that counters the appetite stimulant ghrelin. the secretion of glucagon promotes the release of glucose into the blood by breaking down storage carbohydrates (glycogen). ◦ Both hormones are produced in the pancreas. Diabetes Mellitus ◦ Diabetes mellitus is caused by a deficiency of insulin or a decreased response to insulin in target tissues. leptin suppresses appetite. ghrelin is one of the signals that triggers feelings of hunger as mealtimes approach. ▪ Cells do not take in glucose to break down for energy. ▪ Alpha cells within the pancreatic islets create glucagon and beta cells create insulin. Insulin is produced. ◦ The hormone PYY. ◦ Produced by adipose tissue. ◦ When the blood glucose level drops below the normal range. instead the cells mainly use fat. Among other functions. ◦ A rise in blood sugar level after a meal stimulates the pancreas to secrete insulin. but target cells fail to take up glucose from the blood. ◦ Type 2 diabetes is characterized by a failure of target cells to respond normally to insulin. and appetite increases. thereby decreasing the blood glucose concentration. secreted by the small intestine after meals. Regulation of appetite and consumption ◦ Secreted by the stomach wall. the transport epithelium are the pair of nasal salt glands. including birds. Their body is hypotonic to the environment and water will naturally flow out. land snails. NO DRINKING. Transport epithelia in osmoregulation ◦ In most animals. ▪ Salt glands use active transport to secrete excess salts. meaning water will naturally flow in. ▪ Typically arranged into complex tubular networks with extensive surface areas. ◦ Insects. Their body is hypertonic to the environment. ▪ Excretion of salt ions and large amounts of water in dilute urine form kidneys. ▪ Uptake of salt ions by gills. The advantage is that urea has very low toxicity. ◦ Most terrestrial animals and many marine species secrete urea. 334 Osmoconformers vs. osmoregulators Osmoregulatory challenges and mechanisms ◦ An osmoconformer has its internal osmolarity isoosmotic with its surroundings. Mechanisms: ▪ Gain of water and salt ions from eating food and drinking seawater. osmoregulation and metabolic waste disposal rely on transport epithelia —one or more layers of epithelial cells specialized for moving particular solutes in controlled amounts in specific directions. such as freshwater and terrestrial habitats. and many reptiles. Nitrogen waste Forms of Nitrogenous Waste ◦ Animals that secrete nitrogenous wastes as ammonia need access to lots of water because ammonia can be tolerated at very low concentrations. Most common in aquatic species. They maintain salt balance and allow for saltwater to be drank. ▪ Marine animals are all osmoconformers. ◦ An osmoregulator has its internal osmolarity independent compared to its surroundings. ▪ Osmotic water loss through gills and other pats of the body surface. or to move between marine and freshwater environments. ◦ In birds. ▪ Enables animals to live in environments that are inhabitable for osmoconformers. ▪ Excretion of salt ions and small amounts of water in scanty urine from kidneys. ▪ Osmotic water gain through gills and other parts of body surface. ◦ Freshwater fish are osmoregulators. The disadvantage is that it requires tremendous amounts of energy. ◦ Many marine vertebrates and some marine invertebrates are osmoregulators. create uric acid as their primary . ▪ Gain of water and some ions in food. ▪ Excretion of salt ions from gills. 335 nitrogenous waste. aqueous environment. This is reabsorption. such as toxins and excess ions. where a tubule collects a filtrate from the blood. ▪ During filtration. Proteins and other large molecules can't be filtered out of the blood while small solutes can. ◦ Protists such as paramecium and amoebas possess contractile vacuoules which pump water out of the cell by active transport. releasing filtrate into the tubule network. This is called secretion ◦ The altered filtrate (urine) leaves the system and the body. The advantage is that uric acid is not toxic and it can be disposed with minimal water loss. are extracted from body fluids and added to the contents of the excretory tubule. which form a network of dead-end tubules. Water soluble wastes (i. Excretory systems in simple organisms ◦ All of the cells in protozoans and cnidarians are in contact with the external. ◦ Other substances.e. . carbon dioxide) exit by simple diffusion. ◦ Excess carbon dioxide. and water leave plants by diffusion through stomata and lenticels in a process called transpiration. ▪ Cellular units called flame bulbs cap the branches at each protonephridium. ◦ The transport epithelium then reclaims valuable substances from the filtrate and returns them to body fluids. waste oxygen. Disadvantage is that it requires lots of energy. Protonephridia ◦ Platyhelminthes and Rotifera have units called protonephridia. the beating of the cilia draws water and solutes from the interstitial fluid through the flame bulb. ▪ The filtrate then moves outward through the tubules and empties as urine into the environment. which are connected to external openings. ammonia. branch throughout the flatworm body. Structure of excretory systems Excretory processes ◦ Hydrostatic pressure drives a process of filtration. ▪ The tubules. This is called excretion. most solutes are pumped back into the hemolymph. ▪ Water follows the solutes into the tubule by osmosis. ▪ They extend from dead-end tips immersed in the hemolymph to openings in the digestive tract. ▪ There. . which are immersed in coleomic fluid and enveloped by a capillary network. ▪ There is NO filtration step. and the fluid then passes into the rectum. ▪ As the cilia beat. excretory organs that collect fluid directly from the coelom. and water reabsorption by osmosis follows. Malphagian tubules ◦ Arthropods have organs called malphagian tubules that remove nitrogenous wastes and also function in osmoregualtion. which includes a storage bladder that opens to the outside. ▪ A ciliated funnel surrounds the internal opening of each metanephridium. ▪ Wastes are eliminated as dry matter along with feces. ▪ Each segment of an annelid has a pair of metanephridia. fluid is drawn into a collecting tubule. ▪ The transport epithelium that lines the tubules secretes certain solutes from the hemolymph into the lumen of the tubule. 336 Metanephridia ◦ Annelids have metanephridia. the two ureters drain into a common sac called the urinary bladder. ▪ The liver produces nitrogenous wastes. ▪ During urination. ▪ Urine produced by each kidney exits through a duct called the ureter. ▪ The excretory system consists of kidneys. CO2 and water vapor diffuse from the blood and are continually exhaled. urine is expelled from the bladder through a tube called the urethra ▪ Sphincter muscles near the junction of the urethra and bladder regulate urination. ▪ The fluid that will be excreted as urine is collected in the inner renal pelvis. a pair of organs for transporting and storing urine. and other chemical wastes. blood pigment wastes. ◦ Kidney structure ▪ Each kidney has an outer renal cortex and an inner renal medulla. Within the cortex and the medulla lie tightly packed excretory tubules and associated blood vessels. 337 Mammalian Excretory system ◦ Excretory organs ▪ In the lungs. excess bilirubin causes jaundice (usually a liver issue) ▪ The skin sweat glands excrete water and dissolved salts to regulate body temperature. and exits the kidney via the ureter. Both regions are supplied with blood by a renal artery and drained by a renal vein. ◦ Nephron Types . the functional units of the vertebrate kidney. but not blood cells or large molecules. 338 ▪ Weaving back and forth across the renal cortex and medulla are the nephrons. the juxtamedullary nephrons. which surrounds the glomerulus. Filtrate is formed when blood pressure forces fluid from the blood in the glomerulus into the lumen of Bowman's capsule. ▪ Branches of this vessel form the peritubular capillaries. extend deep into the medulla. ▪ The remainder. and other small molecules. . ▪ 85% of the nephrons are cortical nephrons. nitrogenous wastes. ▪ A collecting duct receives processed filtrate from many nephrons and transports it to the renal pelvis. glucose. ▪ Concentration of these substances in the initial filtrate are the same as those in blood plasma. amino acids. They are essential for production of urine that is hyperosmotic to body fluids. forming an efferent arteriole. and the distal tubule. The capillaries converge as they leave the glomerulus. Other branches extend downward and form the vasa recta. ▪ Processing occurs as the filtrate passes through three major regions of the nephron: the proximal tubule the loop of Henle. including the long loop of Henle of juxtamedullary nephrons. ▪ The filtrate produced in the capsule contains salts. a key adaptation for water conservation in mammals. which surround the proximal and distal tubules. hairpin- shaped capillaries that serve the renal medulla. which reach only a short distance into the medulla. ◦ Nephron organization ▪ Each nephron consists of a single long tubule as well as a ball of capillaries called the glomerulus. vitamins. ▪ Each nephron is supplied with blood by an afferent arteriole an offshoot of the renal artery that branches and forms the capillaries of the glomerulus. called Bowman's capsule. The blind end of the tubule forms a cup-shaped swelling. How the whole excretory process occurs From blood filtrate to urine ◦ The porous capillaries and specialized cells of Bowman's capsule are permeable to water and small solutes. and valuable nutrients from the huge volume of the initial filtrate. As a result. which then combines to form NH4+ in the tubule. amino acids. contributing further to balance pH. ▪ Glucose. ▪ Numerous water channels formed by aquaporins make the transport epithelium freely permeable to water.(bicarbonate) from the filtrate. ▪ Two specialized regions: a thin segment near the loop tip and a thick segment adjacent to the distal tubule. . and this transfer of positive charge out of the tubule drives the passive transport of Cl-. Epithelial cells pump Na+ into interstitial fluid. Proximal tubules also reabsorb the buffer HCO3. the more ammonia the cells secrete into the tubule. ▪ NaCl gets reabsorbed. and K+ ions are reabsorbed through active or passive transportation from the filtrate → interstitial fluid → peritubular capillaries. The more acidic the filtrate is. ▪ Processing of filtrate in proximal tubule help remains constant pH in body fluids: Cells in transport epithelium secrete H+ and NH3 into the tubule. ▪ Water gets reabsorbed through passive transport. water. ◦ Reabsorption of water continues as the filtrate moves into the descending loop of hemle. ◦ The filtrate reaches the tip of the loop and then returns to the cortex in the ascending loop of Henle. ▪ The osmolarity of the interstitial fluid of the kidney increases progressively from the outer cortex to the inner medulla. 339 ◦ Reabsorption in the proximal tubule is critical for the recapture of ions. the kidney osmolarity makes it favorable to water to be reabsorbed. In the thick segment of the ascending limb. the duct becomes permeable to urea. This creates a hyperosomotic urine. ◦ Antidiuretic hormone (ADH) or vasopressin helps increase the reabsorption of water in the collecting duct. NaCl diffuses out passively into the interstitial fluid. NaCl must be pumped out actively into the epithelium. aquaporin channels in the collecting duct allow H2O molecules to be reabsorbed passively. ▪ The nephron uses a countercurrent multiplier system in which it expends energy to create concentration gradients. but their main water conservation adaptation is uric acid. ▪ Water is passively reabsorbed. the epithelium remains impermeable to salt and urea. thus concentrated urine ◦ Reptiles can only produce isoosmotic or hypoosmotic urine. ▪ Contributes to pH regulation by actively secreting H+ into the tuubule and actively reabsorbing HCO3-. ◦ The nephron uses countercurrent system to maximize the activities it wants to do. Final processing of the filtrate by the transport epithelium of the collecting duct forms the urine. ◦ Birds can produce hyperosmotic urine. The amount reabsorbed will regulate NaCl concentration in body fluids. Types of urine produced in other animals ◦ Mammals can produce hyperosmotic urine. birds have a long loop of henle. ▪ The countercurrent multiplier system makes the medulla very salty which facilitates water reabsorption. the kidney actively reabsorbs NaCl without allowing water to follow by osmosis. The amount secreted will regulate the K+ concentration in body fluids. When kidneys are conserving water. 340 As filtrate ascends in the thin segment. In the inner medulla. Since the urine is hyperosmotic. ◦ The collecting duct carries the filtrate through the medulla to the renal pelvis. ▪ ADH is produced in the posterior pituitary gland. ▪ K+ is actively secreted from the epithelium and into the distal tubule. ▪ When blood osmolarity rises. . the hypothalamus trigger release of ADH from the posterior pituitary. ◦ Amphibians cannot produce hyperosmotic urine. Homeostatic regulation of the kidney Hormonal control ◦ The hypothalamus in the brain controls hormones that regulate osmolarity. urea passively gets reabsorbed. This helps maintains the osmolarity of the interstitial fluid of the medulla. ▪ NaCl is actively reabsorbed from the filtrate. At the same time. ◦ Freshwater fishes cannot produce hyperosmotic urine. Solute gradients and water conservation ◦ The primary solutes affecting osmolarity are NaCl and urea. ◦ The distal tubule plays a key role in regulating K+ and NaCl concentration of body fluids and pH regulation. When kidneys are producing dilute urine. ▪ Hormonal control determines the extent to which the urine becomes concentrated. ▪ ANP inhibits the release of renin from the JGA. ◦ The second regulatory mechanism that helps maintain homeostasis by acting upon the kidney is the renin-angiotensisn-aldosterone system (RAAS). 341 ▪ ADH brings about changes that make the epithelium more permeable to water (recruits more aquaporins to the epthelium) and thus able to reabsorb more water. a specialized tissue consisting of cells of and around the afferent arteriole. and lowers blood osmolarity back toward the set point. as a result of dehydration). ▪ The RAAS system involves the juxtaglomerular apparatus (JGA). reduces urine volume. ▪ Angiotension II stimulates the adrenal glands to release a hormone called aldosterone. ▪ Renin initiates a sequence of steps that cleave a plasma protein secreted from the liver called angiotensinogen ultimately yielding a peptide called angiotensin II. and ADH secretion is reduced. the JGA releases the enzyme renin. ▪ The walls of the atria of the heart release ANP in response to an increase in blood volume and blood pressure. . which supplies blood to the glomerulus. Aldosterone causes the nephrons' distal tubules and collecting duct to excrete K+ and reabsorb more Na+ and water. ▪ As the osmolarity of the blood falls. ◦ Atrial natriuretic peptide (ANP) opposes the RAS. ▪ The increase in water reabsorption concentrates urine. ▪ When blood pressure or volume drops in the afferent arteriole (for instance. a negative-feedback mechanism reduces the activity of osmoreceptor cells in the hypothalamus. increasing blood volume and pressure. ▪ Axons are much longer than dendrites. ▪ The part of each axon branch that forms this specialized junction is a synaptic terminal. This is typically where signals that travel down the axon are generated. ◦ The connection shaped base of an axon connected to the cell body is called the axon hillock. ◦ Mylein sheath is an electrically insulating material (made of lipid) that forms around the axon of a neuron. muscle. ◦ Most of a neuron's organelles. or gland cell that receives the signal as the postsynatpic cell. ▪ The greater the diameter of the axon. are located in the cell body. ▪ At most synapses. we refer to the transmitting neuron as the presynaptic cell and the neuron. the faster impulses will propagate. ▪ The axon divides into many branches at its end. . This is because larger diameter axons have less resistance to “flow” of ions. ▪ The dendrites receive signals from other neurons. because the action potential appears to “jump” along the axon from node to node. The extracellular fluid is only in contact with the axon membranes at the nodes. ◦ A neuron as a single axon. This increases the speed at which an action potential moves down the axon. ▪ Mylein sheath is created by glial cells: Central nervous system neuronal mylein sheath is created by glial cells called oligodendrocytes. ◦ A typical neuron has numerous highly branched extensions called dendrites. ◦ Each branched end of an axon transmits information to another cell at a junction called a synapse. ▪ In describing a synapse. 342 Neuron structure and organization Neuron structure and function ◦ Neurons are cells that transformation within the body. The mechanism for propagating action potentials along an axon is called saltatory conduction. voltage-gated sodium channels are restricted to gaps in the mylein sheath called nodes of Ranvier. including its nucleus. Peripheral nervous system neuronal mylein sheath is created by glial cells called Schwann cells. ▪ In myleinated axons. an extension that transmits signals to other cells. chemical messengers called neurotransmitters pass information from the transmitting neuron to the receiving cell. Depolarization occurs at the nodes of Ranvier. regulate nutrient and dissolved gas concentrations. or glia. and regulate the extracellular fluid surrounding neurons. ▪ Sensory (afferent) neurons transmit information about external stimuli or internal . Introduction to information processing Introduction ◦ Information processing by a nervous system occurs in three stages: ▪ sensory input: the conduction of signals from sensory receptors to the central nervous system ▪ integration: analysis and interpretation of the sensory signals and the formulation of the appropriate responses ▪ motor output: the conduction of signals from the integration centers to effector cells. 343 ◦ The neurons of vertebrates and most invertebrates require supporting cells called glial cells. specialized populations of neurons handle each stage of information processing. ▪ Nissl bodies are areas of the rough ER that are involved in neuron protein synthesis. and monitoring of cerebrospinal fluid. ◦ Special cells in the CNS: ▪ Astrocytes maintain the integrity of the blood-brain barrier. ▪ Glial cells vastly outnumber neurons. and absorb and recycle neurotransmitters. ▪ Microglia are the phagocytic cells of the CNS. ▪ Glia sometimes function in replenishing certain groups of neurons and in transmitting information. insulate the axons of neurons. ◦ In all but the simplest animals. ▪ Ependymal cells line the brain ventricles and aid in the production circulation. which perform the body's responses. ▪ They nourish neurons. 344 conditions ▪ Neurons in the brain or ganglia integrate (analyze and interpret) the sensory input. The vast majority of the neurons in the brain are interneurons (association neurons). Ganglia are clusters of neuron cell bodies. the axons of neurons form nerves. a communication line consisting of a bundle of neurons tightly rapped in connective tissue. the membrane potential is called the resting potential and is typically between -60 and -80 mV. These ion channels are called leak channels and only allow the passive movement of potassium ions. a neuron can vary from simple to quite complex. ▪ These constitute all nerves that ARE NOT DIRECTLY inside the brain and spinal cord. A vast majority of nerves (~99%) are interneurons ▪ Neurons that extend out of the processing centers trigger output in the form of muscle or gland activity. ▪ These constitute all nerves DIRECTLY inside the brain and spinal cord. the neurons that carry out integration are organized in a central nervous system (CNS). . These are called motor (efferent) neurons. ▪ The vagus nerve is one very important parasympahetic nerve that innverates many of the thoracic and abdominal viscera. ▪ Satellite cells surround the neuron cell bodies in the ganglia. ◦ For a resting neuron. ▪ This pump uses the energy of ATP hydrolysis to actively transport out 3 Na+ and actively pump in 2 K+ into the cell. ▪ A plexus is a network of nerve fibers. This charge difference is called a membrane potential. ◦ The concentration gradients of ions across the plasma membrane represent a form of potential energy that can be harnessed for cellular processes. ◦ Some ion channels along the membrane of the neuron are always open. which form the local circuits connecting neurons in the brain. Ion pumps and channels establish resting potential Formation of resting potential ◦ There is a charge gradient between the interior of a neuron and the extracellular space. ◦ In many animals. ◦ Depending on its role in information processing. ◦ When bundled together. ◦ The neurons that carry information into and out of the CNS constitute the peripheral nervous system (PNS). ◦ The sodium-potassium pump plays a key role in establishing the resting potential. one that is not sending a signal. the threshold is -55 mV. there will be a net movement of potassium ions out of the cell. Action potentials basics Hyperpolarization and depolarization ◦ Changes in membrane potential occur because neurons contain gated ion channels. ◦ Graded potentials are shifts in the membrane potential that do not reach the threshold needed for an action potential. ▪ Can be a hyperpolarization or a depolarization. ▪ In many mammalian neurons. ◦ An action potential occurs when a depolarization causes the membrane potential to reach the threshold. Graded potentials and action potentials ◦ Threshold is the membrane potential to which an action potential will occur if reached. meaning that if the membrane potential hits the threshold. This helps generate the internal negative charge of the neuron. ▪ Once a certain membrane potential is experienced. an action potential will occur. opening or closing when the membrane potential passes a particular level. the voltage-gated ion channels will . The membrane potential moves closer to 0. ▪ As there are no leak channels for Na+. sodium cannot move in or out of the neuron freely. changing the membrane potential. ◦ Hyperpolarization is an increase in the absolute value of Vm. 345 ▪ Since the internal [K+] is greater than the external [K+]. ▪ Action potentials are all-or-nothing. ions flow the channel. ◦ Depolarization is a decrease in the absolute value of Vm. ◦ Action potentials arise because some of the ion channels in neurons are voltage-gated ion channels. ion channels that open or close in response to stimuli. ▪ When the gate opens. The membrane potential moves farther from 0. ▪ When the voltage-gated ion channels open. Na+ are allowed to passively diffuse to either side. the positive-feedback cycle of the voltage-gated ion channels rapidly brings the membrane potential close to ENa. If the depolarization reaches the threshold. The gated potassium channels eventually close and the membrane potential returns to resting potential. The sodium-potassium pump generates an electrochemical gradient between the inside of the neuron and the extracellular space via active transport. This stage is called the falling phase. there is a net movement of Na+ ions into the neuron. causing a rapid outflow of K+. halting Na+ inflow and (2) Most voltage-gated potassium channels open. ▪ At the site where the action potential is imitated. causing further depolarization. Higher concentration of K+ inside than outside. ▪ This is also called the refractory period. Sub-maximal vs. ◦ Two events prevent the membrane potential from actually reaching ENa: (1) Voltage-gated Na+ channels inactivate soon after opening. ◦ In the final phase of an action potential. called the undershoot. most voltage-gated sodium and voltage-gated potassium channels are closed. the membrane's permeability to K+ is higher than at rest. K+ can passively diffuse to either side. It is due to inactivation of sodium channels. This brings the internal membrane potential down toward EK. ◦ A stimulus (any factor that causes a nerve signal to be generated) opens up some sodium channels. K+ will spontaneously move out into the extracellular space. This causes the neuron to become positively charged. ▪ When the voltage-gated ion channels open. ◦ Once threshold is crossed. causing an action potential in the neighboring region. so the membrane potential is closer to EK than it is to the resting potential. The depolarization is large enough to reach threshold. This . This is called the rising phase ▪ ENa is the equilibrium value of sodium. usually the axon hillock. Since an electrochemical gradient is generated at the resting potential. ◦ Maximal stimulus is the amount of voltage necessary to elicit a maximal response. The sodium-potassium pump generates an electrochemical gradient between inside the neuron and the extracellular space via active transport. Higher concentration of Na+ outside than inside. Mechanism of action potential Mechanism ◦ When the membrane of the axon is at the resting potential. Na+ inflow during the rising phase creates an electrical current that depolarizes the neighboring region of the axon membrane (zone of depolarization). 346 open. ▪ EK is the equilibrium value for potassium. This limits the maximum frequency at which an action potential can be generated. Conduction of action potential across axon ◦ Action potential that starts at the axon hillock moves along the axon only toward the synaptic terminals. ▪ This positive-feedback mechanism explains the all-or-nothing phenomenon of action potentials. maximal stimulus ◦ A sub-maximal stimulus is the amount of voltage necessary to elicit a response between the threshold and the maximum response. where a second action potential cannot be initiated. Both events quickly bring the membrane potential back toward EK. Na+ inflow through those channels depolarizes the membrane. it triggers an action potential. 347 process is repeated across the axon. Therefore. ◦ Greater diameter and more heavily myelinated axons will propagate faster impulses. In this zone. the less resistance to “flow” of ions ▪ A more heavily myelinated axon will have more saltatory conduction ◦ The rate at which action potentials are produced conveys information about the strength of the input signal. an action potential cannot be generated here. ▪ The larger the diameter. sodium channels remain activated. ▪ Behind the zone of depolarization is the zone of repolarization caused by K+ outflow. . 348 . the gap that separates the presynaptic and the postsynaptic neurons. ◦ At some synapses. This is called a . the membrane potential depolarizes to a value midway between EK and ENa. When this receptor opens. ▪ The leftover neurotransmitter in the synaptic cleft may be taken back into the nerve terminal (active transport). the neurotransmitter binds binds to an activates a specific response in the membrane. often called an ionotropic receptor. ▪ Once released. ▪ The resulting rise in Ca2+ concentration in the terminal causes the neurotransmitter to be released. ▪ Upon reaching the postsynaptic membrane. ▪ The arrival of an action potential at the presynaptic terminal depolarizes the plasma membrane. ▪ The result is a postsynaptic potential. Basic steps: ▪ At the terminal of the presynaptic neuron. opening voltage-gated channels that allow Ca2+ ions to diffuse into the terminal. 349 Synaptic communication Introduction ◦ Information is transmitted at the synaptic terminals. Generation of postsynatpic potentials ◦ The receptor protein that binds and responds to neurotransmitters is a ligand-gated ion channel. the neuron synthesizes the neurotransmitter and packages it in multiple membrane-enclosed compartments called synaptic vesicles. ▪ Binding of the neurotransmitter to a particular part of the receptor opens the channel and allows specific ions to diffuse across the postsynaptic membrane. ▪ This depolarization brings the postsynaptic neuron above the threshold. a graded potential in the postsynaptic cell. or diffuse out of the synapse. the neurotransmitter diffuses across the synaptic cleft. be degraded by enzymes. the ionotropic receptor is permeable to Na+ and K+. the site where a motor neuron forms a synapse with a skeletal muscle cell. the postsynaptic membrane hyperpolarizes. or an inhibitory effect. ▪ When this happens. ▪ Metabotropic receptors have a slower onset than ionotropic receptors but last longer. ◦ At other synapses. ◦ Neurotransmitters can also bind to metabotropic receptors. When this receptor opens. the 2+ postsynaptic potentials add up in effect to produce one main effect. a receptor that activates a signal transduction pathway in a postsynaptic neuron that creates a second messenger. ▪ The second messenger can alter the postsynaptic neuron in diverse ways. ◦ One neuron is linked up to many other neurons. so it can receive multiple postsynaptic potentials in rapid succession from different presynaptic neurons. the central nervous system develops from the notochord— a hallmark of chordates. and learning. Neurotransmitters Types ◦ Acetylcholine is vital for nervous system function that includes muscle stimulation. an effect called spatial summation. ▪ The hyperpolarization produce din this manner is called an inhibitory postsynaptic potential (IPSP) because it moves the membrane potential further from threshold. This is excitatory. the ionotropic receptor is selectively permeable for only K+ and Cl-. When acetylcholine is released by a motor neuron binds to this receptor. 350 excitatory postysynaptic potential (EPSP). . Nervous systems Vertebrate central nervous system ◦ During embryonic development. the EPSPs add together. a branch of the PNS. two EPSPs can occur at a single synapse in such a rapid succession that the postsynaptic neuron's membrane potential hasn't returned to resting potential before the arrival of the second EPSP. ◦ Gamma-aminobutyric acid (GABA) is the neurotransmitter at most inhibitory synapses in the brain. ▪ Binding of GABA to receptors in postsynatpic cells increases membrane permeability to Cl-. memory formation. resulting in an IPSP. such as altering the number of open potassium channels. ◦ Norepinephrine is an excitatory neurtornasmiter in the autonomic nervous system. This is an IPSP. ◦ Dopamine and seratonin are released at many sites in the brain and affect sleep. When this happens. an effect called temporal summation. ◦ In addition. and learning. mood. ▪ EPSPs produced nearly simultaneously by DIFFERENT synapses on the same postsynaptic neuron can add together. Acetylcholine released by neurons activate a G protein signal transudction pathway that leads to open potassium channels. which functions at the vertebrate neuromuscular junction. attention. Two main acetylcholine receptors: ▪ One is a ligand-gated ion channel. the ion channel opens forming an EPSP. ▪ The second is a metabotropic receptor found in locations that include the vertebrate CNS and heart. ▪ Metabotropic receptors do not directly pump ions like ionotropic receptors! Summation of postsynaptic potentials ◦ One postsynaptic potential usually isn't strong enough to produce an effect. The hypothalamus constitutes the control center that includes the body's thermostat as well as the central biological clock. ▪ Under the corpus callosum. . such as blood circulation. The cerebral cortex is mostly made up of association areas—sites of higher mental activities (thinking). parts of speech. In a phenomenon known as lateralization. regulation of sleep. the left hemisphere becomes adept at language. ▪ The forebrain has activities that include the processing of olfactory input (smells). telencephalon = cerebral cortex + olfactory bulb diencephalon = thalamus + hypothalamus ▪ The midbrain. temperature and pain. Controls muscular coordination. motor. The right cerebral hemisphere is stronger at spatial relations. ◦ The brain is made up of outer gray matter and inner white matter. The inner portion is called the medulla. and nonverbal thinking. located centrally in the brain. groups of neurons called the basal nuclei are important in motor coordination. pattern. ▪ There are 12 pairs of cranial nerves that are sensory. Olfactory bulb controls smell. ▪ The hindbrain controls involuntary activities. as well as detailed skeletal motor control and the processing of fine visual and auditory details. and any complex processing.and gastrointesitnal activity. The pons is a relay center to allow communication between the cortex and the cerebllum. planning. areas in the two hemispheres become specialized for different functions during brain development in humans and children. ◦ The outer layer of the cerebrum is called the cerebral cortex and is vital for perception. ▪ Occipital lobe – concerned with many aspects of vision. and mixed. movement. emotions and problem solving. and learning. Takes in sensory information and relays it to the correct areas. In most people. Medulla oblongata controls breathing. 351 ◦ Meninges cover around the brain and spinal cord. and mathematical operations. and face recognition. ▪ Temporal lobe – concerned with perception and recognition of auditory stimuli (hearing) and memory. logic. Left hemisphere controls right side of body and vice versa. coordinates routing of sensory input. heart rate . pressure. The cerebrum is the largest part of the brain. ◦ Divided into 4 lobes: ▪ Frontal lobe – concerned with reasoning. ▪ Parietal lobe – concerned with perception of stimuli such as touch. The cerebellum coordinates movement and balance and helps in learning and remembering motor skills. Surrounded by cerebrospinal fluid. ▪ The midbrain and portions of the hindbrain give rise to the brainstem. the part of the brain that is connected to the spinal cord. voluntary movement. learning. ◦ Divided into the left and right cerebral hemispheres. ◦ A thick band of axons called the corpus calossum enables the right and left hemmispheres to communicate. The thalamus is the main input center for sensory information going to the cerebrum. Most cranial nerves are mixed. 3 subdivisions: The enteric division of the autonomic nervous system are active in controlling the digestive tract. Major neurotransmitter is acetylcholine. ◦ Makes up the outer layer of the spinal cord. It is filled with cerebrospinal fluid. Does NOT travel through brain! ▪ Sensory information enters through the dorsal horn and motor information exits through the ventral horn. and controls basic body functions such as breathing. It is generally involuntary. ▪ The central canal is the space that runs longitudinally through the length of the entire spinal cord. The sympathetic division corresponds to the “fight-or-flight” response. instructions travel to muscles glands. It conveys information to and from the brain and generates basic patterns of locomotion. The paraympathetic division causes the opposite response of the sympathetic division and promotes calming and a return to self-maintenance functions. known as the spine. and endocrine cells along PNS neurons called efferent neurons. ▪ Acts independently of the brain as part of simple nerve circuits that produce reflexes. heart rate. Consists of the midbrain. pons. ▪ The autonomic nervous system consists of neurons that carry signals to smooth and cardiac muscles. ◦ PNS has two different components: ▪ The motor system consists of neurons that carry signals to skeletal muscles. ◦ The spinal cord runs lengthwise inside the vertebral column. ◦ Following processing within the CNS. blood pressure. 352 It controls the flow of messages between the brain and the rest of the body. the body's automatic responses to certain stimuli. Peripheral nervous system ◦ Sensory information reaches CNS along PNS neurons designated as afferent neurons. and the medulla oblongata. Can be voluntary or involuntary. which supplies the CNS with nutrients and hormones and carrying away wastes. and whether one is awake or sleepy. and gallbladder. Major neurotransmitter is norepinephrine. White matter consists mainly of bundled axons. swallowing. ▪ Made up of gray and white matter: Gray matter is primarily made up of neuron cell bodies. . consciousness. pancreas. 353 . ◦ Many pathogens that get through barrier defenses are engulfed by phagocytic cells that use several types of receptors to detect pathogens. The skin functions as not only a physical barrier but also a hostile barrier. unlike the adaptive immune system. the exoskeleton provides an effective barrier defense against most pathogens. ▪ Binding of an innate immune receptor to a foreign molecule activates internal defenses. enabling responses to a very broad range of pathogens. saliva. as well as a variety of other molecules that activate tissue damage. ▪ Symbiotic bacteria in the digestive tract and vagina out-competes many other organisms. ▪ Toll-like receptors can detect a broad range of human pathogens. Also release chemicals that kill pathogens and entrap large parasites. by a process called pattern recognition. which kills most pathogens. which are short chains of amino acids that circulate throughout the body of the insect and inactivate or kill fungi and bacteria by disrupting their plasma membranes. ▪ Microbes that go through the digestive tract must contend with the acidic environment of the stomach. making it hard for life to grow on it. ▪ Immune cells of insects bind to molecules found only on the outer layers of fungi or bacteria. and mucous secretions destroys the cell walls of susceptible bacteria as they enter the openings around the eyes or the upper respiratory tract. The mucous membranes produce mucus. ▪ Encounters with pathogens in the hymolymph can cause hemocytes and other cells to secrete antimicrobial peptides. but. does not confer long-lasting or protective immunity to the host. respiratory. 354 Innate immunity Innate immunity of invertebrates ◦ Innate immunity provides an immediate defense against infection. the circulatory fluid. an enzyme that breaks down bacterial cell walls. and reproductive tracts. where it blocks infection by many pathogens ingested with food. It is covered with oily and acidic (pH 3-5) secretions from sweat glands. urinary. ▪ Hemocytes travel throughout the body in the hemolymph. Nonspecific immune system. ▪ They include the skin and the mucous membranes lining the digestive. ◦ Found in all animals Innate immunity in invertebrates ◦ Insects rely on their exoskeleton as a first line of defense against infection. Innate immunity in vertebrates ◦ Barrier defenses block the entry of pathogens. ▪ Innate immune responses are distinct for different classes of pathogens. ◦ Chitin also lines insect's intestine. ◦ Any pathogen that breaches the barrier defenses encounters a number of internal immune defenses. a viscous fluid that traps pathogens and other particles. further protects the insect's digestive system. They ingest and break down bacteria and other foreign substances through phagocytosis. . ▪ Lysozymes in tears. ▪ Composed largely of the polysaccharide chitin. ◦ Lysozyme. Cells of innate system recognize and responds to pathogens in a generic way. macrophages that reside there engulf the invaders as part of the innate immune response. such as skin. lymph that circulates around carries microbes. ◦ Move into tissues via diapedesis. Eosinofils. which phagocytize cell debris and pathogens. Some macrophages reside in lymph nodes. The lymphatic system consists of a branching network of vessels. Dendritic cells can migrate to the lymph nodes after interacting with pathogens. Also stimulates adaptive immunity within the lymph nodes. and several organs. instead. they secrete chemicals that lead to cell death. Lymph nodes fill with huge numbers of defensive cells. Dendritic cells mainly populate tissues. are important in defending against multicellular invaders. ▪ Mast cells secrete histamine and work in the allergic and inflammatory response. Lymph drains from the lymphatic capillaries into larger lymphatic vessels. ◦ Many cellular innate defenses in vertebrates involve the lymphatic system. Eventually fluid reenters the circulatory system via two large lymphatic vessels that fuse with the vein in the chest. ▪ Basophils store histamine and work in inflammatory response. ◦ Are also antigen-presenting cells. numerous lymph nodes—little round organs packed with macrophages and white blood cells called lymphocytes—the bone marrow. . They do not engulf cells. Fluid enters the lymphatic system by diffusing into tiny. dead-end lymphatic capillaries that are intermingled among the blood capillaries. ◦ Are the most common WBC. parts of microbes. 355 These receptors initiate the innate and the adaptive immune response. which circulate in the blood. often found beneath mucosal surfaces. ▪ The lymphatic vessels carry a fluid called lymph. and their toxins picked up from infections. that contact the environment. ▪ Types of phagocytic cells: Neutrophils. Monocytes move into tissues (diapedesis) where they develop into macrophages. ▪ Two main functions: to return tissue fluid back to the circulatory system and to fight infection. which is similar to the interstitial fluid that surrounds body cells but contains less oxygen and fewer nutrients. are attracted by chemicals from infected tissues in a process called chemotaxis and then engulf and destroy the infecting pathogens. They stimulate adaptive immunity against pathogens as they encounter and engulf. ◦ Antigen-presenting cells. ▪ Natural killer cells circulate through the body and detect the abnormal array of surface proteins characteristic of some virus-infected and cancerous cells. causing the tender “swollen glands” in your neck and armpits that your doctor looks for as a sign of infection. Are the least common WBC. Once inside lymphatic organs. ▪ When your body fights infection. ▪ Some of the fluid that enters tissue spaces from the blood in a capillary bed does not reenter the blood capillaries but instead is returned to the blood via lymphatic vessels. a fluid rich in white blood cells. ▪ Complement system helps phagocytes engulf foreign cells and help lyse foreign cells. and cell debris from damaged tissue. They limit the cell-to-cell spread of viruses in the body. engulf pathogens and damaged cells. Activation also can help attract phagocytes to these foreign cells. found in connective tissue. causing localized swelling. dead pathogens. ◦ The inflammatory response is the changes brought about by signaling molecules released upon injury or infection. These proteins circulate around the blood in an inactive form and are activated by substances on the surfaces of pathogens. 356 ◦ In mammals. ▪ Interferons are proteins that provide innate defense by interfering with viral infections. ▪ When macrophages and neutrophils are activated. ▪ The complement system consists of roughly 30 proteins in blood plasma. pathogen recognition triggers the production and release of a variety of peptides and proteins that attack pathogens or impede their production. signaling molecules that modulate immune responses. the cells discharge cytokines. . ▪ Histamine released at sites of damage triggers nearby blood vessels to dilate and become more permeable. Functions in the inflammatory response as well as the adaptive defenses. The dilation causes capillaries to leak fluid into the neighboring tissues. ▪ Phagocytes are attracted to injury by chemical gradients of complement. ▪ One important inflammatory molecule is histamine. which is stored in densely packed vesicles of mast cells. Activation leads to lysis of the cells. ◦ Fever is a systemic inflammatory response. ▪ The result in the of the increased blood flow is the accumulation of pus. Cytokines promote blood flow to the injury site or infection. Adaptive immunity players Introduction ◦ In adaptive immunity. ▪ Lymphocytes originate from stem cells in the bone marrow. . enabling it to respond to any pathogen that produces molecules containing that epitope. either proteins or polysaccharides that protrude from the surface of foreign cells or viruses. ◦ Any substance that elicits a B or T cell response is called an antigen. ▪ Recognition and response occurs with tremendous specificity. ▪ Is activated after the innate immune response and develops more slowly. molecular recognition relies on a vast arsenal of receptors. ▪ In adaptive immunity. ▪ Each antigen receptor binds to just one part of one molecule from a particular pathogen. A single antigen usually has several epitopes. ▪ Higher temperature is beneficial to help fighting off infections. Lymphocytes of a third type remain in the blood and become natural killer cells active in innate immunity. Lymphocytes that remain and mature in the bone marrow develop as B cells. Lymphocytes that go to the thymus (an organ above the heart) mature into T cells. Receptors provide pathogen-specific recognition ◦ The adaptive response relies on T and B cells. recognition occurs when a B or T cell binds to an antigen via a protein called an antigen receptor. each binding to a receptor with different specificity. ▪ The small. which are types of white blood cells called lymphocytes. They are typically foreign and are large molecules. substances released by activated macrophages cause the body's thermostat to reset to a higher temperature. Each B or T cell displays specificity for a particular epitope. accessible portion of an antigen that binds to an antigen receptor is called an epitope. ▪ The antigen receptors of the B cells can bind to epitopes of intact antigens on pathogens or circulating free in body fluids. each of which recognizes a feature typically found on only a particular part of a particular molecule in a particular pathogen. 357 ▪ In response to certain pathogens. ▪ All of the antigen receptors made by a single B or T cell are identical. linked by a disulfide bridge. so named because its amino acid sequence varies extensively from one B cell to another. leading to the formation of cells that secrete a soluble form of the receptor. ▪ Antibodies bind to intact antigens in the blood and the lymph. ▪ T cells can bind only to fragments of antigens that are displayed. ▪ The light and heavy chains each have a constant region. an alpha and beta chain. ▪ Within the two tips of the Y shape. The remainder of the molecule is made up of the constant regions. The secreted protein is called an antibody. where amino acid sequences vary very little among the receptors. heavy and light chains are linked by hydrogen bonds Antigen recognition by T cells ◦ The T cell antigen receptor consists of two different polypeptide chains. unlike B cells. on the surface of host cells. each chain has a variable region. At the base of the T cell antigen receptor is a transmembrane region that anchors the receptor. Note that the antigen-binding site is at the N-terminus! ◦ Binding of a B cell antigen receptor to an antigen is an early step in B cell activation. A transmembrane region anchors the receptor. ▪ in a typical antibody. The combination of the V region makes up the antigen binding site. . ▪ Antibodies have the same Y-shaped structure as B cell antigen receptors but are secreted rather than membrane bound. 358 Antigen recognition by B cells and Antibodies ◦ Each B cell antigen receptor is a Y-shaped molecule consisting of 4 polypeptide chains: two identical heavy chains and two identical light chains. or presented. A short tail region at the end of the transmembrane region extends into the cytoplasm. with disulfide bridges linking the chains together. the variable regions o the alpha and beta chains together form a single-antigen binding site. At the outer tip of the molecule. display of the antigen fragment in an exposed groove of the MHC protein. ▪ Mutations in VJ recombination can add additional variation. enzymes cleave the antigen into smaller peptides and then the antigen fragments bind to the MHC molecules inside the cell. enabling immune system to detect pathogens never encountered ▪ adaptive immunity normally has self-tolerance. This is called VJ recombination. ▪ Assembling a functional Ig gene requires rearranging the DNA. This leads to the creation of many different types of short and long chains. a joining (J) segment. ▪ A receptor light chain is encoded by three gene segments: a variable (V) segment. the lack of reactivity against an animal's own molecules and cells ▪ cell proliferation triggered by activation greatly increases number of B and T cells specific for the antigen ▪ there is a stronger and more rapid response to an antigen encountered previously ◦ The capacity to generate diversity in B and T cells is built into the structure of Ig genes. B and T cell development ◦ 4 major characteristics of adaptive immunity: ▪ immense diversity of lymphocytes and receptors. and a constant (C) segment. ▪ The V and J segments together encode the variable region of the receptor chain while the C segment encodes for the constant region. ▪ Movement of the MHC molecule and the bound antigen fragment up to the cell surface results in antigen presentation. and thus many different types of antigen-binding sites. an enzyme complex called recombinase links one light-chain V segment to one J segment. Most body cells only have MHC II but antigen presenting cells have MHC II and I. ▪ Inside the host cell. 359 ◦ The host protein that displays the antigen fragment on the cell surface is called the major histocompatibility complex (MHC) molecule. . ▪ Recognition of a protein antigens by T cells begin when a pathogen or part of a pathogen either infects or is taken by a host cell. Early in B cell development. ▪ The appropriate T cell can then bind to the antigen fragment and the MHC molecule. The effector forms of T cells are helper T cells and cytotoxic T cells. Proliferating of B and T cells ◦ An antigen is presented to a steady stream of lymphocytes in the lymph nodes until a match is made. they are destroyed by apoptosis. ◦ This whole process is called clonal selection because an encounter with an antigen selects which lymphocyte will divide to produce a clonal population for a particular epitope. the B or T cell undergoes multiple cell divisions. ▪ The remaining cells in the clone become memory cells. of greater . secondary immune response ◦ Immunological memory is responsible for the long-term protection that a prior infection provides against many diseases. long-lived cells that can give rise to effector cells if the same antigen is encountered later in the animal's life. 360 Origin of self-tolerance ◦ As lymphocytes mature in the bone marrow or thymus. which secretes antibodies. The effector forms of B cells are plasma cells. Primary vs. If this fails the test. ◦ The production of effector cells from a clone of lymphocytes during the first exposure to an antigen is the basis for the primary immune response ◦ If an individual is exposed again to the same antigen. ▪ Some of the clones become effector cells. The daughter cells are clones of the original cell. short-lived cells that take effect immediately against the antigen and any pathogens producing that antigens. their antigen receptors are tested for self-reactivity. ◦ Once the match is made. the response is faster. Adaptive immunity mechanism Humoral vs. An accessory protein called CD4 helps the helper T cell bind to the class II MHC molecule. 361 magnitude. but by binding to pathogens. ◦ When an antigen first binds to receptors on the surface of a B cell. ◦ The class II MHC protein of the B cell presents an antigen fragment to a helper T cell. ◦ In the cell-mediated immune response. specialized T cells destroy infected host cells. cytotoxic T cells require signals from helper T cells and interaction with an antigen-presenting cell. the cell takes in a few foreign molecules by receptor-mediated endocytosis. The direct cell-to-cell contact is usually critical to B cell activation. macrophage. and more prolonged. but antigen-presenting cells have class I and class II molecules. The T cell attaches to that antigen. ▪ To become active. When the helper T cell binds to the antigen-presenting cell cytokines are exchanged. ◦ A single activated B cell gives rise to thousands of clones. Can be a dendritic cell. Antibody function ◦ Antibodies do not actually kill pathogens. Cytotoxic T cells ◦ Cytotoxic T cells use toxic proteins to kill cells infected by viruses or other intracellular pathogens before fully mature. or B cell. they produce interleukins to stimulate proliferation of T cells. Helper T cells: A response to nearly all antigens ◦ A type of T cell called a helper T cell triggers the humoral and cell-mediated immune responses. This is called the secondary immune response. Most body cells have class I MHC molecules. ◦ Types of antibodies: . B cells and macrophages. In the humoral response. ▪ The cytotoxic T protein kills the host cell by secreting proteins that disrupt membrane integrity and trigger cell death. they interfere with pathogen activity or mark pathogens in various ways for inactivation or destruction. Two requirements for helper T cells to activate: ▪ A foreign molecule must be present that can bind specifically to the antigen receptor of the T cell ▪ The antigen must be displayed on the surface of an antigen-presenting cell. cell-mediated response ◦ The humoral immune response occurs in the blood and lymph. ◦ Once the helper T cell has been activated. T suppressor cells ◦ T suppressor cells serve to town down the T cell response to self cells or following an infection. antibodies help neutralize or eliminate toxins in the blood and lymph. They secrete signals which help initiate productions of antibodies that neutralize pathogens and activate T cells that will kill the infected cells. ▪ The accessory protein CD8 binds to the class I MHC molecule to keep the 2 cells in contact. These clones begin producing and secreting antibodies. Activation and function of B cells ◦ Activation of B cells involve both helper T cells and proteins on the surface of pathogens. ▪ Binding of complement protein to an antigen-antibody complex on a foreign cell triggers the generation of a membrane attack complex that forms a pore in the membrane of the cell and causes lysis. ◦ In opsonization. the introduction of a live microorganism will stimulate a swift response by the immune system before any disease can become established. or other microorganisms are used as vaccines. Once memory cells have formed. ◦ Vaccines are substances that stimulate the production of memory cells. ◦ Antibodies can also work with proteins of the complement system. passive immunity ◦ Active immunity are the defenses that arise when a pathogen infects the body and prompts a primary or secondary immune response. ▪ Newborn infants are protected by passive immunity also by drinking breast milk. Active vs. . not the recipient. antibodies bound to antigens on bacteria do not block infection. bacteria. ▪ vaccine = active immunity that is artificially acquired Transplant rejection (immune system) ◦ Transplanted tissues or organs are detected as nonself by the recipient’s immune system because the antigens on the donated organ are those of the donor. ◦ Antibiotics are chemicals derived from bacteria or fungi that are harmful to other microorganisms. but instead present a readily recognized structure for macrophages or neutrophils. ◦ Passive immunity is when the antibodies in the blood of a pregnant female cross the placenta to her fetus. Inactivated viruses or fragments of viruses. Breast milk contains antibodies. 362 ▪ IgG is most abundant antibody ▪ IgM is the first antibody to appear in response to an antigen ▪ IgA is present in mucosal secretions ▪ IgE is present in the allergic response ▪ IgD crosses the placenta and activates T-cells ◦ Neutralization is a process in which antibodies bind to proteins on the surface of a virus and makes it impossible for the virus to infect the cell. ▪ Autoimmune diseases result when the immune system goes awry and turns against some of the body's own molecules. Some of these antibodies attach by their base to the surface of mast cells. itchy skin. ▪ The recipient who is taking these drugs are immunocompromised because the immune system is not functioning at full capacity. ◦ Allergies ▪ Allergies are hypersensitive (exaggerated) responses to otherwise harmless antigens in our surroundings. binds to antibodies attached to mast cells. The B cells then proliferate through clonal selection and secrete large amount of antibodies to this allergen. AIDS). protein molecules on pollen grains) ▪ Two stages of an allergy attack: (1) sensitization: Occurs when a person is first exposed to an allergen. ◦ Take immunosuppressing drugs to help prevent transplant rejection. the recipient's immune system will attack the transplanted organ. serious disease can result. body cells that produce histamine and other chemicals that trigger the inflammatory response. They work by lowering the body's immune response to antigens. it binds to effector B cells (plasma cells) with complementary receptors. ▪ Antigens that cause allergies are called allergens (i. After an allergen enters the bloodstream. These people are susceptible to frequent and recurrent infections (i. . and tears. Like in inflammation.e. 363 ◦ As a result. Disorders of the immune system ◦ Malfunction or failure of the immune system causes disease ▪ When the immune system fails to function properly. ▪ Antihistamines are drugs that interfere with histamine's action and give temporary relief from an allergy. ▪ Immunodeficiency diseases are when an immune response is defective or absent.e. histamine causes blood vessels to dilate and leak fluid so it causes nasal irritation. causing the mast cells to release histamine which triggers the allergic symptoms. (2) when the person is exposed to the same allergen later: the allergen enters the body. Structure of skeletal muscle ◦ Vertebrate skeletal muscle. which are the basic contractile units of skeletal muscle. It can propagate an action potential It is invaginated by transverse tubules. channels for ion flow. ▪ Sarcolemma is the plasma membrane of muscle cells. ▪ Thin filaments attach at Z lines which are located at the boundary of a single sarcomere. A different muscle is needed to reverse the action. back-and-forth movement of body parts involves antagonists. The interaction between thick and thin filaments produces muscle cell contraction. which are staggered arrays of myosin molecules. Thus. ▪ A muscle pulls the bone to which it is attached—it can only move the bone in one direction. has a hierarchy of smaller and smaller units. ◦ Each fiber is a single cell with multiple nuclei. ◦ The myofibrils in muscle fibers are made up of repeating sections called sarcomeres. ▪ Each nucleus is derived from one of the embryonic cells that fused to form the muscle cell. the alternating between the thin actin filaments and the thick myosin filaments is responsible for striations in the skeletal muscle. Thin filaments is comprised of two strands of actin that are coiled around each other. which contain the thick and thin filaments. which moves bones and body. ◦ fascia is loose connective tissue that covers the surface of muscle ◦ Within a typical skeletal muscle is a bundle of muscle fibers that run parallel to the length of the muscle. a pair of muscles (or muscle groups) that can pull the same bone in opposite directions. It wraps several myofibrils together to form a muscle cell/muscle fiber ▪ Mitochondria is present in large amounts for ATP synthesis ◦ Inside a muscle cell lies a longitudinal bundle of myofibrils. Thick filaments. ▪ An example of antagonists are the biceps and triceps. 364 Vertebrate skeletal muscle structure and function The skeleton and muscles interact in movement ◦ Muscles are connected to bones by tendons. ▪ Sarcoplasm is the cytoplasm of a fiber cell. . while thick filaments are anchored at M lines centered in the sarcomere. The H zone and I band reduce during contraction. ▪ The H zone is the region containing thick filaments. 365 ▪ The I band is the region containing thin filaments. ▪ The A band is the region of actin and myosin overlapping. The sliding-filament model . but the A band does NOT. ◦ 3) The myosin head binds to actin on its myosin-binding site. ◦ 5) Binding of a new molecule of ATP releases the myosin head from actin. ◦ During intense muscle activity. oxygen becomes a limiting reagent and ATP is instead generated by lactic acid fermentation. powered by myosin muscles. ◦ 1) The myosin head is bound to ATP and it is in its low-energy configuration. . 366 ◦ According to the well-accepted sliding-filament model. This is why dead corpses are stiff. which will transfer a group from phosphocreatine to ADP in an enzyme-catalyzed transphosphorylation reaction. and a new cycle begins. sliding the thin filament toward the center of the sarcomere. ▪ This generates much less ATP per glucose molecule and creates the burning sensation in the muscles. ▪ Glycogen can be broken down into glucose. ◦ Without new ATP. the thin and thick filaments ratchet past each other. Powering repetitive contractions requires two other storage compounds: ▪ Creatine phosphate. ◦ At rest. ◦ 2) The myosin head hydrolyzes ATP to ADP and phosphate and is now in its high-energy conformation. ◦ 4) Releasing ADP and Pi. forming a cross-bridge. the cross bridges remain attached to the myosin head. myosin returns to its low-energy configuration. which can be metabolized quickly to create ATP. most muscle fibers contain only enough ATP for a few contractions. tropomyosin covers the myosin-binding sites on the actin (thin) filaments. ◦ The strength of a contraction of a single muscle fiber cannot increase but the strength of overall contraction can be increased by recruiting more muscle fibers. and contraction stops. and the troponin complex. . ▪ Fine movement uses small motor units only. contraction ends. ▪ In a muscle fiber at rest. it binds to the troponin complex. the binding sites are covered. a set of additional regulatory proteins. 367 The role of calcium and regulatory proteins ◦ Tropomyosin. ▪ When Ca2+ ions accumulates in the cytosol. This creates a smooth increase in force. ▪ The nervous system produces graded contractions of whole muscles by varying (1) the number of muscle fibers that contract and (2) the rate at which muscle fibers are stimulated. exposing the myosin binding sites. contraction of a whole muscle is graded. ◦ A motor unit consists of a single motor neuron and all the muscle fibers it controls. The muscle contracts. then larger ones are activated as needed. When the Ca2+ concentration falls. triggering an action potential in the muscle fiber. a specialized endoplasmic reticulum. are bound to the actin strands of thin filaments. slide thin filament toward center of sacromere. ◦ 6) Cytosolic Ca2+ is removed by active transport into the SR after the action potential ends. preventing actin from interacting. and the muscle fiber relaxes. ◦ 3) The action potential propogating down the T tubules make close contact with the sarcoplasmic reticulum (SR). ◦ 1) Acetylcholine (Ach) is released at the synaptic terminal of a motor neuron. It diffuses across the synaptic cleft and binds to the receptor proteins on the muscle fiber's plasma membrane. ◦ 5) Cycles of myosin cross-bridge formation and the breakdown. ▪ Usually small motor units are activated first. ◦ 7) Tropomyosin blockage of myosin-binding sites is restored. ◦ Whereas contraction of a single skeletal muscle fiber is a brief all-or-none twitch. you can voluntarily alter the extend and strength of its contraction. causing tropomyosin bound along the actin strands to shift position and expose the myosin- binding sites. coupled with ATP hydrolysis. Close contact of the AP with the SR triggers the release of Ca2+ ions from the SR. a regulatory protein. ◦ 4) Ca2+ ions bind to the troponin complex in the thin filament. ◦ 2) The action potential is propagated along the plasma membrane and down transverse tubules. the action potential propagates along the sacrolemma and Ca2+ ions are released to open up the myosin-binding sites. Three phases: ▪ Latent period is the time between stimulation and onset of contraction. ▪ This occurs when a second action potential arrives before the muscle fiber has completely relaxed. The muscle is now unresponsive to a stimulus during this time. ◦ Summation occurs when two contractions combine additively and become stronger. ▪ Contraction ▪ Relaxation is the absolute refractory period. . ◦ Tonus is the unconscious low level contraction of your muscles while they are rest. 368 Types of muscles Types of muscle responses ◦ Simple twitch is the response of a single muscle fiber to a brief stimulus. During this time. They are more prolonged than a simple twitch. ◦ Tetanus is the continuous sustained contraction because the rate of muscle stimulation is so fast that the twitches blur into one smooth constant. It is a state of partial contraction. Fast oxidative muscle fibers have a high rate of myosin ATPase activity. meaning that they contract slowly but they contract for a much longer period of time than fast-twitch fibers. ▪ High amounts of mitochondria ▪ NO summation or tetanus due to long refractory period ▪ Ion channels in the plasma membrane of cardiac muscle cells cause rhythmic depolarizations that trigger action potentials WITHOUT nervous system input (myogenic). powerful contractions. Fast-twitch fibers enable brief. Types of muscle fibers ◦ Skeletal muscle is voluntary. They are fast-twitch fibers. Muscles that need to be active continuously have many of these fibers. They have the largest diameter and the low concentrations of myoglobin. ◦ Smooth muscle is found mainly in hollow organs such as the digestive tract and blood . Have a large amount of the oxygen-storing protein myoglobin. It is striated and involuntary. rapid. It is multi-nucleated. There are multiple types: ▪ Fibers that rely mostly on aerobic respiration are called oxidated fibers. ▪ Adjacent cardiac muscle cells are electrically coupled by specialized regions called intercalated disks. Action potentials last much longer than skeletal muscles. They have many mitochondria for ATP synthesis. 369 ▪ Your muscles are never completely relaxed. Usually used for power. but the tension increases. meaning that they contract very fast. ◦ An isometric contraction occur when both ends of the muscle are fixed and no change in length occurs during the contraction. and moves bone. They are mono- nucleated or bi-nucleated. They have high myosin ATPase activity. causing the whole heart to contract. ▪ In contrast. Red color. ◦ Cardiac muscle is only found in the heart. They have a rich blood supply for easy access to nutrients. ◦ Dynamic contraction involves both concentric and eccentric type of contractions. This enables the action potential generated by specialized cells in one part of the heart to spread. They generally don't undergo mitosis to create new cells (hyperplasia). Red to pink color. Fast-twitch fiber Typically white color. They have the smallest diameter and are the most highly resistant to fatigue. Slow oxidative muscle fibers have a low rate of myosin ATPase activity. ◦ An eccentric contraction is a type of dynamic contraction where the muscle fiber lengthens and the tension on the muscle increases. Are slow-twitch fibers. 5 types of muscle contractions ◦ Isotonic contraction is when a muscle shortens against a fixed load while the tension on the muscle remains constant ◦ A concentric contraction is a type of dynamic contraction where the muscle fibers shorten and the tension on the muscle fiber increases. glycolytic fibers rely on glycolysis as their major source of ATP production. They have an intermediate diameter and are intermediate in resistance to fatigue. striated. ▪ This is what makes your muscles feel somewhat firm while you are resting and not intentionally tensing them. but will increase in size (hypertrophy). Invertebrate locomotion ◦ A hydrostatic skeleton consists of fluid held under pressure in a closed body compartments. ▪ These muscles are stimulated by the autonomic nervous system. Invertebrates with these skeletons control their form and movement by using muscles to change the shape of the fluid filled compartments. This causes the cell to get smaller and contract as a whole. ▪ Thick filaments are scattered throughout the cytoplasm and thin filaments are attached to structures called dense bodies. ▪ Two main types: Single unit (visceral) smooth muscle is connected by gap junctions and contract as a single unit (stomach uterus. some of which are tethered to the plasma membrane. temperatures on top of neuronal responses. and are involuntary. advancing the cell membrane as it extends forward. ▪ The contraction of the thin and thick filaments causes the dense bodies to move closer. In multiunit smooth muscle. . Contraction causes hydrostatic skeleton to flow longitudinally. are mono-nucleated. urinary bladder). ◦ Amoeba extend pseudopodia. which causes the shortening of the intermediate filaments found throughout the cell. anchor the worm in the earth while muscles push ahead. each fiber is directly attached to neurons and can contract independently (iris. change in pH. ▪ Flatworms uses bi-layered longitudinal and circular muscles to contract against the hydrostatic skeleton. bronchioles). 370 vessels. Movement in lower forms Unicellular locomotion ◦ Protozoans and primitive algae use flagella by means of power stroke or recovery stroke. Bristles in the lower part of each segment setae. They lack striations. oxygen and carbon dioxide levels. ▪ Smooth muscle can respond to hormones. lengthening the animal ▪ Segmented worms (annelids) advance by action of muscles on hydrostatic skeleton. ▪ There is less myosin than in skeletal muscle and the myosin is not associated with specific actin strands. watery fluid that fills the space between the cornea and the iris. Rod pigment rhodopsin is struck by photons from light. \ . ◦ Chemoreceptors include both general receptors. ◦ Thermoreceptors detect heat and cold. 371 Sensory receptors Types ◦ Mechanoreceptors sense physical deformation caused by forms of mechanical energy such as pressure. ◦ The neural pathways separate for each type of receptor and all terminate somewhere in the CNS. It is jelly like. and do not detect color. ◦ Electromagnetic receptors detect forms of electromagnetic energy such as light. Important information ◦ Sensory receptors respond strongly to own stimuli and weakly to others. causing hyperpolarization transduction into neural action potential sent to brain. those that transmit information about total solute concentration and specific receptors. ▪ Photoreceptor cells synapse to bipolar cells → ganglion cells → axons of ganglion cells bundle to optic nerve. motion and sound. diameter controlled by iris) → lens (focuses image. This fluid nourishes the cornea and the lens and give the eye its shape. maintains eye shape and optical properties. touch. those that respond to individual kinds of molecules (Taste and smell). are important in night vision. The Eye Pathway of light stimuli ◦ Cornea (focuses light) → pupil (controls amount of light that enters the eye. ▪ Aqueous humor is the thin. ▪ Cones detect high-intensity illumination and are sensitive to color. ◦ Nociceptors detect pain. controlled by cilliary muscles) → Retina (location of rods and cones). and magnetism. ▪ Rods detect low intensity illumination. stretch. Point at which optic nerve exits is called the blind spot (no photoreceptors here) ◦ Eye has virtrous and aqueous humor: ▪ Virtrous humor is the clear gel that fills the space between the lens and retina of the eyeball. electricity. The ear Structure ◦ The Ear transduces sound energy into impulses. direct sound into external auditory canal → ◦ Middle ear – amplifies sound. and stapes (transmit sounds from the air to the cochlea) ◦ Inner eat – wave moves through the cochlea as the vibration of ossicles exert pressure on fluid. this movement is detected by hair cells (sensory receptors of the ear) that are located in the organ of Corti → transduced neural signal → action potential ◦ The inner ear also has semicircular canals that are responsible for balance (fluid + hair cells sense orientation + motion) . 372 Eye disorders ◦ Myopia – nearsightedness ◦ Hyperopia – farsightedness ◦ Astigmatism – irregularly shaped cones. tympanic membrane (eardrum) begins the middle ear and vibrates at the same frequency as incoming sound → ossicles: malleus. ◦ Cataracts – lens becomes opaque and light cannot enter ◦ Glaucoma – increase in pressure of eye due to blocking of outflow of aqueous humor. Causes blurred vision at any distance. or vision loss. moving the vestibular membrane in and out. ◦ Outer ear – auricle/pinna (what we think of as the ear) and the auditory canal. distorted vision. Causes blurred vision. incus. As waves move through the ear the pressure alternates. 373 Invertebrate sekeletons ◦ Arthropods have an exoskeleton composed of hart chitin. Chitin helps necessitate molting for growth. Vertebrate skeleton organization ◦ Axial skeleton is the part of the skeleton that consists of the bones of the heat and the trunk of a vertebrate. ◦ The appendular skeleton supports the attachment and functions of the upper and lower limbs of the human body. Consist of pectoral girdle, pelvic girdle, upper limbs (arms) and lower limbs (legs). ◦ Joints are areas where different bones meet: ▪ Stutures are immovable joints that holds together the bones of the skull. ▪ Moveable joints are bones that move relative to each-other. Ligaments are bone-to-bone connectors that strengthen joints. ◦ ACL ligament limits rotational knee movement and connects femur and tibia. Tendons are muscle-to-bone connectors that bend skeleton at moveable joints. ▪ Origin is the point of attachment of muscle to stationary bone. ▪ Insertion is the point of attachment of muscle to bone that moves. ▪ Extension is the straightening of a joint. ▪ Flexion is the bending of a joint. ▪ A fibrous joint connect bones without allowing any movement. ▪ Cartilaginous joints are bones that are attached by cartilage that allow for little movement. ▪ Synovial joints allow for much more movement. They are most common. They are filled with synovial fluid which acts as a lubricant. ▪ Ball-and socket joints (I.e where the humerus joins the pectoral girdle), enable us to rotate our arms and legs and move them in several places. ▪ Hinge joints permit movement in a single plane (i.e. elbows and knees) ▪ A pivot joint enables us to rotate the forearm at the elbow and move the head from side to side. Vertebrate sekeleton parts ◦ vertical column: cervical, thoracic, lumbar, sacrum, coccyx ◦ upper limbs: humerous, radius, ulna, carpal, metacarpal ◦ lower limbs: femur, tibia, fibula patella, tarsal, metatarsal ◦ Cartillage – avascular connective tissue (supplied with nutrients via diffusion) and it is softer and more flexible. ▪ Made up of specialized cells called chondrocytes that produce a ground substance (supports the cells and fibers and helps determine the consistency of the ECM). ▪ Made up of mostly collagen 374 ▪ Found on the ear, nose, larynx, trachea, and joints ▪ In fetal development, the greater part of the skeleton is cartilaginous. The cartilage is replaced by bone, a process that ends at puberty. ▪ 3 types (differ in the amount of cartillage): hyaline is most common – reduced friction/absorbs shock in joints fibrocartilage elastic ▪ How cartilage is made (chondrogenesis): 1) Condensed mesenchyme tissue differentiates into chondroblasts 2) Chondroblasts secrete collagen, hydroxylysine, ground substance, and elastin fiber. Chondroblasts that get trapped in the ECM are called chondrocytes. ◦ Bone is connective tissue that is hard and strong, while elastic and lightweight. ▪ Functions: supports soft tissue, protects internal organs, assists in body movement, stores minerals (mainly calcium), produces blood cells, and stores energy in the form of adipose cells in bone marrow. ▪ Contains blood and nerves. ▪ 4 different types of cells: Osteoprogenitor/Ostreogenic cells differentiate into osteoblasts Osteoblasts (Bone Building) secrete collagen and organic compounds upon which bone is formed. ◦ Incapable of mitosis ◦ As matrix is released around them, they are enveloped by the matrix and differentiate into osteocytes. Osteocytes are incapable of mitosis and exchange nutrients and waste material with the blood. Osteoclasts reabsorb (destroy) bone matrix, releasing minerals back into the blood. ▪ Develop from monocytes. Structure: Areas of the bone: ◦ The epipheysis is the is one of the rounded ends of the long bones of the body which makes up a joint. ◦ Metaphysis is the area of the bone which grows during childhood ◦ Below the metaphysis is the diaphysis, or the shaft of the bone, which makes up the main section of the bone. Compact bone is highly organized, dense bone that doesn't appear to have cavities from the outside. ◦ Osteoclasts burrow tunnels called Haversian canals throughout. They contain 375 blood and lymph vessels and are connected by Volkmann's canals. ◦ Osteoclasts are followed by osteoblasts, which lay down new matrix onto tunnel walls, forming concentric rings called lamellae. ◦ Osteocytes traped between the lamella in spaces called lacunae exchange nutrients via canaliculi, small canals between the lacunae of bone. ◦ An entire system of haversian canals and lamellae is called an osteon, or a Haversian system. ◦ Also filled with yellow bone marrow that contains adipose cells for fat storage. Spongy (cancellous) bone is less dense and consists of an interconnecting lattice of bony spicules called trabeculae. Filled with red bone marrow, which is the site of RBC development. Bone growth occurs at cartilaginous epiphyseal plates (occurs at the metaphysis) that are replaced by bone in adulthood. Bone increases in length but also in diameter along the diaphysis as well. When a person reaches full maturity, the new bone slowly hardens and the plate turns into the epiphyseal line Most of the Ca2+ in body is stored in bone matrix as hydroxyapatite. 376 Bones can be made from a combination of compact and spongy bone. ▪ Bone formation occurs during the fetal stage of development in a developing human. Endochondral ossification is when existing cartilage is replaced by bone (long bones, limbs, fingers, toes) Intramembranous ossification is when undifferentiated connective tissue is replaced by bone (flat bones, skull, sternum, mandible, clavicles) Osteoporosis ◦ Osteoporosis is characterized by low bone mass and structural deterioration of bone tissue. The weakness emerges from an imbalance in the process of bone maintenance—the destruction of bone material exceeds the rate of replacement. ◦ Ways to prevent osteoporosis: ▪ Weight-bearing exercise such as walking or running strengthens bones. ▪ Strong bones also require an adequate intake of dietary calcium and enough vitamin D which are both essential to bone replacement. ▪ Estrogen the hormone can help maintain bone density. 377 Functions of the skin Functions ◦ Thermoregulation: helps regulate body temperature ◦ Protection: skin is a physical barrier to abrasion, bacteria, dehydration, many chemicals, and UV radiation. ◦ Environmental sensory input: skin gathers information about environment by sensing temperature, pressure, pain and touch ◦ Excretion: water and salts excreted through skin ◦ Immunity: specialized cells of the epidermis are components of the immune system ◦ Blood reservoir: Vessels in the dermis hold up to 10% of the blood in resting adult ◦ Vitamin D synthesis: UV radiation on skin catalyzes the synthesis of vitamin D from a precursor molecule Structure of the skin Epidermis ◦ Epidermis is the superficial epithelial tissue. ▪ It is avascular, meaning it has no blood vessels linking to it. ▪ It depends on the dermis for oxygen and nutrients. ◦ Layers from top to bottom: ▪ Stratum corneum – 25 to 30 layers of dead cells. Filled with keratin (fibrous protein responsible for protective properties of the epidermis) and surrounded by lipids. Lamellar granulues makes it water repellent ▪ Stratum lucidum – 3-5 layers of clear, dead cell. Only located in the palms, soles of feet, and finger tips ▪ Stratum granulosum – 3-5 layers of dying cells lamellar bodies release hydrophobic lipids the stratum granulosum is that layer containing granules which can easily strain ▪ Stratum spinosum – 8-10 layers of cells Cells are held together by desmosomes—keratin involving adhesion proteins Provides strength and flexibility ▪ Stratum basale (germinativum) – contains merkel cells and stem cells that divide to produce keratinocytes; attached by basement membrane. 378 Melanocytes are most likely found in the stratum germinativum The keratinocytes are pushed from this layer to the stratum corneum. As they rise, they accumulate keratin and die. When they die, they lose cytoplasm, nucleus, and other organelles. At the outermost layer of the skin, they slough off the body. ◦ Cells of the epidermis ▪ Keratinocytes produce the protein keratin that helps waterproof the skin ▪ Melanocytes transfer skin pigment melanin to keratinocytes Melanin protects the cell nucleus from the destructive effects of UV radiation. Individual and racial differences in skin coloring are probably due to differences in melanocyte activity. ▪ Langerhans cells interact with helper T-cells of the immune system. They are macrophages. ▪ Merkel cells attach to sensory neurons and function in touch sensation Dermis ◦ Dermis is the primary connective tissue of the skin. ▪ Contains collagen and elastic fibers ▪ Contains hair follicles, glands, nerves, and blood vessels ◦ Layers of the dermis ▪ Papillary region makes up the top 20% of the dermis ▪ Reticular region is the dense connective tissue that is made up of collagen and elastic fibers Provides strength and elasticity (stretch marks are dermal tears!) Packed with oil glands, sweat gland ducts, fat, and hair follicles Hypodermis (subcutaneous) ◦ The hypodermis is not part of the skin. It is the innermost and the thickest layer. ▪ Mainly composed of adipocytes, cells that are specialized in accumulating and storing fats. These cells are grouped together in lobules separated by connective tissue. Acts as energy reserve and as a thermoregulatory insulator. ▪ Has pressure sensing nerve endings ▪ Passage for blood vessels 379 Glands of the skin ◦ Sebaceous (oil) glands are connected to hair follicles except on the palms and soles. Secrete an oily secretion called sebum. ▪ Sebum is usually ducted into a hair follicle where it softens and lubricates the hair and skin and has a bactericidal action. ◦ Ceruminous glands secrete ear wax ◦ Mammary glands secrete milk ◦ Sudoriferous glands are sweat glands. Two types: ▪ Eccrine glands are on most of the body. They regulate temperature through perspiration and eliminate urea. ▪ Apocrine glands are on the armpits, pubic region, and nipples. They secrete viscous secretions with an unknown function. Activated by the sympathetic nervous system. ◦ Members of a particular animal species sometimes communicate with each other via pheromones. chemicals that are released into the external environment. which create the actual effects. aldosterone. Secondary messengers are created along the pathways. ◦ Steroid hormones are synthesized from cholesterol in the smooth ER. which increases blood flow to the tissues. ▪ They attach to a membrane receptor and initiate signal transduction pathways. progesterone. hormones secreted into extracellular fluid by endocrine cells reach target cells via the bloodstream or hemolymph. prolactin. 380 Signaling Intracellular communication ◦ In endocrine signaling. so they are able to diffuse through the plasma membrane. This is indirect stimulation. When the level of oxygen in the blood falls. ▪ Steroid hormones attaches to a receptor in the cytoplasm or the nucleus. ADH. ▪ In autocrine signaling. Classes of hormones ◦ Hormones are transported throughout the body in blood. ▪ Includes: FSH. which diffuse from nerve cell endings into the bloodstream. ◦ In synaptic signaling. ◦ Peptide hormones are synthesized in the rough ER as a larger preprohormone (precursor to one or more prohormones). neurons form specialized junctions called synapses with target cells. ▪ Nitrous oxide (NO) is a gas that functions as a local regulator and a neurotransmitter. The hormone+receptor binds to an active portion of DNA and alters the transcription rate. cortisol. ◦ Local regulators are molecules that act over short distances and reach their target cells solely by diffusion. ▪ Cytokines and growth factors are typically local regulators. Types of local regulators ▪ Prostaglandins are local regulators that promote inflammation and the sensation of pain in response to injury. ▪ These molecules bind to receptors that are highly specific to their structure. LH. ▪ They are lipid-soluble hormones. ▪ In paracrine signaling. so they cannot diffuse through the plasma membrane. neurons secrete neurotransmitters. and testosterone. PTH. They tend to have slower effects. ▪ Includes: glucocorticoids. mineralocorticoids. ACTH. They are modified fatty acids. ◦ In neuroendocrine signaling. the local regulator targets the secreting cell itself. A small amount generates a large impact. ▪ Some hormones have receptors on almost all cells. This is an example of direct stimulation since the hormone itself is generating the . TSH. endothelial cells in blood vessel walls synthesize and release NO. HGH. ▪ Many hormones elicit more than one type of response in the body. specialized neurons called neurosecretory cells secrete neurohormones. glucagon and insulin ▪ They are water-soluble hormones. some have receptors only on specific tissues. NO causes vasodilation. esterogen. the local regulator targets cells that lie near the secreting cell. oxytocin. cleaved in the ER lumen to a prohormone (committed precursor of a single hormone) and then cleaved again (and possibly modified with carbs) in the golgi body to the final form. such as other neurons and muscle cells. ▪ At most synapses. . which stimulates a neurosecretory cell. ◦ Positive feedback reinforces a stimulus. in which the response reduces the initial stimulus. ◦ In a simple neuroendocrine pathway. T3. The neurosecretory cell then secretes a neurohormone. ◦ Tyrosine derivatives are formed by enzymes in the cytosol or on the rough ER. 381 effects. where it will elicit the appropriate responses. Feedback regulation ◦ Regulation often involves negative feedback. endocrine cells respond directly to an internal or environmental stimulus by a secreting a particular hormone. T4 ▪ They are either water-soluble or lipid-soluble. The hormone will travel in the bloodstream to the target cells. Feedback regulation and coordination with the nervous system Simple pathways ◦ In a simple endocrine pathway. leading to an even greater response. the stimulus is received by a sensory neuron. which will diffuse into the bloodstream and travel to target cells. ▪ Includes: catecholamines. 382 . This blood flows directly into the anterior pituitary. Hormones that it stores/secretes: ▪ Antidiuretic hormone (ADH/vasopressin) increases the reabsorption of water by increasing the amount of aquaporins in the epithelium cells in the collecting duct. which stimulates the anterior pituitary to secretes FSH and LH. ▪ The anterior pituitary is regulated by the hypothalamus. Hypothalamus ◦ The hypothalamus monitors the external environment and internal conditions of the body. Types of direct hormones produced/stored in the anterior pituitary: Somatotropin (HGH). ▪ Oxytocin is secreted during childbirth. ▪ Contains neurosecretory cells that link the hypothalamus to the pituitary gland. It increases the strength of uterine contractions and stimulates milk ejection. Thyroid-stimulating hormone (TSH) stimulates the thyroid gland (increases size and cell number) to release thyroid hormone. Prolactin stimulates milk production in females. In males. In males. Pineal gland ◦ Pineal gland secretes melatonin. Endorphins inhibit perception of pain (technically a neurohormone). . ◦ Synthesizes gonadotropin releasing hormone (GnRH) from neurons. a hormone that participates in regulation of biological rhythms. Anterior pituitary ◦ The anterior pituitary mainly regulates hormone production by other grands. Follicle-stimulating hormone (FSH) in females stimulates maturation of ovarian follices to secrete estrogen. 383 Organs of the endocrine system Endocrine glands vs. where the releasing hormones stimulate the release of tropic or direct hormones produced/stored and secreted in the anterior pituitary. which stimulates bone and muscle growth. exocrine glands ◦ Endocrine glands synthesizes and secretes hormones into the bloodstream. FSH stimulates sertoli cells to help mature sperm cells. ▪ Direct hormones directly stimulate target organs. ◦ Synthesizes ADH (vasopressin) and oxytcin to be stored in the posterior pituitary. leutinzing hormone stimulates leydig cells of the testes to produce testosterone. ◦ Exocrine glands secrete substances by way of a duct to the exterior of the body. it stores hormones produced by the hypothalamus. Lutenizing hormone (LH) in females stimluates the formation of the corpus luteum. ◦ Releasing hormones are produced by neurosecretory cells in the hypothalamus and are secreted into the blood. which are involved in regulation of metabolism of glucose. Posterior pituitary ◦ The posterior pituitary does not synthesize hormones. Types of tropic hormones produced/stored in the anterior pituitary: Adrenocrticotrophic hormone (ACTH) stimulates the adrenal cortex to release glucocorticoids. Coffee and alcohol blocks ADH. ◦ Synthesizes releasing and inhibiting hormones to regulate the anterior pituitary. ▪ Tropic hormones stimulate other endocrine glands. and hyperthyroidism lead to goiter. increased heartbeat. Parathyroid ◦ The Parathyroid is four pea-shaped structures attached to the back of thyroid. Increases osteocyte absorption of Ca + P from bone. Hormones that it produces/secretes: Glucocorticoids (cortisol and cortisone) raise blood glucose levels (stimulates gluconeogenesis in liver). and mainly act via a second messenger. meaning high amounts of T3 and T4 will decrease production of TSH. stimulates osteoclast proliferation Increases renal Ca absorption Thymus ◦ Thymus is involved in the immune response. Provide a negative feedback on TSH. Hypo. vasoconstrictor to internal organs and skin but vasodilator to skeletal muscle. results in increased metabolic rate and sweating. Causes passive reabsorption of water in the nephron. ◦ These hormones are catecholamines – they are water soluble. . Hypothyroidism means undersecretion of T3 and T4. Hormones that it produces/secretes: ▪ Parathyroid hormone (PTH) is antagonistic to calcitonin. the abnormal enlargement of the thyroid gland. results in low heart and respiratory rate. Hyperthryoidism means oversecretion of T3 and T4. which will cause a rise in blood volume/pressure. ▪ Calcitonin “tones down” Ca2+ in blood. bind to receptors on target tissue membranes. ▪ Thyroxine (T4) and Triiodothyronine (T3) are necessary for the growth and neurological development in children and increase basal metabolic rate in body. ◦ Glycogen → glucose. It decreases plasma Ca2+ by inhibiting its release from bone Decreases osteoclast activity and number. affect fat and protein metabolism. Hormones that it produces/secretes: Epinephrine and norepinephrine – “fight or flight” hormones. however. Raises Ca2+ concentrations in the blood by stimulating release from bone. ▪ Adrenal medulla. Hormones that it produces/secretes: ▪ Thymosins stimulate lymphocytes (WBCs) to become T-cells Adrenal gland ◦ Adrenal gland is located on the top of kidneys and consists of two main parts: ▪ Adrenal cortex secretes only steroid hormones. Hormones that it produces/secretes: ▪ Achondroplasia is dwarfism of the thyroid. Androgenic steroids – these hormones are converted elsewhere in the body to form estrogens and androgens. these steroid hormones are produced in much larger amounts by the gonads. stress hormones Mineralocorticoids (aldosterone) increaes reabsorption of Na+ and secretion of K+. 384 Thyroid ◦ Thryoid glands are located on the ventral surface of the trachea. ▪ Progeria is premature aging of the thyroid. a hormone that induces spermatogenesis and secondary male sex characteristics. raises blood glucose levels. secreted from the small intestine. released when energy charge low. ◦ Secretin. ◦ Ovaries produces and secretes estrogen and progesterone: ▪ Estrogen is involved in the menstrual cycle and produces secondary female sex characteristics. neutralizes the acidity of chyme by enhancing the secretion of alkaline bicarbonate. Stimulates liver and most other body cells to absorb glucose. inhibits both insulin and glucagon. secreted from the small intestine. Possibly increases nutrient absorption time Testis and Ovaries ◦ Testis produces and secretes testosterone. 385 Pancreas ◦ Pancreas (exocrine and endocrine) has bundles of cells called islets of Landerhans which contains two cell types: ▪ Alpha cells secrete glucagon: catabolic. Provokes liver and muscles to turn glucose into glycogen and fat cells to turn glucose into fat. causes the contraction of the gallbladder to release bile in the presence of high fatty food. ▪ Progesterone is involved in the menstrual cycle and pregnancy. Gastrointestinal hormones ◦ Gastrin secretes stimulation of HCl when food is in the stomach. lower blood glucose levels. Stimulates liver to break down glycogen into glucose. ▪ Beta cells secrete insulin: anabolic. . released when energy charge is high. ◦ Cholecystokinin. ◦ Somatostatin is released by delta cells of pancreas.