Bibc102, Feng, final exam, WI 2012,

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Bibc102, Metabolic Biochemistry, Feng FINAL EXAM 11:30 2:29 pm, March 21, 2013 Student ID # First name: Questions and scores: 1. (5) 2. (5) 3. (5) 4. (5) 5. (5) 6. (5) 7. (5) 8. (5) 9. (5) 10. (5) 11. (5) 12. (5) 13. (5) 14. (5) 15. (5) 16. (5) 17. (5) 18. (5) 19. (5) 20. (5) 21. (20) 22. (20) 23. (20) 24. (20) 25. (20) Total: Last name:

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Please provide brief answer to the following short questions 1-20 (5 points each). 1. How does protein phosphatase 1 (PP1) activation leads to decrease of glucose level and increase of glycogen synthesis simultaneously? PP1 dephosphorylates and inactivates glycogen phosphorylase, but it also dephosphorylates and activates glycogen synthase.

2. Explain briefly why tetrahydrofolate (H4 folate) can become a target for chemotherapy in cancer treatment. H4 folate is required for nucleotide synthesis.

3. When NADH is generated from glycolysis, how does NAD+ is regenerated in muscle cells in order to keep the glycolytic pathway actively going with the relative shortage of O2. NAD+ is regenerated from NADH by reducing pyruvate to lactate.

4. How does the chemical energy stored in NADH that is generated in cytosol get extracted for ATP synthesis via oxidative phosphorylation in mitochondria? NADH equivalent is transferred from cytosol into mitochondria via the malateaspartate shuttle.

5. Explain briefly why a few amino acids can be both glucogenic and ketogenic? These AAs can be metabolized to either oxaloacetate or acetate.

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6. Explain how pyruvate is used to transport NH4+ from muscle cells to hepatocytes.

Pyruvate is condensed with NH4 to become alanine and transported to the liver.

7. Is O2 produced in purple bacterial cells through photosynthesis? and why? NO, it doe not have the system to split H2O.

8. Why is glyceroneogenesis viewed as a truncated version of gluconeogenesis?

The enzymes that catalyze glyceroneogenesis are the same as those for the initial steps of gluconeogenesis.

9. Is ATP required for production of glucose 1-phosphate from glycogen degradation and why?

No, glycogen phosphorylase uses inorganic Pi, not ATP.

10. How does glucose work cooperatively with PP1 to inactivate the phosphorylase activity? Glucose binds phosphorylated glycogen phosphorylase, which makes it more accessible to PP1.

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11. Which enzyme is a giant protein that can catalyze all four reactions in a biosynthetic pathway? Fatty acid synthase (FAS) in fatty acid biosynthesis.

12. How is NADPH linked to cellular protection against reactive oxidative species (ROS)? NADPH is used to regenerate reduced glutathione that is required for disposal of ROS.

13. Synthesis of one urea molecule consumes 3 ATP directly, but the actual expense is less than that, why?

The urea cycle is connected with the TCA cycle, via fumarate or malate, to generate NADH and therefore ATP.

14. The synthesis of both purine and pyrimidine requires amino acids, because of the need for which atom? nitrogen

15. Cholesterol is a complicated molecule that has multiple ring structure, but it is synthesized from which simple molecule? Write down the small molecule structure. Acetate, CH3-COO-

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16. The HAT medium is designed to select the hybridoma cells, based on which metabolic pathways? De novo and salvage pathways for nucleotide synthesis.

17. In many genetic diseases that are associated with loss or dysfunction of an enzyme responsible for amino acid metabolism, the symptom of a patient is often caused by what type of metabolic change? Accumulation of upstream metabolites.

18. Draw out the structure of PRPP, is it required for the de novo or salvage pathway? Or both?

PRPP is required for both pathways.

19. Does !-oxidation require a H2O molecule? How? Yes, in the 2nd step of hydration.

20. Arginine is a molecule that generates urea directly, but it can also be used to generate which molecule that can serve as a signaling factor for relaxation of blood vessel? NO

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21. The following reaction is part of which metabolic pathway? Describe the reverse reactions by which pyruvate is converted to phosphoenolpyruvate, including the chemical structure of molecules involved and the enzymes that catalyze the reactions (20 points)

This is the last step of glycolysis. In gluconeogenesis, converting pyruvate to Phosphoenolpyruvate involves two steps Catalyzed by pyruvate carboxylase And PEP carboxykinase.

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22. Draw out the chemical structure of citrate and discuss how citrate is synthesized and how it is involved in the TCA cycle or fatty acid synthesis, with no need to draw out the chemical structure of molecules involved (20 points).

Citrate is synthesized from oxaloacetate and acetyl-CoA. Citrate can be transported out of the mitochondria to regenerate Acetyl-CoA in the cytosol for FA synthesis. Citrate can also be converted to isocitrate by aconitase, to continue the TCA cycle.

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!"# Please take a look at the following chemical molecules, and answer the following questions (20 points).$ a) what is the name that they can be called collectively? %& What is their common substrate? $ '& Under what kind of physiological or pathological conditions are they synthesized? $ (& Why are they produced under these physiological or pathological conditions (20 points).$ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ )&$*+,-,$./0,'10,-$)2,$'/00,'345,06$')00,($7,3/8,$%/(4,-#$ $ %&$*+,42$'/../8$-1%-32)3,-$)2,$)',3609:/;#$ $ '&$7,3/8,$%/(4,-$)2,$</2.,($18(,2$-3)25)34/8$/2$48$(4)%,34'$-1%=,'3-#$ $ (&$>8(,2$<)-348?$/2$48$(4)%,3,-@$/A)0/)',3)3,@$3+,$)'',B348?$./0,'10,$</2$)',3609:/;$ 48$*:;$'6'0,@$4-$%,48?$1-,($</2$?01'/8,/?,8,-4-@$2,-10348?$48$)''1.10)34/8$/<$)',3609 :/;@$C+4'+$,8+)8',-$7,3/8,$%/(6$</2.)34/8#$ $ $ $ $ $ $ $ $ $ $ $ $ $

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$ 24. Describe the mechanism and reactions of how oxaloacetate contributes to and participates in the urea cycle. (20 points).

Just need to write down the relevant part of urea cycle. Oxaloacetate is converted to aspartate by taking up one NH4 from glutamate, catalyzed by aspartate aminotransferase. Aspartate is condensed with Citrullyl-AMP to become Argininosuccinate, catalyzed by argininosuccinase.

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$ !D# Draw out the chemical structure of malonyl-CoA, and answer the following four questions:$(20 points).$ a). How is it synthesized, what are the substrates? b). Why should it be made, does it become chemically more active or less active, as compare to its main immediate organic substrate? c). what is the reaction that involves use of malonyl-CoA as a substrate? $ $ $ $ $ $ $ $ $ $ $ )&$E)0/8609:/;$4-$-683+,-4F,($<2/.$)',3609:/;$)8($%4')2%/8)3,#$ $ $ %&$E)0/8609:/;$4-$'+,.4')006$./2,$)'345,$3+)8$)',3609:/;#$ $ $ '&$G)336$)'4($%4/-683+,-4-#$ $ $ $ $ $ $ $ $ $ $ $ $