Henderson-Hasselbach Equation Right Ans - pH = pKa + log ([A-] / [HA])
FMOC Chemical Synthesis Right 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.
Salting Out (Purification) Right Ans - Changes soluble protein to solid
precipitate. Protein precipitates when the charges on the protein match the
charges in the solution.
Size-Exclusion Chromatography Right Ans - Separates sample based on
size with smaller molecules eluting later.
Ion-Exchange Chromatography Right 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 Right Ans - Beads are coated
with a carbon chain. Hydrophobic proteins stick better. Elute with non-H-
bonding solvent (acetonitrile).
Affinity Chromatography Right Ans - Attach a ligand that binds a protein to
a bead. Elute with harsh chemicals or similar ligand.
SDS-PAGE Right 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 Right Ans - Sodium dodecyl sulfate. Unfolds proteins and gives them
uniform negative charge.
Isoelectric Focusing Right 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) Right 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) Right Ans - Reduces disulfide bonds.
Iodoacetate Right Ans - Adds carboxymethyl group on free -SH groups.
Blocks disulfide bonding.
Homologs Right Ans - Shares 25% identity with another gene
Orthologs Right Ans - Similar genes in different organisms
Paralogs Right Ans - Similar "paired" genes in the same organism
Ramachandran Plot Right Ans - Shows favorable phi-psi angle
combinations. 3 main "wells" for α-helices, ß-sheets, and left-handed α-
helices.
Glycine Ramachandran Plot Right Ans - Glycine can adopt more angles. (H's
for R-group).
Proline Ramachandran Plot Right Ans - Proline adopts fewer angles. Amino
group is incorporated into a ring.
α-helices Right 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 Right 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 Right Ans - Either parallel or anti-parallel. Often twisted to
increase strength.
Anti-parallel ß-sheet Right Ans - Alternating sheet directions (C & N-
termini don't line-up). Has straight H-bonds.
, Parallel ß-sheet Right Ans - Same sheet directions (C & N-termini line up).
Has angled H-bonds.
ß-turns Right 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 Right Ans - Not highly structured. Not necessary highly flexible, but
can occasionally move. Very variable in sequence.
Circular Dichroism Right Ans - Uses UV light to measure 2° structure. Can
be used to measure destabilization.
Disulfide-bonds Right Ans - Bonds between two -SH groups that form
between 2° and 3° structure.
ß-mercaptoethanol Right Ans - Breaks disulfide bonds.
α-keratin Right Ans - formed from 2 α-helices twisted around each other.
"Coiled coil". Cross-linked by disulfide bonds.
Collagen Right Ans - Repeating sequence of Gly-X-Pro. 3 stranded "coiled
coil". Contains gly core.
Myoglobin 4° Structure Right Ans - Symmetric homodimer,
Hemoglobin 4° Structure Right Ans - Tetramer. Dimer of dimers. α2ß2
tetramer.
α/ß Protein Folding Right Ans - Less distinct areas of α and ß folding.
α+ß Protein Folding Right Ans - Two distinct areas of α and ß folding.
Mechanism of Denaturants Right Ans - Highly soluble, H-binding
molecules. Stabilize protein backbone in water. Allows denatured state to be
stabilized.
Temperature Denaturation of Protein Right Ans - Midpoint of reaction is
Tm.
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