04. the Three-Dimentional Structure of Proteins by Lihninger

Chapter 4 The Three-Dimensional Structure of Proteins

Multiple Choice Questions

1. Overview of protein structurePages: 114115 Difficulty: 1 Ans: DAll 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 structurePages: 114115 Difficulty: 2 Ans: AThe 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 structurePage: 115 Difficulty: 1 Ans: DIn 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 structurePage: 115 Difficulty: 2 Ans: BPauling 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.

Chapter 4 The Three-Dimensional Structure of Proteins

5. Overview of protein structurePage: 116 Difficulty: 3 Ans: AIn 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.

6. Overview of protein structurePage: 116 Difficulty: 2 Ans: DWhich 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 E) C—C—C—N—C—C—C

7. Overview of protein structurePage: 116 Difficulty: 2 Ans: AWhich 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

8. Protein secondary structurePage: 117 Difficulty: 2 Ans: CRoughly how many amino acids are there in one turn of an helix?

A) 1 B) 2.8C) 3.6 D) 4.2 E) 10

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Chapter 4 The Three-Dimensional Structure of Proteins

9. Protein secondary structurePages: 117-119 Difficulty: 2 Ans: AIn the helix the hydrogen bonds:

F) are roughly parallel to the axis of the helix. G) are roughly perpendicular to the axis of the helix. H) occur mainly between electronegative atoms of the R groups. I) occur only between some of the amino acids of the helix. J) occur only near the amino and carboxyl termini of the helix.

10. Protein secondary structurePages: 117-118 Difficulty: 2 Ans: BIn 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.

11. Protein secondary structurePage: 119 Difficulty: 2 Ans: DThr 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.

12. Protein secondary structurePage: 119 Difficulty: 1 Ans: DA 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.

13. Protein secondary structurePages: 119-120 Difficulty: 3 Ans: EAn 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.

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Chapter 4 The Three-Dimensional Structure of Proteins

14. Protein secondary structurePages: 120-121 Difficulty: 1 Ans: E 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.

15. Protein secondary structurePage: 121 Difficulty: 1 Ans: CAmino 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.

16. Protein secondary structurePage: 121 Difficulty: 2 Ans: EA 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.

17. Protein tertiary and quaternary structuresPage: 123 Difficulty: 1 Ans: BThe 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.

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Chapter 4 The Three-Dimensional Structure of Proteins

18. Protein tertiary and quaternary structuresPage: 125 Difficulty: 3 Ans: DThe -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

19. Protein tertiary and quaternary structuresPages: 124-125 Difficulty: 2 Ans: AWhich 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.

20. Protein tertiary and quaternary structuresPages: 129-130 Difficulty: 2 Ans: DKendrew’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.

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Chapter 4 The Three-Dimensional Structure of Proteins

21. Protein tertiary and quaternary structuresPages: 132133 Difficulty: 1 Ans: EDetermining the precise arrangement of atoms within a large protein is possible only through the use of:

A) electron microscopy. B) light microscopy. C) molecular model building. D) Ramachandran plots. E) x-ray diffraction.

22. Protein tertiary and quaternary structuresPages: 132134 Difficulty: 3 Ans: DAnalysis of x-ray diffraction data yields a(n) ; analysis of 2D NMR data yields a(n) .

A) electron density map; count of hydrogen atoms in the molecule B) shadow of protein’s outline; estimate of protein’s molecular volume C) table of interatomic distances; electron density map D) electronic density map; table of interatomic distancesE) 3-d protein structure; 2-d protein structure

23. Protein tertiary and quaternary structuresPage: 135 Difficulty: 1 Ans: AProteins often have regions that show specific, coherent patterns of folding or function. These regions are called:

A) domains. B) oligomers. C) peptides. D) sites. E) subunits.

24. Protein tertiary and quaternary structuresPage: 135 Difficulty: 2 Ans: EWhich 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 structuresPages: 136-138 Difficulty: 2 Ans: DThe 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.

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Chapter 4 The Three-Dimensional Structure of Proteins

26. Protein tertiary and quaternary structuresPages: 136-138 Difficulty: 1 Ans: CProteins 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 structuresPages: 138-140 Difficulty: 1 Ans: BWhich 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 structuresPage: 138-140 Difficulty: 1 Ans: DA repeating structural unit in a multimeric protein is known as a(n):

A) domain. B) motif. C) oligomer. D) protomer. E) subunit.

29. Protein tertiary and quaternary structuresPage: 139140 Difficulty: 2 Ans: AWhich of the following statements concerning rotational symmetry in proteins is false?

A) It involves rotation of proteins inside the cell. B) It is frequently seen in the subunits of oligomeric proteins. C) It is frequently seen in viruses. D) It may involve rotation about one or more axes. E) It results in closed, packed structures.

30. Protein denaturation and foldingPages: 140-141 Difficulty: 2 Ans: CAn 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.

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Chapter 4 The Three-Dimensional Structure of Proteins

31. Protein denaturation and foldingPages: 140-141 Difficulty: 1 Ans: BWhich of the following is least likely to result in protein denaturation?

A) Altering net charge by changing pHB) Changing the salt concentrationC) Disruption of weak interactions by boilingD) Exposure to detergentsE) Mixing with organic solvents such as acetone

32. Protein denaturation and foldingPage: 141 Difficulty: 2 Ans: EExperiments 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 foldingPages: 142143 Difficulty: 2 Ans: AWhich 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 foldingPages: 144145 Difficulty: 1 Ans: BProtein 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) ligand B) molecular chaperone C) protein precursor D) structural motif E) supersecondary structural unit

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Chapter 4 The Three-Dimensional Structure of Proteins

35. Protein denaturation and foldingPages: 144145 Difficulty: 2 Ans: DWhich of the following is not known to be involved in the process of assisted folding of proteins?

A) Chaperonins B) Disulfide interchange C) Heat shock proteins D) Peptide bond hydrolysis E) Peptide bond isomerization

Short Answer Questions

36. Overview of protein structurePage: 113 Difficulty: 2Any given protein is characterized by a unique amino acid sequence (primary structure) and three-dimensional (tertiary) structure. How are these related?

Ans: 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.

37. Overview of protein structurePages: 114-115, 140-141 Difficulty: 2Name 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.

Ans: Among forces that stabilize native protein structures are (a) disulfide bonds, (b) hydrogen bonds, (c) hydrophobic interactions, and (d) ionic interactions. Agents that interfere with these forces are (a) mercaptoethanol or dithiothreitol, (b) pH extremes, (c) detergents and urea, and (d) changes in pH or ionic strength, respectively.

38. Overview of protein structurePages: 114115 Difficulty: 2When 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?

Ans: 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.

39. Overview of protein structurePage: 116 Difficulty: 2Draw the resonance structure of a peptide bond, and explain why there is no rotation around theC—N bond.

Ans: The intermediate resonance structure imparts a partial double bond characteristic to the C—N bond, thereby prohibiting rotation. (See Fig. 4-2, p. 116.)

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Chapter 4 The Three-Dimensional Structure of Proteins

40. Overview of protein structurePage: 116 Difficulty: 1Pauling 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), and indicate which six atoms are part of the planar structure of the peptide bond.

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 C atoms, which are diagonally opposite relative to the C—N bond. (See Fig. 4-2, p. 119.)

41. Protein secondary structurePage: 116 Difficulty: 1Draw the hydrogen bonding typically found between two residues in an helix.

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. (See Fig. 4-2, p. 116.)

42. Protein secondary structurePage: 117-118 Difficulty: 2Describe three of the important features of the -helical polypeptide structure predicted by Pauling and Corey. Provide one or two sentences for each feature.

Ans: The -helical structure of a polypeptide is tightly wound around a long central axis; each turn of the right-handed helix contains 3.6 residues and stretches 5.4 Å along the axis. The peptide NH is hydrogen-bonded to the carbonyl oxygen of the fourth amino acid along the sequence toward the amino terminus. The R groups of the amino acid residues protrude outward from the helical backbone.

43. Protein secondary structurePage: 120 Difficulty: 2Describe three of the important features of a sheet polypeptide structure. Provide one or two sentences for each feature.

Ans: In the sheet structure, several extended polypeptides, or two regions of the same polypeptide, lie side by side and are stabilized by hydrogen bonding between adjacent chains. Adjacent chains may be either parallel (with a repeat distance of about 6.5 Å) or antiparallel (7 Å repeat). The R groups are often small and alternately protrude from opposite faces of the sheet.

44. Protein secondary structurePage: 120-121 Difficulty: 2Why are glycine and proline often found within a turn?

Ans: A turn results in a tight 180° reversal in the direction of the polypeptide chain. Glycine is the smallest and thus most flexible amino acid, and proline can readily assume the cis configuration, which facilitates a tight turn.

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Chapter 4 The Three-Dimensional Structure of Proteins

45. Protein secondary structurePage: 122, 140-141 Difficulty: 3Explain how circular dichroism spectroscopy could be used to measure the denaturation of a protein.

Ans: 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.

46. Protein tertiary and quaternary structuresPages: 124125 Difficulty: 2In superhelical proteins, such as collagen, several polypeptide helices are intertwined. 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.

47. Protein tertiary and quaternary structuresPage: 128 Difficulty: 2Why is silk fibroin so strong, but at the same time so soft and flexible?

Ans: Unlike collagen and keratin, silk fibroin has no covalent crosslinks between adjacent strands, or between its stacked sheets, making it very flexible. Fibroin’s unusual tensile strength derives from the fact that the peptide backbone of antiparallel -strands is fully extended, and that the R-groups in the stacked pleated sheets interdigitate, preventing any longitudinal sliding of the sheets across one another.

48. Protein tertiary and quaternary structuresPage: 130 Difficulty: 1What 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, so much of the protein’s interior is a tightly packed combination of hydrocarbon and aromatic ring R groups with very few water molecules.

49. Protein tertiary and quaternary structuresPages: 132134 Difficulty: 3How does one determine the three-dimensional structure of a protein? Your answer should be more than the name of a technique.

Ans: The protein is crystallized, and the crystal structure is determined by x-ray diffraction. The pattern of diffracted x-rays yields, by Fourier transformation, the three-dimensional distribution of electron density. 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. Sometimes, the three-dimensional structure of a small protein or peptide can be determined in solution by sophisticated analysis of the NMR spectrum of the polypeptide. This technique can also reveal dynamic aspects of protein structure such as conformational changes. Computer analysis of two-dimensional NMR spectra can be used to generate a picture of the three-dimensional structure of a protein.

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Chapter 4 The Three-Dimensional Structure of Proteins

50. Protein tertiary and quaternary structuresPage: 132-134 Difficulty: 2Describe a reservation about the use of x-ray crystallography in determining the three-dimensional structures of biological molecules.

Ans: To obtain an x-ray picture of a biomolecule, the molecule must be purified and crystallized under laboratory conditions far different from those encountered by the native molecule. Biomolecules in the cell also have more flexibility and freedom of motion than can be accommodated in a rigid crystal structure. Therefore, 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.

51. Protein tertiary and quaternary structuresPages: 135136 Difficulty: 1Explain what is meant by motifs in protein structure.

Ans: Motifs are particularly stable arrangements of elements of secondary structure (e.g., helix and conformation), including the connections between them, which are found in a variety of proteins.

52. Protein tertiary and quaternary structuresPages: 136-137 Difficulty: 2Draw a loop, and describe what is found in the interior of the loop.

Ans: Hydrophobic amino acid residues are usually found in the interior of the loop; these help stabilize the arrangement through hydrophobic interactions. (See Fig. 4-20, p. 140.)

53. Protein tertiary and quaternary structuresPage: 136 Difficulty: 1Describe the quaternary structure of hemoglobin.

Ans: Each protein molecule is composed of two copies each of two different subunits and . The two protomers are arranged with C2 symmetry.

54. Protein tertiary and quaternary structuresPages: 138140 Difficulty: 2Describe briefly the two major types of symmetry found in oligomeric proteins and give an example of each.

Ans: 1) Rotational: In rotational symmetry, subunits are superimposable after rotation about one or more of the axes. Some examples are hemoglobin and thepoliovirus capsid. 2) Helical: In helical symmetry, subunits are superimposable after a helical rotation. Some examples are actin filaments and the tobacco mosaic virus capsid.

55. Protein tertiary and quaternary structuresPages: 139-140 Difficulty: 2What 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. It is therefore more efficient to have fewer genes, encoding shorter polypeptides that can be used to construct many large proteins.

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Chapter 4 The Three-Dimensional Structure of Proteins

56. Protein denaturation and foldingPages: 141-142 Difficulty: 2Explain (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.”

Ans: Anfinsen showed that a completely denatured enzyme (ribonuclease) could fold spontaneously into its native, enzymatically active form with only the primary sequence to guide it.

57. Protein denaturation and foldingPages: 140-142 Difficulty: 2Each 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

Ans: (a) Urea acts primarily by disrupting hydrophobic interactions. (b) High temperature provides thermal energy greater than the strength of the weak interactions (hydrogen bonds, electrostatic interactions, hydrophobic interactions, and van der Waals forces, breaking these interactions. (c) Detergents bind to hydrophobic regions of the protein, preventing hydrophobic interactions among several hydrophobic patches on the native protein. (d) Low pH causes protonation of the side chains of Asp, Glu, and His, preventing electrostatic interactions.

58. Protein denaturation and foldingPages: 140-141 Difficulty: 2How 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. 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.

59. Protein denaturation and foldingPages: 141142 Difficulty: 2Once a protein has been denatured, how can it be renatured? If renaturation does not occur, 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, 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.

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Chapter 4 The Three-Dimensional Structure of Proteins

60. Protein denaturation and foldingPages: 143145 Difficulty: 2What 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. They can also provide a microenvironment that promotes correct folding.

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