MCAT Biochemistry Study Guide Exam
Questions and Verified Answers | A+
Graded | Latest Update 2025/2026
Concept Check 1.1
Amino Acids Found in Proteins
What are the four groups attached to the central (a) carbon of
a proteinogenic amino acid?
The four groups are an amino group (-NH2), a carboxylic group (-
COOH), a hydrogen atom, and an R group
What is the stereochemistry of the chiral amino acids that
appear in eukaryotic proteins? L or D? (R) or (S)?
(Exception:____________)
All chiral eukaryotic amino acids are L. All chiral eukaryotic amino
acids are (S), with the exception of cysteine (because cysteine is
the only amino acid with an R group that has a higher priority than
a carboxylic acid according to the Cahn-Ingold-Prelog rules)
Which amino acids fir into each of these categories?
Nonpolar, nonaromatic (7):
Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Proline
Which amino acids fir into each of these categories?
Aromatic (3):
Tryptophan, Phenylalanine, Tyrosine
Which amino acids fir into each of these categories?
Polar (5):
Serine, Threonine, Asparagine, Glutamine, Cysteine
Which amino acids fir into each of these categories?
Negatively charged/acidic (2):
Aspartate, Glutamate
Which amino acids fir into each of these categories?
Positively charged/basic (3):
Lysine, Arginine, Histidine
,Where do hydrophobic amino acids tend to reside within a
protein? What about a hydrophilic ones?
Hydrophobic amino acids tend to reside in the interior of a protein,
away from water. Hydrophilic amino acids tend to remain on the
surface of the protein, in contact with water.
Concept Check 1.2:
Acid-Base Chemistry of Amino Acids
For a generic amino acid NH2CRHCOOH, with an uncharged
side chain, what would be the predominant form at each of
the following pH values?
pH = 1 :_______________
pH = 7 :______________
pH = 11: ______________
pH = 1 : +NH3CRHCOOH
pH = 7 :+NH3CRHCOO-
pH = 11: NH2CRHCOO-
Given the following pKa values, what is the value of the pI for
each of the amino acids listed below?
Aspartic acid (pKa1=1.88, pKa2=3.65, pKa3=9.60)
Arginine (pKa1=2.17, pKa2=9.04, pKa3=12.48)
Valine (pKa1=2.32, pKa2=9.62)
Aspartic acid pI=(1.88+3.65) /2 = 2.77
Arginine pI=(9.04+12.48) /2 = 10.76
Valine pI= (2.32_9.62) /2 =5.97
Concept Check 1.3:
Peptide Bond Formation and Hydrolysis
What is the difference between an amino acid, a dipeptide, a
tripeptide, an oligopeptide, and a polypeptide?
These species differ by the number of amino acids that make
them up:
,amino acid=1
dipeptide=2
tripeptide=3
oligopeptide="few" (<20)
polypeptide = "many" (>20)
What molecule is released during formation of a peptide
bond?
Water (H2O)
If chymotrypsin cleaves at the carboxyl end of phenylalanine,
tryptophan, and tyrosine, how many oligopeptides would be
formed in enzymatic cleavage of the following molecule with
chymotrypsin?
Val-Phe-Glu-Lys-Tyr-Phe-Trp-Ile-Met-Tyr-Gly-Ala
4: Val-Phe; Glu-Lys-Tyr; Ile-Met-Tyr; Gly-Ala.
A single amino acid on its own is not considered an oligopeptide
Concept Check 1.4:
Primary and Secondary Protein Structure
Define Primary Structure:
Linear sequence of amino acids in chain
Subtypes of Primary Structure:
(none)
Stabilizing Bonds of Primary Structure:
Peptide (amide) bond
Define Secondary Structure:
Local structure determined by nearby amino acids
Subtypes of Secondary Structure:
a-helix
B-pleated sheets
Stabilizing Bonds of Secondary Structure:
Hydrogen Bonds
What role does proline serve in secondary structure?
Proline's rigid structure causes it to introduce kinks in a-helices, or
create turns in B-pleated sheets.
Concept Check 1.5:
, Tertiary and Quaternary Protein Structure
Define Tertiary Structure:
Three-dimensional shape of protein
Subtypes of Primary Structure
-Hydrophobic interactions
-Acid-base/salt-bridges
-Disulfide links
Stabilizing Bonds of Tertiary Structure:
-Van der Waals forces
-Hydrogen bonds
-Ionic bonds
-Covalent bonds
Define Quaternary Structure:
Interaction between separate subunits of a multisubunit protein
Subtypes of Quaternary Structure:
(none)
Stabilizing Bonds of Quaternary Structure:
Same as tertiary structure
-Van der Waals forces
-Hydrogen bonds
-Ionic bonds
-Covalent bonds
What is the primary motivation for hydrophobic residues in a
polypeptide to move to the interior of the protein?
Moving hydrophobic residues to the interior of a protein increases
entropy by allowing water molecules on the surface of the protein
to have more possible positions and configurations. This positive
deltaS makes deltaG<0, stabilizing the protein.
Concept Check 1.6:
Denaturation
Why are proteins denatured by heat and solutes,
respectively?
Heat denatures proteins by increasing their average kinetic
energy, thus disrupting hydrophobic
Questions and Verified Answers | A+
Graded | Latest Update 2025/2026
Concept Check 1.1
Amino Acids Found in Proteins
What are the four groups attached to the central (a) carbon of
a proteinogenic amino acid?
The four groups are an amino group (-NH2), a carboxylic group (-
COOH), a hydrogen atom, and an R group
What is the stereochemistry of the chiral amino acids that
appear in eukaryotic proteins? L or D? (R) or (S)?
(Exception:____________)
All chiral eukaryotic amino acids are L. All chiral eukaryotic amino
acids are (S), with the exception of cysteine (because cysteine is
the only amino acid with an R group that has a higher priority than
a carboxylic acid according to the Cahn-Ingold-Prelog rules)
Which amino acids fir into each of these categories?
Nonpolar, nonaromatic (7):
Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Proline
Which amino acids fir into each of these categories?
Aromatic (3):
Tryptophan, Phenylalanine, Tyrosine
Which amino acids fir into each of these categories?
Polar (5):
Serine, Threonine, Asparagine, Glutamine, Cysteine
Which amino acids fir into each of these categories?
Negatively charged/acidic (2):
Aspartate, Glutamate
Which amino acids fir into each of these categories?
Positively charged/basic (3):
Lysine, Arginine, Histidine
,Where do hydrophobic amino acids tend to reside within a
protein? What about a hydrophilic ones?
Hydrophobic amino acids tend to reside in the interior of a protein,
away from water. Hydrophilic amino acids tend to remain on the
surface of the protein, in contact with water.
Concept Check 1.2:
Acid-Base Chemistry of Amino Acids
For a generic amino acid NH2CRHCOOH, with an uncharged
side chain, what would be the predominant form at each of
the following pH values?
pH = 1 :_______________
pH = 7 :______________
pH = 11: ______________
pH = 1 : +NH3CRHCOOH
pH = 7 :+NH3CRHCOO-
pH = 11: NH2CRHCOO-
Given the following pKa values, what is the value of the pI for
each of the amino acids listed below?
Aspartic acid (pKa1=1.88, pKa2=3.65, pKa3=9.60)
Arginine (pKa1=2.17, pKa2=9.04, pKa3=12.48)
Valine (pKa1=2.32, pKa2=9.62)
Aspartic acid pI=(1.88+3.65) /2 = 2.77
Arginine pI=(9.04+12.48) /2 = 10.76
Valine pI= (2.32_9.62) /2 =5.97
Concept Check 1.3:
Peptide Bond Formation and Hydrolysis
What is the difference between an amino acid, a dipeptide, a
tripeptide, an oligopeptide, and a polypeptide?
These species differ by the number of amino acids that make
them up:
,amino acid=1
dipeptide=2
tripeptide=3
oligopeptide="few" (<20)
polypeptide = "many" (>20)
What molecule is released during formation of a peptide
bond?
Water (H2O)
If chymotrypsin cleaves at the carboxyl end of phenylalanine,
tryptophan, and tyrosine, how many oligopeptides would be
formed in enzymatic cleavage of the following molecule with
chymotrypsin?
Val-Phe-Glu-Lys-Tyr-Phe-Trp-Ile-Met-Tyr-Gly-Ala
4: Val-Phe; Glu-Lys-Tyr; Ile-Met-Tyr; Gly-Ala.
A single amino acid on its own is not considered an oligopeptide
Concept Check 1.4:
Primary and Secondary Protein Structure
Define Primary Structure:
Linear sequence of amino acids in chain
Subtypes of Primary Structure:
(none)
Stabilizing Bonds of Primary Structure:
Peptide (amide) bond
Define Secondary Structure:
Local structure determined by nearby amino acids
Subtypes of Secondary Structure:
a-helix
B-pleated sheets
Stabilizing Bonds of Secondary Structure:
Hydrogen Bonds
What role does proline serve in secondary structure?
Proline's rigid structure causes it to introduce kinks in a-helices, or
create turns in B-pleated sheets.
Concept Check 1.5:
, Tertiary and Quaternary Protein Structure
Define Tertiary Structure:
Three-dimensional shape of protein
Subtypes of Primary Structure
-Hydrophobic interactions
-Acid-base/salt-bridges
-Disulfide links
Stabilizing Bonds of Tertiary Structure:
-Van der Waals forces
-Hydrogen bonds
-Ionic bonds
-Covalent bonds
Define Quaternary Structure:
Interaction between separate subunits of a multisubunit protein
Subtypes of Quaternary Structure:
(none)
Stabilizing Bonds of Quaternary Structure:
Same as tertiary structure
-Van der Waals forces
-Hydrogen bonds
-Ionic bonds
-Covalent bonds
What is the primary motivation for hydrophobic residues in a
polypeptide to move to the interior of the protein?
Moving hydrophobic residues to the interior of a protein increases
entropy by allowing water molecules on the surface of the protein
to have more possible positions and configurations. This positive
deltaS makes deltaG<0, stabilizing the protein.
Concept Check 1.6:
Denaturation
Why are proteins denatured by heat and solutes,
respectively?
Heat denatures proteins by increasing their average kinetic
energy, thus disrupting hydrophobic
