Question 1

Which of the following statements best explains why proline is rarely found in α-helices?

Accepted Answer

Proline's side chain forms a rigid ring that restricts rotation around the N-Cα bond, disrupting the helical structure.

Question 2

A protein is found to have a high content of β-branched amino acids such as valine and isoleucine. Which secondary structure is this protein most likely to favor?

Accepted Answer

β-sheet

Question 3

Which of the following best describes the hydrogen bonding pattern in an antiparallel β-sheet?

Accepted Answer

Hydrogen bonds are linear and nearly perpendicular to the direction of the strands.

Question 4

A helical wheel projection of a peptide reveals that hydrophobic residues cluster on one side of the helix. What property does this suggest about the helix?

Accepted Answer

The helix is amphipathic, with one hydrophobic and one hydrophilic face.

Question 5

Which of the following amino acids is most likely to be found at the third position of a type II β-turn?

Accepted Answer

Glycine

Question 6

What is the primary driving force for protein folding into its native tertiary structure?

Accepted Answer

The hydrophobic effect, which increases the entropy of water molecules.

Question 7

According to Anfinsen’s experiments with RNase A, which statement is correct?

Accepted Answer

The primary amino acid sequence contains all the information required for correct protein folding.

Question 8

Which of the following best describes the role of molecular chaperones in protein folding?

Accepted Answer

They prevent inappropriate interactions and aggregation during folding.

Question 9

A mutation replaces a hydrophobic residue in the core of a globular protein with a charged residue. What is the most likely effect on protein stability?

Accepted Answer

The protein will be destabilized due to the unfavorable desolvation cost of burying a charge.

Question 10

Which of the following Ramachandran plot regions corresponds to the allowed dihedral angles for a right-handed α-helix?

Accepted Answer

$$\varphi \approx -60^\circ$$, $$\psi \approx -45^\circ$$

Question 11

Which of the following best explains why hydrogen bonds are not the primary driving force for protein folding?

Accepted Answer

Hydrogen bonds are already formed with water in the unfolded state, so folding does not provide a net gain in hydrogen bonding.

Question 12

A β-sheet is found to have alternating polar and nonpolar side chains. If this sheet is located at the surface of a protein, what is the most likely arrangement?

Accepted Answer

The polar face is exposed to solvent, and the nonpolar face is buried or interacts with other hydrophobic regions.

Question 13

Which of the following is a characteristic of a coiled-coil supersecondary structure?

Accepted Answer

It is formed by two amphipathic α-helices with hydrophobic residues at the i and i+3 positions.

Question 14

Which of the following best describes the folding funnel model of protein folding?

Accepted Answer

Proteins fold through multiple pathways, reducing free energy and entropy until reaching the native state.

Question 15

Which of the following is true regarding salt bridges in proteins?

Accepted Answer

Interior salt bridges contribute more to specificity than exterior salt bridges.

Question 16

A protein is denatured by heating. What is the most likely observation if the protein is monitored by circular dichroism?

Accepted Answer

An abrupt two-state transition in the CD signal, indicating cooperative unfolding.

Question 17

Which of the following best explains why glycine is commonly found in turn regions of proteins?

Accepted Answer

Glycine's small side chain allows for the tight conformational flexibility required in turns.

Question 18

Which of the following diseases is associated with protein misfolding and aggregation into amyloid fibrils?

Accepted Answer

Alzheimer’s disease

Question 19

What is the effect of a chaotrope such as urea on protein structure?

Accepted Answer

It disrupts the hydrophobic core, leading to protein denaturation.

Three-Dimensional Structure of Proteins: Secondary and Tertiary Structure

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