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Chapter 4 The Three-Dimensional Structure of Proteins
Multiple Choice Questions
1. Overview of protein structure
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. Overview of protein structure
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
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.
4. Overview of protein structure
Which of the following is not an appropriate description for van der Waals interactions?
A) They involve dipole-dipole interactions.
B) Their strength depends on the distance between the two interacting atoms.
C) They are highly specific.
D) An individual van der Waals interaction does not contribute significantly to the stability of a
protein.
Chapter 4 The Three-Dimensional Structure of Proteins
39
E) They can involve hydrophobic amino acids.
5. Overview of protein structure
Which statement about intrinsically disordered proteins is true?
A) They contain small hydrophobic cores.
B) They represent misfolded conformations of cellular proteins.
C) They have no stable three-dimensional structure and therefore have no cellular function.
D) They are responsible for proteostasis.
E) They can interact with multiple protein-binding partners and are central to protein interaction
networks.
6. Overview of protein structure
Pauling and Corey’s studies of the peptide bond showed that:
A) at pH 7, many different peptide bond conformations are equally probable.
B) peptide bonds are essentially planar, with no rotation about the C—N axis.
C) peptide bonds in proteins are unusual, and unlike those in small model compounds.
D) peptide bond structure is extraordinarily complex.
E) primary structure of all proteins is similar, although the secondary and tertiary structure may
differ greatly.
7. Overview of protein structure
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.
8. Overview of protein structure
Which of the following best represents the backbone arrangement of two peptide bonds?
A) C—N—C—C—C—N—C—C
Chapter 4 The Three-Dimensional Structure of Proteins
40
B) C—N—C—C—N—C
C) C—N—C—C—C—N
D) C—C—N—C—C—N
E) C—C—C—N—C—C—C
9. Overview of protein structure
Which of the following pairs of bonds within a peptide backbone show free rotation around both bonds?
A) C—C and N—C
B) C=O and N—C
C) C=O and N—C
D) N—C and C—C
E) N—C and N—C
10. Protein secondary structure
Roughly how many amino acids are there in one turn of an helix?
A) 1
B) 2.8
C) 3.6
D) 4.2
E) 10
11. Protein secondary structure
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.
12. Protein secondary structure
In an helix, the R groups on the amino acid residues:
A) alternate between the outside and the inside of the helix.
B) are found on the outside of the helix spiral.
C) cause only right-handed helices to form.
D) generate the hydrogen bonds that form the helix.
E) stack within the interior of the helix.
13. Protein secondary structure
Chapter 4 The Three-Dimensional Structure of Proteins
41
Thr and/or Leu residues tend to disrupt an helix when they occur next to each other in a protein because:
A) an amino acids like Thr is highly hydrophobic.
B) covalent interactions may occur between the Thr side chains.
C) electrostatic repulsion occurs between the Thr side chains.
D) steric hindrance occurs between the bulky Thr side chains.
E) the R group of Thr can form a hydrogen bond.
A D-amino acid would interrupt an helix made of L-amino acids. Another naturally occurring
hindrance to the formation of an helix is the presence of:
A) a negatively charged Arg residue.
B) a nonpolar residue near the carboxyl terminus.
C) a positively charged Lys residue.
D) a Pro residue.
E) two Ala residues side by side.
15. Protein secondary structure
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.
16. Protein secondary structure
The major reason that antiparallel -stranded protein structures are more stable than parallel -
stranded structures is that the latter:
A) are in a slightly less extended configuration than antiparallel strands.
B) do not have as many disulfide crosslinks between adjacent strands.
C) do not stack in sheets as well as antiparallel strands.
D) have fewer lateral hydrogen bonds than antiparallel strands.
E) have weaker hydrogen bonds laterally between adjacent strands.
17. Protein secondary structure
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.
Chapter 4 The Three-Dimensional Structure of Proteins
42
18. Protein secondary structure
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.
19. Protein tertiary and quaternary structures
The three-dimensional conformation of a protein may be strongly influenced by amino acid residues
that are very far apart in sequence. This relationship is in contrast to secondary structure, where the
amino acid residues are:
A) always side by side.
B) generally near each other in sequence.
C) invariably restricted to about 7 of the 20 standard amino acids.
D) often on different polypeptide strands.
E) usually near the polypeptide chain’s amino terminus or carboxyl terminus.
20. Protein tertiary and quaternary structures
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?
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
21. Protein tertiary and quaternary structures
Chapter 4 The Three-Dimensional Structure of Proteins
43
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.
22. Protein tertiary and quaternary structures
Kendrew’s studies of the globular myoglobin structure demonstrated that:
A) “corners” between -helical regions invariably lacked proline residue.
B) highly polar or charged amino-acid residues tended to be located interiorally.
C) myoglobin was completely different from hemoglobin, as expected.
D) the structure was very compact, with virtually no internal space available for water.
E) the helix predicted by Pauling and Corey was not found in myoglobin.
23. Protein tertiary and quaternary structures
Proteins often have regions that can fold and function as an independent entity from the whole
protein. These regions are called:
A) domains.
B) oligomers.
C) peptides.
D) sites.
E) subunits.
24. Protein tertiary and quaternary structures
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.
25. Protein tertiary and quaternary structures
The structural classification of proteins (based on motifs) is based primarily on their:
A) amino-acid sequence.
B) evolutionary relationships.
C) function.
D) secondary structure content and arrangement.
E) subunit content and arrangement.
Chapter 4 The Three-Dimensional Structure of Proteins
44
26. Protein tertiary and quaternary structures
Proteins are classified within families or superfamilies based on similarities in:
A) evolutionary origin.
B) physico-chemical properties.
C) structure and/or function.
D) subcellular location.
E) subunit structure.
27. Protein tertiary and quaternary structures
Which of the following statements about oligomeric proteins is false?
A) A subunit may be similar to other proteins.
B) All subunits must be identical.
C) Many have regulatory roles.
D) Some oligomeric proteins can further associate into large fibers.
E) Some subunits may have nonprotein prosthetic groups.
28. Protein tertiary and quaternary structures
A repeating structural unit in a multimeric protein is known as a(n):
A) domain.
B) motif.
C) oligomer.
D) protomer.
E) subunit.
29. Protein denaturation and folding
Proteostasis is the cellular process by which:
A) proteins are synthesized.
B) proteins are folded.
C) proteins are modified.
D) proteins are degraded.
E) protein levels are maintained.
30. Protein denaturation and folding
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
45
31. Protein denaturation and folding
Which of the following is least likely to result in protein denaturation?
A) Altering net charge by changing pH
B) Changing the salt concentration
C) Disruption of weak interactions by boiling
D) Exposure to detergents
E) Mixing with organic solvents such as acetone
32. Protein denaturation and folding
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, active conformation, requires the input of energy in
the form of heat.
B) native ribonuclease does not have a unique secondary and tertiary structure.
C) the completely unfolded enzyme, with all —S—S— bonds broken, is still enzymatically active.
D) the enzyme, dissolved in water, is thermodynamically stable relative to the mixture of amino
acids whose residues are contained in RNase.
E) the primary sequence of RNase is sufficient to determine its specific secondary and tertiary
structure.
33. Protein denaturation and folding
Which of the following statements concerning the process of spontaneous folding of proteins is false?
A) It may be an essentially random process.
B) It may be defective in some human diseases.
C) It may involve a gradually decreasing range of conformational species.
D) It may involve initial formation of a highly compact state.
E) It may involve initial formation of local secondary structure.
34. Protein denaturation and folding
Protein S will fold into its native conformation only when protein Q is also present in the solution.
However, protein Q can fold into its native conformation without protein S. Protein Q, therefore,
may function as a ____________ for protein S.
A) proteasome
B) molecular chaperone
C) protein precursor
D) structural motif
E) supersecondary structural unit
35. Protein denaturation and folding
Which of the following is not known to be involved in the process of assisted folding of proteins?
Chapter 4 The Three-Dimensional Structure of Proteins
46
A) Chaperonins
B) Disulfide interchange
C) Heat shock proteins
D) Peptide bond condensation
E) Peptide bond isomerization
Short Answer Questions
36. Overview of protein structure
Page: 113 Difficulty: 2
Any given protein is characterized by a unique amino acid sequence (primary structure) and three-
dimensional (tertiary) structure. How are these related?
37. Overview of protein structure
Pages: 114−115, 140−141 Difficulty: 2
Name four factors (bonds or other forces) that contribute to stabilizing the native structure of a
protein, and describe one condition or reagent that interferes with each type of stabilizing force.
38. Overview of protein structure
Pages: 114−115 Difficulty: 2
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?
39. Overview of protein structure
Page: 116 Difficulty: 2
Draw the resonance structure of a peptide bond, and explain why there is no rotation around the
C—N bond.
40. Overview of protein structure
Page: 116 Difficulty: 1
Pauling and Corey showed that in small peptides, 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),
Chapter 4 The Three-Dimensional Structure of Proteins
47
and indicate which six atoms are part of the planar structure of the peptide bond.
41. Overview of protein structure
Page 116−117 Difficulty: 2-3
Provide a brief explanation for the statement “Soluble globular proteins can be distinguished from
soluble intrinsically disordered proteins on the basis of their amino acid content.”
42. Protein secondary structure
Page: 116 Difficulty: 1
Draw the hydrogen bonding typically found between two residues in an helix.
43. Protein secondary structure
Page: 117−118 Difficulty: 2
Describe three of the important features of the -helical polypeptide structure predicted by Pauling
and Corey. Provide one or two sentences for each feature.
44. Protein secondary structure
Page: 120 Difficulty: 2
Describe three of the important features of a sheet polypeptide structure. Provide one or two
sentences for each feature.
45. Protein secondary structure
Page: 120−121 Difficulty: 2
Why are glycine and proline often found within a turn?
Chapter 4 The Three-Dimensional Structure of Proteins
48
46. Protein secondary structure
Page: 122, 140−141 Difficulty: 3
Explain how circular dichroism spectroscopy could be used to measure the denaturation of a protein.
47. Protein tertiary and quaternary structures
Pages: 124−125 Difficulty: 2
In superhelical proteins, such as collagen, several polypeptide helices are intertwined. What is the
function of this superhelical twisting?
48. Protein tertiary and quaternary structures
Page: 128 Difficulty: 2
Why is silk fibroin so strong, but at the same time so soft and flexible?
49. Protein tertiary and quaternary structures
Page: 130 Difficulty: 1
What is typically found in the interior of a water-soluble globular protein?
50. Protein tertiary and quaternary structures
Pages: 132−134 Difficulty: 3
How does one determine the three-dimensional structure of a protein? Your answer should be more
than the name of a technique.
Chapter 4 The Three-Dimensional Structure of Proteins
49
51. Protein tertiary and quaternary structures
Page: 132−134 Difficulty: 2
Describe a reservation about the use of x-ray crystallography in determining the three-dimensional
structures of biological molecules.
52. Protein tertiary and quaternary structures
Pages: 135−136 Difficulty: 1
Explain what is meant by motifs in protein structure.
53. Protein tertiary and quaternary structures
Pages: 136−137 Difficulty: 2
Draw a loop, and describe what is found in the interior of the loop.
54. Protein tertiary and quaternary structures
Page: 136 Difficulty: 1
Describe the quaternary structure of hemoglobin.
55. Protein tertiary and quaternary structures
Pages: 139−140 Difficulty: 2
What is the rationale for many large proteins containing multiple copies of a polypeptide subunit?
56. Protein denaturation and folding
Pages: 141−142 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.”
57. Protein denaturation and folding
Pages: 140−142 Difficulty: 2
Chapter 4 The Three-Dimensional Structure of Proteins
50
Each of the following reagents or conditions will denature a protein. For each, describe in one or two
sentences what the reagent/condition does to destroy native protein structure.
(a) urea
(b) high temperature
(c) detergent
(d) low pH
58. Protein denaturation and folding
Pages: 140−141 Difficulty: 2
How can changes in pH alter the conformation of a protein?
50. Protein denaturation and folding
Pages: 141−142 Difficulty: 2
Once a protein has been denatured, how can it be renatured? If renaturation does not occur, what
might be the explanation?
60. Protein denaturation and folding
Pages: 143−145 Difficulty: 2
What are two mechanisms by which “chaperone” proteins assist in the correct folding of
polypeptides?
61. Protein denaturation and folding
Pages: 143−145 Difficulty: 2
What important concepts regarding protein thermal denaturation can be inferred from the egg white
of a boiled egg?
Chapter 4 The Three-Dimensional Structure of Proteins
51
