ACS BIOCHEMISTRY EXAM QUESTION WITH
COMPLETE SOLUTIONS LATEST 2023/2024
Henderson-Hasselbach Equation - ANSWER--pH = pKa + log ([A-] / [HA])
FMOC Chemical Synthesis - ANSWER--Used in synthesis of a growing amino acid
chain to a polystyrene bead. FMOC is used as a protecting group on the N-
terminus.
Salting Out (Purification) - ANSWER--Changes soluble protein to solid precipitate.
Protein precipitates when the charges on the protein match the charges in the
solution.
Size-Exclusion Chromatography - ANSWER--Separates sample based on size with
smaller molecules eluting later.
Ion-Exchange Chromatography - ANSWER--Separates sample based on charge.
CM attracts +, DEAE attracts -. May have repulsion effect on like charges. Salt or
acid used to remove stuck proteins.
Hydrophobic/Reverse Phase Chromatography - ANSWER--Beads are coated with a
carbon chain. Hydrophobic proteins stick better. Elute with non-H-bonding
solvent (acetonitrile).
Affinity Chromatography - ANSWER--Attach a ligand that binds a protein to a
bead. Elute with harsh chemicals or similar ligand.
, ACS BIOCHEMISTRY EXAM QUESTION WITH
COMPLETE SOLUTIONS LATEST 2023/2024
SDS-PAGE - ANSWER--Uses SDS. Gel is made from cross-linked polyacrylamide.
Separates based off of mass with smaller molecules moving faster. Visualized with
Coomassie blue.
SDS - ANSWER--Sodium dodecyl sulfate. Unfolds proteins and gives them uniform
negative charge.
Isoelectric Focusing - ANSWER--Variation of gel electrophoresis where protein
charge matters. Involves electrodes and pH gradient. Protein stops at their pI
when neutral.
FDNB (1-fluoro-2,3-dinitrobenzene) - ANSWER--FDNB reacts with the N-terminus
of the protein to produce a 2,4-dinitrophenol derivative that labels the first
residue. Can repeat hydrolysis to determine sequential amino acids.
DTT (dithiothreitol) - ANSWER--Reduces disulfide bonds.
Iodoacetate - ANSWER--Adds carboxymethyl group on free -SH groups. Blocks
disulfide bonding.
Homologs - ANSWER--Shares 25% identity with another gene
Orthologs - ANSWER--Similar genes in different organisms
Paralogs - ANSWER--Similar "paired" genes in the same organism
, ACS BIOCHEMISTRY EXAM QUESTION WITH
COMPLETE SOLUTIONS LATEST 2023/2024
Ramachandran Plot - ANSWER--Shows favorable phi-psi angle combinations. 3
main "wells" for α-helices, ß-sheets, and left-handed α-helices.
Glycine Ramachandran Plot - ANSWER--Glycine can adopt more angles. (H's for R-
group).
Proline Ramachandran Plot - ANSWER--Proline adopts fewer angles. Amino group
is incorporated into a ring.
α-helices - ANSWER--Ala is common, Gly & Pro are not very common. Side-chain
interactions every 3 or 4 residues. Turns once every 3.6 residues. Distance
between backbones is 5.4Å.
Helix Dipole - ANSWER--Formed from added dipole moments of all hydrogen
bonds in an α-helix. N-terminus is δ+ and C-terminus is δ-.
ß-sheet - ANSWER--Either parallel or anti-parallel. Often twisted to increase
strength.
Anti-parallel ß-sheet - ANSWER--Alternating sheet directions (C & N-termini don't
line-up). Has straight H-bonds.
Parallel ß-sheet - ANSWER--Same sheet directions (C & N-termini line up). Has
angled H-bonds.
, ACS BIOCHEMISTRY EXAM QUESTION WITH
COMPLETE SOLUTIONS LATEST 2023/2024
ß-turns - ANSWER--Tight u-turns with specific phi-psi angles. Must have gly at
position 3. Proline may also be at ß-turn because it can have a cis-omega angle.
Loops - ANSWER--Not highly structured. Not necessary highly flexible, but can
occasionally move. Very variable in sequence.
Circular Dichroism - ANSWER--Uses UV light to measure 2° structure. Can be used
to measure destabilization.
Disulfide-bonds - ANSWER--Bonds between two -SH groups that form between 2°
and 3° structure.
ß-mercaptoethanol - ANSWER--Breaks disulfide bonds.
α-keratin - ANSWER--formed from 2 α-helices twisted around each other. "Coiled
coil". Cross-linked by disulfide bonds.
Collagen - ANSWER--Repeating sequence of Gly-X-Pro. 3 stranded "coiled coil".
Contains gly core.
Myoglobin 4° Structure - ANSWER--Symmetric homodimer,
Hemoglobin 4° Structure - ANSWER--Tetramer. Dimer of dimers. α2ß2 tetramer.
COMPLETE SOLUTIONS LATEST 2023/2024
Henderson-Hasselbach Equation - ANSWER--pH = pKa + log ([A-] / [HA])
FMOC Chemical Synthesis - ANSWER--Used in synthesis of a growing amino acid
chain to a polystyrene bead. FMOC is used as a protecting group on the N-
terminus.
Salting Out (Purification) - ANSWER--Changes soluble protein to solid precipitate.
Protein precipitates when the charges on the protein match the charges in the
solution.
Size-Exclusion Chromatography - ANSWER--Separates sample based on size with
smaller molecules eluting later.
Ion-Exchange Chromatography - ANSWER--Separates sample based on charge.
CM attracts +, DEAE attracts -. May have repulsion effect on like charges. Salt or
acid used to remove stuck proteins.
Hydrophobic/Reverse Phase Chromatography - ANSWER--Beads are coated with a
carbon chain. Hydrophobic proteins stick better. Elute with non-H-bonding
solvent (acetonitrile).
Affinity Chromatography - ANSWER--Attach a ligand that binds a protein to a
bead. Elute with harsh chemicals or similar ligand.
, ACS BIOCHEMISTRY EXAM QUESTION WITH
COMPLETE SOLUTIONS LATEST 2023/2024
SDS-PAGE - ANSWER--Uses SDS. Gel is made from cross-linked polyacrylamide.
Separates based off of mass with smaller molecules moving faster. Visualized with
Coomassie blue.
SDS - ANSWER--Sodium dodecyl sulfate. Unfolds proteins and gives them uniform
negative charge.
Isoelectric Focusing - ANSWER--Variation of gel electrophoresis where protein
charge matters. Involves electrodes and pH gradient. Protein stops at their pI
when neutral.
FDNB (1-fluoro-2,3-dinitrobenzene) - ANSWER--FDNB reacts with the N-terminus
of the protein to produce a 2,4-dinitrophenol derivative that labels the first
residue. Can repeat hydrolysis to determine sequential amino acids.
DTT (dithiothreitol) - ANSWER--Reduces disulfide bonds.
Iodoacetate - ANSWER--Adds carboxymethyl group on free -SH groups. Blocks
disulfide bonding.
Homologs - ANSWER--Shares 25% identity with another gene
Orthologs - ANSWER--Similar genes in different organisms
Paralogs - ANSWER--Similar "paired" genes in the same organism
, ACS BIOCHEMISTRY EXAM QUESTION WITH
COMPLETE SOLUTIONS LATEST 2023/2024
Ramachandran Plot - ANSWER--Shows favorable phi-psi angle combinations. 3
main "wells" for α-helices, ß-sheets, and left-handed α-helices.
Glycine Ramachandran Plot - ANSWER--Glycine can adopt more angles. (H's for R-
group).
Proline Ramachandran Plot - ANSWER--Proline adopts fewer angles. Amino group
is incorporated into a ring.
α-helices - ANSWER--Ala is common, Gly & Pro are not very common. Side-chain
interactions every 3 or 4 residues. Turns once every 3.6 residues. Distance
between backbones is 5.4Å.
Helix Dipole - ANSWER--Formed from added dipole moments of all hydrogen
bonds in an α-helix. N-terminus is δ+ and C-terminus is δ-.
ß-sheet - ANSWER--Either parallel or anti-parallel. Often twisted to increase
strength.
Anti-parallel ß-sheet - ANSWER--Alternating sheet directions (C & N-termini don't
line-up). Has straight H-bonds.
Parallel ß-sheet - ANSWER--Same sheet directions (C & N-termini line up). Has
angled H-bonds.
, ACS BIOCHEMISTRY EXAM QUESTION WITH
COMPLETE SOLUTIONS LATEST 2023/2024
ß-turns - ANSWER--Tight u-turns with specific phi-psi angles. Must have gly at
position 3. Proline may also be at ß-turn because it can have a cis-omega angle.
Loops - ANSWER--Not highly structured. Not necessary highly flexible, but can
occasionally move. Very variable in sequence.
Circular Dichroism - ANSWER--Uses UV light to measure 2° structure. Can be used
to measure destabilization.
Disulfide-bonds - ANSWER--Bonds between two -SH groups that form between 2°
and 3° structure.
ß-mercaptoethanol - ANSWER--Breaks disulfide bonds.
α-keratin - ANSWER--formed from 2 α-helices twisted around each other. "Coiled
coil". Cross-linked by disulfide bonds.
Collagen - ANSWER--Repeating sequence of Gly-X-Pro. 3 stranded "coiled coil".
Contains gly core.
Myoglobin 4° Structure - ANSWER--Symmetric homodimer,
Hemoglobin 4° Structure - ANSWER--Tetramer. Dimer of dimers. α2ß2 tetramer.
