(3) 1. Draw the complete structure for ATP
(20) 2. For each of the pathways
listed below fill in the table to describe its regulation in terms
of main regulatory enzymes, types of control (e.g. substrate availability,
allosteric effectors, product inhibition, etc), and the substance(s)
involved as effector, inhibitor etc.
|Pathway||Enzyme(s) or rxn||Type of Control||Substance(s)|
|a.||G-6-P DH (G-6-P + NADP+ to lactone + NADPH)||substrate avilability||NADP+|
|b.||Gluconate DH (Gluconate + NADP+ to Ru-2-P + CO2 + NADPH)||substrate avilability||NADP+|
|a.||Hexokinase (Glu + ATP to G-6-P + ADP)||product feedback inhibition||G-6-P|
|b.||Phosphokinase (F-6-P + ATP to F-1,6-bisP + ADP)||allosteric inhibition/activation||ATP/AMP & F-2,6-bisP|
|c.||Pyruvate Kinase (PEP + ADP to Pyruvate + ATP)||feed-forward activation||F-1,6-bisP|
|Kreb's Cycle (overall)||Dehydrogenase reactions||substrate availability||NAD+ & FAD|
(15) 3. Calculate the net energy gain or loss in (ATP equivalents) for the complete oxidation of alpha-ketoglutarate (-O2CCH2CH2COCO2-) to oxaloacetate (-O2CCH2COCO2-). Show your work in a table with one reaction per line as we have done in class [i.e.: glycerol DH x 2; 2 NADH; () ATP etc].
|Reaction||Energy Product||factor||ATP (@2.5) Equivalents||ATP (@3) Equivalents|
|Succ CoA Synthase||GTP||1||1||1|
(22) 4. Outline a pathway for the breakdown of glucose to carbon dioxide and water Structures are not required (names or abbreviations are OK), but all cofactors and enzyme types must be identified at the appropriate locations, and the production/use of Pi, NTP, FADH2, and NADH must be noted.
(18) 5 a. Write out a detailed mechanism for Aldolase, starting with F-6-P to give DHAP and GALP.
b. Name the types of catalysis used in your mechanism, and identify (i.e. circle and label) where each occurs.
See diagram above (blue)
c. Draw a kinetic mechanism diagram for your mechanism and name it using Cleland nomenclature.
Ordered Sequential Uni Bi
(12) 6. Describe and/or explain thefollowing:
a. lipid bilayer:
A two dimensional sheet (membrane) made of lipids, usually phospholipids, having polar, hydrophilic groups facing the outside, usually aqueous, environment, and the non-polar 'tails' on the interior of the bilayer.
b. High energy compound:
A compound with a large negative value of the standard free energy measured a pH = 7 (DG°') of Hydrolysis.
c. futile cycle:
A set of two or more reactions in which a substance is modified and then returned to its original state with a loss of energy. e.g. PFK anf F-1,6-bisPase where F-6-P is used up and regenerated with the loss of an ATP.
d. Energy charge:
A measure of available cell energy based on the concentrations of adenylates:
E.C. = ([ATP] + 0.5[ADP])/([ATP] + [ADP] + [AMP])
(10) 7. Consider the strategies of the reactions in the Kreb's cycle starting with Citrate
(-OOCCH2CH(COO)CH2COO-) and leading to succinate.
a. What kind of chemical transformation first occurs with citrate and why?
A tertiasry alcohol (citrate) is isomerized to a secondary alcohol (isocitrate) so that the alcohol can be oxidized to a ketone with the subsequent reduction of NAD+ to NADH.
b. In going from oxaloacetate to citrate to succinyl CoA an acetyl group (2 Cís) is added and two CO2's are lost, with carbon now being in its most oxidized state. Can you now consider that the acetyl group is now completely oxidized? Why or why not? (Hint: why do we need to make oxalacetate now?)
No - in th eoxidation of two carbons of the citrate molecule to CO2 some of the other carbons were reduced - thus the acetyl group which was added to oxaloacetate has not been completely oxidized until the remaining carbons are brought to the oxidation states in oxaloacetate. In other words, the oxidastion of acetate is not complete until all catalytic compounds have been regenerated.
Last modified 5 March 2004