Q: Which of the following best describes the relationship between $pK_a$ and the ionization state of an amino acid side chain?

When $pH < pK_a$, the side chain is predominantly protonated.

Q: Which of the following best explains why a protein can exist in two stable conformations at room temperature?

The protein has two distinct energy minima separated by an energy barrier that is not easily overcome at room temperature.

Q: Which of the following is most likely to occur if a peptide contains a high proportion of glycine and proline residues?

The peptide will have increased flexibility and may form turns or loops rather than regular secondary structures.

Q: Which of the following best describes the effect of adding a reducing agent to a protein with multiple disulfide bonds?

The reducing agent will break the disulfide bonds, converting them to free thiol groups ($\mathrm{R-SH}$).

Question 1

Which of the following best describes the origin of hydrogen bonds in proteins?

Accepted Answer

They arise from the attraction between the partial positive charge on a hydrogen atom covalently bonded to an electronegative atom and the partial negative charge on another electronegative atom.

Question 2

Given the peptide sequence MTWQHEQHPNV, which amino acid is at the C-terminus?

Accepted Answer

Valine

Question 3

Which of the following amino acids in the peptide MTWQHEQHPNV can be phosphorylated?

Accepted Answer

Histidine

Question 4

At pH 1.9, what is the net charge of the peptide MTWQHEQHPNV? (Assume N-terminus and C-terminus are free, and side chain pKa values: Asp/Glu ≈ 4, His ≈ 6, Lys ≈ 10, Arg ≈ 12)

Accepted Answer

$+2$

Question 5

Which of the following best explains why proline-rich sequences cannot form standard secondary structures?

Accepted Answer

Proline's rigid ring structure restricts rotation around the peptide bond, disrupting regular hydrogen bonding patterns.

Question 6

Which of the following amino acids in the peptide MTWQHEQHPNV can be glycosylated?

Accepted Answer

Asparagine

Question 7

Which of the following is a correct statement about the effect of pH on the charge of a peptide?

Accepted Answer

At low pH, the peptide will have more positive charges due to protonation of amino and carboxyl groups.

Question 8

Which of the following amino acids in the peptide MTWQHEQHPNV can be methylated?

Accepted Answer

Histidine

Question 9

Which of the following best describes the role of reducing agents in protein chemistry?

Accepted Answer

They break disulfide bonds by donating electrons, converting $\mathrm{S-S}$ to $\mathrm{SH}$ groups.

Question 10

Which of the following is a polar side chain in the peptide MTWQHEQHPNV?

Accepted Answer

Glutamine

Question 11

A mutation changes the peptide MTWQHEQHPNV to MTWQHEQHPNA. At pH 7.3, what is the most likely effect on the net charge of the peptide?

Accepted Answer

The net charge will remain the same because asparagine is neutral like valine.

Question 12

Which of the following best explains why tertiary structure is disrupted by denaturing agents?

Accepted Answer

Denaturing agents disrupt non-covalent interactions such as hydrogen bonds, ionic bonds, and hydrophobic interactions that stabilize tertiary structure.

Question 13

Which of the following is a non-polar side chain in the peptide MTWQHEQHPNV?

Accepted Answer

Valine

Question 14

Which of the following best describes the relationship between $pK_a$ and the ionization state of an amino acid side chain?

Accepted Answer

When $pH < pK_a$, the side chain is predominantly protonated.

Question 15

Which of the following best explains why a protein can exist in two stable conformations at room temperature?

Accepted Answer

The protein has two distinct energy minima separated by an energy barrier that is not easily overcome at room temperature.

Question 16

Which of the following is most likely to occur if a peptide contains a high proportion of glycine and proline residues?

Accepted Answer

The peptide will have increased flexibility and may form turns or loops rather than regular secondary structures.

Question 17

Which of the following best describes the effect of adding a reducing agent to a protein with multiple disulfide bonds?

Accepted Answer

The reducing agent will break the disulfide bonds, converting them to free thiol groups ($\mathrm{R-SH}$).

Question 18

Which of the following is a correct statement about the planarity of peptide bonds?

Accepted Answer

Peptide bonds are planar due to partial double-bond character from resonance between the carbonyl and amide nitrogen.

Question 19

Which of the following best explains the effect of phosphorylation on a peptide?

Accepted Answer

Phosphorylation adds a negative charge to the peptide, which can alter its structure and function.

Biochemistry Peptide Structure, Properties, and Protein Folding Study Notes

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