ACS BIOCHEMISTRY EXAM | QUESTIONS AND ANSWERS | LATEST
EXAM
Henderson-Hasselbach Equation - CORRECT ANSWER - pH = pKa + log
([A-] / [HA])
FMOC Chemical Synthesis - CORRECT 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) - CORRECT ANSWER - Changes soluble protein to
solid precipitate. Protein precipitates when the charges on the protein match the
charges in the solution.
Size-Exclusion Chromatography - CORRECT ANSWER - Separates sample
based on size with smaller molecules eluting later.
Ion-Exchange Chromatography - CORRECT 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 - CORRECT ANSWER - Beads
are coated with a carbon chain. Hydrophobic proteins stick better. Elute with
non-H-bonding solvent (acetonitrile).
Affinity Chromatography - CORRECT ANSWER - Attach a ligand that binds
a protein to a bead. Elute with harsh chemicals or similar ligand.
,SDS-PAGE - CORRECT 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 - CORRECT ANSWER - Sodium dodecyl sulfate. Unfolds proteins and
gives them uniform negative charge.
Isoelectric Focusing - CORRECT 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) - CORRECT 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) - CORRECT ANSWER - Reduces disulfide bonds.
Iodoacetate - CORRECT ANSWER - Adds carboxymethyl group on free -SH
groups. Blocks disulfide bonding.
Homologs - CORRECT ANSWER - Shares 25% identity with another gene
Orthologs - CORRECT ANSWER - Similar genes in different organisms
Paralogs - CORRECT ANSWER - Similar "paired" genes in the same
organism
Ramachandran Plot - CORRECT ANSWER - Shows favorable phi-psi angle
combinations. 3 main "wells" for α-helices, ß-sheets, and left-handed α-helices.
, Glycine Ramachandran Plot - CORRECT ANSWER - Glycine can adopt more
angles. (H's for R-group).
Proline Ramachandran Plot - CORRECT ANSWER - Proline adopts fewer
angles. Amino group is incorporated into a ring.
α-helices - CORRECT 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 - CORRECT 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 - CORRECT ANSWER - Either parallel or anti-parallel. Often twisted
to increase strength.
Anti-parallel ß-sheet - CORRECT ANSWER - Alternating sheet directions (C
& N-termini don't line-up). Has straight H-bonds.
Parallel ß-sheet - CORRECT ANSWER - Same sheet directions (C & N-
termini line up). Has angled H-bonds.
ß-turns - CORRECT 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 - CORRECT ANSWER - Not highly structured. Not necessary highly
flexible, but can occasionally move. Very variable in sequence.
Circular Dichroism - CORRECT ANSWER - Uses UV light to measure 2°
structure. Can be used to measure destabilization.
EXAM
Henderson-Hasselbach Equation - CORRECT ANSWER - pH = pKa + log
([A-] / [HA])
FMOC Chemical Synthesis - CORRECT 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) - CORRECT ANSWER - Changes soluble protein to
solid precipitate. Protein precipitates when the charges on the protein match the
charges in the solution.
Size-Exclusion Chromatography - CORRECT ANSWER - Separates sample
based on size with smaller molecules eluting later.
Ion-Exchange Chromatography - CORRECT 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 - CORRECT ANSWER - Beads
are coated with a carbon chain. Hydrophobic proteins stick better. Elute with
non-H-bonding solvent (acetonitrile).
Affinity Chromatography - CORRECT ANSWER - Attach a ligand that binds
a protein to a bead. Elute with harsh chemicals or similar ligand.
,SDS-PAGE - CORRECT 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 - CORRECT ANSWER - Sodium dodecyl sulfate. Unfolds proteins and
gives them uniform negative charge.
Isoelectric Focusing - CORRECT 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) - CORRECT 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) - CORRECT ANSWER - Reduces disulfide bonds.
Iodoacetate - CORRECT ANSWER - Adds carboxymethyl group on free -SH
groups. Blocks disulfide bonding.
Homologs - CORRECT ANSWER - Shares 25% identity with another gene
Orthologs - CORRECT ANSWER - Similar genes in different organisms
Paralogs - CORRECT ANSWER - Similar "paired" genes in the same
organism
Ramachandran Plot - CORRECT ANSWER - Shows favorable phi-psi angle
combinations. 3 main "wells" for α-helices, ß-sheets, and left-handed α-helices.
, Glycine Ramachandran Plot - CORRECT ANSWER - Glycine can adopt more
angles. (H's for R-group).
Proline Ramachandran Plot - CORRECT ANSWER - Proline adopts fewer
angles. Amino group is incorporated into a ring.
α-helices - CORRECT 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 - CORRECT 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 - CORRECT ANSWER - Either parallel or anti-parallel. Often twisted
to increase strength.
Anti-parallel ß-sheet - CORRECT ANSWER - Alternating sheet directions (C
& N-termini don't line-up). Has straight H-bonds.
Parallel ß-sheet - CORRECT ANSWER - Same sheet directions (C & N-
termini line up). Has angled H-bonds.
ß-turns - CORRECT 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 - CORRECT ANSWER - Not highly structured. Not necessary highly
flexible, but can occasionally move. Very variable in sequence.
Circular Dichroism - CORRECT ANSWER - Uses UV light to measure 2°
structure. Can be used to measure destabilization.
