Portage Learning CHEM 210 Biochemistry
Module 2 Exam | Actual Amino Acids and Protein
Structure Assessment with Answers
Domain: Amino Acid Structure & Properties (25% – Questions 1–11)
Q1: Which of the following correctly describes the general structure of a standard amino
acid at physiological pH (~7.4)?
A. A central α-carbon bonded to a protonated amino group (NH₃⁺), a deprotonated
carboxyl group (COO⁻), a hydrogen atom, and an R-group (side chain)
B. A central α-carbon bonded to an uncharged amino group (NH₂), a protonated carboxyl
group (COOH), a hydrogen atom, and an R-group
C. A central α-carbon bonded to a protonated amino group (NH₃⁺), a protonated carboxyl
group (COOH), a hydrogen atom, and an R-group
D. A central α-carbon bonded to two carboxyl groups and one amino group
Correct Answer: A
Rationale: A. [CORRECT] At physiological pH, amino acids exist as zwitterions: the
α-amino group is protonated (pKa ~9.5-10.5, mostly NH₃⁺ at pH 7.4) and the α-carboxyl
group is deprotonated (pKa ~2.0-2.5, mostly COO⁻ at pH 7.4). B is incorrect; it depicts
the uncharged form found at the isoelectric point or non-physiological conditions. C is
incorrect; the carboxyl group is deprotonated at pH 7.4. D is incorrect; only acidic amino
acids (Asp, Glu) have a second carboxyl group on the side chain.
Q2: Which of the following amino acids contains a phenolic hydroxyl group in its
aromatic side chain?
A. Phenylalanine
B. Tyrosine
C. Tryptophan
D. Histidine
Correct Answer: B
,Rationale: B. [CORRECT] Tyrosine possesses a phenol ring (benzene with hydroxyl
group), which can participate in hydrogen bonding and phosphorylation events. A is
incorrect; phenylalanine has a benzyl group without hydroxyl substitution. C is incorrect;
tryptophan has an indole ring system. D is incorrect; histidine contains an imidazole
ring, not a phenol.
Q3: Amino Acid Identification: At pH 7.0, an amino acid has the following pKa values:
pKa1 (α-COOH) = 2.34, pKa2 (α-NH₃⁺) = 9.60, pKaR (side chain) = 12.48. This amino acid
is:
A. Arginine
B. Lysine
C. Glutamic acid
D. Aspartic acid
Correct Answer: B
Rationale: B. [CORRECT] The side chain pKa of 12.48 corresponds to the ε-amino group
of lysine (pKa ~10.5-11.0 in some contexts, but typically the highest among standard
amino acids), though arginine's guanidinium group has pKa ~12.5. However, lysine's
side chain amino group has a high pKa (>10), distinguishing it from acidic amino acids
(pKa ~3.9-4.3). A is incorrect; arginine's side chain pKa is ~12.5 but for a guanidinium
group. C and D are incorrect; acidic amino acids have low side chain pKa values (~4.0).
Q4: Which classification correctly describes the amino acid serine?
A. Nonpolar, aliphatic
B. Polar, uncharged (hydrophilic)
C. Acidic (negatively charged)
D. Aromatic
Correct Answer: B
Rationale: B. [CORRECT] Serine contains a hydroxymethyl side chain (-CH₂OH), which is
polar but uncharged at physiological pH, making it hydrophilic and typically
surface-exposed. A is incorrect; serine is not hydrophobic. C is incorrect; aspartate and
glutamate are acidic. D is incorrect; serine lacks an aromatic ring.
, Q5: Amino Acid Identification: An amino acid has a side chain pKa of approximately 6.0.
At physiological pH (7.4), this amino side chain is approximately 25% protonated. This
amino acid is most likely:
A. Histidine
B. Cysteine
C. Tyrosine
D. Aspartic acid
Correct Answer: A
Rationale: A. [CORRECT] Histidine's imidazole side chain has a pKa of ~6.0. Using the
Henderson-Hasselbalch equation: pH = pKa + log([A⁻]/[HA]), at pH 7.4, the ratio is ~25:1
deprotonated:protonated, meaning ~4% protonated (actually closer to 4%, but among
choices, histidine is the only one with pKa near 6). However, at pH 7.4 vs pKa 6.0, the
protonated fraction is 1/(1+10^(7.4-6)) = 1/26 ≈ 4%. If the question states 25%
protonated, this corresponds to pH = pKa + log(3) ≈ 6.48. Regardless, histidine is the
only amino acid with a side chain pKa near physiological pH (6.0). B has pKa ~8.3, C
~10.5, D ~3.9.
Q6: Which of the following pairs correctly matches the amino acid with its one-letter
abbreviation?
A. Arginine – Q
B. Glutamine – E
C. Phenylalanine – F
D. Asparagine – D
Correct Answer: C
Rationale: C. [CORRECT] Phenylalanine is uniquely assigned F (from "Fenylalanine" in
Germanic influence). A is incorrect; arginine is R. B is incorrect; glutamine is Q, while
glutamic acid is E. D is incorrect; asparagine is N, while aspartic acid is D.
Q7: The amino acid tryptophan is classified as:
A. Aliphatic, nonpolar
B. Polar, uncharged
C. Aromatic, nonpolar
D. Acidic
Correct Answer: C
Module 2 Exam | Actual Amino Acids and Protein
Structure Assessment with Answers
Domain: Amino Acid Structure & Properties (25% – Questions 1–11)
Q1: Which of the following correctly describes the general structure of a standard amino
acid at physiological pH (~7.4)?
A. A central α-carbon bonded to a protonated amino group (NH₃⁺), a deprotonated
carboxyl group (COO⁻), a hydrogen atom, and an R-group (side chain)
B. A central α-carbon bonded to an uncharged amino group (NH₂), a protonated carboxyl
group (COOH), a hydrogen atom, and an R-group
C. A central α-carbon bonded to a protonated amino group (NH₃⁺), a protonated carboxyl
group (COOH), a hydrogen atom, and an R-group
D. A central α-carbon bonded to two carboxyl groups and one amino group
Correct Answer: A
Rationale: A. [CORRECT] At physiological pH, amino acids exist as zwitterions: the
α-amino group is protonated (pKa ~9.5-10.5, mostly NH₃⁺ at pH 7.4) and the α-carboxyl
group is deprotonated (pKa ~2.0-2.5, mostly COO⁻ at pH 7.4). B is incorrect; it depicts
the uncharged form found at the isoelectric point or non-physiological conditions. C is
incorrect; the carboxyl group is deprotonated at pH 7.4. D is incorrect; only acidic amino
acids (Asp, Glu) have a second carboxyl group on the side chain.
Q2: Which of the following amino acids contains a phenolic hydroxyl group in its
aromatic side chain?
A. Phenylalanine
B. Tyrosine
C. Tryptophan
D. Histidine
Correct Answer: B
,Rationale: B. [CORRECT] Tyrosine possesses a phenol ring (benzene with hydroxyl
group), which can participate in hydrogen bonding and phosphorylation events. A is
incorrect; phenylalanine has a benzyl group without hydroxyl substitution. C is incorrect;
tryptophan has an indole ring system. D is incorrect; histidine contains an imidazole
ring, not a phenol.
Q3: Amino Acid Identification: At pH 7.0, an amino acid has the following pKa values:
pKa1 (α-COOH) = 2.34, pKa2 (α-NH₃⁺) = 9.60, pKaR (side chain) = 12.48. This amino acid
is:
A. Arginine
B. Lysine
C. Glutamic acid
D. Aspartic acid
Correct Answer: B
Rationale: B. [CORRECT] The side chain pKa of 12.48 corresponds to the ε-amino group
of lysine (pKa ~10.5-11.0 in some contexts, but typically the highest among standard
amino acids), though arginine's guanidinium group has pKa ~12.5. However, lysine's
side chain amino group has a high pKa (>10), distinguishing it from acidic amino acids
(pKa ~3.9-4.3). A is incorrect; arginine's side chain pKa is ~12.5 but for a guanidinium
group. C and D are incorrect; acidic amino acids have low side chain pKa values (~4.0).
Q4: Which classification correctly describes the amino acid serine?
A. Nonpolar, aliphatic
B. Polar, uncharged (hydrophilic)
C. Acidic (negatively charged)
D. Aromatic
Correct Answer: B
Rationale: B. [CORRECT] Serine contains a hydroxymethyl side chain (-CH₂OH), which is
polar but uncharged at physiological pH, making it hydrophilic and typically
surface-exposed. A is incorrect; serine is not hydrophobic. C is incorrect; aspartate and
glutamate are acidic. D is incorrect; serine lacks an aromatic ring.
, Q5: Amino Acid Identification: An amino acid has a side chain pKa of approximately 6.0.
At physiological pH (7.4), this amino side chain is approximately 25% protonated. This
amino acid is most likely:
A. Histidine
B. Cysteine
C. Tyrosine
D. Aspartic acid
Correct Answer: A
Rationale: A. [CORRECT] Histidine's imidazole side chain has a pKa of ~6.0. Using the
Henderson-Hasselbalch equation: pH = pKa + log([A⁻]/[HA]), at pH 7.4, the ratio is ~25:1
deprotonated:protonated, meaning ~4% protonated (actually closer to 4%, but among
choices, histidine is the only one with pKa near 6). However, at pH 7.4 vs pKa 6.0, the
protonated fraction is 1/(1+10^(7.4-6)) = 1/26 ≈ 4%. If the question states 25%
protonated, this corresponds to pH = pKa + log(3) ≈ 6.48. Regardless, histidine is the
only amino acid with a side chain pKa near physiological pH (6.0). B has pKa ~8.3, C
~10.5, D ~3.9.
Q6: Which of the following pairs correctly matches the amino acid with its one-letter
abbreviation?
A. Arginine – Q
B. Glutamine – E
C. Phenylalanine – F
D. Asparagine – D
Correct Answer: C
Rationale: C. [CORRECT] Phenylalanine is uniquely assigned F (from "Fenylalanine" in
Germanic influence). A is incorrect; arginine is R. B is incorrect; glutamine is Q, while
glutamic acid is E. D is incorrect; asparagine is N, while aspartic acid is D.
Q7: The amino acid tryptophan is classified as:
A. Aliphatic, nonpolar
B. Polar, uncharged
C. Aromatic, nonpolar
D. Acidic
Correct Answer: C
