ACS Biochemistry Exam Questions and
Answers | Verified | A+
• 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 -✓✓formed from 2 α-helices twisted around each other. "Coiled coil".
Cross-linked by disulfide bonds.
• Collagen -✓✓Repeating sequence of Gly-X-Pro. 3 stranded "coiled coil".
Contains gly core.
• Myoglobin 4° Structure -✓✓Symmetric homodimer,
• Hemoglobin 4° Structure -✓✓Tetramer. Dimer of dimers. α2ß2 tetramer.
• α/ß Protein Folding -✓✓Less distinct areas of α and ß folding.
• α+ß Protein Folding -✓✓Two distinct areas of α and ß folding.
• Mechanism of Denaturants -✓✓Highly soluble, H-binding molecules. Stabilize
protein backbone in water. Allows denatured state to be stabilized.
• Temperature Denaturation of Protein -✓✓Midpoint of reaction is Tm.
• Cooperative Protein Folding -✓✓Folding transition is sharp. More reversible.
• Folding Funnel -✓✓Shows 3D version of 2D energy states. Lowest energy is
stable protein. Rough funnel is less cooperative.
Answers | Verified | A+
• 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 -✓✓formed from 2 α-helices twisted around each other. "Coiled coil".
Cross-linked by disulfide bonds.
• Collagen -✓✓Repeating sequence of Gly-X-Pro. 3 stranded "coiled coil".
Contains gly core.
• Myoglobin 4° Structure -✓✓Symmetric homodimer,
• Hemoglobin 4° Structure -✓✓Tetramer. Dimer of dimers. α2ß2 tetramer.
• α/ß Protein Folding -✓✓Less distinct areas of α and ß folding.
• α+ß Protein Folding -✓✓Two distinct areas of α and ß folding.
• Mechanism of Denaturants -✓✓Highly soluble, H-binding molecules. Stabilize
protein backbone in water. Allows denatured state to be stabilized.
• Temperature Denaturation of Protein -✓✓Midpoint of reaction is Tm.
• Cooperative Protein Folding -✓✓Folding transition is sharp. More reversible.
• Folding Funnel -✓✓Shows 3D version of 2D energy states. Lowest energy is
stable protein. Rough funnel is less cooperative.
