MCAT Biochemistry Review Questions and Answers Rated A
Amino Acid - -Dipolar compound
containing an amino group and a carboxyl group Alanine - -Alkyl side chain (1C)
Amino Group - --NH2 Valine - -Alkyl side chain (3C)
Carboxyl Group - --COOH Leucine - -Alkyl side chain (4C)
Alpha Carbon - -Central carbon atom in Isoleucine - -Alkyl side chain (4C)
amino acid
Attached to amino & carboxyl groups, H atom,
and side chain Methionine - -Methyl side chain (-CH3)
Contains S atom in side chain
Side Chain - -The variable component of
an amino acid that gives the amino acid its Proline - -Cyclic amino acid
identity and chemical properties N from amino group becomes part of side chain,
also called R-group forming five-part ring, limiting where is can
appear on a protein
Rigid/constraints on flexibility
Chiral - -A molecule with a
nonsuperimposable mirror image
All amino acids (except glycine) are chiral Aromatic Amino Acids - -Tryptophan,
phenylalanine, tyrosine
(S) Absolute Configuration - -All amino
acids (except cysteine) have an (S) absolute Aromaticity - -The ability of a molecule to
configuration delocalize pi electrons around a conjucated ring,
creating exceptional stability
L-amino Acid - -All amino acids found in
eukaryotes Tryptophan - -Double-ring system
Contains N atom in one ring
Largest of aromatic amino acids
Nonpolar, Nonaromatic Amino Acids - -
Glycine, alanine, valine, leucine, isoleucine,
methionine, proline Phenylalanine - -Benzyl side chain
(benzene ring + -CH2 group)
Smallest aromatic amino acid
Glycine - -Single H atom as side chain Relatively nonpolar
Achiral
Smallest amino acid
Tyrosine - -Phenylalanine + -OH group
,MCAT Biochemistry Review Questions and Answers Rated A
Relatively polar Glutamic Acid (Glutamate) - -Carboxylate (-
COO(-)) group in side chain
Deprotonated form of glutamine
Polar Amino Acids - -Serine, threonine,
asparagine, glutamine, cysteine
Positively-charged (Basic) Amino Acids - -
Lysine, arginine, histidine
Polarity - -An uneven sharing of electrons
in a molecule, creating a slightly positive side
and a slightly negative side Lysine - -Terminal primary amino group
Serine - --OH group in side chain Arginine - -Has 3 N atoms in side chain
Highly polar - participate in H-bonding Charge delocalized over all three N atoms
Threonine - --OH group in side chain Histidine - -Has aromatic ring with 2 N
Highly polar - participate in H-bonding atoms (ring is called an imidazole)
At pH 7.4, one N is protonated and the other isn't
Under acidic conditions, the 2nd N becomes
Asparagine - -Amide (-NH2) side chain protonated, making it positively charged
Amide N do not gain or lose protons with
changes in pH - do not become charged
Hydrophobic Amino Acids - -Being repelled
by water
Glutamine - -Amide (-NH2) side chain Alanine, isoleucine, leucine, valine, phenylalanine
Amide N do not gain or lose protons with More likely to be found in center of protein
changes in pH - do not become charged Nonpolar, uncharged compounds
Long alkyl chains
Cysteine - -Thiol (-SH) side chain - weaker
than OH bond Hydrophilic Amino Acids - -Being attracted
Prone to oxidation to water
Histidine, arginine, lysine, glutamate, aspartate,
asparagine, glutamine
Negatively-charged (Acidic) Amino Acids - Polar and charged compounds and those that
-Aspartic acid (aspartate), glutamic acid participate in H-bonding
(glutamate)
Neither Really Hydrophobic/-philic - -
Aspartic Acid (Aspartate) - -Carboxylate (- Cysteine, threonine, serine, tyrosine, tryptophan,
COO(-)) group in side chain proline, methionine, glycine
Deprotonated form of asparagine
Amphoteric - -Ability to act as an acid or a
,MCAT Biochemistry Review Questions and Answers Rated A
base Predominantly in zwitterion form
Can either accept or donate a proton
For ionizable groups: tend to be protonated at
low pH; deprotonated at high pH pI(neutral amino acid) = - -(pKa(NH3+) +
pKa(COOH))/2
For amino acids with neutral side chains
pKa - -The pH at which half of the species Have relatively neutral pI values (~6)
are deprotonated
[HA] = [A(-)]
Buffer - -When pH of a solution is
approximately = pKa of solute
pKa1 - -pKa for carboxyl group The pH doesn't change very much, even when
Usually around 2 acid or base are added to solution
pKa2 - -pKa for amino group pI(acidic amino acid) = - -(pKa(R group) +
Usually between 9 and 10 pKa(COOH))/2
For amino acids with negatively charged side
chains
pKa3 - -For amino acids with ionizable side Have relatively low pI values (~3.2)
chains
pI(basic amino acid) = - -(pKa(NH3+) +
Amino Acids in Acidic Conditions - -Amino pKa(R group))/2
acid is fully protonated For amino acids with positively charged side
i.e. (-NH3+) and (-COOH) chains
Have relatively high pI values (~9.75)
Amino Acids in Neutral Conditions - -Form
zwitterions Titration - -A laboratory technique in which
pH is near pI of amino acid a solution of unknown concentration is mixed with
i.e. (-COO(-)) and (-NH3(+)) a solution of known concentration to determine
the unknown concentration
Zwitterion - -A molecule that contains
charges, but is neutral overall Titration Curves for Amino Acids - -Curve is
nearly flat at pKa values of amino acids
Nearly vertical at pI of amino acid
Amino Acids in Basic Conditions - -Amino
acid is fully deprotonated
i.e. (-COO(-)) and (-NH2) Peptides - -A molecule composed of more
than one amino acid
Can be subdivided into dipeptides, tripeptides,
Isoelectric Point (pI) - -The pH at which oligopeptides, and polypeptides
every molecule in solution is electrically neutral
, MCAT Biochemistry Review Questions and Answers Rated A
Dipeptide - -Two amino acid residues
Trypsin - -Hydrolytic enzyme
Cleaves carboxyl end of arginine and lysine
Tripeptide - -Three amino acid residues
Chymotrypsin - -Hydrolytic enzyme
Oligopeptide - -Relatively small peptides Cleaves carboxyl end of tryptophan,
(up to ~20 residues) phenylalanine, and tyrosine
(Single amino acid does not count as
oligopeptide)
Proteins - -Polypeptides
Can be enzymes, hormones, membrane pores
Polypeptides - -Long chains of residues and receptors, elements of cell structure
(>20 residue)
Primary Protein Structure - -Linear
Peptide Bonds - -An amide bond between sequence of amino acids in a polypeptide
the carboxyl group of one amino acid and the Stabilized by formation of covalent peptide bonds
amino group of another amino acid between adjacent amino acids
Forms functional group -C(O)NH(-) Encodes all info needed for folding at all higher
structural levels
Peptide (Amide) Bond Formation - -
Condensation/Dehydration Secondary Protein Structure - -Local
Loss of H2O molecule structure of neighboring amino acids - most
So strong because of resonance commonly alpha-helices and beta-pleated sheets
Primarily result of intramolecular H-bonds
between residues
N-terminus - -Free amino end of a Proline can interrupt secondary structure
polypeptide because of rigid structure
On left side of drawings
Read from N-terminus -> C-terminus
Alpha-Helices - -An element of secondary
structure, marked by clockwise coiling of amino
C-terminus - -Free carboxyl end of a acids around a central axis
polypeptide Stabilized by intramolecular H-bonds between
On right side of drawings carbonyl O and amide H atom 4 residues down
Read from N-terminus -> C-terminus the chain
Side chains point away from center
Cleavage of Peptides - -Hydrolysis -
hydrolytic enzymes break the amide bond by Beta-Pleated Sheets - -An element of
adding an H atom to amide nitrogen and adding secondary structure, marked by peptide chains
an OH group to the carbonyl carbon. lying alongside one another, forming rows or
Amino Acid - -Dipolar compound
containing an amino group and a carboxyl group Alanine - -Alkyl side chain (1C)
Amino Group - --NH2 Valine - -Alkyl side chain (3C)
Carboxyl Group - --COOH Leucine - -Alkyl side chain (4C)
Alpha Carbon - -Central carbon atom in Isoleucine - -Alkyl side chain (4C)
amino acid
Attached to amino & carboxyl groups, H atom,
and side chain Methionine - -Methyl side chain (-CH3)
Contains S atom in side chain
Side Chain - -The variable component of
an amino acid that gives the amino acid its Proline - -Cyclic amino acid
identity and chemical properties N from amino group becomes part of side chain,
also called R-group forming five-part ring, limiting where is can
appear on a protein
Rigid/constraints on flexibility
Chiral - -A molecule with a
nonsuperimposable mirror image
All amino acids (except glycine) are chiral Aromatic Amino Acids - -Tryptophan,
phenylalanine, tyrosine
(S) Absolute Configuration - -All amino
acids (except cysteine) have an (S) absolute Aromaticity - -The ability of a molecule to
configuration delocalize pi electrons around a conjucated ring,
creating exceptional stability
L-amino Acid - -All amino acids found in
eukaryotes Tryptophan - -Double-ring system
Contains N atom in one ring
Largest of aromatic amino acids
Nonpolar, Nonaromatic Amino Acids - -
Glycine, alanine, valine, leucine, isoleucine,
methionine, proline Phenylalanine - -Benzyl side chain
(benzene ring + -CH2 group)
Smallest aromatic amino acid
Glycine - -Single H atom as side chain Relatively nonpolar
Achiral
Smallest amino acid
Tyrosine - -Phenylalanine + -OH group
,MCAT Biochemistry Review Questions and Answers Rated A
Relatively polar Glutamic Acid (Glutamate) - -Carboxylate (-
COO(-)) group in side chain
Deprotonated form of glutamine
Polar Amino Acids - -Serine, threonine,
asparagine, glutamine, cysteine
Positively-charged (Basic) Amino Acids - -
Lysine, arginine, histidine
Polarity - -An uneven sharing of electrons
in a molecule, creating a slightly positive side
and a slightly negative side Lysine - -Terminal primary amino group
Serine - --OH group in side chain Arginine - -Has 3 N atoms in side chain
Highly polar - participate in H-bonding Charge delocalized over all three N atoms
Threonine - --OH group in side chain Histidine - -Has aromatic ring with 2 N
Highly polar - participate in H-bonding atoms (ring is called an imidazole)
At pH 7.4, one N is protonated and the other isn't
Under acidic conditions, the 2nd N becomes
Asparagine - -Amide (-NH2) side chain protonated, making it positively charged
Amide N do not gain or lose protons with
changes in pH - do not become charged
Hydrophobic Amino Acids - -Being repelled
by water
Glutamine - -Amide (-NH2) side chain Alanine, isoleucine, leucine, valine, phenylalanine
Amide N do not gain or lose protons with More likely to be found in center of protein
changes in pH - do not become charged Nonpolar, uncharged compounds
Long alkyl chains
Cysteine - -Thiol (-SH) side chain - weaker
than OH bond Hydrophilic Amino Acids - -Being attracted
Prone to oxidation to water
Histidine, arginine, lysine, glutamate, aspartate,
asparagine, glutamine
Negatively-charged (Acidic) Amino Acids - Polar and charged compounds and those that
-Aspartic acid (aspartate), glutamic acid participate in H-bonding
(glutamate)
Neither Really Hydrophobic/-philic - -
Aspartic Acid (Aspartate) - -Carboxylate (- Cysteine, threonine, serine, tyrosine, tryptophan,
COO(-)) group in side chain proline, methionine, glycine
Deprotonated form of asparagine
Amphoteric - -Ability to act as an acid or a
,MCAT Biochemistry Review Questions and Answers Rated A
base Predominantly in zwitterion form
Can either accept or donate a proton
For ionizable groups: tend to be protonated at
low pH; deprotonated at high pH pI(neutral amino acid) = - -(pKa(NH3+) +
pKa(COOH))/2
For amino acids with neutral side chains
pKa - -The pH at which half of the species Have relatively neutral pI values (~6)
are deprotonated
[HA] = [A(-)]
Buffer - -When pH of a solution is
approximately = pKa of solute
pKa1 - -pKa for carboxyl group The pH doesn't change very much, even when
Usually around 2 acid or base are added to solution
pKa2 - -pKa for amino group pI(acidic amino acid) = - -(pKa(R group) +
Usually between 9 and 10 pKa(COOH))/2
For amino acids with negatively charged side
chains
pKa3 - -For amino acids with ionizable side Have relatively low pI values (~3.2)
chains
pI(basic amino acid) = - -(pKa(NH3+) +
Amino Acids in Acidic Conditions - -Amino pKa(R group))/2
acid is fully protonated For amino acids with positively charged side
i.e. (-NH3+) and (-COOH) chains
Have relatively high pI values (~9.75)
Amino Acids in Neutral Conditions - -Form
zwitterions Titration - -A laboratory technique in which
pH is near pI of amino acid a solution of unknown concentration is mixed with
i.e. (-COO(-)) and (-NH3(+)) a solution of known concentration to determine
the unknown concentration
Zwitterion - -A molecule that contains
charges, but is neutral overall Titration Curves for Amino Acids - -Curve is
nearly flat at pKa values of amino acids
Nearly vertical at pI of amino acid
Amino Acids in Basic Conditions - -Amino
acid is fully deprotonated
i.e. (-COO(-)) and (-NH2) Peptides - -A molecule composed of more
than one amino acid
Can be subdivided into dipeptides, tripeptides,
Isoelectric Point (pI) - -The pH at which oligopeptides, and polypeptides
every molecule in solution is electrically neutral
, MCAT Biochemistry Review Questions and Answers Rated A
Dipeptide - -Two amino acid residues
Trypsin - -Hydrolytic enzyme
Cleaves carboxyl end of arginine and lysine
Tripeptide - -Three amino acid residues
Chymotrypsin - -Hydrolytic enzyme
Oligopeptide - -Relatively small peptides Cleaves carboxyl end of tryptophan,
(up to ~20 residues) phenylalanine, and tyrosine
(Single amino acid does not count as
oligopeptide)
Proteins - -Polypeptides
Can be enzymes, hormones, membrane pores
Polypeptides - -Long chains of residues and receptors, elements of cell structure
(>20 residue)
Primary Protein Structure - -Linear
Peptide Bonds - -An amide bond between sequence of amino acids in a polypeptide
the carboxyl group of one amino acid and the Stabilized by formation of covalent peptide bonds
amino group of another amino acid between adjacent amino acids
Forms functional group -C(O)NH(-) Encodes all info needed for folding at all higher
structural levels
Peptide (Amide) Bond Formation - -
Condensation/Dehydration Secondary Protein Structure - -Local
Loss of H2O molecule structure of neighboring amino acids - most
So strong because of resonance commonly alpha-helices and beta-pleated sheets
Primarily result of intramolecular H-bonds
between residues
N-terminus - -Free amino end of a Proline can interrupt secondary structure
polypeptide because of rigid structure
On left side of drawings
Read from N-terminus -> C-terminus
Alpha-Helices - -An element of secondary
structure, marked by clockwise coiling of amino
C-terminus - -Free carboxyl end of a acids around a central axis
polypeptide Stabilized by intramolecular H-bonds between
On right side of drawings carbonyl O and amide H atom 4 residues down
Read from N-terminus -> C-terminus the chain
Side chains point away from center
Cleavage of Peptides - -Hydrolysis -
hydrolytic enzymes break the amide bond by Beta-Pleated Sheets - -An element of
adding an H atom to amide nitrogen and adding secondary structure, marked by peptide chains
an OH group to the carbonyl carbon. lying alongside one another, forming rows or
