Ultimate ACS Biochemistry Exam Study Guide: 105 Practice Questions on Enzyme Kinetics, Metabolism, DNA Replication & Lab Techniques (With Answers & Explanations)

Ultimate ACS Biochemistry Exam Study Guide: 105 Practice
Questions on Enzyme Kinetics, Metabolism, DNA Replication &
Lab Techniques (With Answers & Explanations)

Amino Acids & Protein Structure (1-15)
Q1. Which amino acid contains a secondary amine group rather than a primary amine?
 A) Glycine
 B) Alanine
 C) Proline
 D) Lysine
Proline has a cyclic side chain that bonds back to the nitrogen atom, forming a
secondary amine (imino acid). This rigid structure disrupts alpha helices.
Q2. Which of the following amino acids has a side chain that can form hydrogen bonds and
is often found in active sites?
 A) Leucine
 B) Serine
 C) Valine
 D) Phenylalanine
Serine contains a hydroxyl group (-OH) that acts as a hydrogen bond
donor/acceptor and serves as a nucleophile in many enzyme active sites (e.g.,
serine proteases).
Q3. At pH 7.4, what is the net charge of a free histidine amino acid? (pKa values: α-COOH
~2.2, α-NH₃⁺ ~9.0, side chain ~6.0)
 A) +2
 B) +1
 C) 0
 D) -1
*At pH 7.4: α-COOH is deprotonated (-1), α-NH₃⁺ is protonated (+1), side chain

, imidazole is protonated (+1) because pH > pKa? Wait — pKa side chain is 6.0, pH
7.4 > pKa, so side chain is deprotonated (0). Net = +1 -1 +0 = 0? Correction: α-
COO⁻ (-1), α-NH₃⁺ (+1), side chain (0) = net 0. But common ACS trick: histidine side
chain pKa ~6, at pH 7.4 it's mostly deprotonated, so net 0. However, many ACS
exams list answer as 0. Let me verify — actually correct calculation: α-NH₃⁺ (+1), α-
COO⁻ (-1), side chain neutral (0) = 0. Answer is 0.*
Q4. Which technique separates proteins primarily by molecular weight?
 A) SDS-PAGE
 B) Ion exchange chromatography
 C) Affinity chromatography
 D) Isoelectric focusing
SDS denatures proteins and coats them with negative charge, so migration in
polyacrylamide gel depends only on molecular weight (smaller = faster).
Q5. The alpha helix is stabilized primarily by:
 A) Disulfide bonds
 B) Hydrophobic interactions
 C) Hydrogen bonds between backbone amide and carbonyl groups
 D) Ionic interactions between side chains
*Each carbonyl oxygen (residue n) hydrogen bonds with the amide hydrogen
(residue n+4), forming a regular helical pattern.*
Q6. Which level of protein structure describes the three-dimensional arrangement of
multiple polypeptide chains?
 A) Primary
 B) Secondary
 C) Tertiary
 D) Quaternary
Quaternary structure refers to the assembly of two or more separate
polypeptide subunits into a functional protein (e.g., hemoglobin α₂β₂).
Q7. The β-pleated sheet is characterized by:

,  A) Helical turns every 3.6 residues
 B) Extended polypeptide chains stabilized by hydrogen bonds between
adjacent strands
 C) Covalent crosslinks between cysteine residues
 D) Complete absence of hydrogen bonding
Adjacent β-strands run parallel or antiparallel, with backbone hydrogen bonds
forming between strands perpendicular to the strand direction.
Q8. Which reagent reduces disulfide bonds?
 A) Urea
 B) β-Mercaptoethanol
 C) SDS
 D) Protease K
β-Mercaptoethanol (BME) breaks disulfide bonds (-S-S-) by reducing them to
free thiols (-SH). Urea denatures via hydrogen bond disruption but doesn't
reduce disulfides.
Q9. A protein binds to a specific DNA sequence. Which structure is most directly involved?
 A) Primary structure only
 B) A motif such as a helix-turn-helix
 C) Quaternary structure alone
 D) Random coil
DNA-binding proteins often contain structural motifs like helix-turn-helix, zinc
fingers, or leucine zippers that recognize specific DNA sequences.
Q10. Which amino acid residue is phosphorylated most commonly in eukaryotic signaling?
 A) Serine
 B) Phenylalanine
 C) Isoleucine
 D) Methionine
Serine, threonine, and tyrosine are phosphorylated, with serine being the most
frequent (approx. 86% of phosphorylation sites).