ACS BIOCHEMISTRY EXAM
ACTUAL EXAM 2026 GRADED
A+
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.
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.
,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.
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.
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).
ACTUAL EXAM 2026 GRADED
A+
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.
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.
,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.
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.
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).
