C485 Final Exam Fall ‘13
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. (15pts) There are three major photosynthetic assemblies used in the light reactions of
photosynthesis. Briefly describe the important components of each, and state what the
function and goal of each assembly is.
2. (8pts) 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) Rubisco catalyzes an undesirable side reaction. What is this reaction? Draw
the mechanism of this reaction in full. You MUST use structure and arrows as
appropriate.
4. (10 pts) List the environmental conditions/small molecules that activate rubisco and/or
enzymes of the Calvin cycle.
a_____________________
b_____________________
c_____________________
d_____________________
e_____________________
5. (10pts) The pentose phosphate pathway yields energy in the form of what molecule?
What reactions generate these molecules and how are they driven to completion?
6. (15pts) Starting from ribulose 1,5- bisphosphate, draw the reactions of the Calvin
cycle. Which of these reaction do NOT take place in the pentose phosphate pathway.
Explain the logic for why these pathways differ based on thermodynamic principles,
taking the goals of the pathway into account.
7. (16 pts) There are two types of carbon-carbon bond forming reaction that take place in
the pentose phosphate pathway. Draw the mechanism of these reactions.
8. (10 pts) Explain the difference between regulation of glycogen breakdown in the liver,
and the muscle. What is the physiological rational for these differences? What reaction
takes place in the liver that does not take place in the muscle?
9. (10 pts) Draw the reactions for activation of a monomer and its use in glycogen
synthesis. Explain the seemingly unusual feature of the thermodynamics associated with
this reaction.
10. (8 pts) Draw the pathway for insulin signaling. You should indicate any chemical
reactions, or structural changes that occur during this process.
11. (10 pts). Explain the difference between type 1 and type 2 diabetes. Explain likely
molecular mechanisms for the cause of type 2 diabetes.
12. (10 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. Do not consider the energy
from the remnant. Please show how you do this calculation.
13. (6 pts) In which ways are fatty acid synthesis and breakdown different?
14. (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?
15. (9 pts) Show the three pathways for the degradation of threonine.
16. (8 pts) Diagram the pathway for the breakdown of lysine. Structures please.
17. (20 pts) Branched chain amino acids are all broken down in the muscle via the same
first two steps. Outline these steps and draw the full mechanism by which they occur.
What is the ultimate fate of the byproduct produced in the first step?
18. (15 pts) Show the biosynthetic origin of all the heavy atoms of histidine, AMP, and
CTP (phosphate groups not required). You must clearly label the atoms in both the
product and its source. Any ambiguities will be marked wrong. For example, you cannot
simply draw the starting material, you must number it and indicate which atom becomes
which part of the products.
19. (8 pts) Describe the role of the following structures:
High-density lipoproteins-
Chylomicrons-
Leptins-
Low-density lipoproteins-
20. (10 pts) Draw the mechanism for the final step in tryptophan biosynthesis
21. (10 pts) Draw the mechanism for the conversion of S-adenosyl homocysteine to
homocysteine and adenosine.
22. (8 pts) Outline the biosynthesis of phosphatidyl choline, starting from ethanolamine,
and diacylglycerol.
23. (6pts) Outline the two basic strategies for screening for drug candidates.
24. (10 pts) Describe how you would synthesized a mixed combinatorial library of
peptides. How would you select for binding to a particular peptide in a mixed library?
Point breakdown
Possible
actual
1)
15
________
2)
8
________
3)
10
________
4)
10
________
5)
10
________
6)
15
________
7)
16
________
8)
10
________
9)
10
________
10)
8
________
11)
10
________
12)
10
________
13)
6
________
14)
8
________
15)
9
________
16)
8
________
17)
20
________
18)
15
________
19)
8
________
20)
10
________
21)
10
________
22) 8
________
23) 6
________
24) 10
________
Total Out of 240
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