Exam 3, BICH 410 (MWF 3-3:50P), Monday November 22, 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) Starting with glucose radiolabeled at carbon 5, draw the structures of the following metabolites, specifying which carbon(s) are derived from glucose C-5 via glycolysis and/or the pentose phosphate pathway and/or an anaerobic fermentation pathway. In other words, clearly denote the labeled carbon atom in each metabolite that was derived from the radiolabeled carbon in glucose.

(a) fructose-1,6-bisphosphate
Answer: see structure on pg. 388; carbon-5 of FBP derived from carbon-5 of glucose

(b) dihydroxyacetone phosphate
Answer: see structure on pg. 388; no carbons of DHAP are derived from carbon-5 of glucose

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

(d) lactate
Answer: see structure on pg. 402; middle carbon (C-2) of lactate is derived from glucose carbon-5

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) How many turns of an alpha helix are required to span a lipid bilayer (Hint: remember that the pitch of an alpha helix is 0.54 nm)?
Answer: width of lipid bilayer = 3 nm
pitch of alpha helix = 0.54 nm/turn
number of turns = 3 nm / 0.54 nm/turn = 5.5 turns

4) (5 pts) Draw the enediol intermediate of the reaction catalyzed by triosephosphate isomerase.
Answer: structure on pg. 391

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 2-phosphoglycerate is 2.0 mM, what concentration of 3-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 3-PG at equilibrium (deltaG = 0):
0 = 4.7 kJ/mole + (8.315 J/mol-K)(310 K)/(1000 J/kJ) ln (.002)/[3-PG]
Solve for [3-PG] = 0.0124 M = 12.4 mM
For deltaG to be less than 0, [3-PG] must be greater than 12.4 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 protein is used to prime glycogen synthesis?
Answer: glycogenin

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

D) Name the enzyme that is deficient in individuals suffering from lactose intolerance.
Answer: lactase

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

F) Name an inhibitor of the sodium-potassium ATPase.
Answer: ouabain or digitoxin or vanadate

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

H) Write the reaction catalyzed by nucleoside diphosphokinase that interconverts GTP and ATP.
Answer: GDP + ATP <-> GTP + ADP

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

J) Write the names (or structures) of two intermediates that can be used to effectively shuttle oxaloacetate between the mitochondria and the cytosol.
Answer: aspartate, malate

K) Name two allosteric activators for the major control point enzyme in glycolysis.
Answer: ADP, AMP, fructose-2,6-bisphosphate