BIOCHEMISTRY - All 20 Amino Acids Final
Exam Study guide |Test bank Verified Practice
Questions with A+ Answers | Final Exam Guide
FOR 2025/2026
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.
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.
Anti-parallel ß-sheet
Alternating sheet directions (C & N-termini don't line-up). Has straight H-bonds.
Parallel ß-sheet
Same sheet directions (C & N-termini line up). Has angled H-bonds.
ß-turns
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
Not highly structured. Not necessary highly flexible, but can occasionally move. Very variable in
sequence.
Circular Dichroism
Uses UV light to measure 2° structure. Can be used to measure destabilization.
Disulfide-bonds
Bonds between two -SH groups that form between 2° and 3° structure.
ß-mercaptoethanol
Breaks disulfide bonds.
α-keratin
Exam Study guide |Test bank Verified Practice
Questions with A+ Answers | Final Exam Guide
FOR 2025/2026
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.
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.
Anti-parallel ß-sheet
Alternating sheet directions (C & N-termini don't line-up). Has straight H-bonds.
Parallel ß-sheet
Same sheet directions (C & N-termini line up). Has angled H-bonds.
ß-turns
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
Not highly structured. Not necessary highly flexible, but can occasionally move. Very variable in
sequence.
Circular Dichroism
Uses UV light to measure 2° structure. Can be used to measure destabilization.
Disulfide-bonds
Bonds between two -SH groups that form between 2° and 3° structure.
ß-mercaptoethanol
Breaks disulfide bonds.
α-keratin
