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ACS BIOCHEMISTRY EXAM Terms in this set (252) 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-te CA$13.67   Add to cart
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ACS BIOCHEMISTRY EXAM Terms in this set (252) 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-te
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ACS BIOCHEMISTRY EXAM Terms in this set (252) 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) ...

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  • August 20, 2024
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  • acs biochemistry exam terms in this set 2

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8/20/24, 4:40 PM




ACS BIOCHEMISTRY EXAM
Jeremiah




Terms in this set (252)

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

Used in synthesis of a growing amino acid chain to a polystyrene bead. FMOC is used
FMOC Chemical Synthesis
as a protecting group on the N-terminus.

Changes soluble protein to solid precipitate. Protein precipitates when the charges on
Salting Out (Purification)
the protein match the charges in the solution.

Size-Exclusion Chromatography Separates sample based on size with smaller molecules eluting later.

Separates sample based on charge. CM attracts +, DEAE attracts -. May have repulsion
Ion-Exchange Chromatography
effect on like charges. Salt or acid used to remove stuck proteins.

Hydrophobic/Reverse Phase Beads are coated with a carbon chain. Hydrophobic proteins stick better. Elute with
Chromatography non-H-bonding solvent (acetonitrile).

Attach a ligand that binds a protein to a bead. Elute with harsh chemicals or similar
Affinity Chromatography
ligand.

Uses SDS. Gel is made from cross-linked polyacrylamide. Separates based off of mass
SDS-PAGE
with smaller molecules moving faster. Visualized with Coomassie blue.

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

Variation of gel electrophoresis where protein charge matters. Involves electrodes and
Isoelectric Focusing
pH gradient. Protein stops at their pI when neutral.

FDNB reacts with the N-terminus of the protein to produce a 2,4-dinitrophenol
FDNB (1-fluoro-2,3-dinitrobenzene) 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


ACS BIOCHEMISTRY EXAM




1/5

, 8/20/24, 4:40 PM
Shows favorable phi-psi angle combinations. 3 main
"wells" for α-helices, ß-sheets, and left-handed α-
Ramachandran Plot
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.

Ala is common, Gly & Pro are not very common. Side-chain interactions every 3 or 4
α-helices
residues. Turns once every 3.6 residues. Distance between backbones is 5.4Å.

Formed from added dipole moments of all hydrogen bonds in an α-helix. N-terminus is
Helix Dipole
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.

Tight u-turns with specific phi-psi angles. Must have gly at position 3. Proline may also
ß-turns
be at ß-turn because it can have a cis-omega angle.

Not highly structured. Not necessary highly flexible, but can occasionally move. Very
Loops
variable in sequence.

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



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

ß-mercaptoethanol Breaks disulfide bonds.

formed from 2 α-helices twisted around each other. "Coiled coil". Cross-linked by
α-keratin
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.

Highly soluble, H-binding molecules. Stabilize protein backbone in water. Allows
Mechanism of Denaturants
denatured state to be stabilized.

Temperature Denaturation of Protein Midpoint of reaction is Tm.

Cooperative Protein Folding Folding transition is sharp. More reversible.

Shows 3D version of 2D energy states. Lowest energy is stable protein. Rough funnel is
Folding Funnel
less cooperative.

"Core" and "fringe" of the interfaces. Core is more hydrophobic and is on the inside
Protein-Protein Interfaces
when interfaced. Fringe is more hydrophilic.

π-π Ring Stacking Weird interaction where aromatic rings stack on each other in positive interaction.

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

Fe2+ binds to O2 reversible. Fe3+ has an additional + charge and binds to O2
Fe Binding of O2
irreversibly. Fe3+ rusts in O2 rich environments.
ACS BIOCHEMISTRY EXAM

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