Q: Which of the following equations correctly describes the fraction of ligand binding sites occupied (θ) for a protein-ligand interaction?

$\theta = \frac{[L]}{[L] + K_d}$

Question 1

Which of the following statements best explains why the peptide bond in proteins is rigid and planar?

Accepted Answer

The peptide bond has partial double bond character due to resonance, restricting rotation.

Question 2

A protein is purified using size-exclusion chromatography (SEC) and then analyzed by SDS-PAGE. The SEC elution volume corresponds to a molecular weight of 120 kDa, while SDS-PAGE shows a single band at 30 kDa. What is the most likely quaternary structure of this protein?

Accepted Answer

The protein is a tetramer of 30 kDa subunits.

Question 3

Which amino acid is most likely to be found at the N-terminus of a protein after treatment with Sanger’s reagent (FDNB) and acid hydrolysis?

Accepted Answer

The amino acid with a free amino group not involved in a peptide bond.

Question 4

During ion-exchange chromatography using a DEAE column at pH 8.0, which protein will bind most strongly to the column?

Accepted Answer

A protein with a pI of 5.0

Question 5

Which of the following best describes the effect of 2,3-bisphosphoglycerate (BPG) on hemoglobin?

Accepted Answer

BPG binds to the central cavity of hemoglobin, stabilizing the T state and decreasing oxygen affinity.

Question 6

A protein sample is analyzed by isoelectric focusing. At pH 6.0, the protein migrates toward the cathode (negative electrode). What does this indicate about the protein’s isoelectric point (pI)?

Accepted Answer

The pI is greater than 6.0.

Question 7

Which of the following amino acid substitutions is most likely to be a conservative substitution?

Accepted Answer

Leucine replaced by isoleucine

Question 8

Which of the following best explains why proline is considered a 'helix breaker' in alpha helices?

Accepted Answer

Proline lacks an amide hydrogen, preventing intrahelical hydrogen bonding and introduces a rigid kink.

Question 9

A researcher is using affinity chromatography to purify a His-tagged protein. Which elution method is most appropriate to specifically release the His-tagged protein from a Ni-NTA column?

Accepted Answer

Add imidazole to compete with the His-tag for nickel binding.

Question 10

Which of the following equations correctly describes the fraction of ligand binding sites occupied (θ) for a protein-ligand interaction?

Accepted Answer

$	heta = \frac{[L]}{[L] + K_d}$

Question 11

A patient with sickle cell anemia has a mutation in the β-globin gene. Which amino acid substitution is responsible for the disease, and what is the consequence at the molecular level?

Accepted Answer

Glutamate is replaced by valine at position 6, creating a hydrophobic patch that promotes hemoglobin aggregation.

Question 12

Which of the following best describes the Bohr effect in hemoglobin?

Accepted Answer

A decrease in pH (increase in H+) promotes oxygen release from hemoglobin by stabilizing the T state.

Question 13

Which of the following statements about the Ramachandran plot is correct?

Accepted Answer

It plots the phi ($\phi$) and psi ($\psi$) backbone dihedral angles, indicating allowed regions for secondary structures.

Question 14

A protein is denatured by urea. Which level(s) of protein structure are disrupted by this treatment?

Accepted Answer

Secondary, tertiary, and quaternary structures are disrupted, but the primary structure remains intact.

Question 15

Which of the following best explains why myoglobin is a poor oxygen transport protein compared to hemoglobin?

Accepted Answer

Myoglobin binds oxygen with high affinity and does not release it efficiently at tissue oxygen pressures.

Question 16

Which of the following is a correct statement about the use of absorbance at 280 nm to estimate protein concentration?

Accepted Answer

It can overestimate protein concentration if the protein has many tryptophan residues.

Question 17

Which of the following best describes the role of the distal histidine (His E7) in myoglobin?

Accepted Answer

It forms a hydrogen bond with bound oxygen, stabilizing the O$_2$ binding and reducing CO binding affinity.

Question 18

A protein is subjected to Edman degradation. What is the main advantage of this method over Sanger’s method for N-terminal sequencing?

Accepted Answer

Edman degradation can sequentially identify multiple N-terminal residues without destroying the peptide.

Question 19

Which of the following best describes the effect of a negatively charged environment on the pKa of a carboxyl group in a protein?

Accepted Answer

The pKa increases because the negative environment destabilizes the deprotonated form.

Protein Structure, Purification, and Function: Study Notes for Biochemistry

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