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.ACS BIOCHEMISTRY EXAM QUESTION WITH COMPLETE SOLUTIONS LATEST 2024 DTT (dithiothreitol) - CORRECT ANSWER - Reduces disulfide bonds.
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.
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. Disulfide-bonds - CORRECT ANSWER - Bonds between two -SH groups that form
between 2° and 3° structure.
Circular Dichroism - CORRECT ANSWER - Uses UV light to measure 2° structure. Can
be used to measure destabilization.
ß-mercaptoethanol - CORRECT ANSWER - Breaks disulfide bonds.
α-keratin - CORRECT ANSWER - formed from 2 α-helices twisted around each other.
"Coiled coil". Cross-linked by disulfide bonds.
Collagen - CORRECT ANSWER - Repeating sequence of Gly-X-Pro. 3 stranded "coiled
coil". Contains gly core.
Myoglobin 4° Structure - CORRECT ANSWER - Symmetric homodimer,
Hemoglobin 4° Structure - CORRECT ANSWER - Tetramer. Dimer of dimers. α2ß2
tetramer.
α/ß Protein Folding - CORRECT ANSWER - Less distinct areas of α and ß folding.
α+ß Protein Folding - CORRECT ANSWER - Two distinct areas of α and ß folding.
Mechanism of Denaturants - CORRECT ANSWER - Highly soluble, H-binding
molecules. Stabilize protein backbone in water. Allows denatured state to be stabilized.
Temperature Denaturation of Protein - CORRECT ANSWER - Midpoint of reaction is
Tm.
Cooperative Protein Folding - CORRECT ANSWER - Folding transition is sharp. More
reversible.
Folding Funnel - CORRECT ANSWER - Shows 3D version of 2D energy states. Lowest
energy is stable protein. Rough funnel is less cooperative.
Protein-Protein Interfaces - CORRECT ANSWER - "Core" and "fringe" of the interfaces.
Core is more hydrophobic and is on the inside when interfaced. Fringe is more
hydrophilic.
π-π Ring Stacking - CORRECT ANSWER - Weird interaction where aromatic rings
stack on each other in positive interaction.
σ-hole - CORRECT ANSWER - Methyl group has area of diminished electron density in
center; attracts electronegative groups
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.ACS BIOCHEMISTRY EXAM QUESTION WITH COMPLETE SOLUTIONS LATEST 2024 DTT (dithiothreitol) - CORRECT ANSWER - Reduces disulfide bonds.
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.
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. Disulfide-bonds - CORRECT ANSWER - Bonds between two -SH groups that form
between 2° and 3° structure.
Circular Dichroism - CORRECT ANSWER - Uses UV light to measure 2° structure. Can
be used to measure destabilization.
ß-mercaptoethanol - CORRECT ANSWER - Breaks disulfide bonds.
α-keratin - CORRECT ANSWER - formed from 2 α-helices twisted around each other.
"Coiled coil". Cross-linked by disulfide bonds.
Collagen - CORRECT ANSWER - Repeating sequence of Gly-X-Pro. 3 stranded "coiled
coil". Contains gly core.
Myoglobin 4° Structure - CORRECT ANSWER - Symmetric homodimer,
Hemoglobin 4° Structure - CORRECT ANSWER - Tetramer. Dimer of dimers. α2ß2
tetramer.
α/ß Protein Folding - CORRECT ANSWER - Less distinct areas of α and ß folding.
α+ß Protein Folding - CORRECT ANSWER - Two distinct areas of α and ß folding.
Mechanism of Denaturants - CORRECT ANSWER - Highly soluble, H-binding
molecules. Stabilize protein backbone in water. Allows denatured state to be stabilized.
Temperature Denaturation of Protein - CORRECT ANSWER - Midpoint of reaction is
Tm.
Cooperative Protein Folding - CORRECT ANSWER - Folding transition is sharp. More
reversible.
Folding Funnel - CORRECT ANSWER - Shows 3D version of 2D energy states. Lowest
energy is stable protein. Rough funnel is less cooperative.
Protein-Protein Interfaces - CORRECT ANSWER - "Core" and "fringe" of the interfaces.
Core is more hydrophobic and is on the inside when interfaced. Fringe is more
hydrophilic.
π-π Ring Stacking - CORRECT ANSWER - Weird interaction where aromatic rings
stack on each other in positive interaction.
σ-hole - CORRECT ANSWER - Methyl group has area of diminished electron density in
center; attracts electronegative groups
