Exam for D. Nelson's lectures on TCA, electron transport, OxPhos, amino acid and 
nucleotide metabolism and evolution.  Dec. 18, 2002

This part of the exam is 70 points with three questions per lecture.  

1. (3 pts) Why can't acetyl CoA be converted to glucose in animals?






2. (2 pts) What enzyme of the TCA cycle is also part of the electron transport 
chain that passes electrons to oxygen?



3. (2 pts) Ribonucleotide reductase has a pair of sulfhydryls in the active site 
that are oxidized and reduced in the catalytic cycle.  What cofactor of pyruvate 
dehydrogenase has a pair of sulfhydryl groups that are also oxidized and reduced 
in catalysis?  



4. (3 pts) The malate aspartate shuttle brings electrons from cytosolic NADH into 
the mitochondria at the level of NADH.  The glycero-phosphate shuttle brings 
electrons from cytosolic NADH in at the level of ubiquinone.  Which shuttle gets 
more energy ot of the cytosolic NADH?  Why is this true?







5. (2 pts) In the Q cycle, the two electrons from ubiquinone are split and forced 
to go in two different directions.  Why don't they both go to the Rieske iron 
sulfur protein since it has the most positive reduction potential?






6. (2 pts) In cytochrome c oxidase (complex IV) what is the difference between a 
pumped proton and a chemical proton?

7. (2 pts) Why did Peter Mitchell's chemiosmotic hypothesis predict that the inner 
membrane of the mitochondrion would be impermeable to protons?



8. (2 pts) What is the importance of the gamma subunit in the function of the ATP 
synthase?







9. (3 pts) Suppose that the number of c subunits (also called DCCD binding 
protein) in the Fo part of the ATP synthase was variable and the organism could 
change the number of subunits.  The normal number is 10, but what if the organism 
could make it work with only 7 c subunits.  Would this be more efficient or less 
efficient?  Please explain why.







10. (3 pts) In the de novo pathway of purine biosynthesis, the first step is 
synthesis of PRPP.  This step is feeedback inhibited by the purine nucleotide end 
products.  The second step is also inhibited by these end products.  Why is it 
necessary to inhibit the first step and the second step to regulate this pathway?






11. (2 pts) How does allopurinol prevent gout?






12. (2 pts) Why is the enzyme hypoxanthine guanine phosphoribosyltransferase 
(HGPRT) called a salvage pathway enzyme?


13. (2 pts) Why is thymidylate synthase an ideal drug target for chemotherapy?





14. (3 pts) Ribonucleotide reductase has activity and specificity conferring sites 
for its regulation.  How does ADA (adenosine deaminase) deficiency [also called 
SCID] affect ribonucleotide reductase?







15. (2 pts) Carbamoyl phosphate synthase II is the committed step in animals for 
pyrimidine synthesis.  It is not the committed step in E. coli.  Why is this true?






16. (2 pts) Many amino acid pathways activate a carboxyl group before reducing it 
to an aldehyde.  What are two ways of activating the carboxyl?






17. (2 pts) Where does the amino group come from in all 20 amino acids?




18. (3 pts) Why is the shikimate pathway for aromatic amino acids a potential drug 
target for human pathogens like malaria?





19. (3 pts) What is the purpose of the urea cycle?

20. (2 pts) Why do defects in amino acid breakdown often cause diseases, while 
defects in in amino acid biosynthesis do not?




21. (2 pts) What two methods are used to remove amino groups from amino acids?




22. (2 pts) EF1 alpha, tubulin, and actin have been combined into an artificial 
super protein to make phylogenetic trees to understand early eukaryotic evolution. 
Why is it useful to join proteins together to make these trees?







23. (3 pts) In the hydrogen hypothesis, did the methanogen host benefit right away 
from the oxidative phosphorylation capability of the endosymbiont?  Explain 
briefly.









24. (2 pts) What is the concept of the RNA world?





25. (3 pts) What evidence suggests that eukaryotes without mitochondria today 
(like Giardia and Trichomonas) had them once, but lost them?






26. (2 pts) Why is mitochondrial DNA a faster molecular clock that nuclear DNA?







27. (2 pts) DHFR (dihydrofolate reductase) is fused to thymidylate synthase in 
some eukaryotes, but not in others.  What can be said about the evolution of these 
organisms based on these gene fusions?







28. (3 pts) There is no sequence similarity between vertebrate rhodopsin and 
bacteriorhodopsin.  What does this tell us about their 3 dimensional structures?








29. (2 pts) Do nuclear receptors need to have a ligand to regulate gene 
expression?  Please explain.








30. (2 pts) Why are there no naturally occurring blue roses?