Question 1

Which property of the peptide bond is primarily responsible for the limited flexibility of polypeptide chains?

Accepted Answer

The peptide bond is planar due to resonance, restricting rotation around the C-N bond.

Question 2

Which of the following best describes the secondary structure of proteins?

Accepted Answer

Regular, repeating patterns of backbone hydrogen bonding, such as alpha helices and beta sheets.

Question 3

A Ramachandran plot is used to visualize which aspect of protein structure?

Accepted Answer

The allowed values of phi ($\phi$) and psi ($\psi$) backbone dihedral angles.

Question 4

Which of the following statements about alpha helices is TRUE?

Accepted Answer

Alpha helices are stabilized by hydrogen bonds between the backbone C=O of residue $i$ and the N-H of residue $i+4$.

Question 5

What is the energetic penalty for rotating the peptide C-N bond, and what is the consequence for protein structure?

Accepted Answer

About 88 kJ/mol; this makes the peptide bond planar and limits backbone flexibility.

Question 6

Which of the following best describes the difference between parallel and antiparallel beta sheets?

Accepted Answer

Antiparallel beta sheets have more linear and thus stronger hydrogen bonds compared to parallel beta sheets.

Question 7

Which level of protein structure is directly determined by the sequence of amino acids?

Accepted Answer

Primary structure

Question 8

A mutation causes a single amino acid substitution in a protein. Which level(s) of structure could potentially be affected?

Accepted Answer

Primary, secondary, tertiary, and quaternary structures.

Question 9

Which of the following is a characteristic of globular proteins?

Accepted Answer

They are spherical, well-folded, and generally water soluble.

Question 10

Which of the following statements about protein folding is correct?

Accepted Answer

The amino acid sequence alone can determine the native structure of some proteins.

Question 11

Which of the following best explains why evolution can repurpose existing protein structures for new functions?

Accepted Answer

Many protein folds are stable and can accommodate changes in sequence that allow new functions.

Question 12

Which of the following interactions is primarily responsible for stabilizing tertiary structure in proteins?

Accepted Answer

Long-range interactions between side chains, including hydrophobic interactions, ionic bonds, and disulfide bridges.

Question 13

A protein is found to consist of two identical polypeptide chains. Which level of structure does this describe?

Accepted Answer

Quaternary structure

Question 14

Which of the following is a consequence of the planarity of the peptide bond?

Accepted Answer

It restricts rotation, resulting in a rigid, planar structure.

Question 15

Which of the following best describes a protein domain?

Accepted Answer

A structurally distinct part of a protein that can often fold independently into a stable structure.

Question 16

Which of the following statements about motifs and domains is correct?

Accepted Answer

Domains are larger structural units that can often fold independently, while motifs are smaller, recurring structural elements.

Question 17

Which of the following is NOT a typical classification criterion for proteins?

Accepted Answer

Type of nucleic acid present

Question 18

Which of the following statements about membrane proteins is TRUE?

Accepted Answer

They are associated with lipid membranes and are generally not water soluble.

Question 19

Which of the following best explains why only a few combinations of phi ($\phi$) and psi ($\psi$) angles are allowed in proteins?

Accepted Answer

Steric clashes between atoms restrict the accessible conformations.

Question 20

Which of the following is a correct statement about the cis and trans configurations of the peptide bond?

Accepted Answer

The trans configuration is generally favored because it minimizes steric clashes between side chains.

Protein Three-Dimensional Structure: Levels, Bonds, and Folding

Study Guide - Practice Questions