ACS BIOCHEMISTRY FINAL PAPER EXAM QUESTIONS WITH
SOLUTIONS GRADED A+
✔✔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.
✔✔Non-Competitive Inhibition Graph - ✔✔Form of mixed inhibition where the pivot point
is on the x-axis. Only happens when K1 is equal to K1'.
✔✔Ionophore - ✔✔Hydrophobic molecule that binds to ions and carries them through
cell membranes. Disrupts concentration gradients.
✔✔ΔGtransport Equation - ✔✔ΔGtransport = RTln([S]out / [S]in) + ZFΔΨ
✔✔Pyranose vs. Furanose - ✔✔Pyranose is a 6-membered ring.
Furanose is a 5-membered ring.
✔✔Mutarotation - ✔✔Conversion from α to ß forms of the sugar at the anomeric carbon.
✔✔Anomeric Carbon - ✔✔Carbon that is cyclized. Always the same as the aldo or keto
carbon in the linear form.
✔✔α vs. ß sugars - ✔✔α form has -OR/OH group opposite from the -CH2OH group.
ß form has -OR/OH group on the same side as the -CH2OH group.
✔✔Starch - ✔✔Found in plants. D-glucose polysaccharide. "Amylose chain".
Unbranched. Has reducing and non-reducing end.
✔✔Amylose Chain - ✔✔Has α-1,4-linkages that produce a coiled helix similar to an α-
helix. Has a reducing and non-reducing end.
✔✔Amylopectin - ✔✔Has α-1,4-linkages. Has periodic α-1,6-linkages that cause
branching. Branched every 24-30 residues. Has reducing and non-reducing end.
SOLUTIONS GRADED A+
✔✔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.
✔✔Non-Competitive Inhibition Graph - ✔✔Form of mixed inhibition where the pivot point
is on the x-axis. Only happens when K1 is equal to K1'.
✔✔Ionophore - ✔✔Hydrophobic molecule that binds to ions and carries them through
cell membranes. Disrupts concentration gradients.
✔✔ΔGtransport Equation - ✔✔ΔGtransport = RTln([S]out / [S]in) + ZFΔΨ
✔✔Pyranose vs. Furanose - ✔✔Pyranose is a 6-membered ring.
Furanose is a 5-membered ring.
✔✔Mutarotation - ✔✔Conversion from α to ß forms of the sugar at the anomeric carbon.
✔✔Anomeric Carbon - ✔✔Carbon that is cyclized. Always the same as the aldo or keto
carbon in the linear form.
✔✔α vs. ß sugars - ✔✔α form has -OR/OH group opposite from the -CH2OH group.
ß form has -OR/OH group on the same side as the -CH2OH group.
✔✔Starch - ✔✔Found in plants. D-glucose polysaccharide. "Amylose chain".
Unbranched. Has reducing and non-reducing end.
✔✔Amylose Chain - ✔✔Has α-1,4-linkages that produce a coiled helix similar to an α-
helix. Has a reducing and non-reducing end.
✔✔Amylopectin - ✔✔Has α-1,4-linkages. Has periodic α-1,6-linkages that cause
branching. Branched every 24-30 residues. Has reducing and non-reducing end.
