ACS BIOCHEMISTRY EXAM study
exams and study guides EXAM
QUESTIONS AND ANSWERS SOLVED
CORRECT
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.
Disulfide-bonds - CORRECT ANSWER✅✅✅Bonds between two -SH groups that form
between 2° and 3° structure.
exams and study guides EXAM
QUESTIONS AND ANSWERS SOLVED
CORRECT
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.
Disulfide-bonds - CORRECT ANSWER✅✅✅Bonds between two -SH groups that form
between 2° and 3° structure.
