Page 1 of 41
ACS Biochemistry Exam | Complete
Study Guide & Practice Test for
American Chemical Society Certification
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.
, Page 2 of 41
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.
, Page 3 of 41
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.
, Page 4 of 41
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.
ACS Biochemistry Exam | Complete
Study Guide & Practice Test for
American Chemical Society Certification
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.
, Page 2 of 41
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.
, Page 3 of 41
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.
, Page 4 of 41
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.
