BCH 2333DGD 1 & 2 – Mondays 11:30 – 1pm 2:30 – 4pm Thao Nguyen ([email protected]) My cave/lab/office: Marion 02 Feel free to email me with questions. You can come to visit me as well but let me know first so I can prepare cookies. (although not desired, you may talk to me about your questions for lab materials) Goal of this course • Overview of fundamental concepts in biochemistry for a strong foundation for future study of biological system • Focus: 1) major macromolecules (amino acids. lipids. carbohydrates) .Physical properties of water. Metabolism. nucleic acids. pH and buffers 3) Enzyme kinetics and metabolic regulation • Successful students can: Demonstrate a broad knowledge of biochemical concepts Good biochemical vocabulary Be able to critically review experimental evidence in the scientific literature . function and metabolism of those 2) chemical properties of living systems (ie.Structure.Roles of membranes and organelles in cell function . pathways etc) . 1. autonomous learning behavior Know the factual information presented in the lecture Be able to synthesize those info into a logical whole – the big picture Consider biochemistry in your other courses Discover how the concepts presented impact your health.Expection of this course & Dr. Know the basic structures of every macromolecules (YES. know their basic chemical reactivity Appreciate the importance of chirality in biochemistry (more relevant in amino acids & carbohydrates) Simple reactions & mechanisms (YES. 2. environment & the biological world Open to new ways of thinking and challenge old ways of thinking . you will be asked to DRAW in the exam) Hence. Shuhendler We stress on structures this is bio-CHEMISTRY. you have to review your ORGANIC CHEMISTRY II) Exhibit self-regulated. your university study. • Come to class: regular class attendance is essential for success especially for BIOCHEMSITRY • Take note: take your own note – pick up the important clues in class • Form a study group: good practice for this class. pictures. concept maps etc • Keep up • Read the text before class if the material is new to you • .Tips to do well in this course • Live your life: eat well. Last minute usually is a waste of time. “drink” well – and understand the biochemistry behind all of these processes • Schedule saves times Develop a schedule BEFORE even begin to think about studying • Study when you are rested. summary charts. science career & future • Make diagrams. jog. play sports. alert and have planned for it. T (2012).Trust me – Biochem is awesome Erythropoietin Nguyen. A study on human erythropoietin. . The Vampire Legend The Biosynthesis of Heme Heme Precursor Derivative of glycine & succinyl-CoA • 4 porphobilinogen form the porphyrin ring • Final incorporation of iron into the ring form the heme prosthetic group • Hereditary defects in the enzyme uroporphyrinogen III cosynthase results to congenital erythropoietic porphyria SYMPTOMS Urine turns red Skin becomes photosensitive Teeth become fluorescent due to deposition of strongly light-absorbing porphyrins . 3389/fphys.2013. Physiol. SAL et al (2013).The biochemistry of lipids Dynamic phospholipid remodeling is important for neuronal membrane function Bennett.00168 . Front. 4:168/ doi: 10. Polar molecules dissolve well in water • Exclusion of nonpolar substances by water is called hydrophobic effect This effect is critical for the folding of proteins & self-assembly of biological membranes • Molecules that are both. are amphipathic • When a sufficiently high concentration of amphipathic compounds is dispersed in water. they form micelles .Hydrophobicity vs Hydrophilicity • Nonpolar molecules are hydrophobic . Hydrophobicity vs Hydrophilicity To predict hydrophilicity. The presence of ions 2. Hydrophilicity is the determination factor of solubility . The presence of a dipole moment 3. Molecules with greater London forces are more hydrophilic. The presence of London dispersion forces (van der Waals attractive force) Points to note: Ions are easy for water to solvate around because they are charged Polar = dipole moments Substances that lack ions or dipole moment are hydrophobic. look at: 1. But uncharged. nonpolar gases can still exhibit London forces. London forces are larger as the size of the atom or molecule increases. Water molecules are small relative to other solvents. allowing them to associate with many solute particles to increase it solubility (Osmotic Pressure) Physical properties of water make it an excellent solvent. Water viscosity does not impede movement of dissolve molecule (Important in cellular concentrations and diffusion) 3. .Why is water a good solvent ? 1. Water molecules are polar dissolve ionic & polar substances easily 2. water can dissolve crystalline electrolytes.Water 1. the water molecule has a permanent dipole 2. these micelles can trap insoluble substances in a hydrophobic interior. Chaotropes enhance the solubility of nonpolar compounds in water. Hydrogen bonding contributes to the high specific heat and heat of vaporization of water 3. form micelles when suspended in water. Detergents – contain both hydrophobic and hydrophilic portions. Eg. Water molecules form a solvation sphere around each dissolved ion. Organic molecules may be soluble in water if they contain ionic or polar functional groups that can form hydrogen bonds with water molecules. Because it is polar. 4. . Hydrophobic effect is the exclusion of non-polar substances by water molecules. Because of the uneven distribution of charge in O-H bonds and their angled arrangement. Water molecules can form hydrogen bonds with each other.Summary of week 1 . Covalent bond has dissociation energy of approximately 340 – 450 kJ/mol (C-H or C-C) . macromolecules do not spontaneously hydrolyze.4 to 4kJ/mol versus 2 to 20 kJ/mol) 5. hydrogen bonds. 2.Summary of week 2 . Under cellular conditions. Hydrophobic interactions: dissociation energy depends on the increased entropy of surrounding water molecules rather than on direct attraction between nonpolar groups. 3. van der Waals forces (London dispersion force) are much weaker than hydrogen bonds (0. despite the presence of high concentration of water.Bonds 1. 4. Electrostatic interactions include charge-charge interactions. Specific enzymes catalyze their hydrolysis and other enzymes catalyze their energy-requiring synthesis. and van der Waals forces. The major noncovalent interactions that determine the structure and function of biomolecules are electrostatic interactions and hydrophobic interactions. Buffered solutions resist changes in pH. The strength of a weak acid is indicated by its pKa value. And acid/base is the utmost importance.4 is maintained by the carbon dioxide-carbonic acid-bicarbonate buffer system. a constant pH of 7.0 x 10-14 M2 = Kw – the ion-product constant for water (This means pure water ionizes to produce 10-7 M of H+ and 10-7 M of OH.) The acidity and basicity of an aqueous solution depends on the concentration of H + and is described by a pH value.Hasselbalch equation defines the pH of a solution of weak acid in terms of the pKa and the concentration of the weak acid and its conjugate base. . [H+][OH-] has a value of 1.In preparation for this week content Review your acid/base chemistry – the most important chemistry in biochemistry If you like biochemistry. In human blood. Prelude At 25oC. The Henderson. you must know the chemistry in that word. DGD wednesdays eyy074@uottawa?? . youtube.youtube.com/watch?v=C2GfoGXfySQ .com/watch?v=gq-rWb0fmzQ Part 2: https://www.Memorizing aa’s Part 1: https://www. Know pkas KNOW HOW TO DERIVE THE HENDERSON HASSLEBACH eqn…. . HW Q: RNA world hypothesis provides further detail as to the early evolution of primoridal life Answer a) In early organisms and proto-organisms. RNA was the predominant biomolecule responsible for both information storage and chemical catalysis . overlap them.Q: Rank from lowest to highest dissociation constant a PH of 2. To rank items as equivalent. . Lysine will be protonate**d/unprotonated? @ a PH of 2 Asparatic acid will be protonated** / unprotonated? @ pH of 2 What are favourable and unfavourable interactions? Kd will be high .