CHEM 219 Final Exam Comprehensive
Questions on Biomolecular Structure,
Function & Chemical Biology | UCI
1. The type of chemical linkage involved in the
polymerization of amino acids into proteins is:
A) Phosphodiester bond
B) Peptide bond
C) Hydrogen bond
D) Carbon-carbon sigma bond
Answer: B | Rationale: Amino acids are linked by peptide
(amide) bonds formed between the carboxyl group of one
amino acid and the amino group of the next, with the
elimination of water .
2. The native conformation of a protein is most dependent
on what aspect of protein structure?
A) Primary amino acid sequence
B) Secondary structure
C) α-helix and β-pleated sheets
D) The total number of hydrogen bonds present
Answer: A | Rationale: The primary amino acid sequence
determines the native three-dimensional conformation of a
protein. The sequence encodes all the information required
for folding into the native structure .
,3. Which amino acid most restricts the configuration of a
peptide backbone?
A) Arg
B) Asp
C) Pro
D) Gly
Answer: C | Rationale: Proline restricts peptide backbone
configuration because its side chain is covalently bonded
back to the nitrogen atom, forming a ring structure that
limits rotation around the N-Cα bond .
4. What force is most dominant in driving a protein from an
ensemble of unfolded states to a compact globular
structure?
A) Hydrogen bonding
B) Hydrophobic collapse
C) Disulfide bonding
D) Formation of helices
Answer: B | Rationale: The hydrophobic effect—the
tendency of nonpolar groups to aggregate to minimize
contact with water—is the dominant driving force in protein
folding, driving the polypeptide chain to collapse into a
compact globular structure .
,5. The rate-limiting step in protein folding is often the cis-
trans isomerization of the peptide bond for which amino
acid?
A) Alanine
B) Proline
C) Lysine
D) Histidine
Answer: B | Rationale: Proline residues have a unique
peptide bond that can exist in cis or trans conformations.
The slow interconversion between these conformations is
often a rate-limiting step in protein folding .
6. Which structural element(s) most commonly stabilize
polar groups in the interior of a protein?
A) Primary structure
B) Secondary structure
C) Quaternary structure
D) Disulfide bonds
Answer: B | Rationale: Secondary structure elements (α-
helices and β-sheets) commonly stabilize polar groups in the
protein interior through hydrogen bonding networks that
satisfy the hydrogen-bonding potential of the peptide
backbone .
7. The absorption spectrum of a protein is related to which
group of amino acids?
, A) He, Leu, Met
B) Phe, Tyr, Trp
C) Asp, Glu
D) Lys, His, Arg
Answer: B | Rationale: Aromatic amino acids—
phenylalanine, tyrosine, and tryptophan—absorb UV light
due to their conjugated ring systems. This property is used
in protein quantification at 280 nm .
8. Which reagent could best be used to cleave disulfide
bonds in proteins?
A) p-nitrophenylacetate
B) Iodoacetamide
C) Phenyl isothiocyanate
D) β-mercaptoethanol
Answer: D | Rationale: β-mercaptoethanol (and DTT) are
reducing agents that cleave disulfide bonds by reducing
them to free thiols. This is a key step in protein denaturation
and sequencing workflows .
9. Which reagent would be most useful in producing a small
number of fragmentation products from a protein?
A) Dilute HCl hydrolysis
B) Chymotrypsin digestion
C) Pepsin digestion
Questions on Biomolecular Structure,
Function & Chemical Biology | UCI
1. The type of chemical linkage involved in the
polymerization of amino acids into proteins is:
A) Phosphodiester bond
B) Peptide bond
C) Hydrogen bond
D) Carbon-carbon sigma bond
Answer: B | Rationale: Amino acids are linked by peptide
(amide) bonds formed between the carboxyl group of one
amino acid and the amino group of the next, with the
elimination of water .
2. The native conformation of a protein is most dependent
on what aspect of protein structure?
A) Primary amino acid sequence
B) Secondary structure
C) α-helix and β-pleated sheets
D) The total number of hydrogen bonds present
Answer: A | Rationale: The primary amino acid sequence
determines the native three-dimensional conformation of a
protein. The sequence encodes all the information required
for folding into the native structure .
,3. Which amino acid most restricts the configuration of a
peptide backbone?
A) Arg
B) Asp
C) Pro
D) Gly
Answer: C | Rationale: Proline restricts peptide backbone
configuration because its side chain is covalently bonded
back to the nitrogen atom, forming a ring structure that
limits rotation around the N-Cα bond .
4. What force is most dominant in driving a protein from an
ensemble of unfolded states to a compact globular
structure?
A) Hydrogen bonding
B) Hydrophobic collapse
C) Disulfide bonding
D) Formation of helices
Answer: B | Rationale: The hydrophobic effect—the
tendency of nonpolar groups to aggregate to minimize
contact with water—is the dominant driving force in protein
folding, driving the polypeptide chain to collapse into a
compact globular structure .
,5. The rate-limiting step in protein folding is often the cis-
trans isomerization of the peptide bond for which amino
acid?
A) Alanine
B) Proline
C) Lysine
D) Histidine
Answer: B | Rationale: Proline residues have a unique
peptide bond that can exist in cis or trans conformations.
The slow interconversion between these conformations is
often a rate-limiting step in protein folding .
6. Which structural element(s) most commonly stabilize
polar groups in the interior of a protein?
A) Primary structure
B) Secondary structure
C) Quaternary structure
D) Disulfide bonds
Answer: B | Rationale: Secondary structure elements (α-
helices and β-sheets) commonly stabilize polar groups in the
protein interior through hydrogen bonding networks that
satisfy the hydrogen-bonding potential of the peptide
backbone .
7. The absorption spectrum of a protein is related to which
group of amino acids?
, A) He, Leu, Met
B) Phe, Tyr, Trp
C) Asp, Glu
D) Lys, His, Arg
Answer: B | Rationale: Aromatic amino acids—
phenylalanine, tyrosine, and tryptophan—absorb UV light
due to their conjugated ring systems. This property is used
in protein quantification at 280 nm .
8. Which reagent could best be used to cleave disulfide
bonds in proteins?
A) p-nitrophenylacetate
B) Iodoacetamide
C) Phenyl isothiocyanate
D) β-mercaptoethanol
Answer: D | Rationale: β-mercaptoethanol (and DTT) are
reducing agents that cleave disulfide bonds by reducing
them to free thiols. This is a key step in protein denaturation
and sequencing workflows .
9. Which reagent would be most useful in producing a small
number of fragmentation products from a protein?
A) Dilute HCl hydrolysis
B) Chymotrypsin digestion
C) Pepsin digestion
