ACS BIOCHEMISTRY EXAM STUDY
QUESTIONS AND ANSWERS UPDATED
2024
BESTZONE
ACS BIOCHEM
8/29/24
,ACS BIOCHEMISTRY EXAM
Henderson-Hasselbach Equation - pH = pKa + log ([A-] / [HA])
FMOC Chemical Synthesis - 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) - Changes soluble protein to solid precipitate. Protein
precipitates when the charges on the protein match the charges in the solution.
Size-Exclusion Chromatography - Separates sample based on size with smaller
molecules eluting later.
Ion-Exchange Chromatography - 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 - Beads are coated with a carbon chain.
Hydrophobic proteins stick better. Elute with non-H-bonding solvent (acetonitrile).
Affinity Chromatography - Attach a ligand that binds a protein to a bead. Elute with
harsh chemicals or similar ligand.
SDS-PAGE - Uses SDS. Gel is made from cross-linked polyacrylamide. Separates
based off of mass with smaller molecules moving faster. Visualized with Coomassie
blue.
SDS - Sodium dodecyl sulfate. Unfolds proteins and gives them uniform negative
charge.
Isoelectric Focusing - Variation of gel electrophoresis where protein charge matters.
Involves electrodes and pH gradient. Protein stops at their pI when neutral.
ACS BIOCHEMISTRY EXAM
, ACS BIOCHEMISTRY EXAM
FDNB (1-fluoro-2,3-dinitrobenzene) - 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) - Reduces disulfide bonds.
Iodoacetate - Adds carboxymethyl group on free -SH groups. Blocks disulfide bonding.
Homologs - Shares 25% identity with another gene
Orthologs - Similar genes in different organisms
Paralogs - Similar "paired" genes in the same organism
Ramachandran Plot - Shows favorable phi-psi angle combinations. 3 main "wells" for α-
helices, ß-sheets, and left-handed α-helices.
Glycine Ramachandran Plot - Glycine can adopt more angles. (H's for R-group).
Proline Ramachandran Plot - Proline adopts fewer angles. Amino group is incorporated
into a ring.
α-helices - 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 - Formed from added dipole moments of all hydrogen bonds in an α-helix.
N-terminus is δ+ and C-terminus is δ-.
ß-sheet - Either parallel or anti-parallel. Often twisted to increase strength.
ACS BIOCHEMISTRY EXAM
QUESTIONS AND ANSWERS UPDATED
2024
BESTZONE
ACS BIOCHEM
8/29/24
,ACS BIOCHEMISTRY EXAM
Henderson-Hasselbach Equation - pH = pKa + log ([A-] / [HA])
FMOC Chemical Synthesis - 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) - Changes soluble protein to solid precipitate. Protein
precipitates when the charges on the protein match the charges in the solution.
Size-Exclusion Chromatography - Separates sample based on size with smaller
molecules eluting later.
Ion-Exchange Chromatography - 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 - Beads are coated with a carbon chain.
Hydrophobic proteins stick better. Elute with non-H-bonding solvent (acetonitrile).
Affinity Chromatography - Attach a ligand that binds a protein to a bead. Elute with
harsh chemicals or similar ligand.
SDS-PAGE - Uses SDS. Gel is made from cross-linked polyacrylamide. Separates
based off of mass with smaller molecules moving faster. Visualized with Coomassie
blue.
SDS - Sodium dodecyl sulfate. Unfolds proteins and gives them uniform negative
charge.
Isoelectric Focusing - Variation of gel electrophoresis where protein charge matters.
Involves electrodes and pH gradient. Protein stops at their pI when neutral.
ACS BIOCHEMISTRY EXAM
, ACS BIOCHEMISTRY EXAM
FDNB (1-fluoro-2,3-dinitrobenzene) - 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) - Reduces disulfide bonds.
Iodoacetate - Adds carboxymethyl group on free -SH groups. Blocks disulfide bonding.
Homologs - Shares 25% identity with another gene
Orthologs - Similar genes in different organisms
Paralogs - Similar "paired" genes in the same organism
Ramachandran Plot - Shows favorable phi-psi angle combinations. 3 main "wells" for α-
helices, ß-sheets, and left-handed α-helices.
Glycine Ramachandran Plot - Glycine can adopt more angles. (H's for R-group).
Proline Ramachandran Plot - Proline adopts fewer angles. Amino group is incorporated
into a ring.
α-helices - 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 - Formed from added dipole moments of all hydrogen bonds in an α-helix.
N-terminus is δ+ and C-terminus is δ-.
ß-sheet - Either parallel or anti-parallel. Often twisted to increase strength.
ACS BIOCHEMISTRY EXAM
