ACS Biochemistry Study Guide
Updated 2025/2026 Syllabus | 100+ Answered Questions
1. Amino Acids & Protein Structure
Q1: What structural feature distinguishes proline from other standard amino
acids?
ANSWER: Proline contains a secondary amine group, forming a cyclic side chain that
links back to the backbone nitrogen, making it an imino acid. This restricts
conformational flexibility and often introduces kinks in polypeptide chains.
Q2: Which amino acid is most likely to disrupt an alpha helix when placed within
it?
ANSWER: Proline ✓, due to its rigid ring structure, which prevents proper phi bond
rotation and lacks an amide hydrogen for intrahelical hydrogen bonding.
Q3: How does the Henderson-Hasselbalch equation relate to amino acid titration?
ANSWER: It predicts the pH at which an amino acid’s functional group is
half-deprotonated (pKa) and is used to determine the isoelectric point (pI). For amino
acids with two titratable groups, pI = (pKa1 + pKa2)/2.
Q4: What defines the primary structure of a protein?
ANSWER: The linear sequence of amino acids linked by peptide bonds.
Q5: What stabilizes the alpha-helix secondary structure?
ANSWER: Intramolecular hydrogen bonds between the carbonyl oxygen of
residue *i* and the amide hydrogen of residue *i+4*.
Q6: In a beta-sheet, what is meant by “antiparallel” versus “parallel”?
ANSWER: Antiparallel beta-sheets have adjacent strands running in opposite directions
(N→C opposite C→N), forming linear H-bonds. Parallel sheets have strands running in
the same direction, with angled H-bonds.
Q7: What role do chaperone proteins play in protein folding?
ANSWER: They assist in proper folding by providing an isolated environment,
preventing aggregation, and sometimes using ATP to unfold misfolded proteins for
another folding attempt.
, Q8: What is the thermodynamic driving force for protein folding?
ANSWER: The hydrophobic effect (burial of nonpolar residues) is the major driver, along
with formation of hydrogen bonds and van der Waals interactions, despite the
conformational entropy loss.
Q9: How does urea denature proteins?
ANSWER: Urea disrupts hydrogen bonding and hydrophobic interactions by acting as
both a hydrogen-bond donor/acceptor and by increasing water solubility of nonpolar
groups.
Q10: What is the significance of the Ramachandran plot?
ANSWER: It visualizes allowed dihedral angle (phi/psi) combinations for polypeptide
backbones, identifying sterically permitted conformations for secondary structures like
alpha-helices and beta-sheets.
2. Enzymes & Kinetics
Q11: Define the Michaelis constant KmKm.
ANSWER: KmKm is the substrate concentration at which the reaction velocity is half
of VmaxVmax. It reflects the enzyme’s apparent affinity for the substrate (lower KmKm
= higher affinity).
Q12: What does the Lineweaver-Burk plot allow you to determine?
ANSWER: A double-reciprocal plot (1/v1/v vs. 1/[S]1/[S]) used to
determine VmaxVmax and KmKm from the intercepts, and to diagnose enzyme
inhibition patterns.
Q13: How does competitive inhibition affect KmKm and VmaxVmax?
ANSWER: Increases apparent KmKm (lowers apparent affinity); VmaxVmax remains
unchanged because sufficient substrate can outcompete the inhibitor.
Q14: Contrast competitive vs. noncompetitive inhibition.
ANSWER: Competitive inhibitors bind the active site; noncompetitive inhibitors bind a
site distinct from the active site, often altering enzyme conformation and
reducing VmaxVmax without changing KmKm.
Q15: What is allosteric regulation?
ANSWER: Regulation of an enzyme’s activity by binding of an effector molecule at a site
Updated 2025/2026 Syllabus | 100+ Answered Questions
1. Amino Acids & Protein Structure
Q1: What structural feature distinguishes proline from other standard amino
acids?
ANSWER: Proline contains a secondary amine group, forming a cyclic side chain that
links back to the backbone nitrogen, making it an imino acid. This restricts
conformational flexibility and often introduces kinks in polypeptide chains.
Q2: Which amino acid is most likely to disrupt an alpha helix when placed within
it?
ANSWER: Proline ✓, due to its rigid ring structure, which prevents proper phi bond
rotation and lacks an amide hydrogen for intrahelical hydrogen bonding.
Q3: How does the Henderson-Hasselbalch equation relate to amino acid titration?
ANSWER: It predicts the pH at which an amino acid’s functional group is
half-deprotonated (pKa) and is used to determine the isoelectric point (pI). For amino
acids with two titratable groups, pI = (pKa1 + pKa2)/2.
Q4: What defines the primary structure of a protein?
ANSWER: The linear sequence of amino acids linked by peptide bonds.
Q5: What stabilizes the alpha-helix secondary structure?
ANSWER: Intramolecular hydrogen bonds between the carbonyl oxygen of
residue *i* and the amide hydrogen of residue *i+4*.
Q6: In a beta-sheet, what is meant by “antiparallel” versus “parallel”?
ANSWER: Antiparallel beta-sheets have adjacent strands running in opposite directions
(N→C opposite C→N), forming linear H-bonds. Parallel sheets have strands running in
the same direction, with angled H-bonds.
Q7: What role do chaperone proteins play in protein folding?
ANSWER: They assist in proper folding by providing an isolated environment,
preventing aggregation, and sometimes using ATP to unfold misfolded proteins for
another folding attempt.
, Q8: What is the thermodynamic driving force for protein folding?
ANSWER: The hydrophobic effect (burial of nonpolar residues) is the major driver, along
with formation of hydrogen bonds and van der Waals interactions, despite the
conformational entropy loss.
Q9: How does urea denature proteins?
ANSWER: Urea disrupts hydrogen bonding and hydrophobic interactions by acting as
both a hydrogen-bond donor/acceptor and by increasing water solubility of nonpolar
groups.
Q10: What is the significance of the Ramachandran plot?
ANSWER: It visualizes allowed dihedral angle (phi/psi) combinations for polypeptide
backbones, identifying sterically permitted conformations for secondary structures like
alpha-helices and beta-sheets.
2. Enzymes & Kinetics
Q11: Define the Michaelis constant KmKm.
ANSWER: KmKm is the substrate concentration at which the reaction velocity is half
of VmaxVmax. It reflects the enzyme’s apparent affinity for the substrate (lower KmKm
= higher affinity).
Q12: What does the Lineweaver-Burk plot allow you to determine?
ANSWER: A double-reciprocal plot (1/v1/v vs. 1/[S]1/[S]) used to
determine VmaxVmax and KmKm from the intercepts, and to diagnose enzyme
inhibition patterns.
Q13: How does competitive inhibition affect KmKm and VmaxVmax?
ANSWER: Increases apparent KmKm (lowers apparent affinity); VmaxVmax remains
unchanged because sufficient substrate can outcompete the inhibitor.
Q14: Contrast competitive vs. noncompetitive inhibition.
ANSWER: Competitive inhibitors bind the active site; noncompetitive inhibitors bind a
site distinct from the active site, often altering enzyme conformation and
reducing VmaxVmax without changing KmKm.
Q15: What is allosteric regulation?
ANSWER: Regulation of an enzyme’s activity by binding of an effector molecule at a site
