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Name Test 3PHYS 0213 (Biochem) Spring 2005
1. (8 pts.) In glycolysis, ATP is formed during the conversion of phosphoenolpyruvate topyruvate. What is the driving force for this reaction?
C
COPO3
2–H2C
O O
+ ADPC
COH3C
O O
+ ATP
2. In glycolysis, fructose-1,6-bisphophate is converted to dihydroxyacetonephosphate andglyceraldehyde-3-phosphate via a reverse aldol condensation.
C
C O
H2C OPO32-CH
C OHH
H2C OPO32-
O
OH
H
H
CH2OPO32–
C O
C HHO
C OHH
C OHH
CH2OPO32–
HC
C OH
C HHO
C OHH
C OHH
CH2OPO32–
O
H
Reverse aldol condensation of fructose-1,6-bisphosphate glucose-6-phosphate
a. (3 pts.) Between which C atoms is fructose cleaved.
b. (3 pts.) Imagine that glucose-6-phosphate underwent a reverse aldol condensation.Between which C atoms would glucose be cleaved?
c. (2 pts.) Draw the products of the reverse aldol condensation described in part b.
d. (3 pts) What advantage does the reverse aldol condensation of fructose have over thereverse aldol condensation of glucose? (Hint: consider the size of the resulting productmolecules.)
1. _______
2. _______
3. _______
4. _______
5. _______
6. _______
7. _______
8. _______
9. _______
10. ______
11. ______
12. ______
13. ______
14. ______
15. ______
16. ______
17. ______
3. (8 pts.) For each of the following pairs of carbon atoms indicate (circle) which carbon is the moreoxidized carbon atom.
a.
C
C
O H
CH2 OPO32–
OHH
b.
C
CCO2H
H2C CO2
CO2 c.
C
C
O OPO32–
CH2 OPO32–
OHH
d.C
C
O OPO32–
CH2 OPO32–
OHH
4. The reactions in the glycolytic pathway are summarized below.
O
OHOH
HOCH2
HOOH
ATP ADP O
OHOH
PiOCH2
HOOH
O CH2OHPiOCH2
OH
HO OHATP ADP
O CH2OPiPiOCH2
OH
HO OH
C
C
O H
CH2OPi
OHH
CH2OPi
C
CH2OH
O
C
C
O OPi
CH2OPi
OHH
NAD+ + Pi
C
C
O O
CH2OPi
OHH
ATP ADP
C
C
CH2OH
OO
OPiHC
COPiH2C
O OC
C
O O
OH3C
ATP ADP
NADH
a. (4 pts.) In which step is the sugar being oxidized?
b. (4 pts.) Which part of the sugar molecule is being oxidized?
c. (4 pts.) How many ATP molecules are synthesized for each glucose molecule that entersglycolysis?
After mannose is phosphorylated, phosphomannose isomerase performs the following conversion:
O OHOH
HOOH phosphomannose
isomerase
CH2OPO
O
OCH2OPO
O
OO CH2OH
OH
HOOH
d. (4 pts.) Phosphomannose isomerase converts mannose to what sugar?
e. (4 pts.) At what step does mannose get fed into glycolysis?
5. Gluconeogenesis is basically glycolysis run in reverse, but there are three important steps wereglycolysis cannot run in reverse. Two of those steps from the glycolytic pathway are drawnbelow.
Glycolysis Glycolysis in reverse
O
OHOH
HOCH2
HOOH
ATP ADP O
OHOH
PiOCH2
HOOH
glu glu-6-Pi
O CH2OHPiOCH2
OH
HO OHATP ADP
O CH2OPiPiOCH2
OH
HO OH
fru-6-Pi fru-1,6-bisPi
a. (2 pts.) Draw the reactions in reverse (you can use the abbreviations if you wish).
b. (4 pts.) Why don’t these reactions run in reverse?
c. (4 pts.) How does gluconeogenesis get around these two irreversible steps?
6. (2 pts. each) Which of the following molecules could be candidates for controlling glycolysis viafeedback inhibition?
a. glucose b. ADP c. ATP
d. AMP e. citrate f. pyruvate
7. (2 pts. each) Which of the following molecules could be candidates for activators of glycolysis?
a. NADH b. ADP c. ATP
d. AMP e. citrate f. pyruvate
8. A version of the citric acid cycle is drawn below.
CO2–
HC
CO2
CH
CO2–
O OC
CH2
CH2
O2C
H
C CO2
CH2
CoA
HO
CO2
C
CoA
O
S CO2–
H H
C
C
CH2
CO2–
CH2
CH2
CO2–
O
HHO
CO2–
H CO2–
C
C
CH2
CO2–
CO2–
HO
CH2
CO2–
CH2
CCO2
O
C
H2C
O2C
CoAC
O
H3C S
SH
CoA
+ H+H2O
SHCoA SH
a. (6 pts.) Identify the reactions were both CO2 and NADH are produced.
b. (4 pts.) In terms of ΔG, what is the significance of the release of CO2 in the steps in part a?
c. (4 pts.) In addition to the steps where both CO2 and NADH are produced, there are two moresteps where “reducing power” (NADH or FADH2) are produced. Identify those steps. (It is notnecessary to specify whether NADH or FADH2 is formed.)
9. In the pyruvate decarboxylase complex, an acetyl group is transferred fromthiaminepyrophosphate to lipoyl amide. One step of that reaction is drawn below.
NC
SC
C SS
O
NLYSHR'
R
H3CC
H3CO
H
SS
O
NLYSN
C
SC
C
R'
R
H3CC
H3CO
H
H+
(6 pts.) Redox wise, what is the significance of this step for the S atoms of the lipoyl amide?
10. Considering only the carbon atoms, for one crank of the citric acid cycle the overallstoichiometry of the reaction is... (One crank means start at the top and go all the way arounduntil you get back to the top.)
a. (4 pts.)
CC
CH2
C
O O
O
O
O +H3C
C
O
S CoA
Drawn below is a representation of the glyoxylate cycle. Considering only the carbon atoms, forone crank of the glyoxylate cycle the overall stoichiometry of the reaction is... (One crankmeans start at the top and go all the way around until you get back to the top.)
CO2–
HC
CO2
CH
CO2–
O OC
CH2
CH2
O2C
H
C CO2
CH2
CoA
HO
CO2
C
CoA
O
S CO2–
H H
C
C
CH2
CO2–
CH2
CH2
CO2–
O
HHO
CO2–
H CO2–
C
C
CH2
CO2–
CO2–
HO
CH2
CO2–
CH2
CCO2
O
C
H2C
O2C
CoAC
O
H3C S
SH
CoA
+ H+H2O
SHCoA SH
OC
HC
O
O
+ CH3CO-CoA
b. (4 pts.)
CC
CH2
C
O O
O
O
O +H3C
C
O
S CoA2
c. (2 pts.) Which pathway is better suited for building molecules containing four carbon atoms fromtwo-carbon atom precursors, the citric acid cycle or the glyoxalate cycle?
d. (6 pts.) Explain why one path is better suited for the task described in part c.
11. Although it is complicated, when it comes to getting NADH from the cytosol into themitochondrial matrix the aspartate-malate shuttle has a distinct advantage over the glycerolphosphate shuttle. In the glycerol phosphate shuttle the reducing power of NADH is used toreduce dihydroxyacetone phosphate to glycerol phosphate which is then delivered to themitochondrion and used to form FADH2. However, in the aspartate-malate shuttle, thereducing power of NADH is used to convert oxaloacetate to malate, which is then delivered inthe matrix of the mitochondrion.
(8 pts.) Why would delivering malate (in the aspartate-malate shuttle) into the mitochondrialmatrix be better than converting NADH to FADH2 (in the glycerol phosphate shuttle)? (Feelfree to flip back through the test and see where malate appears in other important pathways.You may also want to flip to the last page where some supplemental information has beenattached.)
H
C
CH2
CO2
CO2HO
malate
12. (6 pts.) Describe the traits that make vitamin E an effective intramembrane antioxidant.
O
O
H
H
13. (6 pts.) Describe two strategies that cells use to deal with radicals.
14. (8 pts.) The primary goal of the electron transport chain is to do what?
15. (8 pts.) Explain why radicals are potentially so damaging to cells.
16. (10 pts.) ATP Sythase is a large molecular machine that synthesizes ATP. What provides theenergy to drive this machine.
17. A cartoon of ATP Synthase from Biochemistry by McKee and McKee is pictured below.
a.
b.
c.
d.
(4 pts.) Which subunits move (list them by letterhere)?
(4 pts.) Which subunits are stationary (list them byletter here)?
(4 pts) Which side of the drawing represents thematrix of the mitochondrion ?
(6 pts.) What is the role of the γ and ε subunits?
Supplemental information for question 11.
FMNH2
NADH + H+
mitochondrial matrix
2 H+
2 e–
2 H+
UQ
UQH2
4Fe–4Scomplex2 H+
intermembrane space
2 e–
2Fe–2Scomplex
2 H+
2 H+2 H+
UQ
UQH2
to Complex III(Cytochrome bc1Complex)
Complex I
NADH Dehydrogenase Complex
FMN
NAD+
ETC Complex II
succinateFAD–succinatedehydrogenase
Fe–Scomplexes
UQH2
UQ
mitochondrial matrix
intermembrane space
C
H2C C
H2
C O
O
O
O
C
HC C
H
C O
O
O
Ofumarate
Cytochrome bc1 complex
Complex III
UQH2 UQH•
Fe–S
cyt c1
cyt c cyt c•
H+
cyt bL
cyt bH
UQH2
UQ2 2
2
2
2
2 2
1
UQH•
H+
H+
2
2
Cytochrome OxidaseComplex IV
cyt c•CuA
cyt a
cyt a3
CuB
2 H+ + 1/2 O2H2O
Glycerol Phosphate Shuttle
mitochondrial matrix
intermembrane space
NADH + H+
FAD
CH2OH
CH2OPi
O
CH2OH
CH2OPi
HHO
CH2OH
CH2OPi
HHO
CH2OH
CH2OPi
O
cytosol
UQH2UQ
Acyl-CoAdehydrogenase complex
FAD
UQH2UQ
FADH2
NAD+
FADH2
