Exam on TCA, electron transport, oxphos, amino acid and nucleotide metabolism 
D. Nelson Nov. 7, 2001
7 points per lecture (49 points total)

1. (2.5 pts) The pyruvate dehydrogenase complex is similar to what other enzyme 
complexes? Check all that are related by having the same mechanism.

X	Branch chain alpha keto acid dehydrogenase (BCKDH)

	Isocitrate dehydrogenase

	Malate dehydrogenase

X	Alpha keto glutarate dehydrogenase

X	Alpha keto acid dehydrogenase (lysine, methionine and tryptophan breakdown)

2. (2.5 pts) You have all TCA cycle enzymes in a reaction mixture.  Acetyl-CoA, NAD+, 
GDP, CoA and all needed ions and other cofactors are present, but the reaction does 
not produce any NADH.  Circle any intermediates that will get the catalytic TCA cycle 
running.

The structures shown were 

     alpha keto adipate (6 carbons) 

     aspartate

X    fumarate 

X    oxaloacetate

     lactate

3. (2 pts) Why does the glyoxylate cycle permit synthesis of sugar from acetyl-CoA?

It bypasses the two decarboxylation steps of the TCA cycle so a two carbon compound 
like acetyl CoA can be built into a four carbon compound like malate.  Malate can go 
to gluconeogenesis

4. (2.5 pts) Ubiquinone (coenzyme Q) carries electrons from: [check all that are true]

	complex III (bc1 complex) to complex IV (cytochrome c oxidase)

X	complex II (succinate dehydrogenase) to complex III

	complex I (NADH dehydrogenase) to complex II

X	complex I to complex III

	complex III to complex V (ATP synthase)


5. (2 pts) In the electron transport chain, energy from NADH and FADH2 is captured in 
what form? (ATP is not the answer)

a proton and electrochemical gradient across the inner membrane

6. (2.5 pts) List five different redox active centers used in the mitochondrial 
electron transport chain. (not proteins or complexes, not oxygen)

FMN, FAD, iron sulfur centers, hemes, ubiquinone, Cu 
I did not want mutiple types of the same thing, like three iron sulfur centers.
Or BH and BL hemes

7. (2.5 pts) In the elevator model of the ATP synthase mechanism, the number of 
protons required to synthesize one ATP might vary depending on the number of c 
subunits in the Fo part of the protein.  How many protons would be needed to make one 
ATP if there were 11 c subunits in the ATP synthase?

11/3 = 3.67 protons per ATP (11 protons per complete rotation and three ATP)

8. (2.5 pts) The formation of a disulfide bond by oxidation of two sulfhydryls has 
been used to test what subunits turn in the ATPase (are part of the rotor), and what 
subunits are fixed (part of the stator).  In a bacterium, a new subunit X was found.  
This subunit X was crosslinked by a disulfide bond to the gamma subunit.  The ATP 
synthase activity was blocked.  Check all of the following that are true.

	Subunit X is part of the rotor.

X	Subunit X is part of the stator.

X	Subunit X and the gamma subunit normally move past one another like a wheel on 
an axle.  

	subunit X and the gamma subunit are normally fixed together and move together.

X	Subunit X is not firmly attached to the c subunits.


9. (2 pts) What does an uncoupler do?

An uncoupler is a small molecule like dinitrophenol or FCCP that carries proteins 
across the membrane to dissipate the proton gradient.

10. (2 pts) all amino acid alpha amino groups come from glutamate.  There are two ways 
to make glutamate.  What are these two ways?

Glutamate synthase and glutamate dehydrogenase
Or you could show the reactions for these two

11. (2.5 pts) Several amino acid biosynthetic pathways use three steps like the first 
three steps of the TCA cycle.  Which pathways share this common strategy?

X	Fungal lysine pathway

	Proline pathway

	Arginine pathway (urea cycle)

X	Leucine pathway

	Shikimate pathway


12. (2.5 pts) What is a metabolon.  Give two observations that support the concept of 
a metabolon.

A metabolon is a loose complex of enzymes in a pathway like TCA cycle or tryptophan 
biosynthesis where substrate is passed by channeling between members of the complex.
The complex may have multifunctional proteins such as ATIC (AICAR transformylase IMP 
cyclohydrolase) in the purine de novo pathway.

Observations that support the metabolon concept are non-contiguous enzymes in a 
pathway that are connected by disulfide bonds, metabolic channeling of radioactive 
labeled compounds.  The tunnel in the 3D structure of tryptophan synthase.  Fusion of 
some enzymes into multienzyme complexes (one of these ATIC was on the cover of Nature 
Structural Biology this fall in living color).  Fusion of different enzymes in the 
pathway in different species.

13. (2 pts) In the urea cycle what enzyme is responsible for eliminating waste 
nitrogen found in the form of ammonia?  In animals, what is the cellular location of 
this enzyme?

CPS I in the mitochondria

14. (2.5 pts) What enzyme complex is defective in maple syrup urine disease?

BCKDH branch chain keto acid dehydrogenase

15. (2.5 pts) Why are more diseases caused by defects in amino acid breakdown than by 
defects in amino acid biosynthesis?

Intermediates that build up from breakdown pathways can be toxic and cannot be 
eliminated.  Diet can correct lack of an amino acid.  

16. (2 pts) The first reaction in the de novo pathway of purine biosynthesis is 
formation of PRPP from ribose-5-P.  Why isn't this the committed step for purine 
biosynthesis in animals?

PRPP is used in other pathways so it cannot be the committed step in purine synthesis.

17. (2.5 pts) allopurinol blocks the enzyme xanthine oxidase.  Why is that an 
effective treatment for gout?

Allopurinol is a hypoxanthine analog that inhibits xanthine oxidase and blocks 
formation of uric acid the main cause of gout.  Xanthine and hypoxanthine build up but 
they are more water soluble and do not cause gout.

18. (2.5 pts) What is the connection between adenosine deaminase deficiency and 
ribonucleotide reductase?

ADA deficiency leads to a build up of dATP which inhibits the ribonucleotide reductase 
enzyme and shuts down DNA synthesis.  dATP is especially toxic to lymphocytes.

19. (2.5 pts) Methotrexate blocks dihydrofolate reductase.  How does this inhibit the 
thymidylate synthase reaction?

Thymidylate synthase requires 5,10 methylene tetrahydrofolate and converts it to 
dihydrofolate (DHF).  The the DHF reductase is required to remake the tetrahydrofolate 
intermediate.  Blocking DHFR blocks this step and prevents TS from having its 
substrate.

20. (2.5 pts) Why are fluoro compounds like 5-fluoro uracil mechanism based enzyme 
inhibitors?

F is a poor leaving group.  Substitution of H for F in a critical part of a compound 
will cause the enzyme to get trapped in a ternary complex with F not coming off as F+.
This will kill the enzyme.

21. (2 pts) How does azaserine inhibit both purine and pyrimidine de novo pathways?

Azaserine is a glutamine analog that covalently modifies the active site of glutamine 
requiring enzymes.  There are three of these in the two de novo pathways.