ACEDS/ACTUAL EXAM LATEST
VERSION 2024-2025 WITH VERIFIED
QUESTIONS AND ANSWERS GRADED A+
Henderson-Hasselbach Equation - ANS✔✔--pH = pKa + log ([A-] / [HA])
FMOC Chemical Synthesis - ANS✔✔--Used in synthesis of a growing amino acid
chain to a polystyrene bead. FMOC is used as a protecting group on the N-terminus.
Collagen - ANS✔✔--Repeating sequence of Gly-X-Pro. 3 stranded "coiled coil".
Contains gly core.
Myoglobin 4° Structure - ANS✔✔--Symmetric homodimer,
Salting Out (Purification) - ANS✔✔--Changes soluble protein to solid precipitate.
Protein precipitates when the charges on the protein match the charges in the solution.
,Size-Exclusion Chromatography - ANS✔✔--Separates sample based on size with
smaller molecules eluting later.
Ion-Exchange Chromatography - ANS✔✔--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 - ANS✔✔--Beads are coated with a
carbon chain. Hydrophobic proteins stick better. Elute with non-H-bonding solvent
(acetonitrile).
Affinity Chromatography - ANS✔✔--Attach a ligand that binds a protein to a bead.
Elute with harsh chemicals or similar ligand.
Low-Spin Fe - ANS✔✔--Electrons are less "spread out" and are compacted by
electron rich porphyrin ring.
T-State - ANS✔✔--Heme is in high-spin state. H2O is bound to heme.
R-State - ANS✔✔--Heme is in low-spin state. O2 is bound to heme.
SDS-PAGE - ANS✔✔--Uses SDS. Gel is made from cross-linked polyacrylamide.
Separates based off of mass with smaller molecules moving faster. Visualized with
Coomassie blue.
SDS - ANS✔✔--Sodium dodecyl sulfate. Unfolds proteins and gives them uniform
negative charge.
Isoelectric Focusing - ANS✔✔--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) - ANS✔✔--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) - ANS✔✔--Reduces disulfide bonds.
Iodoacetate - ANS✔✔--Adds carboxymethyl group on free -SH groups. Blocks
disulfide bonding.
Homologs - ANS✔✔--Shares 25% identity with another gene
Orthologs - ANS✔✔--Similar genes in different organisms
, Paralogs - ANS✔✔--Similar "paired" genes in the same organism
.
α-helices - ANS✔✔--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 - ANS✔✔--Formed from added dipole moments of all hydrogen bonds in
an α-helix. N-terminus is δ+ and C-terminus is δ-.
ß-sheet - ANS✔✔--Either parallel or anti-parallel. Often twisted to increase strength.
Anti-parallel ß-sheet - ANS✔✔--Alternating sheet directions (C & N-termini don't line-
up). Has straight H-bonds.
Parallel ß-sheet - ANS✔✔--Same sheet directions (C & N-termini line up). Has
angled H-bonds.
ß-turns - ANS✔✔--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 - ANS✔✔--Not highly structured. Not necessary highly flexible, but can
occasionally move. Very variable in sequence.
Circular Dichroism - ANS✔✔--Uses UV light to measure 2° structure. Can be used to
measure destabilization.
Disulfide-bonds - ANS✔✔--Bonds between two -SH groups that form between 2° and
3° structure.
ß-mercaptoethanol - ANS✔✔--Breaks disulfide bonds.
α-keratin - ANS✔✔--formed from 2 α-helices twisted around each other. "Coiled coil".
Cross-linked by disulfide bonds.
Hemoglobin 4° Structure - ANS✔✔--Tetramer. Dimer of dimers. α2ß2 tetramer.
α/ß Protein Folding - ANS✔✔--Less distinct areas of α and ß folding.
α+ß Protein Folding - ANS✔✔--Two distinct areas of α and ß folding.
Mechanism of Denaturants - ANS✔✔--Highly soluble, H-binding molecules. Stabilize
protein backbone in water. Allows denatured state to be stabilized.
VERSION 2024-2025 WITH VERIFIED
QUESTIONS AND ANSWERS GRADED A+
Henderson-Hasselbach Equation - ANS✔✔--pH = pKa + log ([A-] / [HA])
FMOC Chemical Synthesis - ANS✔✔--Used in synthesis of a growing amino acid
chain to a polystyrene bead. FMOC is used as a protecting group on the N-terminus.
Collagen - ANS✔✔--Repeating sequence of Gly-X-Pro. 3 stranded "coiled coil".
Contains gly core.
Myoglobin 4° Structure - ANS✔✔--Symmetric homodimer,
Salting Out (Purification) - ANS✔✔--Changes soluble protein to solid precipitate.
Protein precipitates when the charges on the protein match the charges in the solution.
,Size-Exclusion Chromatography - ANS✔✔--Separates sample based on size with
smaller molecules eluting later.
Ion-Exchange Chromatography - ANS✔✔--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 - ANS✔✔--Beads are coated with a
carbon chain. Hydrophobic proteins stick better. Elute with non-H-bonding solvent
(acetonitrile).
Affinity Chromatography - ANS✔✔--Attach a ligand that binds a protein to a bead.
Elute with harsh chemicals or similar ligand.
Low-Spin Fe - ANS✔✔--Electrons are less "spread out" and are compacted by
electron rich porphyrin ring.
T-State - ANS✔✔--Heme is in high-spin state. H2O is bound to heme.
R-State - ANS✔✔--Heme is in low-spin state. O2 is bound to heme.
SDS-PAGE - ANS✔✔--Uses SDS. Gel is made from cross-linked polyacrylamide.
Separates based off of mass with smaller molecules moving faster. Visualized with
Coomassie blue.
SDS - ANS✔✔--Sodium dodecyl sulfate. Unfolds proteins and gives them uniform
negative charge.
Isoelectric Focusing - ANS✔✔--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) - ANS✔✔--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) - ANS✔✔--Reduces disulfide bonds.
Iodoacetate - ANS✔✔--Adds carboxymethyl group on free -SH groups. Blocks
disulfide bonding.
Homologs - ANS✔✔--Shares 25% identity with another gene
Orthologs - ANS✔✔--Similar genes in different organisms
, Paralogs - ANS✔✔--Similar "paired" genes in the same organism
.
α-helices - ANS✔✔--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 - ANS✔✔--Formed from added dipole moments of all hydrogen bonds in
an α-helix. N-terminus is δ+ and C-terminus is δ-.
ß-sheet - ANS✔✔--Either parallel or anti-parallel. Often twisted to increase strength.
Anti-parallel ß-sheet - ANS✔✔--Alternating sheet directions (C & N-termini don't line-
up). Has straight H-bonds.
Parallel ß-sheet - ANS✔✔--Same sheet directions (C & N-termini line up). Has
angled H-bonds.
ß-turns - ANS✔✔--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 - ANS✔✔--Not highly structured. Not necessary highly flexible, but can
occasionally move. Very variable in sequence.
Circular Dichroism - ANS✔✔--Uses UV light to measure 2° structure. Can be used to
measure destabilization.
Disulfide-bonds - ANS✔✔--Bonds between two -SH groups that form between 2° and
3° structure.
ß-mercaptoethanol - ANS✔✔--Breaks disulfide bonds.
α-keratin - ANS✔✔--formed from 2 α-helices twisted around each other. "Coiled coil".
Cross-linked by disulfide bonds.
Hemoglobin 4° Structure - ANS✔✔--Tetramer. Dimer of dimers. α2ß2 tetramer.
α/ß Protein Folding - ANS✔✔--Less distinct areas of α and ß folding.
α+ß Protein Folding - ANS✔✔--Two distinct areas of α and ß folding.
Mechanism of Denaturants - ANS✔✔--Highly soluble, H-binding molecules. Stabilize
protein backbone in water. Allows denatured state to be stabilized.
