Exam 3, BICH 410 (MWF 3-3:50P), Monday November 29, 1999

Write your name on each page. Write concise answers to demonstrate effectively your mastery of the subject material. Show your work in order to receive partial credit where applicable.

gas constant R 8.315 J/mol-K
Faraday constant F 96.5 kJ/mol-V

1) (16 pts) Draw the structures of the following metabolites, specifying which carbon(s) are derived from glucose C-4 via glycolysis and, possibly, the pentose phosphate pathway or an anaerobic fermentation pathway. If none of the carbons in that compound are derived from glucose C-4, then state so. For this question, consider that none of the glycolytic reactions are reversible.

(a) fructose-6-phosphate
Answer: see structure on pg. 387; carbon-4 of F6P derived from carbon-4 of glucose.

(b) dihydroxyacetone phosphate
Answer: see structure on pg. 388; no carbons of DHAP are derived from carbon-4 of glucose

(c) ribose-5-phosphate
Answer: see structure on pg. 418 (furanose ring is OK too); carbon-3 of ribose-5-P is derived from carbon-4 of glucose

(d) lactate
Answer: see structure on pg. 402; carboxyl carbon of lactate is derived from glucose carbon-4

2) (12 pts) Write the reactions, including the names of enzymes, for only those steps in gluconeogenesis that either consume or produce ATP or GTP. Assume that gluconeogenesis starts with pyruvate and ends with glucose.
Answer: three reactions:
pyruvate carboxylase: pyruvate + HCO3- + ATP -> oxaloacetate + ADP + Pi
phosphoenolpyruvate carboxykinase (PEPCK): oxaloacetate + GTP -> phosphoenolpyruvate + CO2 + GDP
phosphoglycerate kinase: 3-phosphoglycerate + ATP -> 1,3-bisphosphoglycerate + ADP

3) (5 pts) List the five classes of lipoproteins.
Answer: chylomicrons, VLDL (very low density lipoproteins), IDL (intermediate density lipoproteins), LDL (low density lipoproteins), HDL (high density lipoproteins)

4) (5 pts) Draw the Schiff base that forms between fructose-1,6-bisphosphate and a lysine side chain of aldolase.
Answer: structure on pg. 390

5) (15 pts) Describe how an increased concentration of cyclic AMP coordinately regulates glycogen phosphorylase, glycogen synthase and phosphoprotein phosphatase-1 in muscle.
Answer: cAMP binds to and activates cAMP-dependent protein kinase (cAPK)
cAPK phosphorylates phosphorylase kinase, making it more active
phosphorylase kinase phosphorylates glycogen phosphorylase, making it more active
cAPK or phosphorylase kinase phosphorylates glycogen synthase, making it less active
cAPK phosphorylates the inhibitor protein of the phosphatase; when the inhibitor protein is phosphorylated, it binds to the phosphatase, making it less active
So overall, glycogen phosphorylase is activated, resulting in phosphorolysis of glycogen (degradation), glycogen synthase is deactivated, resulting in no synthesis of glycogen, and the phosphoprotein phosphatase-1 is deactivated so the phosphorylated forms of the phosphorylase and synthase are maintained.

6) (8 pts) The standard free energy change for the reaction catalyzed by phosphoglycerate mutase is +4.7 kJ/mole. If the concentration of 3-phosphoglycerate is 2.0 mM, what concentration of 2-phosphoglycerate is necessary for the reaction to proceed in the direction of glycolysis? (temp. = 37 C)
Answer: The reaction in the direction of glycolysis is 3-phosphoglycerate -> 2-phosphoglycerate
deltaG = deltaGo' + RT ln [2-PG]/[3-PG]
For the reaction to proceed, deltaG must be less than 0.
First calculate the conc. of 2-PG at equilibrium (deltaG = 0):
0 = 4.7 kJ/mole + (8.315 J/mol-K)(310 K)/(1000 J/kJ) ln [2-PG]/(.002)
Solve for [2-PG] = 0.00032 M = 0.32 mM
For deltaG to be less than 0, [2-PG] must be less than 0.32 mM

7) (15 pts) Draw the reaction mechanism for yeast pyruvate decarboxylase showing the role of the coenzyme thiamine pyrophosphate.
Answer: see Fig. 14-20

8) (24 pts) Fill-in blanks or short answer:
A) Name an enzyme that is deficient in patients suffering from galactosemia.
Answer: galactose-1-phosphate uridylyl transferase or galactokinase or UDP-galactose-4-epimerase

B) What is the name of the ubiquitous calcium-binding protein that is a subunit of phosphorylase kinase?
Answer: calmodulin (CaM)

C) Draw the fused ring system of carboxybiotin.
Answer: see Fig. 15-24

D) Name two enzymes that catalyze reactions that use ATP in the catabolism of fructose in the liver.
Answer: fructokinase, glyceraldehyde kinase, glycerol kinase

E) Name the two enzymes in the pentose phosphate pathway that catalyze reactions generating NADPH.
Answer: glucose-6-phosphate dehydrogenase, 6-phosphogluconate dehydrogenase

F) The "favorable" gradient of this ion is used to transport glucose in the intestinal epithelium by a secondary active transport process.
Answer: sodium (Na+)

G) Name an example of an ionophore.
Answer: valinomycin or gramicidin A

H) Write the reaction catalyzed by creatine kinase (no structures necessary).
Answer: creatine + ATP <-> phosphocreatine + ADP

I) What phosphorylated amino acid sidechain is a key to the reaction mechanism of phosphoglucomutase?
Answer: (phospho)serine

J) What hormone binds to adrenergic receptors?
Answer: adrenalin or epinephrine

K) How many ATPs are generated per glucose released by glycogen phosphorylase and catabolized to pyruvate?
Answer: three; no ATP used by phosphorylase and skip hexokinase step; so, overall, use 1 ATP and gain 4 ATPs; net gain = 3

Question 1 from other version of exam. (15 pts) Draw the reaction mechanism for glyceraldehyde-3-phosphate dehydrogenase.
Answer: see Fig. 14-9 on pg. 395