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ACS BIOCHEMISTRY EXAM WITH COMPLETE SOLUTIONS LATEST UPDATE
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ACS BIOCHEMISTRY EXAM WITHCOMPLETE SOLUTIONS LATEST UPDATE
Henderson-Hasselbach Equation - correct answers pH = pKa + log ([A-] / [HA])
FMOC Chemical Synthesis - correct answers 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 answers Changes soluble protein to solid
precipitate. Protein precipitates when the charges on the protein match the
charges in the solution.
Size-Exclusion Chromatography - correct answers Separates sample based on size
with smaller molecules eluting later.
Ion-Exchange Chromatography - correct answers 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 answers Beads are coated
with a carbon chain. Hydrophobic proteins stick better. Elute with non-H-bonding
solvent (acetonitrile).
,Affinity Chromatography - correct answers Attach a ligand that binds a protein to a
bead. Elute with harsh chemicals or similar ligand.
SDS-PAGE - correct answers 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 answers Sodium dodecyl sulfate. Unfolds proteins and gives them
uniform negative charge.
Isoelectric Focusing - correct answers 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) - correct answers 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) - correct answers Reduces disulfide bonds.
Iodoacetate - correct answers Adds carboxymethyl group on free -SH groups.
Blocks disulfide bonding.
Homologs - correct answers Shares 25% identity with another gene
,Orthologs - correct answers Similar genes in different organisms
Paralogs - correct answers Similar "paired" genes in the same organism
Ramachandran Plot - correct answers Shows favorable phi-psi angle combinations.
3 main "wells" for α-helices, ß-sheets, and left-handed α-helices.
Glycine Ramachandran Plot - correct answers Glycine can adopt more angles. (H's
for R-group).
Proline Ramachandran Plot - correct answers Proline adopts fewer angles. Amino
group is incorporated into a ring.
α-helices - correct answers 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 answers 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 answers Either parallel or anti-parallel. Often twisted to increase
strength.
Anti-parallel ß-sheet - correct answers Alternating sheet directions (C & N-termini
don't line-up). Has straight H-bonds.
, Parallel ß-sheet - correct answers Same sheet directions (C & N-termini line up).
Has angled H-bonds.
ß-turns - correct answers 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 answers Not highly structured. Not necessary highly flexible, but
can occasionally move. Very variable in sequence.
Circular Dichroism - correct answers Uses UV light to measure 2° structure. Can be
used to measure destabilization.
Disulfide-bonds - correct answers Bonds between two -SH groups that form
between 2° and 3° structure.
ß-mercaptoethanol - correct answers Breaks disulfide bonds.
α-keratin - correct answers formed from 2 α-helices twisted around each other.
"Coiled coil". Cross-linked by disulfide bonds.
Collagen - correct answers Repeating sequence of Gly-X-Pro. 3 stranded "coiled
coil". Contains gly core.
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