FMOC Chemical Synthesis - 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) - ANSWER-✅Changes soluble protein to solid precipitate.
Protein precipitates when the charges on the protein match the charges in the
solution.
Size-Exclusion Chromatography - ANSWER-✅Separates sample based on size with
smaller molecules eluting later.
Ion-Exchange Chromatography - 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 - ANSWER-✅Beads are coated with a
carbon chain. Hydrophobic proteins stick better. Elute with non-H-bonding solvent
(acetonitrile).
Affinity Chromatography - ANSWER-✅Attach a ligand that binds a protein to a bead.
Elute with harsh chemicals or similar ligand.
,SDS-PAGE - 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 - ANSWER-✅Sodium dodecyl sulfate. Unfolds proteins and gives them uniform
negative charge.
Isoelectric Focusing - ANSWER-✅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) - 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 - ANSWER-✅Adds carboxymethyl group on free -SH groups. Blocks
disulfide bonding.
Homologs - ANSWER-✅Shares 25% identity with another gene
Orthologs - ANSWER-✅Similar genes in different organisms
Paralogs - ANSWER-✅Similar "paired" genes in the same organism
Ramachandran Plot - ANSWER-✅Shows favorable phi-psi angle combinations. 3
main "wells" for α-helices, ß-sheets, and left-handed α-helices.
Glycine Ramachandran Plot - ANSWER-✅Glycine can adopt more angles. (H's for R-
group).
Proline Ramachandran Plot - ANSWER-✅Proline adopts fewer angles. Amino group
is incorporated into a ring.
α-helices - 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 - 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 - ANSWER-✅Either parallel or anti-parallel. Often twisted to increase
strength.
, Parallel ß-sheet - ANSWER-✅Same sheet directions (C & N-termini line up). Has
angled H-bonds.
ß-turns - 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 - ANSWER-✅Not highly structured. Not necessary highly flexible, but can
occasionally move. Very variable in sequence.
Circular Dichroism - ANSWER-✅Uses UV light to measure 2° structure. Can be used
to measure destabilization.
Disulfide-bonds - ANSWER-✅Bonds between two -SH groups that form between 2°
and 3° structure.
Hemoglobin 4° Structure - ANSWER-✅Tetramer. Dimer of dimers. α2ß2 tetramer.
α/ß Protein Folding - ANSWER-✅Less distinct areas of α and ß folding.
α+ß Protein Folding - ANSWER-✅Two distinct areas of α and ß folding.
Mechanism of Denaturants - ANSWER-✅Highly soluble, H-binding molecules.
Stabilize protein backbone in water. Allows denatured state to be stabilized.
Temperature Denaturation of Protein - ANSWER-✅Midpoint of reaction is Tm.
Cooperative Protein Folding - ANSWER-✅Folding transition is sharp. More
reversible.
Folding Funnel - ANSWER-✅Shows 3D version of 2D energy states. Lowest energy is
stable protein. Rough funnel is less cooperative.
Protein-Protein Interfaces - ANSWER-✅"Core" and "fringe" of the interfaces. Core is
more hydrophobic and is on the inside when interfaced. Fringe is more hydrophilic.
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