MChem Master of Chemistry Biochemistry and Chemical Biology 1 — Questions and Answers
Question 1: What is the function of ATP synthase (Complex V) in oxidative phosphorylation?
- It transfers electrons from NADH to ubiquinone
- It uses the proton gradient across the inner mitochondrial membrane to synthesize ATP from ADP + Pi (Correct answer)
- It directly oxidizes FADH2 to produce ATP
- It pumps protons out of the mitochondrial matrix using electron transport
Correct answer: It uses the proton gradient across the inner mitochondrial membrane to synthesize ATP from ADP + Pi
ATP synthase harnesses the proton motive force (proton gradient + membrane potential) built by the electron transport chain to drive the rotation of the F0 subunit and synthesize ATP.
Question 2: In enzyme kinetics, what does the Michaelis constant (Km) represent?
- The maximum rate of catalysis at saturating substrate
- The substrate concentration at which reaction velocity is half of Vmax (Correct answer)
- The rate of enzyme-product complex dissociation
- The equilibrium constant for the overall reaction
Correct answer: The substrate concentration at which reaction velocity is half of Vmax
Km is the substrate concentration at which reaction velocity equals Vmax/2, reflecting the apparent affinity of an enzyme for its substrate.
Question 3: Which type of enzyme inhibition increases the apparent Km without affecting Vmax?
- Uncompetitive inhibition
- Competitive inhibition (Correct answer)
- Non-competitive inhibition
- Mixed inhibition
Correct answer: Competitive inhibition
Competitive inhibitors bind the active site and increase apparent Km (reduced substrate affinity) but can be overcome by excess substrate, leaving Vmax unchanged.
Question 4: What is the role of coenzyme A (CoA) in metabolic pathways?
- It carries hydride ions between oxidation reactions
- It activates and transfers acyl groups in fatty acid and carbohydrate metabolism (Correct answer)
- It donates methyl groups in methylation reactions
- It carries amino acids during protein synthesis
Correct answer: It activates and transfers acyl groups in fatty acid and carbohydrate metabolism
CoA forms high-energy thioester bonds with acyl groups (e.g., acetyl-CoA), activating them for transfer reactions in the citric acid cycle, fatty acid synthesis, and β-oxidation.
Question 5: What chemical modification is responsible for the activity of serine proteases like chymotrypsin?
- A zinc ion coordinated in the active site that activates water
- A catalytic triad (Ser–His–Asp) that activates the serine hydroxyl as a nucleophile (Correct answer)
- A covalent flavin prosthetic group that accepts electrons
- A heme iron center that binds and activates oxygen
Correct answer: A catalytic triad (Ser–His–Asp) that activates the serine hydroxyl as a nucleophile
The Ser-His-Asp catalytic triad lowers the pKa of serine, enabling it to act as a powerful nucleophile that attacks peptide carbonyl groups, forming an acyl-enzyme intermediate.
Question 6: In DNA replication, what is the chemical basis for the 3'→5' proofreading activity of DNA polymerase?
- A separate exonuclease enzyme removes mismatched bases after replication
- DNA polymerase has an intrinsic 3'→5' exonuclease domain that excises incorrectly incorporated nucleotides (Correct answer)
- The DNA helicase corrects mismatches as it unwinds the double helix
- Mismatch repair proteins act during replication to immediately fix errors
Correct answer: DNA polymerase has an intrinsic 3'→5' exonuclease domain that excises incorrectly incorporated nucleotides
DNA polymerase III possesses a 3'→5' exonuclease domain that recognizes and excises mismatched 3'-terminal nucleotides, then re-synthesizes the correct sequence.
MChem Master of Chemistry Biochemistry and Chemical Biology 1
What is the function of ATP synthase (Complex V) in oxidative phosphorylation?