Download C485 Exam I

C485 Final Exam Fall ‘10
Name___________________
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. (6pts) Which of the following statement about cyclic photophosphorylation are
correct? (Circle the correct ones)
A) It doesn’t involve NADPH formation
B) It uses electrons supplied by photosystem II
C) It is activated when NADP+ is limiting
D) It does not generate O2
E) It leads to ATP production via the cytochrome bf complex
F) It involves a substrate-level phosphorylation.
2. (6pts) What is the overall soichiometry of photosynthesis in chloroplasts? If eight
photons are absorbed, the net yield is:
______ O2
________NADPH
_________ATP
3. (12pts) In one sentence or less, describe the role of each photosystem component
named below:
Pheophytin
Ferredoxin
Plastoquinone
P700
Z
Plastocyanine
4. (6 pts) Draw the mechanism for how the mobile electron carrier associated with PSII
undergoes oxidation (use chemical structures).
5. (10 pts) Rubisco catalyzes a side reaction that is generally considered wasteful. Draw
this reaction and show a notional mechanism by which it occurs. (You must use
chemical structures and appropriate arrows to get credit.)
6. (16pts) The pentose phosphate pathway and the Calvin cycle are very similar. Each
pathway utilizes a transketolase reaction and an aldolase, or transaldolase reaction.
Choosing from either pathway, show the mechanism of a ketolase and an aldolase
(transladolase) reaction. You must show the full structures of products and starting
materials and state which pathway you are drawing from.
7. (6pts) Liver synthesizes fatty acids and lipids for export to other tissues. Would you
expect the pentose phosphate pathway to have a low or a high activity in this organ?
Explain.
8. (10 pts) In addition to fatty acids and glucose-derived material, muscle utilizes another
class of molecules that is not generally utilized by other tissues for energy generation.
What is this energy source.? Diagram the metabolism of one of these molecules (your
choice, but structures please) and make the case for why this molecule is a good source of
energy for muscle.
9. (8 pts ) How does the regulation of glycogen phosphorylase differ between the muscle
and the liver? Explain why this difference may be advantageous for the differing
functions of the organs.
10. (16 pts) Consider the processing of the 11-carbon fatty acid shown below via betaoxidation.
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. Please show how you do this
calculation.
11. (14 pts) The processing of the remnant from oxidation of odd-carbon fatty acids,
such as the one described in problem 9 requires two enzymatic steps that rely on
cofactors. Draw the mechanism utilized in these two enzymatic steps. Make sure to
show the structure of the cofactors and intermediates and use appropriate arrows.
12. (8 pts) Describe the regulation of fatty acid biosynthesis.
13. (8 pts) Show the biosynthetic origin of the carbons and nitrogen in tryptophan.
(Draw tryptophan, circle the relevant atoms and show the compounds of origin, mapping
the atoms correctly.)
14. (8 pts) What enzyme activities are required for glycogen synthesis? Describe what
these enzymes do.
15. (8 Pts) Describe the enzyme activities required to target proteins for degradation.
Use diagrams to ensure clarity. Please show the nature of the bond between the protein
and the targeting molecule. What is the name of the targeting molecule?
16. (10 pts) If you were a triacylglycerol molecule in a choice cut of beef, describe your
journey through the human body from the time you hit the intestinal tract until your final
place of storage. You should outline the various transformations that take place, and any
ancillary molecules that assist in this process.
17. (10 pts) Describe the signal transduction cascade triggered by epinephrine. How are
these signals terminated?
18. (8 pts) First pass metabolism often causes substantial differences in absorption of an
orally administered drug vs. an injected drug. Explain how this happens.
19. (10 pts) Diagram the biosynthesis of IMP starting with PRPP. You must use
chemical structures and show all molecules used (i.e. what are the N and C sources, and
what activating molecules are used).
20. (10 pts) In the urea cycle, arginine is derived from citrulline, aspartate and ATP.
Outline this process (structures please), paying especial attention to the products formed
in addition to arginine. What is the advantage of using ATP in this manner and why do
you think it would be necessary in this reaction? (Hint- one of the products is AMP)
21. (10 pts) Serine may be degraded to glycine. What two cofactors are involved in this
reaction? Draw the mechanism of this transformation.
22. (10 pts) Outline the biosynthesis of uridylate, starting with bicarbonate. Structures
please.
23. (5 Pts) What enzyme is the control point in cholesterol biosynthesis (acronym okay)?
List four methods that organisms use to control this enzyme.
24. (10 pts) Draw the chemical mechanism utilized by ribonucleotide reductase. You
must show starting material and products, as well as crucial active site residues that play
a direct role in the reaction.
25. (8pts) Pyrimidine biosynthesis contains a C-N bond-forming reaction that is unusual
in biosynthesis. What is this reaction and why is it so unusual? What enzymic strategy
is employed to make this reaction feasible?
26. (8 pts) Show the derivation of all the heavy atoms in leucine. Make sure you number
your precursor molecules and leucine so that it is clear how the atoms of leucine map to
the precursors.
Point breakdown
Possible
actual
1)
6
________
2)
6
________
3)
12
________
4)
6
________
5)
10
________
6)
16
________
7)
6
________
8)
10
________
9)
8
________
10)
16
________
11)
14
________
12)
8
________
13)
8
________
14)
8
________
15)
8
________
16)
10
________
17)
10
________
18)
8
________
19)
10
________
20)
10
________
21)
10
________
22)
10
________
23)
5
________
24)
10
________
25)
8
________
26)
8
________
Total Out of 234
________