Download Sample Question Set 5a

Bchm2000
Problem Set 5a
Spring 2008
1. Give brief definitions or unique descriptions of the following terms:
a. Redox reaction
b. Kinase
c. Q cycle
2. A certain metabolic reaction takes the form A -> B. Its standard
transformed free energy change is 7.5 kJ mol-1. (R = 8.3145 J K-1 mol-1)
a. Calculate the equilibrium constant for the reaction at 25°C.
b. Calculate ΔG at 37°C when the concentraiton of A is 0.5 mM and
the concentraiton of B is 0.1 mM. Is the reaction spontaneous
under these conditions?
c. How might the reaction proceed in the cell?
3. Choose the best definition for a near-equilibrium reaction:
(i) always operates with a favorable free energy change
(ii) has a free energy change near zero
(iii) is usually a control point in a metabolic pathway
(iv) operates very slowly in vivo.
4. Creatine kinase catalyzes the following reaction:
ATP + creatine Ù phosphocreatine + ADP, ΔG°’ = + 12.6 kJ mol-1
Predict wether creatine kinase will operate in the direction of ATP
synthesis or phosphocreatine synthesis at 25°C when [ATP] = 4 mM,
[ADP] = 0.15 mM, [phosphocreatine] = 2.5 mM, and [creatine] = 1 mM.
5. Write a balanced equation for the oxidation of uibquinol by cytochrome c.
Calculate ΔG°’ and ΔE°’ for the reaction. (F = 96.485 kJ V-1 mol-1)
Standard Reduction Potentials
Bchm2000
Problem Set 5a
Spring 2008
6. Under standard conditions, will the following reactions proceed
spontaneously as written?
a. Fumarate + NADH + H+ Ù succinate + NAD+
b. Cyt a (Fe2+) + Cyt b (Fe3+) Ù Cyt a (Fe3+) + Cyt b (Fe3+)
7. Which reaction in glycolysis is catalyzed by the following enzyme? Provide
names of all reactants and products (no structures required).
a. Aldolase
b. Hexokinase
c. Pyruvate Kinase
8. Glycolytic Enzymes II:
a. List the glycolytic enzymes which consume ATP.
b. List the glycolytic enzymes which produce ATP.
9. What is the net reaction of glycolysis for 2 glucoses?
10. Phosphohexose isomerase converts Glucose-6-phosphate to Fructose-6phosphate. Write down the structures of both substrate and product.
11. Energetics of glycolysis:
Explain in general words which reactions in glycolysis are favorable, which
operate at equilibrium and which are unfavorable.
Bchm2000
Problem Set 5a
Spring 2008
12. ΔG°’ for the aldolase reaction is 22.8 kJ mol-1. In the cell at 37°C, there is
the following ratio [DHAP]/[GAP] = 5.5. Calculate the equilibrium ratio of
[FBP]/[GAP] when [GAP] = 10-4 M. (abbreviations: DHAP =
dihydroxyacetone phosphate, GAP = glyceraldehyde-3-phosphate, FBP =
fructose-1,6-bisphosphate)
13. Put the following events in the correct order of their occurence:
Citric acid cycle, digestion, glycolysis, oxidative phosphorylation,
electron transport
14. The order of enzyme complexes in the elctron transport pahtway leading
ultimately to oxygen consumption during oxidative phosphorlyation is:
i. cytochrome c -> cytochrome c oxidase -> NADH
dehydrogenase -> ubiquinone
ii. cytochrome c oxidase -> cytochrome c -> NADH
dehydrogenase -> ubiquinone
iii. NADH dehydrogenase -> ubiquinone -> cytochrome c ->
cytochrome c oxidase
iv. NADH dehydrogenase –> cytochrome c -> ubiquinone ->
cytochrome c oxidase
15. Why is it possible for electrons to flow from a redox center with a more
positive E°’ to one with a more negative E°’ within an electron-transfer
complex?
16. In oxidative phosphorylation, which compound is oxidized and which is
phosphorylated?
17. Calculate ΔG°’ for the oxidation of free FADH2 by O2. What is the
maximum number of ATPs that can be synthesized, assuming standard
conditions and 100% conservation of energy? (ΔG°’ = 30.5 kJ mol-1 for
ATP synthesis)
18. When the F1 prtion of the ATP synthase complex is removed from the
mitochondrial membrane and studied in solution, it functions as an
ATPase, i.e. it hydrolyzes ATP. Why does it not function as an ATP
synthase?
Bchm2000
Problem Set 5a
Spring 2008
Answers:
1. a. Redox reactions are all chemical reactions in which atoms change their
oxidation state.
b. Kinases are enzymes that transfer a phosphoryl group from a high
energy donor to an acceptor (i.e. consume or produce ATP).
c. The Q cycle transfers electrons from ubiquinone to complex III in two
steps.
2. Standard free energy and equilibrium constants:
a. Since ΔG°’ = -RT ln K, K = e (-ΔG°’ / RT) , T = 298 K (25 °C)
K = e -7500 J mol-1 / (8.3145 J K-1 mol-1) (298K) = 0.048
b. ΔG = ΔG°’ + RT ln [B]/[A]
= 7500 J mol-1 + (8.3145 J K-1 mol-1) (310 K) ln (0.0001/0.0005)
= 7500 J mol-1 – 4150 J mol-1 = 3.35 kJ mol-1
The reaction is not spontaneous since ΔG >0.
c. The reaction can proceed in the cell if the product B is the substrate
for a second reaction such that the second reaction continually
draws off B, causing the first reaction to continually produce more B
from A.
3. (ii) has a free energy change near zero
4. ΔG = ΔG°’ + RT ln ([phosphocreatine] [ADP] / [creatine] [ATP])
= 12.5 kJ mol-1 + (8.3145 J K-1 mol-1) (298K) ln (2.5mM * 0.15 mM / 1 mM
* 4 mM)
= 12.6 KJ mol-1 – 5.9 kJ mol-1 = 6.7 kJ mol-1
Since ΔG >0, the reaction will proceed in the opposite direction as written
in the quesiton, that is, in the direction of ATP synthesis.
5. 2 cytc (Fe3+) (oxidized) + Ubiquinol (QH2 - reduced)
-> 2 cytc (Fe2+)(reduced) + Ubiquinone (Q -oxidized) + 2 H+
ΔE°’ = E°’(e- acceptor) – E°’ (e- donor) = 0.235 V – 0.045 V= 0.190 V
ΔG°’ = - n F ΔE°’ = - (2) (96.485 kJ V-1 mol-1) (0.190V) = -36.7 kJ mol-1
6. Using the table of reduction potentials:
a. ΔE°’ = E°’(e- acceptor) – E°’ (e- donor) = E°’ (fumarate ) – E°’
(NAD+) = 0.031V – (-0.315V) = 0.346 V. Because ΔE°’ > 0,
ΔG°’ < 0 and the reaction will spontaneously proceed as written.
b. ΔE°’ = E°’(cyt b) – E°’ (cyt a) = 0.077V – (0.290V) = - 0.213V.
Because ΔE°’ < 0, ΔG°’ > 0 and the reaction will spontaneously
proceed in the opposite direction from that written.
7. Glycolytic enzymes:
a. Aldolase catalyzes the cleavage of fructose-1,6-bisphosphate to
dihydroxyacetone phosphate and glyceraldehyde-3-phosphate.
Bchm2000
Problem Set 5a
Spring 2008
b. Hexokinase catalyzes phosphorylation of Glucose at C6. Thus, it
uses glucose and ATP to produce Glucose-6-phosphate and ADP.
c. Pyruvate kinase uses phosphoenolpyruvate (PEP) and ADP to
generate pyruvate and ATP
8. Glycolytic enzymes II:
a. Hexokinase and Fructokinase consume ATP.
b. Phosphoglyceratekinase and Pyruvate Kinase generate ATP.
c.
9. 2 glucose + 4 NAD+ + 8 ADP + 8 Pi
-> 4 pyruvate + 4 NADH + 4 H+ + 8 ATP + 4 H2O
10. Phosphohexose isomerase:
11. All reactions catalyzed by kinases, i.e. all phosphotransferyl reactions are
highly favorable since the phosphate is transferred from a high energy
donor to an acceptor. All isomerizations work at equilibrium, i.e. ΔG’o is
close to zero as both substrate and product have comparable free energy.
The three “special” reactions catalyzed by aldolase, glyceraldehyde-3phosphate dehydrogenase and enolase are unfavorable. These are driven
by removal of the product by the favorable phosphoryltransfer reactions.
12. When [GAP] = 10-4 M, [DHAP] = 5.5 x 10-4 M. ΔG°’ = -RT ln K, thus
K = e (-ΔG°’/RT) = [GAP] [DHAP] / [FBP]
= e (– 22,800 J mol-1) / 8.3145 J K-1 mol-1) (310K) = 1.4 x 10-4
Thus: (10-4) (5.5 x 10-4) / [FBP] = 1.4 x 10-4
Thus: [FBP] = 3.8 x 10-4 M
And [FBP]/[GAP] = (3.8 x 10-4 M) / (10-4 M) = 3.8
13. (1) digestion, (2) glycolysis, (3) citric acid cycle, (4) electron transport, (5)
oxidative phosphorylation
14. Electron transport pathway:
iii. NADH dehydrogenase -> ubiquinone -> cytochrome c -> cytochrome c
oxidase
Bchm2000
Problem Set 5a
Spring 2008
15. E may differ from E°’, depending on the redox center’s microenvironment
and the concentration of reactants and products. In addition, the tight
coupling between successive electron transfers within a complex may
“pull” electrons so that the overall process is spontaneous.
16. In oxidative phosphorylation, NADH + H+ (or FADH2) is oxidized, i.e. it
loses electrons. ADP is phosphorylated and thereby converted to ATP.
17. ΔE°’ = E°’ (e- acceptor) – E°’ (e- donor) = 0.815 V – (-0.219V) = 1.034V
ΔG°’ = -n F ΔE°’ = -2 x 96.485 kJ V-1 mol-1 x 1.034V = - 200 kJ mol-1
The maximum number of ATP that could be snythesized under standard
conditions is therefore 200 kJ mol-1 / 30.5 kJ mol-1 = 6.6 mol ATP / mol
FADH2 oxidized by O2.
18. Like all enzymes, the F1 subunit of the ATP synthase can catalyze a
reaction in both directions ADP + Pi <-> ATP + H2O. Hydrolysis of ATP
sets a large amount of energy free. With no proton gradient (no
membrane!) providing the energy to drive the reaction toward ATP
synthesis, the hydrolysis of ATP, i.e. ATPase activity, occurs
spontaneously as it is energetically favorable (negative ΔG).