CHEMISTRY 153C Study Questions and Problems 2 Fall 2004 1. Compare a reaction selected from the β-oxidation cycle of fatty acid oxidation or the biosynthesis of acetoacetate with a closely analogous reaction of the tricarboxylic acid cycle. Select reactions for comparison in which the chemical changes involved and the mechanistic features bear a close resemblance to one another. Illustrate the reactions and comment on the most important features they have in common. 2. Liver cells lack the succinylCoA 3-ketoacyl:CoA transferase enzyme that is thought to be responsible for the activation of acetoacetate in other tissues. However, recent evidence suggests that activation of acetoacetate is possible in the extramitochondrial compartment of liver cells. Propose a reasonable reaction or set of reactions, other than the 3-ketoacyl:CoA transferase, that might be responsible for the activation of acetoacetate to its coenzyme A thioester in the extramitochondrial compartment. Use structural formulas including enough structure of any coenzymes, to make it clear how they participate. Use a reaction or reactions that would result in a favorable conversion of acetoacetate to acetoacetylCoA. 3. Unless otherwise indicated, use structural formulas for reactants and products except for coenzymes which can be abbreviated in standard fashion: a) Illustrate a reaction that is catalyzed by heart cells but not liver cells and is responsible for the ability of heart cells to use ketone bodies as an energy source. b) Would an auxiliary enzyme (or enzymes) be required to effect the complete oxidation of the activated fatty acid shown below to acetylCoA by β-oxidation? CH3(CH2)5CH (CH2)10OHCOSCoA c) Show the structure of 3-hydroxy-3-methylglutarylCoA and indicate clearly with an asterisk the labeling pattern expected in this substance when it is produced in liver mitochondria that are carrying out the oxidation of 2-[14C]-palmitylCoA. CH3CH2(CH2CH2)6CH2CSCoAO* 14. The cleavage of acetoacetylCoA to 2 acetylCoA catalyzed by the enzyme 3-ketothiolase is thermodynamically favorable under standard state conditions (∆Go = -6.7 kcal mol-1). If this is the case, how could the proposed synthesis of acetoacetylCoA from acetylCoA in a reaction catalyzed by 3-ketothiolase serve as a step in the biosynthesis of ketone bodies in liver mitochondria? Be as specific as you can in describing factors that may be involved. 5. For some years after the general features of the process of β-oxidation of fatty acids to acetylCoA had been elucidated, it was assumed by many biochemists that fatty acid biosynthesis from acetylCoA would be accomplished by the reversal of the β-oxidation pathway. However, experimental efforts to demonstrate this were fruitless. What features of the β-oxidation pathway would appear to make it a poor candidate as the scheme for the biosynthesis of fatty acids when operating in the reverse direction? 6. O-ORO-OCH2(CH2)8R = CH3petroselinate (C18; ∆6-cis)oleate (C18; ∆9-cis) A recent paper describes the isolation of a mutant of the bacterium Escherichia coli that can grow normally on oleate as a sole carbon source, but only poorly on petroselinate as a carbon source. One enzyme that participates in the oxidation of some fatty acids was deficient in the mutant strain. Illustrate with the types of structural designations employed above, the sequence of reactions that would take place with petroselinate as the substrate in the mutant strain. Show the reactions only up to the point where the pathway would be inhibited by the absence of a needed enzyme. For each step, indicate any coenzymes that would participate in the reaction. (Coenzymes can be abbreviated in standard fashion; the names of enzymes are not required.) RO-Opetroselinate 7. (a) Illustrate a pathway that shows the transformation of R-3-hydroxybutyrate to an intermediate, or intermediates, of the central metabolic pathways in heart cells. Use structures for reactants and products except for coenzymes, which may be abbreviated in the normal way. (Note: it is not necessary to show any reaction in the central pathways.) 2CH3COHCH2HCOO- (b) How many molecules of ATP, or its equivalent, would be synthesized during the complete oxidation of one molecule of R-3-hydroxybutyrate to 4 CO2 and water in actively respiring heart cells. Briefly justify how you arrived at this number. 8. For the following transformation, calculate the net yield (+) or net consumption (-) of ATP molecules (or its equivalent e.g. GTP) that would result from the operation of that process. Assume that any reduced coenzymes produced would be reoxidized in the mitochondrion as a part of that process. Justify your answer by summarizing in a table the sources of ATP molecules produced (+) or utilized (-). It is not necessary to show individual reactions or equations; just give a brief indication of how you arrived at the number. liver4CH3COCOO-CH2 palmitic acid (C16) 9. The following pathway has been proposed for lysine catabolism. Each arrow signifies an enzyme-catalyzed reaction. Note that not all intermediates, reactants and products are shown, and that the coenzymes participating in a reaction are not indicated. NH3+CH2CH2CH2-OOCCH2CH COO-NH3+CH2CH2CH2CH COO-NH3+-OOC CH2CH2CH2CSCoAO-OOC CH2CH2CH2COCOO--OOC CH2CH CH CSCoAOCH3CH3CH CH CSCoAOCSCoAO7521098CO26CO24L-lysine231 3Answer the following questions about this pathway. Show reactions with structures of reactants and products where requested; in no case is it necessary to show reaction mechanisms or intermediates. Standard abbreviations may be used to indicate coenzymes. (a) Show a reaction with structures for all reactants and products that would accomplish the transformation shown in step 4. (b) What coenzyme would participate in the reaction shown for step 4? (c) List all of the coenzymes that would participate in the overall transformation shown in step 5. (The coenzymes may participate either as reactants or in catalytic roles.) (d) What coenzyme would participate in the reaction shown in step 6? (e) Illustrate with structures the reactants and products for step 9. Any coenzymes participating in this reaction may be abbreviated in standard fashion. (f) If lysine were fed to a diabetic animal carrying out this catabolic pathway would it be glucogenic, ketogenic, both, or neither? 10. (a) The following overall