ACS BIOCHEMISTRY END OF COURSE EXAM QUESTIONS
AND ANSWERS MARKED A+
✔✔Loops - ✔✔Not highly structured. Not necessary highly flexible, but can occasionally
move. Very variable in sequence.
✔✔Circular Dichroism - ✔✔Uses UV light to measure 2° structure. Can be used to
measure destabilization.
✔✔Disulfide-bonds - ✔✔Bonds between two -SH groups that form between 2° and 3°
structure.
✔✔ß-mercaptoethanol - ✔✔Breaks disulfide bonds.
✔✔α-keratin - ✔✔formed from 2 α-helices twisted around each other. "Coiled coil".
Cross-linked by 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.
✔✔Mechanism of Denaturants - ✔✔Highly soluble, H-binding molecules. Stabilize
protein backbone in water. Allows denatured state to be stabilized.
✔✔Temperature Denaturation of Protein - ✔✔Midpoint of reaction is Tm.
✔✔Cooperative Protein Folding - ✔✔Folding transition is sharp. More reversible.
✔✔Folding Funnel - ✔✔Shows 3D version of 2D energy states. Lowest energy is stable
protein. Rough funnel is less cooperative.
✔✔Protein-Protein Interfaces - ✔✔"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 - ✔✔Weird interaction where aromatic rings stack on each other
in positive interaction.
,✔✔σ-hole - ✔✔Methyl group has area of diminished electron density in center; attracts
electronegative groups
✔✔Fe Binding of O2 - ✔✔Fe2+ binds to O2 reversible. Fe3+ has an additional + charge
and binds to O2 irreversibly. Fe3+ rusts in O2 rich environments.
✔✔Ka for Binding - ✔✔Ka = [PL] / [P][L]
✔✔ϴ-value in Binding - ✔✔ϴ = (bound / total)x100%
ϴ = [L] / ([L] + 1/Ka)
✔✔Kd for binding - ✔✔Kd = [L] when 50% bound to protein.
Kd = 1/Ka
✔✔High-Spin Fe - ✔✔Electrons are "spread out" and result in larger atom.
✔✔Low-Spin Fe - ✔✔Electrons are less "spread out" and are compacted by electron
rich porphyrin ring.
✔✔T-State - ✔✔Heme is in high-spin state. H2O is bound to heme.
✔✔R-State - ✔✔Heme is in low-spin state. O2 is bound to heme.
✔✔O2 Binding Event - ✔✔O2 binds to T-state and changes the heme to R-state.
Causes a 0.4Å movement of the iron.
✔✔Hemoglobin Binding Curve - ✔✔4 subunits present in hemoglobin that can be either
T or R -state. Cooperative binding leads to a sigmoidal curve.
✔✔Binding Cooperativity - ✔✔When one subunit of hemoglobin changes from T to R-
state the other sites are more likely to change to R-state as well. Leads to sigmoidal
graph.
✔✔Homotropic Regulation of Binding - ✔✔Where a regulatory molecule is also the
enzyme's substrate.
✔✔Heterotropic Regulation of Binding - ✔✔Where an allosteric regulator is present that
is not the enzyme's substrate.
✔✔Hill Plot - ✔✔Turns sigmoid into straight lines. Slope = n (# of binding sites). Allows
measurement of binding sites that are cooperative.
, ✔✔pH and Binding Affinity (Bohr Affect) - ✔✔As [H+] increases, Histidine group in
hemoglobin becomes more protonated and protein shifts to T-state. O2 binding affinity
decreases.
✔✔CO2 binding in Hemoglobin - ✔✔Forms carbonic acid that shifts hemoglobin to T-
state. O2 binding affinity decreases. Used in the peripheral tissues.
✔✔BPG (2,3-bisphosphoglycerate) - ✔✔Greatly reduces hemoglobin's affinity for O2 by
binding allosterically. Stabilizes T-state. Transfer of O2 can improve because increased
delivery in tissues can outweigh decreased binding in the lungs.
✔✔Michaelis-Menton Equation - ✔✔V0 = (Vmax[S]) / (Km + [S])
✔✔Km in Michaelis-Menton - ✔✔Km = [S] when V0 = 0.5(Vmax)
✔✔Michaelis-Menton Graph - ✔✔
✔✔Lineweaver-Burke Graph - ✔✔Slope = Km/Vmax
Y-intercept = 1/Vmax
X-intercept = - 1/Km
✔✔Lineweaver-Burke Equation - ✔✔Found by taking the reciprocal of the Michaelis-
Menton Equation.
✔✔Kcat - ✔✔Rate-limiting step in any enzyme-catalyzed reaction at saturation. Known
as the "turn-over number". Kcat = Vmax/Et
✔✔Chymotripsin - ✔✔Cleaves proteins on C-terminal endof Phe, Trp, and Tyr
✔✔Competitive Inhibition Graph - ✔✔Slope changes by factor of α. Slope becomes
αKm/Vmax.
X-intercept becomes 1/αKm
Y-intercept does not change.
Vmax does not change.
✔✔Uncompetitive Inhibition Graph - ✔✔Does not change slope.
Changes Km and Vmax.
Results in vertical shift up and down.
Y-intercept becomes α'/Vmax
X-intercept becomes -α'/Km
✔✔Mixed Inhibition Graph - ✔✔Allosteric inhibitor that binds either E or ES.
Pivot point is between X-intercept and Y-intercept.
AND ANSWERS MARKED A+
✔✔Loops - ✔✔Not highly structured. Not necessary highly flexible, but can occasionally
move. Very variable in sequence.
✔✔Circular Dichroism - ✔✔Uses UV light to measure 2° structure. Can be used to
measure destabilization.
✔✔Disulfide-bonds - ✔✔Bonds between two -SH groups that form between 2° and 3°
structure.
✔✔ß-mercaptoethanol - ✔✔Breaks disulfide bonds.
✔✔α-keratin - ✔✔formed from 2 α-helices twisted around each other. "Coiled coil".
Cross-linked by 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.
✔✔Mechanism of Denaturants - ✔✔Highly soluble, H-binding molecules. Stabilize
protein backbone in water. Allows denatured state to be stabilized.
✔✔Temperature Denaturation of Protein - ✔✔Midpoint of reaction is Tm.
✔✔Cooperative Protein Folding - ✔✔Folding transition is sharp. More reversible.
✔✔Folding Funnel - ✔✔Shows 3D version of 2D energy states. Lowest energy is stable
protein. Rough funnel is less cooperative.
✔✔Protein-Protein Interfaces - ✔✔"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 - ✔✔Weird interaction where aromatic rings stack on each other
in positive interaction.
,✔✔σ-hole - ✔✔Methyl group has area of diminished electron density in center; attracts
electronegative groups
✔✔Fe Binding of O2 - ✔✔Fe2+ binds to O2 reversible. Fe3+ has an additional + charge
and binds to O2 irreversibly. Fe3+ rusts in O2 rich environments.
✔✔Ka for Binding - ✔✔Ka = [PL] / [P][L]
✔✔ϴ-value in Binding - ✔✔ϴ = (bound / total)x100%
ϴ = [L] / ([L] + 1/Ka)
✔✔Kd for binding - ✔✔Kd = [L] when 50% bound to protein.
Kd = 1/Ka
✔✔High-Spin Fe - ✔✔Electrons are "spread out" and result in larger atom.
✔✔Low-Spin Fe - ✔✔Electrons are less "spread out" and are compacted by electron
rich porphyrin ring.
✔✔T-State - ✔✔Heme is in high-spin state. H2O is bound to heme.
✔✔R-State - ✔✔Heme is in low-spin state. O2 is bound to heme.
✔✔O2 Binding Event - ✔✔O2 binds to T-state and changes the heme to R-state.
Causes a 0.4Å movement of the iron.
✔✔Hemoglobin Binding Curve - ✔✔4 subunits present in hemoglobin that can be either
T or R -state. Cooperative binding leads to a sigmoidal curve.
✔✔Binding Cooperativity - ✔✔When one subunit of hemoglobin changes from T to R-
state the other sites are more likely to change to R-state as well. Leads to sigmoidal
graph.
✔✔Homotropic Regulation of Binding - ✔✔Where a regulatory molecule is also the
enzyme's substrate.
✔✔Heterotropic Regulation of Binding - ✔✔Where an allosteric regulator is present that
is not the enzyme's substrate.
✔✔Hill Plot - ✔✔Turns sigmoid into straight lines. Slope = n (# of binding sites). Allows
measurement of binding sites that are cooperative.
, ✔✔pH and Binding Affinity (Bohr Affect) - ✔✔As [H+] increases, Histidine group in
hemoglobin becomes more protonated and protein shifts to T-state. O2 binding affinity
decreases.
✔✔CO2 binding in Hemoglobin - ✔✔Forms carbonic acid that shifts hemoglobin to T-
state. O2 binding affinity decreases. Used in the peripheral tissues.
✔✔BPG (2,3-bisphosphoglycerate) - ✔✔Greatly reduces hemoglobin's affinity for O2 by
binding allosterically. Stabilizes T-state. Transfer of O2 can improve because increased
delivery in tissues can outweigh decreased binding in the lungs.
✔✔Michaelis-Menton Equation - ✔✔V0 = (Vmax[S]) / (Km + [S])
✔✔Km in Michaelis-Menton - ✔✔Km = [S] when V0 = 0.5(Vmax)
✔✔Michaelis-Menton Graph - ✔✔
✔✔Lineweaver-Burke Graph - ✔✔Slope = Km/Vmax
Y-intercept = 1/Vmax
X-intercept = - 1/Km
✔✔Lineweaver-Burke Equation - ✔✔Found by taking the reciprocal of the Michaelis-
Menton Equation.
✔✔Kcat - ✔✔Rate-limiting step in any enzyme-catalyzed reaction at saturation. Known
as the "turn-over number". Kcat = Vmax/Et
✔✔Chymotripsin - ✔✔Cleaves proteins on C-terminal endof Phe, Trp, and Tyr
✔✔Competitive Inhibition Graph - ✔✔Slope changes by factor of α. Slope becomes
αKm/Vmax.
X-intercept becomes 1/αKm
Y-intercept does not change.
Vmax does not change.
✔✔Uncompetitive Inhibition Graph - ✔✔Does not change slope.
Changes Km and Vmax.
Results in vertical shift up and down.
Y-intercept becomes α'/Vmax
X-intercept becomes -α'/Km
✔✔Mixed Inhibition Graph - ✔✔Allosteric inhibitor that binds either E or ES.
Pivot point is between X-intercept and Y-intercept.
