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ACS BIOCHEMISTRY EXAM – QUESTIONS AND ANSWERS

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ACS BIOCHEMISTRY EXAM – QUESTIONS AND ANSWERS

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  • November 25, 2024
  • 23
  • 2024/2025
  • Exam (elaborations)
  • Questions & answers
  • ACS BIOCHEMISTRY
  • ACS BIOCHEMISTRY
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ACS BIOCHEMISTRY EXAM – QUESTIONS AND ANSWERS

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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