CHM 516: BIOPHYSICAL CHEMISTRY II
QUESTIONS AND ANSWERS
1. Protein Folding & Energy Landscapes
Question: Which of the following best describes the energy landscape for protein folding?
A. A flat potential surface with no barriers
B. A rugged funnel with many local minima leading to the native state
C. A single, deep energy well with no intermediates
D. A series of equally spaced energy levels
Correct Answer: B
Rationale: Protein folding is typically visualized as a funnel-shaped energy landscape that is rugged (has
many local minima) yet guides the protein toward its lowest-energy native conformation.
2. Structural Determination Techniques
Question: Which technique is most commonly used to determine the three-dimensional atomic
structure of proteins?
A. X-ray crystallography
B. Nuclear magnetic resonance (NMR) spectroscopy
C. Cryo-electron microscopy (cryo-EM)
D. Circular dichroism (CD) spectroscopy
Correct Answer: A
Rationale: X-ray crystallography remains the gold standard for obtaining high-resolution (atomic level)
structures of proteins, although cryo-EM and NMR are also valuable complementary techniques.
3. Secondary Structure Analysis
Question: Which spectroscopic technique is most sensitive to the secondary structure content (e.g.,
α-helix, β-sheet) of proteins?
Page 1 of 22
,A. UV-visible spectroscopy
B. Infrared (IR) spectroscopy
C. Circular dichroism (CD) spectroscopy
D. Fluorescence spectroscopy
Correct Answer: C
Rationale: Circular dichroism spectroscopy, especially in the far-UV region, is widely used to assess the
secondary structure of proteins.
4. Cooperative Binding
Question: A Hill coefficient (nₕ) greater than 1 in ligand binding studies indicates:
A. Negative cooperativity
B. No cooperativity
C. Positive cooperativity
D. Non-specific binding
Correct Answer: C
Rationale: A Hill coefficient greater than 1 suggests that binding of one ligand increases the affinity for
subsequent ligand binding—i.e., positive cooperativity.
5. Protein Stability
Question: Which thermodynamic parameter best reflects the stability of a folded protein?
A. ΔH (enthalpy change of folding)
B. ΔS (entropy change of folding)
C. ΔG (Gibbs free energy change of folding)
D. The melting temperature (Tm) only
Correct Answer: C
Rationale: Protein stability is governed by the Gibbs free energy change (ΔG) for folding (ΔG = ΔH – TΔS);
a more negative ΔG indicates a more stable folded state.
6. Enzyme Kinetics
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, Question: In Michaelis–Menten kinetics, the Michaelis constant (Kₘ) represents:
A. The maximum reaction rate
B. The substrate concentration at which the reaction rate is half of Vₘₐₓ
C. The turnover number (k_cat)
D. The binding affinity of an inhibitor
Correct Answer: B
Rationale: Kₘ is defined as the substrate concentration at which the reaction rate is half of its maximum
(Vₘₐₓ), reflecting the enzyme’s affinity for its substrate.
7. Enzyme Catalysis
Question: Which of the following is true regarding enzyme catalysis?
A. Enzymes increase the equilibrium constant of a reaction.
B. Enzymes lower the activation energy without affecting the overall free energy change (ΔG).
C. Enzymes are consumed during the reaction.
D. Enzymes change the ΔH of a reaction.
Correct Answer: B
Rationale: Enzymes function by lowering the activation energy required for a reaction, thereby
accelerating the rate without altering the overall equilibrium (ΔG) or the equilibrium constant.
8. Maximum Reaction Rate
Question: In enzyme kinetics, Vₘₐₓ represents:
A. The reaction rate when the enzyme is saturated with substrate
B. The substrate concentration at half-maximum rate
C. The enzyme turnover number
D. The rate constant for the reaction
Correct Answer: A
Rationale: Vₘₐₓ is the maximum velocity achieved when all enzyme active sites are fully occupied by
substrate.
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QUESTIONS AND ANSWERS
1. Protein Folding & Energy Landscapes
Question: Which of the following best describes the energy landscape for protein folding?
A. A flat potential surface with no barriers
B. A rugged funnel with many local minima leading to the native state
C. A single, deep energy well with no intermediates
D. A series of equally spaced energy levels
Correct Answer: B
Rationale: Protein folding is typically visualized as a funnel-shaped energy landscape that is rugged (has
many local minima) yet guides the protein toward its lowest-energy native conformation.
2. Structural Determination Techniques
Question: Which technique is most commonly used to determine the three-dimensional atomic
structure of proteins?
A. X-ray crystallography
B. Nuclear magnetic resonance (NMR) spectroscopy
C. Cryo-electron microscopy (cryo-EM)
D. Circular dichroism (CD) spectroscopy
Correct Answer: A
Rationale: X-ray crystallography remains the gold standard for obtaining high-resolution (atomic level)
structures of proteins, although cryo-EM and NMR are also valuable complementary techniques.
3. Secondary Structure Analysis
Question: Which spectroscopic technique is most sensitive to the secondary structure content (e.g.,
α-helix, β-sheet) of proteins?
Page 1 of 22
,A. UV-visible spectroscopy
B. Infrared (IR) spectroscopy
C. Circular dichroism (CD) spectroscopy
D. Fluorescence spectroscopy
Correct Answer: C
Rationale: Circular dichroism spectroscopy, especially in the far-UV region, is widely used to assess the
secondary structure of proteins.
4. Cooperative Binding
Question: A Hill coefficient (nₕ) greater than 1 in ligand binding studies indicates:
A. Negative cooperativity
B. No cooperativity
C. Positive cooperativity
D. Non-specific binding
Correct Answer: C
Rationale: A Hill coefficient greater than 1 suggests that binding of one ligand increases the affinity for
subsequent ligand binding—i.e., positive cooperativity.
5. Protein Stability
Question: Which thermodynamic parameter best reflects the stability of a folded protein?
A. ΔH (enthalpy change of folding)
B. ΔS (entropy change of folding)
C. ΔG (Gibbs free energy change of folding)
D. The melting temperature (Tm) only
Correct Answer: C
Rationale: Protein stability is governed by the Gibbs free energy change (ΔG) for folding (ΔG = ΔH – TΔS);
a more negative ΔG indicates a more stable folded state.
6. Enzyme Kinetics
Page 2 of 22
, Question: In Michaelis–Menten kinetics, the Michaelis constant (Kₘ) represents:
A. The maximum reaction rate
B. The substrate concentration at which the reaction rate is half of Vₘₐₓ
C. The turnover number (k_cat)
D. The binding affinity of an inhibitor
Correct Answer: B
Rationale: Kₘ is defined as the substrate concentration at which the reaction rate is half of its maximum
(Vₘₐₓ), reflecting the enzyme’s affinity for its substrate.
7. Enzyme Catalysis
Question: Which of the following is true regarding enzyme catalysis?
A. Enzymes increase the equilibrium constant of a reaction.
B. Enzymes lower the activation energy without affecting the overall free energy change (ΔG).
C. Enzymes are consumed during the reaction.
D. Enzymes change the ΔH of a reaction.
Correct Answer: B
Rationale: Enzymes function by lowering the activation energy required for a reaction, thereby
accelerating the rate without altering the overall equilibrium (ΔG) or the equilibrium constant.
8. Maximum Reaction Rate
Question: In enzyme kinetics, Vₘₐₓ represents:
A. The reaction rate when the enzyme is saturated with substrate
B. The substrate concentration at half-maximum rate
C. The enzyme turnover number
D. The rate constant for the reaction
Correct Answer: A
Rationale: Vₘₐₓ is the maximum velocity achieved when all enzyme active sites are fully occupied by
substrate.
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