BIOCHEM 210 FINAL EXAM COMPREHENSIVE
STUDY GUIDE WITH SOLUTIONS
◉ 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,
◉ 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.
STUDY GUIDE WITH SOLUTIONS
◉ 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,
◉ 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.
