Chapter 4 The 3D Structure of Proteins (Ed. 6 test bank)

Question 1

In the diagram below, the plane drawn behind the peptide bond indicates the:

Answer 1

absence of rotation around the C—N bond because of its partial double-bond character.

Question 2

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.

Answer 2

Peptide bonds

Question 3

Which of the following best represents the backbone arrangement of two peptide bonds?

A) Cα—N—Cα—C—Cα—N—Cα—C
B) Cα—N—C—C—N—Cα
C) C—N—Cα—Cα—C—N
D) Cα—C—N—Cα—C—N

E) Cα—Cα—C—N—Cα—Cα—C

Answer 3

Cα—C—N—Cα—C—N

Question 4

In the alpha-helix the hydrogen bonds:

Answer 4

Are roughly parallel to the axis of the helix

Question 5

An alpha-helix would be destabilized most by:

Answer 5

The presence of two Lys residues near the amino terminus of the alpha helix

Question 6

Amino acid residues commonly found in the middle of a beta-turn are:

Answer 6

Pro and Gly

Question 7

A sequence of amino acids in a certain protein is foudn to be -Ser-Gly-Pro-Gly-. The sequence is most probably part of a(n):

Answer 7

Beta-turn

Question 8

The alpha-keratin chains indicated by the diagram have undergone one chemical step. To alter the shape of the alpha-keratin chains – as in hair waving – what subsequent steps are required?

Answer 8

Shape remodeling and then chemical oxidation

Question 9

Which of the following statements is false?

A) Collagen is a protein in which the polypeptides are mainly in the alpha-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 beta conformation.

E) Alpha-keratin is a protein in which the polypeptides are mainly in the alpha-helix conformation.

Answer 9

Collagen is a protein in which the polypeptides are mainly in the alpha-helix conformation

Question 10

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.

Answer 10

They may retain their correct shape even when separated from the rest of the protein

Question 11

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.

Answer 11

Iodoacetic acid

Question 12

Any given protein is characterized by a unique amino acid sequence (primary structure) and three-dimensional (tertiary) structure. How are these related?

Answer 12

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.

Question 13

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 13

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.

Question 14

Explain how circular dichroism spectroscopy could be used to measure the denaturation of a protein.

Answer 14

Circular dichroism spectroscopy measures the amount of alpha-helix in a given protein. As the protein denatures, the amount of alpha-helix should decrease as the protein chain becomes disordered; this change would be detectable using CD spectrography.

Question 15

What is typically found in the interior of a water-soluble globular protein?

Answer 15

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.

Question 16

How can changes in pH alter the conformation of a protein?

Answer 16

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.

Question 17

Once a protein has been denatured, how can it be renatured? If renaturation does not occur, what might be the explanation?

Answer 17

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.