BIOCHEMISTRY 7TH EDITION COMPREHENSIVE
EXAM SCRIPT WITH SOLUTIONS
◉ 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.
◉ DTT (dithiothreitol).
Answer: Reduces disulfide bonds.
◉ 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 5.4A.
,◉ 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.
◉ Anti-parallel ß-sheet.
Answer: Alternating sheet directions (C & N-termini don't line-up).
Has straight H-bonds.
◉ 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.
◉ ß-mercaptoethanol.
Answer: Breaks disulfide bonds.
◉ α-keratin.
Answer: formed from 2 α-helices twisted around each other. "Coiled
coil". Cross-linked by disulfide bonds.
◉ Collagen.
Answer: Repeating sequence of Gly-X-Pro. 3 stranded "coiled coil".
Contains gly core.
◉ Myoglobin 4° Structure.
Answer: Symmetric homodimer,
EXAM SCRIPT WITH SOLUTIONS
◉ 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.
◉ DTT (dithiothreitol).
Answer: Reduces disulfide bonds.
◉ 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 5.4A.
,◉ 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.
◉ Anti-parallel ß-sheet.
Answer: Alternating sheet directions (C & N-termini don't line-up).
Has straight H-bonds.
◉ 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.
◉ ß-mercaptoethanol.
Answer: Breaks disulfide bonds.
◉ α-keratin.
Answer: formed from 2 α-helices twisted around each other. "Coiled
coil". Cross-linked by disulfide bonds.
◉ Collagen.
Answer: Repeating sequence of Gly-X-Pro. 3 stranded "coiled coil".
Contains gly core.
◉ Myoglobin 4° Structure.
Answer: Symmetric homodimer,
