C485 Final Exam Fall 12

C485 Final Exam Fall 12

C485 Final Exam Fall ‘12


Legible please!

Do not use acronyms. Use structures whenever they are asked for, or appropriate. Your explanations should be brief. Overly lengthy answers with irrelevant or erroneous material will receive deductions. GOOD LUCK

1. (10pts) Assume four electrons pass completely through the light reactions of photosynthesis. What is the stoichiometry of the compounds produced or used.

______O2 ______NADPH ______ATP ______H+ pumped out ______H+ taken up

What if cyclic photophosphoryation is operative?

______O2 ______NADPH ______ATP ______H+ released ______H+ taken up

2. (10pts) Diagram the Q cycle of photosynthesis, showing where and how many quinone/quinol molecules are used and where and how protons are taken up and given off. Make sure you account for the stoichiometry of the cycle and show where electrons wind up. Make sure to show where the lumen and stroma are.

3. (10pts) In one sentence or less, describe the role of each photosystem component named below:

Cytochrome bf

Manganese Center




4. (10 pts) List the environmental conditions/small molecules that activate rubisco and/or enzymes of the Calvin cycle.




5.(8pts) Draw a balanced equation for the overall reaction mediated by the Calvin cycle, assuming the production of one glucose molecule from carbon dioxide. How many turnovers are required from Rubisco for each glucose produced?

6. (10pts) Starting from GAP and F-6-P, show all the reactions of the Calvin cycle used to regenerate RuBP. You MUST use structures. No enzyme names required. Please note which of these reaction(s) does NOT occur in the pentose phosphate pathway. Show how glucose is generated as a “by product”.

7. (8 pts) Outline the oxidative portion of the pentose phosphate pathway. What provides the driving force for these reactions?

8. (8 pts) The pentose phosphate pathway operates in four modes. What are they, and how is the pathway altered to accommodate the needs of the cell.

Mode 1Mode 2

Mode 3Mode 4

9. (8pts ) The regulation of glycogen phosphorylase differs between the muscle and liver. Diagram this regulation and show how it differs. What is the physiological rationale for this?

10. (10 pts) Diagram the structure of glycogen, showing all glycosidic linkages and outline the biosynthesis, including the biosynthesis of any required activated intermediates.

11. (8 pts) What are the basic steps of signal transduction?

12. (10 pts) Outline the signaling pathway for glucagon, showing how it exerts its effect on both glycogen breakdown and synthesis.

13. (12pts) Consider the processing of the 11-carbon fatty acid shown below via beta- oxidation.

Outline (structures please) how this molecule would be processed via beta oxidation. (You do not need to enumerate repeated steps.) Make sure you show any products that cannot be processed via beta-oxidation. Outline the intermediates involved in converting this remnant into a commonly used metabolite. To the extent possible, calculate the yield of ATP from the metabolism of this 11-carbon fatty acid. Do not consider the energy from the remnant. Please show how you do this calculation.

14. (6 pts) Outline the process by which substrates of beta oxidation are transported into the mitochondria. Structures please.

15. (8 pts) Outline the process by which the cytoplasm obtains Acetyl CoA for fatty acid synthesis. (structures please). What other benefit does this provide for the cell?

16. (8 pts) List the differences between fatty acid biosynthesis and breakdown.

17. (12 pts) Give the major carbonaceous breakdown product(s) of the following amino acids (structure please): (Must not be an amino acid)



18. (8 pts) For the following reactions, list whether they are oxidations, reductions, or neither. For oxidations and reductions, put down the number of electrons involved.

19.(20 pts) Draw the structure required- label it and below it show where the carbons are derived from at the beginning of the pathway moving forward. You must use structures and labels. Ambiguities will not be counted.



IMP (base only)

CTP (base only)



20. (8 pts) Describe the role of the following structures:

High-density lipoproteins-



Low-density lipoproteins-

21. (10 pts) Draw the mechanism for the final step in tryptophan biosynthesis

22. (10 pts) Draw the mechanism for the conversion of S-adenosyl homocysteine to homocysteine and adenosine.

23. (10 pts) Threonie may be degraded to glycine and acetaldehyde. Draw the mechanism of this transformation. (Show the full transformation from start to finish.)

24. (10 pts) Outline. (structures) the biosynthesis of leucine.

25. Draw a transketolase reaction from the pentose phosphate pathway. Show the mechanism (structures and arrows, please).

Point breakdown











10) 10______











21) 10______

22) 10______

23) 10______

24) 10______

25) 10______

Total Out of 242______