ACS BIOCHEMISTRY EXAM 2023 WITH COMPLETE SOLUTION;VERIFIED CORRECTLY

ACS BIOCHEMISTRY EXAM 2022 WITH

COMPLETE SOLUTION;VERIFIED

CORRECTLY

Henderson-Hasselbach Equation - pH = pKa + log ([A-] / [HA])

FMOC Chemical Synthesis - 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) - Changes soluble protein to solid precipitate. Protein

precipitates when the charges on the protein match the charges in the solution.

Size-Exclusion Chromatography - Separates sample based on size with smaller

molecules eluting later.

Ion-Exchange Chromatography - 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 - Beads are coated with a carbon chain.

Hydrophobic proteins stick better. Elute with non-H-bonding solvent (acetonitrile).

Affinity Chromatography - Attach a ligand that binds a protein to a bead. Elute with

harsh chemicals or similar ligand.

SDS-PAGE - Uses SDS. Gel is made from cross-linked polyacrylamide. Separates

based off of mass with smaller molecules moving faster. Visualized with Coomassie

blue.

SDS - Sodium dodecyl sulfate. Unfolds proteins and gives them uniform negative

charge.

Isoelectric Focusing - 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) - 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) - Reduces disulfide bonds.

Iodoacetate - Adds carboxymethyl group on free -SH groups. Blocks disulfide bonding.

Homologs - Shares 25% identity with another gene

Orthologs - Similar genes in different organisms

Paralogs - Similar "paired" genes in the same organism

Ramachandran Plot - Shows favorable phi-psi angle combinations. 3 main "wells" for αhelices, ß-sheets, and left-handed α-helices.

Glycine Ramachandran Plot - Glycine can adopt more angles. (H's for R-group).

Proline Ramachandran Plot - Proline adopts fewer angles. Amino group is incorporated

into a ring.

α-helices - 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 - Formed from added dipole moments of all hydrogen bonds in an α-helix.

N-terminus is δ+ and C-terminus is δ-.

ß-sheet - Either parallel or anti-parallel. Often twisted to increase strength.

Anti-parallel ß-sheet - Alternating sheet directions (C & N-termini don't line-up). Has

straight H-bonds.

Parallel ß-sheet - Same sheet directions (C & N-termini line up). Has angled H-bonds.

ß-turns - 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 - Not highly structured. Not necessary highly flexible, but can occasionally move.

Very variable in sequence.

Circular Dichroism - Uses UV light to measure 2° structure. Can be used to measure

destabilization.

Disulfide-bonds - Bonds between two -SH groups that form between 2° and 3° structure.

ß-mercaptoethanol - Breaks disulfide bonds.

α-keratin - formed from 2 α-helices twisted around each other. "Coiled coil". Crosslinked by disulfide bonds.

Collagen - Repeating sequence of Gly-X-Pro. 3 stranded "coiled coil". Contains gly

core.

Myoglobin 4° Structure - Symmetric homodimer,

Hemoglobin 4° Structure - Tetramer. Dimer of dimers. α2ß2 tetramer.

α/ß Protein Folding - Less distinct areas of α and ß folding.

α+ß Protein Folding - Two distinct areas of α and ß folding.

Mechanism of Denaturants - Highly soluble, H-binding molecules. Stabilize protein

backbone in water. Allows denatured state to be stabilized.

Temperature Denaturation of Protein - Midpoint of reaction is Tm.

Cooperative Protein Folding - Folding transition is sharp. More reversible.

Folding Funnel - Shows 3D version of 2D energy states. Lowest energy is stable

protein. Rough funnel is less cooperative.

Protein-Protein Interfaces - "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 - Weird interaction where aromatic rings stack on each other in

positive interaction.

σ-hole - Methyl group has area of diminished electron density in center; attracts

electronegative groups

Fe Binding of O2 - Fe2+ binds to O2 reversible. Fe3+ has an additional + charge and

binds to O2 irreversibly. Fe3+ rusts in O2 rich environments.

Ka for Binding - Ka = [PL] / [P][L]

ϴ ϴ -value in Binding - = (bound / total)x100%

ϴ = [L] / ([L] + 1/Ka)

Kd for binding - Kd = [L] when 50% bound to protein.

Kd = 1/Ka

High-Spin Fe - Electrons are "spread out" and result in larger atom.

Low-Spin Fe - Electrons are less "spread out" and are compacted by electron rich

porphyrin ring.