Q: Which feature distinguishes an anti-parallel $b$-sheet from a parallel $b$-sheet?

Anti-parallel $b$-sheets have straight hydrogen bonds, while parallel $b$-sheets have staggered hydrogen bonds.

Q: What is the main reason right-handed $b$-helices are more common and stable than left-handed $b$-helices in proteins?

Right-handed $b$-helices have more favorable hydrogen bonding and less steric clash between side chains.

Question 1

Which statement best defines the primary structure of a protein?

Accepted Answer

The linear sequence of amino acids covalently linked by peptide bonds.

Question 2

Which type of bond is responsible for stabilizing the secondary structure of proteins such as $b$-helices and $b$-sheets?

Accepted Answer

Hydrogen bonds

Question 3

In the protein backbone, which torsion angles are flexible and contribute to the possible conformations of the polypeptide chain?

Accepted Answer

$c$ (phi) and $c$ (psi)

Question 4

Which feature distinguishes an anti-parallel $b$-sheet from a parallel $b$-sheet?

Accepted Answer

Anti-parallel $b$-sheets have straight hydrogen bonds, while parallel $b$-sheets have staggered hydrogen bonds.

Question 5

What is the main reason right-handed $b$-helices are more common and stable than left-handed $b$-helices in proteins?

Accepted Answer

Right-handed $b$-helices have more favorable hydrogen bonding and less steric clash between side chains.

Question 6

Which equation correctly represents the calculation of the dipole moment ($bc$) of a peptide bond?

Accepted Answer

$bc = q 	imes d$

Question 7

A protein is found to have a sequence highly conserved across multiple species. What does this suggest about the protein?

Accepted Answer

It is likely essential and evolves slowly due to functional constraints.

Question 8

Which of the following best describes the Ramachandran plot?

Accepted Answer

A plot of allowed and disallowed values of backbone torsion angles $c$ (phi) and $c$ (psi) in proteins.

Question 9

Which amino acid substitution is considered conservative?

Accepted Answer

Replacing a polar, uncharged amino acid with another polar, uncharged amino acid.

Question 10

In an $b$-helix, which atoms participate in the hydrogen bond that stabilizes the structure?

Accepted Answer

The carbonyl oxygen of residue $i$ and the amide hydrogen of residue $i+4$

Question 11

Which of the following is NOT a function of proteins in cells?

Accepted Answer

Storing genetic information

Question 12

Which statement about the peptide bond in proteins is correct?

Accepted Answer

The peptide bond is planar due to resonance and restricts rotation.

Question 13

Which secondary structure is characterized by side chains alternating above and below the plane of the structure?

Accepted Answer

Anti-parallel $b$-sheet

Question 14

A mutation changes a glycine to a lysine in a protein sequence. What type of substitution is this?

Accepted Answer

Nonconservative substitution

Question 15

Which of the following best explains the formation of the helix dipole in an $b$-helix?

Accepted Answer

Alignment of individual peptide bond dipoles along the helix axis

Question 16

Which method is commonly used to identify homologous proteins by comparing their sequences?

Accepted Answer

BLAST (Basic Local Alignment Search Tool)

Question 17

Which of the following is true about connectors between secondary structure elements in globular proteins?

Accepted Answer

They often consist of loops or turns that allow compact folding.

Question 18

Which of the following best describes the tertiary structure of a protein?

Accepted Answer

The overall three-dimensional folding of secondary structure elements into a domain.

Question 19

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

Accepted Answer

Restriction of rotation around the peptide bond

Question 20

A protein has a total helix dipole of $n 	imes 3.5$ Debye, where $n$ is the number of residues. What is the approximate charge separation at each end of the helix?

Accepted Answer

0.5-0.7 unit charge

Protein Primary and Secondary Structure: Foundations and Analysis

Study Guide - Practice Questions

Study Guide - Flashcards