Chapter 4 The Three-Dimensional Structure of ProteinsMultiple Choice Questions 1. Overview of protein structure Pages: 117−118 Difficulty: 1 Ans: D All of the following are considered “weak” interactions in proteins, except: A) B) C) D) E) hydrogen bonds. hydrophobic interactions. ionic bonds. peptide bonds. van der Waals forces. 2. Overview of protein structure Pages: 117−118 Difficulty: 2 Ans: A The most important contribution to the stability of a protein’s conformation appears to be the: A) entropy increase from the decrease in ordered water molecules forming a solvent shell around it. B) maximum entropy increase from ionic interactions between the ionized amino acids in a protein. C) sum of free energies of formation of many weak interactions among the hundreds of amino acids in a protein. D) sum of free energies of formation of many weak interactions between its polar amino acids and surrounding water. E) stabilizing effect of hydrogen bonding between the carbonyl group of one peptide bond and the amino group of another. 3. Overview of protein structure Page: 118 Difficulty: 1 Ans: D In an aqueous solution, protein conformation is determined by two major factors. One is the formation of the maximum number of hydrogen bonds. The other is the: A) B) C) D) E) formation of the maximum number of hydrophilic interactions. maximization of ionic interactions. minimization of entropy by the formation of a water solvent shell around the protein. placement of hydrophobic amino acid residues within the interior of the protein. placement of polar amino acid residues around the exterior of the protein. 4. Overview of protein structure Page: 118 Difficulty: 2 Ans: B Pauling and Corey’s studies of the peptide bond showed that: A) B) C) D) E) at pH 7, many different peptide bond conformations are equally probable. peptide bonds are essentially planar, with no rotation about the C—N axis. peptide bonds in proteins are unusual, and unlike those in small model compounds. peptide bond structure is extraordinarily complex. primary structure of all proteins is similar, although the secondary and tertiary structure may differ greatly. Overview of protein structure Page: 119 Difficulty: 3 Ans: A In the diagram below. the plane drawn behind the peptide bond indicates the: A) B) C) D) E) absence of rotation around the C—N bond because of its partial double-bond character. . occur only between some of the amino acids of the helix. occur only near the amino and carboxyl termini of the helix.Chapter 4 The Three-Dimensional Structure of Proteins 39 5. plane of rotation around the Cα—N bond. region of steric hindrance determined by the large C=O group. occur mainly between electronegative atoms of the R groups. theoretical space between –180 and +180 degrees that can be occupied by the φ and ψ angles in the peptide bond. Overview of protein structure Page: 119 Difficulty: 2 Ans: A Which of the following pairs of bonds within a peptide backbone show free rotation around both bonds? A) B) C) D) E) Cα—C and N—Cα C=O and N—C C=O and N—Cα N—C and Cα—C N—Cα and N—C 8. Protein secondary structure Pages: 120−121 Difficulty: 2 Ans: A In the α helix the hydrogen bonds: A) B) C) D) E) are roughly parallel to the axis of the helix. region of the peptide bond that contributes to a Ramachandran plot. Overview of protein structure Page: 119 Difficulty: 2 Ans: D Which of the following best represents the backbone arrangement of two peptide bonds? A) B) C) D) E) Cα—N—Cα—C—Cα—N—Cα—C Cα—N—C—C—N—Cα C—N—Cα—Cα—C—N Cα—C—N—Cα—C—N Cα—Cα—C—N—Cα—Cα—C 7. are roughly perpendicular to the axis of the helix. 6. 10. steric hindrance occurs between the bulky Thr side chains. Another naturally occurring hindrance to the formation of an α helix is the presence of: A) B) C) D) E) a negatively charged Arg residue. the R groups on the amino acid residues: A) B) C) D) E) alternate between the outside and the inside of the helix. Protein secondary structure Page: 121 Difficulty: 2 Ans: D Thr and/or Leu residues tend to disrupt an α helix when they occur next to each other in a protein because: A) B) C) D) E) an amino acids like Thr is highly hydrophobic. Protein secondary structure Page: 122 Difficulty: 3 Ans: E An α helix would be destabilized most by: A) B) C) D) E) an electric dipole spanning several peptide bonds throughout the α helix. Protein secondary structure Page: 120 Difficulty: 2 Ans: B In an α helix. generate the hydrogen bonds that form the helix. the R group of Thr can form a hydrogen bond.40 Chapter 4 The Three-Dimensional Structure of Proteins 9. are found on the outside of the helix spiral. electrostatic repulsion occurs between the Thr side chains. cause only right-handed helices to form. two Ala residues side by side. the presence of two Lys residues near the amino terminus of the α helix. interactions between two adjacent hydrophobic Val residues. 12. a positively charged Lys residue. . interactions between neighboring Asp and Arg residues. a nonpolar residue near the carboxyl terminus. 11. stack within the interior of the helix. Protein secondary structure Page: 122 Difficulty: 1 Ans: D A D-amino acid would interrupt an α helix made of L-amino acids. covalent interactions may occur between the Thr side chains. a Pro residue. the presence of an Arg residue near the carboxyl terminus of the α helix. The sequence is most probably part of a(n): A) B) C) D) E) antiparallel β sheet. have fewer lateral hydrogen bonds than antiparallel strands. usually near the polypeptide chain’s amino terminus or carboxyl terminus. hydrophobic. where the amino acid residues are: A) B) C) D) E) always side by side. often on different polypeptide strands. do not have as many disulfide crosslinks between adjacent strands. Pro and Gly. Protein secondary structure Page: 124 Difficulty: 2 Ans: E A sequence of amino acids in a certain protein is found to be -Ser-Gly-Pro-Gly-. . parallel β sheet. have weaker hydrogen bonds laterally between adjacent strands.Chapter 4 The Three-Dimensional Structure of Proteins 41 13. α helix. two Cys. β turn. Protein tertiary and quaternary structures Page: 125 Difficulty: 1 Ans: B The three-dimensional conformation of a protein may be strongly influenced by amino acid residues that are very far apart in sequence. α sheet. do not stack in sheets as well as antiparallel strands. 16. invariably restricted to about 7 of the 20 standard amino acids. 15. Protein secondary structure Page: 124 Difficulty: 1 Ans: C Amino acid residues commonly found in the middle of β turn are: A) B) C) D) E) Ala and Gly. generally near each other in sequence. Protein secondary structure Page: 123 Difficulty: 1 Ans: E The major reason that antiparallel β-stranded protein structures are more stable than parallel βstranded structures is that the latter: A) B) C) D) E) are in a slightly less extended configuration than antiparallel strands. 14. those with ionized R-groups. This relationship is in contrast to secondary structure. as expected. Silk fibroin is a protein in which the polypeptide is almost entirely in the β conformation. with virtually no internal space available for water. Protein tertiary and quaternary structures Page: 127 Difficulty: 3 Ans: D The α-keratin chains indicated by the diagram below have undergone one chemical step. α-keratin is a protein in which the polypeptides are mainly in the α-helix conformation. Gly residues are particularly abundant in collagen. the α helix predicted by Pauling and Corey was not found in myoglobin. Disulfide linkages are important for keratin structure. Protein tertiary and quaternary structures Page: 127 Difficulty: 2 Ans: A Which of the following statements is false? A) B) C) D) E) Collagen is a protein in which the polypeptides are mainly in the α-helix conformation.42 Chapter 4 The Three-Dimensional Structure of Proteins 17. the structure was very compact. To alter the shape of the α-keratin chains—as in hair waving—what subsequent steps are required? A) B) C) D) E) Chemical oxidation and then shape remodeling Chemical reduction and then chemical oxidation Chemical reduction and then shape remodeling Shape remodeling and then chemical oxidation Shape remodeling and then chemical reduction 18. myoglobin was completely different from hemoglobin. 19. . Protein tertiary and quaternary structures Pages: 133−134 Difficulty: 2 Ans: D Kendrew’s studies of the globular myoglobin structure demonstrated that: A) B) C) D) E) “corners” between α-helical regions invariably lacked proline residue. highly polar or charged amino acid residues tended to be located interiorally. They may retain their correct shape even when separated from the rest of the protein. 43 . These regions are called: A) B) C) D) E) domains. function. sites. Protein tertiary and quaternary structures Page: 141 Difficulty: 1 Ans: C Proteins are classified within families or superfamilies based on similarities in: A) B) C) D) E) evolutionary origin. physico-chemical properties. subunit structure. peptides. subunit content and arrangement. x-ray diffraction. Protein tertiary and quaternary structures Page: 141 Difficulty: 2 Ans: D The structural classification of proteins (based on motifs) is based primarily on their: A) B) C) D) E) amino acid sequence. Ramachandran plots. 23. Protein tertiary and quaternary structures Page: 140 Difficulty: 1 Ans: A Proteins often have regions that show specific. coherent patterns of folding or function. They consist of separate polypeptide chains (subunits). They have been found only in prokaryotic proteins. light microscopy. secondary structure content and arrangement. 22. Protein tertiary and quaternary structures Pages: 136−137 Difficulty: 1 Ans: E Determining the precise spacing of atoms within a large protein is possible only through the use of: A) B) C) D) E) electron microscopy. structure and/or function. oligomers. 21. Protein tertiary and quaternary structures Page: 140 Difficulty: 2 Ans: E Which of the following statements concerning protein domains is true? A) B) C) D) E) They are a form of secondary structure. evolutionary relationships.Chapter 4 The Three-Dimensional Structure of Proteins 20. subunits. subcellular location. They are examples of structural motifs. molecular model building. 24. 27.44 Chapter 4 The Three-Dimensional Structure of Proteins 25. Protein tertiary and quaternary structures Page: 144 Difficulty: 1 Ans: B Which of the following statements about oligomeric proteins is false? A) B) C) D) E) A subunit may be similar to other proteins. urea. heating to 90°C. oligomer. Protein tertiary and quaternary structures Page: 144 Difficulty: 1 Ans: D A repeating structural unit in a multimeric protein is known as a(n): A) B) C) D) E) domain. 28. iodoacetic acid. It is frequently seen in the subunits of oligomeric proteins. It is frequently seen in viruses. It results in closed. Many have regulatory roles. Protein tertiary and quaternary structures Page: 144−146 Difficulty: 2 Ans: A Which of the following statements concerning rotational symmetry in proteins is false? A) B) C) D) E) It involves rotation of proteins inside the cell. 29. protomer. packed structures. motif. It may involve rotation about one or more axes. pH 10. Some subunits may have nonprotein prosthetic groups. Protein denaturation and folding Page: 147 Difficulty: 1 Ans: B Which of the following is least likely to result in protein denaturation? A) B) C) D) E) Altering net charge by changing pH Changing the salt concentration Disruption of weak interactions by boiling Exposure to detergents Mixing with organic solvents such as acetone . 26. Protein denaturation and folding Page: 147 Difficulty: 2 Ans: C An average protein will not be denatured by: A) B) C) D) E) a detergent such as sodium dodecyl sulfate. subunit. Some oligomeric proteins can further associate into large fibers. All subunits must be identical. requires the input of energy in the form of heat. with all —S—S— bonds broken. C) the completely unfolded enzyme.Chapter 4 The Three-Dimensional Structure of Proteins 45 30. E) the primary sequence of RNase is sufficient to determine its specific secondary and tertiary structure. D) the enzyme. Protein denaturation and folding Pages: 151−152 Difficulty: 1 Ans: B Protein S will fold into its native conformation only when protein Q is also present in the solution. A) B) C) D) E) ligand molecular chaperone protein precursor structural motif supersecondary structural unit 33. It may involve initial formation of a highly compact state. may function as a ____________ for protein S. It may involve a gradually decreasing range of conformational species. However. 31. It may be defective in some human diseases. active conformation. is thermodynamically stable relative to the mixture of amino acids whose residues are contained in RNase. B) native ribonuclease does not have a unique secondary and tertiary structure. Protein denaturation and folding Pages: 148−149 Difficulty: 2 Ans: A Which of the following statements concerning the process of spontaneous folding of proteins is false? A) B) C) D) E) It may be an essentially random process. protein Q can fold into its native conformation without protein S. 32. therefore. It may involve initial formation of local secondary structure. dissolved in water. Protein Q. is still enzymatically active. Protein denaturation and folding Pages: 151−153 Difficulty: 2 Ans: D Which of the following is not known to be involved in the process of assisted folding of proteins? A) B) C) D) E) Chaperonins Disulfide interchange Heat shock proteins Peptide bond hydrolysis Peptide bond isomerization . Protein denaturation and folding Page: 148 Difficulty: 2 Ans: E Experiments on denaturation and renaturation after the reduction and reoxidation of the —S—S— bonds in the enzyme ribonuclease (RNase) have shown that: A) folding of denatured RNase into the native. and describe one condition or reagent that interferes with each type of stabilizing force. and indicate which six atoms are part of the planar structure of the peptide bond. (See Fig. 4-2. (b) hydrogen bonds. (c) detergents and urea. Overview of protein structure Pages: 117. The number of water molecules involved in such ordered shells is reduced when the protein folds. (c) hydrophobic interactions. there are weak interactions between its R groups. 4-2. However. the lower free energy of the native conformation. Overview of protein structure Pages: 117−118 Difficulty: 2 When a polypeptide is in its native conformation.46 Chapter 4 The Three-Dimensional Structure of Proteins Short Answer Questions 34. p. and (d) changes in pH or ionic strength. Overview of protein structure Page: 119 Difficulty: 2 Draw the resonance structure of a peptide bond. and explain why there is no rotation around the C—N bond. Ans: The intermediate resonance structure imparts a partial double bond characteristic to the C—N bond. 35. Ans: The N and H of the amino and the C and O of the carbonyl are all in the same plane with the two Cα atoms. How are these related? Ans: The three-dimensional structure is determined by the amino acid sequence. which are diagonally opposite relative to the C—N bond. 36. 119. respectively. six atoms associated with the peptide bond all lie in a plane. Draw a dipeptide of two amino acids in trans linkage (side-chains can be shown as —R). resulting in higher entropy.) 38. Ans: Among forces that stabilize native protein structures are (a) disulfide bonds. Overview of protein structure Page: 119 Difficulty: 1 Pauling and Corey showed that in small peptides. What then accounts for the greater stability of the native conformation? Ans: In the unfolded polypeptide. Overview of protein structure Page: 116 Difficulty: 2 Any given protein is characterized by a unique amino acid sequence (primary structure) and threedimensional (tertiary) structure. (b) pH extremes. p. 37. there are ordered solvation shells of water around the protein groups. Agents that interfere with these forces are (a) mercaptoethanol or dithiothreitol. (See Fig. 147 Difficulty: 2 Name four factors (bonds or other forces) that contribute to stabilizing the native structure of a protein. and (d) ionic interactions. thereby prohibiting rotation. Hence. This means that the amino acid sequence contains all of the information that is required for the polypeptide chain to fold up into a discrete three-dimensional shape. 119. when it is denatured there are similar interactions between the protein groups and water.) . lie side by side and are stabilized by hydrogen bonding between adjacent chains. several extended polypeptides. What is the function of this superhelical twisting? Ans: The superhelical twisting of multiple polypeptide helices makes the overall structure more compact and increases its overall strength. Ans: Hydrogen bonds occur between every carbonyl oxygen in the polypeptide backbone and the peptide —NH of the fourth amino acid residue toward the amino terminus of the chain. and proline can readily assume the cis configuration.Chapter 4 The Three-Dimensional Structure of Proteins 47 39. Protein secondary structure Page: 119 Difficulty: 1 Draw the hydrogen bonding typically found between two residues in an α helix. several polypeptide helices are intertwined. p. Protein secondary structure Page: 120 Difficulty: 2 Describe three of the important features of the α-helical polypeptide structure predicted by Pauling and Corey. such as collagen. 43. Protein tertiary and quaternary structures Page: 129 Difficulty: 2 . Protein tertiary and quaternary structures Pages: 127−128 Difficulty: 2 In superhelical proteins. (See Fig. Provide one or two sentences for each feature. 119. 41. Ans: The α-helical structure of a polypeptide is tightly wound around a long central axis.5 Å) or antiparallel (7 Å repeat). 44. Protein secondary structure Page: 123 Difficulty: 2 Why are glycine and proline often found within a β turn? Ans: A β turn results in a tight 180° reversal in the direction of the polypeptide chain. each turn of the right-handed helix contains 3.6 residues and stretches 5. Protein secondary structure Page: 123 Difficulty: 2 Describe three of the important features of a β sheet polypeptide structure. Adjacent chains may be either parallel (with a repeat distance of about 6. Glycine is the smallest and thus most flexible amino acid. The peptide NH is hydrogen-bonded to the carbonyl oxygen of the fourth amino acid along the sequence toward the amino terminus. 42. which facilitates a tight turn.4 Å along the axis. Provide one or two sentences for each feature. or two regions of the same polypeptide.) 40. The R groups are often small and alternately protrude from opposite faces of the β sheet. The R groups of the amino acid residues protrude outward from the helical backbone. 4-2. Ans: In the β sheet structure. 48 Chapter 4 The Three-Dimensional Structure of Proteins Why is silk fibroin so strong. Ans: To obtain an x-ray picture of a biomolecule. the threedimensional structure of a small protein or peptide can be determined in solution by sophisticated analysis of the NMR spectrum of the polypeptide. The pattern of diffracted x-rays yields. Sometimes. the three-dimensional distribution of electron density. and the crystal structure is determined by x-ray diffraction. Ans: Motifs are particularly stable arrangements of elements of secondary structure (e. but at the same time so soft and flexible? Ans: Unlike collagen and keratin. Therefore. By matching electron density with the known sequence of amino acids in the protein. each region of electron density is identified as a single atom. Computer analysis of two-dimensional NMR spectra can be used to generate a picture of the three-dimensional structure of a protein. 45. by Fourier transformation. 46. α helix and β conformation). which are found in a variety of proteins. and that the R-groups in the stacked pleated sheets interdigitate. Biomolecules in the cell also have more flexibility and freedom of motion than can be accommodated in a rigid crystal structure. so much of the protein’s interior is a tightly packed combination of hydrocarbon and aromatic ring R groups with very few water molecules. 48. the static picture obtained from an x-ray analysis of a crystal may not provide a complete or accurate representation of the biomolecule in vivo. Protein tertiary and quaternary structures Page: 140 Difficulty: 2 . or between its stacked sheets. Fibroin’s unusual tensile strength derives from the fact that the peptide backbone of antiparallel β-strands is fully extended. Ans: The protein is crystallized. 49. Protein tertiary and quaternary structures Pages: 139−141 Difficulty: 1 Explain what is meant by motifs in protein structure. the molecule must be purified and crystallized under laboratory conditions far different from those encountered by the native molecule. This technique can also reveal dynamic aspects of protein structure such as conformational changes. including the connections between them. Protein tertiary and quaternary structures Page: 133 Difficulty: 1 What is typically found in the interior of a water-soluble globular protein? Ans: Hydrophobic amino acid residues cluster away from the surface in globular proteins. Protein tertiary and quaternary structures Page: 136-137 Difficulty: 2 Describe a reservation about the use of x-ray crystallography in determining the three-dimensional structures of biological molecules.g. silk fibroin has no covalent crosslinks between adjacent strands.. preventing any longitudinal sliding of the sheets across one another. making it very flexible. Protein tertiary and quaternary structures Pages: 136−139 Difficulty: 3 How does one determine the three-dimensional structure of a protein? Your answer should be more than the name of a technique. 47. 2) Helical: In helical symmetry. describe in one or two sentences what the reagent/condition does to destroy native protein structure. these help stabilize the arrangement through hydrophobic interactions. Protein denaturation and folding Page: 147 Difficulty: 2 Each of the following reagents or conditions will denature a protein. Protein denaturation and folding Page: 148 Difficulty: 2 Explain (succinctly) the theoretical and/or experimental arguments in support of this statement: “The primary sequence of a protein determines its three-dimensional shape and thus its function. Protein tertiary and quaternary structures Page: 144 Difficulty: 1 Describe the quaternary structure of hemoglobin. (a) (b) (c) (d) urea high temperature detergent low pH Ans: (a) Urea acts primarily by disrupting hydrophobic interactions. 52. 4-20. p. For each. Some examples are actin filaments and the tobacco mosaic virus capsid. Some examples are hemoglobin and thepoliovirus capsid. Protein tertiary and quaternary structures Pages: 145−146 Difficulty: 2 Describe briefly the two major types of symmetry found in oligomeric proteins and give an example of each. subunits are superimposable after a helical rotation. electrostatic . subunits are superimposable after rotation about one or more of the axes. (b) High temperature provides thermal energy greater than the strength of the weak interactions (hydrogen bonds. It is therefore more efficient to have fewer genes. 51.Chapter 4 The Three-Dimensional Structure of Proteins 49 Draw a βαβ loop. 54. Ans: Hydrophobic amino acid residues are usually found in the interior of the loop. Ans: Each protein molecule is composed of two copies each of two different subunits α and β. and describe what is found in the interior of the loop.” Ans: Anfinsen showed that a completely denatured enzyme (ribonuclease) could fold spontaneously into its native. 53. encoding shorter polypeptides that can be used to construct many large proteins. 140. The two αβ protomers are arranged with C2 symmetry.) 50. Protein tertiary and quaternary structures Page: 146 Difficulty: 2 What is the rationale for many large proteins containing multiple copies of a polypeptide subunit? Ans: Each different polypeptide requires a separate gene that must be replicated and transcribed. Ans: 1) Rotational: In rotational symmetry. enzymatically active form with only the primary sequence to guide it. (See Fig. 55. what might be the explanation? Ans: Because a protein may be denatured through the disruption of hydrogen bonds and hydrophobic interactions by salts or organic solvents.g. Glu. it may be because the denaturing treatment removed a required prosthetic group. insulin). Denatured insulin would not refold easily. (d) Low pH causes protonation of the side chains of Asp. and His. If the protein does not renature.. removal of those conditions will reestablish the original aqueous environment. 57. preventing electrostatic interactions. Protein denaturation and folding Page: 147 Difficulty: 2 How can changes in pH alter the conformation of a protein? Ans: Changes in pH can influence the extent to which certain amino acid side chains (or the amino and carboxyl termini) are protonated. often permitting the protein to fold once again into its native conformation. which can lead to electrostatic attractions or repulsions between different regions of the protein. preventing hydrophobic interactions among several hydrophobic patches on the native protein. breaking these interactions. 56. Protein denaturation and folding Pages: 151−153 Difficulty: 2 What are two mechanisms by which “chaperone” proteins assist in the correct folding of polypeptides? Ans: Chaperones protect unfolded polypeptides from aggregation by binding to hydrophobic regions. The result is a change in net charge on the protein. (c) Detergents bind to hydrophobic regions of the protein. how can it be renatured? If renaturation does not occur. The final effect is a change in the protein’s three-dimensional shape or even complete denaturation. Protein denaturation and folding Pages: 148−149 Difficulty: 2 Once a protein has been denatured. . and van der Waals forces. hydrophobic interactions. or because the normal folding pathway requires the presence of a polypeptide chain binding protein or molecular chaperone. which is then cleaved (e. The normal folding pathway could also be mediated by a larger polypeptide. They can also provide a microenvironment that promotes correct folding.50 Chapter 4 The Three-Dimensional Structure of Proteins interactions.
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