ACS BIOCHEMISTRY EXAM Q&A With
complete solution
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.
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
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.
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.
α/ß Protein Folding - ANSWER Less distinct areas of α and ß folding.
α+ß Protein Folding - ANSWER Two distinct areas of α and ß folding.
Mechanism of Denaturants - ANSWER Highly soluble, H-binding molecules. Stabilize
protein backbone in water. Allows denatured state to be stabilized.
Temperature Denaturation of Protein - ANSWER Midpoint of reaction is Tm.
Cooperative Protein Folding - ANSWER Folding transition is sharp. More reversible.
Folding Funnel - ANSWER Shows 3D version of 2D energy states. Lowest energy is
stable protein. Rough funnel is less cooperative.
Protein-Protein Interfaces - ANSWER "Core" and "fringe" of the interfaces. Core is more
hydrophobic and is on the inside when interfaced. Fringe is more hydrophilic.
π-π Ring Stacking - ANSWER Weird interaction where aromatic rings stack on each
other in positive interaction.
σ-hole - ANSWER Methyl group has area of diminished electron density in center;
attracts electronegative groups
Fe Binding of O2 - ANSWER Fe2+ binds to O2 reversible. Fe3+ has an additional +
charge and binds to O2 irreversibly. Fe3+ rusts in O2 rich environments.
Ka for Binding - ANSWER Ka = [PL] / [P][L]
ϴ-value in Binding - ANSWER ϴ = (bound / total)x100%
ϴ = [L] / ([L] + 1/Ka)
Kd for binding - ANSWER Kd = [L] when 50% bound to protein.
Kd = 1/Ka
High-Spin Fe - ANSWER Electrons are "spread out" and result in larger atom.
Low-Spin Fe - ANSWER Electrons are less "spread out" and are compacted by electron
rich porphyrin ring.
complete solution
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.
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
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.
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.
α/ß Protein Folding - ANSWER Less distinct areas of α and ß folding.
α+ß Protein Folding - ANSWER Two distinct areas of α and ß folding.
Mechanism of Denaturants - ANSWER Highly soluble, H-binding molecules. Stabilize
protein backbone in water. Allows denatured state to be stabilized.
Temperature Denaturation of Protein - ANSWER Midpoint of reaction is Tm.
Cooperative Protein Folding - ANSWER Folding transition is sharp. More reversible.
Folding Funnel - ANSWER Shows 3D version of 2D energy states. Lowest energy is
stable protein. Rough funnel is less cooperative.
Protein-Protein Interfaces - ANSWER "Core" and "fringe" of the interfaces. Core is more
hydrophobic and is on the inside when interfaced. Fringe is more hydrophilic.
π-π Ring Stacking - ANSWER Weird interaction where aromatic rings stack on each
other in positive interaction.
σ-hole - ANSWER Methyl group has area of diminished electron density in center;
attracts electronegative groups
Fe Binding of O2 - ANSWER Fe2+ binds to O2 reversible. Fe3+ has an additional +
charge and binds to O2 irreversibly. Fe3+ rusts in O2 rich environments.
Ka for Binding - ANSWER Ka = [PL] / [P][L]
ϴ-value in Binding - ANSWER ϴ = (bound / total)x100%
ϴ = [L] / ([L] + 1/Ka)
Kd for binding - ANSWER Kd = [L] when 50% bound to protein.
Kd = 1/Ka
High-Spin Fe - ANSWER Electrons are "spread out" and result in larger atom.
Low-Spin Fe - ANSWER Electrons are less "spread out" and are compacted by electron
rich porphyrin ring.
