CHEM 210 Biochemistry | Portage Learning |
Academic Year 2026/2027 | Comprehensive
Examination
Module 1: Amino Acids & Protein Structure
1. Which of the following amino acids is classified as both glucogenic and
ketogenic?
A. Leucine
B. Alanine
C. Isoleucine
D. Lysine
C. Isoleucine
Rationale: Isoleucine is one of the few amino acids that is both glucogenic and
ketogenic. Its carbon skeleton is degraded into both acetyl-CoA (ketogenic) and
propionyl-CoA (glucogenic). Leucine and Lysine are purely ketogenic. Alanine is
purely glucogenic.
2. A patient presents with a genetic defect in the enzyme phenylalanine
hydroxylase. Which of the following is the most likely diagnosis?
A. Maple Syrup Urine Disease
B. Alkaptonuria
C. Phenylketonuria (PKU)
D. Homocystinuria
C. Phenylketonuria (PKU)
Rationale: Phenylalanine hydroxylase (PAH) converts phenylalanine to
tyrosine. A defect in this enzyme leads to a buildup of phenylalanine, which is the
biochemical hallmark of Phenylketonuria (PKU). Maple Syrup Urine Disease is
caused by a defect in branched-chain alpha-keto acid dehydrogenase.
Alkaptonuria is a defect in homogentisate oxidase. Homocystinuria is a defect in
cystathionine beta-synthase.
3. SATA: Which of the following statements about the peptide bond are true?
A. It has partial double-bond character.
,B. It allows for free rotation around the C-N bond.
C. It is a planar structure.
D. It is usually found in the cis conformation.
E. It is formed by a dehydration reaction.
A. It has partial double-bond character.
C. It is a planar structure.
E. It is formed by a dehydration reaction.
Rationale: The peptide bond has partial double-bond character due to
resonance, which restricts rotation (making B false). This partial double bond
enforces a planar structure around the bond. The trans conformation is strongly
favored over the cis conformation due to steric hindrance (making D false). The
bond is formed by removing a water molecule in a dehydration/condensation
reaction.
4. In the context of protein structure, a motif such as the helix-turn-helix is an
example of:
A. Primary structure
B. Secondary structure
C. Tertiary structure
D. Quaternary structure
B. Secondary structure
Rationale: A motif, like the helix-turn-helix or a beta-hairpin, is a specific
combination of secondary structural elements (alpha-helices and beta-sheets).
Therefore, it is a component of secondary structure. Tertiary structure refers to
the overall 3D fold of a single polypeptide chain.
5. Which amino acid has a side chain that can act as a nucleophile in the active
site of an enzyme at physiological pH?
A. Aspartate
B. Lysine
C. Serine
D. Phenylalanine
C. Serine
Rationale: The hydroxyl group on the side chain of serine is a potent
,nucleophile, especially when activated in the catalytic triad of enzymes like
chymotrypsin. Aspartate and Lysine are charged at physiological pH and can
participate in acid-base catalysis or ionic bonding, but are not typically strong
nucleophiles. Phenylalanine is nonpolar and non-reactive.
6. The unfolding of a protein, leading to the loss of its native three-dimensional
structure and function, is known as:
A. Hydrolysis
B. Denaturation
C. Oxidation
D. Renaturation
B. Denaturation
Rationale: Denaturation is the process where a protein loses its quaternary,
tertiary, and secondary structure due to the disruption of non-covalent bonds
(e.g., by heat, pH, or chemicals). This results in a loss of function. Renaturation is
the reverse process.
7. Which of the following is an example of a protein with a quaternary
structure?
A. Myoglobin
B. Alpha-keratin
C. Hemoglobin
D. Cytochrome c
C. Hemoglobin
Rationale: Hemoglobin is a tetramer composed of four polypeptide subunits
(two alpha and two beta chains), making it a classic example of a protein with
quaternary structure. Myoglobin and Cytochrome c are single polypeptide chains.
Alpha-keratin is primarily composed of alpha-helices.
8. SATA: Which of the following amino acids are considered essential and must
be obtained from the diet?
A. Valine
B. Aspartate
C. Methionine
, D. Glutamine
E. Tryptophan
A. Valine
C. Methionine
E. Tryptophan
Rationale: Valine, Methionine, and Tryptophan are all essential amino acids.
Aspartate and Glutamine are non-essential, as they can be synthesized by the
body.
9. The primary structure of a protein is determined by:
A. The number of alpha-helices and beta-sheets.
B. The sequence of amino acids.
C. The overall 3D shape of the protein.
D. The association of multiple polypeptide subunits.
B. The sequence of amino acids.
Rationale: Primary structure is defined as the linear sequence of amino acids
in a polypeptide chain, determined by the peptide bonds and the order of
residues.
10. A disulfide bond is a covalent bond formed between the side chains of which
two amino acids?
A. Two Alanine residues
B. A Lysine and a Glutamate residue
C. Two Cysteine residues
D. A Serine and a Threonine residue
C. Two Cysteine residues
Rationale: A disulfide bond is formed by the oxidation of two sulfhydryl (-SH)
groups on the side chains of two cysteine residues. This bond is important for
stabilizing the tertiary and quaternary structure of many proteins.
11. Which of the following techniques separates proteins based on their size?
A. Ion-exchange chromatography
B. Affinity chromatography
Academic Year 2026/2027 | Comprehensive
Examination
Module 1: Amino Acids & Protein Structure
1. Which of the following amino acids is classified as both glucogenic and
ketogenic?
A. Leucine
B. Alanine
C. Isoleucine
D. Lysine
C. Isoleucine
Rationale: Isoleucine is one of the few amino acids that is both glucogenic and
ketogenic. Its carbon skeleton is degraded into both acetyl-CoA (ketogenic) and
propionyl-CoA (glucogenic). Leucine and Lysine are purely ketogenic. Alanine is
purely glucogenic.
2. A patient presents with a genetic defect in the enzyme phenylalanine
hydroxylase. Which of the following is the most likely diagnosis?
A. Maple Syrup Urine Disease
B. Alkaptonuria
C. Phenylketonuria (PKU)
D. Homocystinuria
C. Phenylketonuria (PKU)
Rationale: Phenylalanine hydroxylase (PAH) converts phenylalanine to
tyrosine. A defect in this enzyme leads to a buildup of phenylalanine, which is the
biochemical hallmark of Phenylketonuria (PKU). Maple Syrup Urine Disease is
caused by a defect in branched-chain alpha-keto acid dehydrogenase.
Alkaptonuria is a defect in homogentisate oxidase. Homocystinuria is a defect in
cystathionine beta-synthase.
3. SATA: Which of the following statements about the peptide bond are true?
A. It has partial double-bond character.
,B. It allows for free rotation around the C-N bond.
C. It is a planar structure.
D. It is usually found in the cis conformation.
E. It is formed by a dehydration reaction.
A. It has partial double-bond character.
C. It is a planar structure.
E. It is formed by a dehydration reaction.
Rationale: The peptide bond has partial double-bond character due to
resonance, which restricts rotation (making B false). This partial double bond
enforces a planar structure around the bond. The trans conformation is strongly
favored over the cis conformation due to steric hindrance (making D false). The
bond is formed by removing a water molecule in a dehydration/condensation
reaction.
4. In the context of protein structure, a motif such as the helix-turn-helix is an
example of:
A. Primary structure
B. Secondary structure
C. Tertiary structure
D. Quaternary structure
B. Secondary structure
Rationale: A motif, like the helix-turn-helix or a beta-hairpin, is a specific
combination of secondary structural elements (alpha-helices and beta-sheets).
Therefore, it is a component of secondary structure. Tertiary structure refers to
the overall 3D fold of a single polypeptide chain.
5. Which amino acid has a side chain that can act as a nucleophile in the active
site of an enzyme at physiological pH?
A. Aspartate
B. Lysine
C. Serine
D. Phenylalanine
C. Serine
Rationale: The hydroxyl group on the side chain of serine is a potent
,nucleophile, especially when activated in the catalytic triad of enzymes like
chymotrypsin. Aspartate and Lysine are charged at physiological pH and can
participate in acid-base catalysis or ionic bonding, but are not typically strong
nucleophiles. Phenylalanine is nonpolar and non-reactive.
6. The unfolding of a protein, leading to the loss of its native three-dimensional
structure and function, is known as:
A. Hydrolysis
B. Denaturation
C. Oxidation
D. Renaturation
B. Denaturation
Rationale: Denaturation is the process where a protein loses its quaternary,
tertiary, and secondary structure due to the disruption of non-covalent bonds
(e.g., by heat, pH, or chemicals). This results in a loss of function. Renaturation is
the reverse process.
7. Which of the following is an example of a protein with a quaternary
structure?
A. Myoglobin
B. Alpha-keratin
C. Hemoglobin
D. Cytochrome c
C. Hemoglobin
Rationale: Hemoglobin is a tetramer composed of four polypeptide subunits
(two alpha and two beta chains), making it a classic example of a protein with
quaternary structure. Myoglobin and Cytochrome c are single polypeptide chains.
Alpha-keratin is primarily composed of alpha-helices.
8. SATA: Which of the following amino acids are considered essential and must
be obtained from the diet?
A. Valine
B. Aspartate
C. Methionine
, D. Glutamine
E. Tryptophan
A. Valine
C. Methionine
E. Tryptophan
Rationale: Valine, Methionine, and Tryptophan are all essential amino acids.
Aspartate and Glutamine are non-essential, as they can be synthesized by the
body.
9. The primary structure of a protein is determined by:
A. The number of alpha-helices and beta-sheets.
B. The sequence of amino acids.
C. The overall 3D shape of the protein.
D. The association of multiple polypeptide subunits.
B. The sequence of amino acids.
Rationale: Primary structure is defined as the linear sequence of amino acids
in a polypeptide chain, determined by the peptide bonds and the order of
residues.
10. A disulfide bond is a covalent bond formed between the side chains of which
two amino acids?
A. Two Alanine residues
B. A Lysine and a Glutamate residue
C. Two Cysteine residues
D. A Serine and a Threonine residue
C. Two Cysteine residues
Rationale: A disulfide bond is formed by the oxidation of two sulfhydryl (-SH)
groups on the side chains of two cysteine residues. This bond is important for
stabilizing the tertiary and quaternary structure of many proteins.
11. Which of the following techniques separates proteins based on their size?
A. Ion-exchange chromatography
B. Affinity chromatography
