Chapter 4 The Three-Dimensional Structure of Proteins
Multiple Choice Questions
1. Answer: D All of the following are considered “weak” interactions in proteins, except:
A) hydrogen bonds. B) hydrophobic interactions. C) ionic bonds. D) peptide bonds. E) van der Waals forces.
2. Answer: 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) formation of the maximum number of hydrophilic interactions. B) maximization of ionic interactions. C) minimization of entropy by the formation of a water solvent shell around the protein. D) placement of hydrophobic amino acid residues within the interior of the protein. E) placement of polar amino acid residues around the exterior of the protein.
3. 3 Answer: A In the diagram below, the plane drawn behind the peptide bond indicates the:
A) absence of rotation around the C—N bond because of its partial double-bond character.
B) plane of rotation around the C—N bond. C) region of steric hindrance determined by the large C=O group. D) region of the peptide bond that contributes to a Ramachandran plot. E) theoretical space between –180 and +180 degrees that can be occupied by the and angles in the peptide bond.
4. Answer: D Which of the following best represents the backbone arrangement of two peptide bonds?
A) C—N—C—C—C—N—C—C B) C—N—C—C—N—C C) C—N—C—C—C—N D) C—C—N—C—C—N Chapter 4 The Three-Dimensional Structure of Proteins
E) C—C—C—N—C—C—C
5. Answer: A In the helix the hydrogen bonds:
A) are roughly parallel to the axis of the helix. B) are roughly perpendicular to the axis of the helix. C) occur mainly between electronegative atoms of the R groups. D) occur only between some of the amino acids of the helix. E) occur only near the amino and carboxyl termini of the helix.
6. Answer: E An helix would be destabilized most by:
A) an electric dipole spanning several peptide bonds throughout the helix. B) interactions between neighboring Asp and Arg residues. C) interactions between two adjacent hydrophobic Val residues. D) the presence of an Arg residue near the carboxyl terminus of the helix. E) the presence of two Lys residues near the amino terminus of the helix.
7. Answer: C Amino acid residues commonly found in the middle of turn are:
A) Ala and Gly. B) hydrophobic. C) Pro and Gly. D) those with ionized R-groups. E) two Cys.
8. Answer: E A sequence of amino acids in a certain protein is found to be -Ser-Gly-Pro-Gly-. The sequence is most probably part of a(n):
A) antiparallel sheet. B) parallel sheet. C) helix. D) sheet. E) turn.
9. Answer: D The -keratin chains indicated by the diagram below have undergone one chemical step. To alter the shape of the -keratin chains—as in hair waving—what subsequent steps are required?
Chapter 4 The Three-Dimensional Structure of Proteins
A) Chemical oxidation and then shape remodeling B) Chemical reduction and then chemical oxidation C) Chemical reduction and then shape remodeling D) Shape remodeling and then chemical oxidation E) Shape remodeling and then chemical reduction
10. Answer: A Which of the following statements is false?
A) Collagen is a protein in which the polypeptides are mainly in the -helix conformation. B) Disulfide linkages are important for keratin structure. C) Gly residues are particularly abundant in collagen. D) Silk fibroin is a protein in which the polypeptide is almost entirely in the conformation. E) -keratin is a protein in which the polypeptides are mainly in the -helix conformation.
11. Answer: E Which of the following statements concerning protein domains is true?
A) They are a form of secondary structure. B) They are examples of structural motifs. C) They consist of separate polypeptide chains (subunits). D) They have been found only in prokaryotic proteins. E) They may retain their correct shape even when separated from the rest of the protein.
12. Answer: C An average protein will not be denatured by:
A) a detergent such as sodium dodecyl sulfate. B) heating to 90°C. C) iodoacetic acid. D) pH 10. E) urea.
Chapter 4 The Three-Dimensional Structure of Proteins
Short Answer Questions
13. Any given protein is characterized by a unique amino acid sequence (primary structure) and three-dimensional (tertiary) structure. How are these related?
Answer: The three-dimensional structure is determined by the amino acid sequence. 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.
14. When a polypeptide is in its native conformation, there are weak interactions between its R groups. However, when it is denatured there are similar interactions between the protein groups and water. What then accounts for the greater stability of the native conformation?
Answer: In the unfolded polypeptide, there are ordered solvation shells of water around the protein groups. The number of water molecules involved in such ordered shells is reduced when the protein folds, resulting in higher entropy. Hence, the lower free energy of the native conformation.
15. Explain how circular dichroism spectroscopy could be used to measure the denaturation of a protein.
Answer: Circular dichroism spectroscopy measures the amount of -helix in a given protein. As the protein denatures, the amount of -helix should decrease as the protein chain becomes disordered; this change would be detectable using CD spectrography.
16. What is typically found in the interior of a water-soluble globular protein?
Answer: Hydrophobic amino acid residues cluster away from the surface in globular proteins, so much of the protein’s interior is a tightly packed combination of hydrocarbon and aromatic ring R groups with very few water molecules.
17. How can changes in pH alter the conformation of a protein?
Answer: Changes in pH can influence the extent to which certain amino acid side chains (or the amino and carboxyl termini) are protonated. The result is a change in net charge on the protein, which can lead to electrostatic attractions or repulsions between different regions of the protein. The final effect is a change in the protein’s three-dimensional shape or even complete denaturation.
18. Once a protein has been denatured, how can it be renatured? If renaturation does not occur, what might be the explanation?
Answer: Because a protein may be denatured through the disruption of hydrogen bonds and hydrophobic interactions by salts or organic solvents, removal of those conditions will reestablish the original aqueous environment, often permitting the protein to fold once again into its native conformation. If the protein does not renature, it may be because the denaturing treatment removed a required prosthetic group, or because the normal folding pathway requires the presence of a polypeptide chain binding protein or molecular chaperone. The normal folding pathway could also be mediated by a larger polypeptide, which is then cleaved (e.g., insulin). Denatured insulin would not refold easily.