ACS BIOCHEMISTRY STUDY GUIDE WITH
SOLVED QUESTIONS AND ANSWERS
◉ 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.
◉ π-π Ring Stacking.
, Answer: Weird interaction where aromatic rings stack on each other
in positive interaction.
◉ σ-hole.
Answer: Methyl group has area of diminished electron density in
center; attracts electronegative groups
◉ Fe Binding of O2.
Answer: Fe2+ binds to O2 reversible. Fe3+ has an additional +
charge and binds to O2 irreversibly. Fe3+ rusts in O2 rich
environments.
◉ Ka for Binding.
Answer: Ka = [PL] / [P][L]
◉ ϴ-value in Binding.
Answer: ϴ = (bound / total)x100%
ϴ = [L] / ([L] + 1/Ka)
◉ Kd for binding.
Answer: Kd = [L] when 50% bound to protein.
Kd = 1/Ka
SOLVED QUESTIONS AND ANSWERS
◉ 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.
◉ π-π Ring Stacking.
, Answer: Weird interaction where aromatic rings stack on each other
in positive interaction.
◉ σ-hole.
Answer: Methyl group has area of diminished electron density in
center; attracts electronegative groups
◉ Fe Binding of O2.
Answer: Fe2+ binds to O2 reversible. Fe3+ has an additional +
charge and binds to O2 irreversibly. Fe3+ rusts in O2 rich
environments.
◉ Ka for Binding.
Answer: Ka = [PL] / [P][L]
◉ ϴ-value in Binding.
Answer: ϴ = (bound / total)x100%
ϴ = [L] / ([L] + 1/Ka)
◉ Kd for binding.
Answer: Kd = [L] when 50% bound to protein.
Kd = 1/Ka
