chapter 16
How does covalent modification regulate the pyruvate dehydrogenase complex?
Acyl groups are covalently linked to the thiol group forming thioesters. Because of their relative standard free energies, they can donate/transfer their acyl groups to a variety of acceptor molecules.
The DG'o of the aconitase reaction is 13.3 kJ/mol. What drives the aconitase reaction forward?
Although this part of the citric acid cycle is reversible and endergonic, the reaction is pulled to the right (forward) becuase isocitrate is rapidly consumed in the next step of the cycle, lowering its steady state concentration. This energy status is most favorable for the cylce and therefore, despite its initial tendency to want to proceed in the reverse direction, that immediate lowering of total energy drives the aconitase reaction forward.
Why is it advantageous to have 3 different enzymatic activities clustered into a single enzyme complex?
Having 3 different enzymatic activities in a single enzyme complex is advantageous because it is more efficient. The structure has been conserved through evolution and is used in a number of similar reactions. This allows it to be very diverse.
How is the energy of oxidation of a-ketoglutarate conserved?
It is consereved through the formation of the thioester bond of succinyl CoA.
What are roles of lipoate in enzymatic reactions? Be sure to understand the 3 different enzyme subunits in pyruvate dehydrogenase and their cofactors act together to catalyze the decarboxylation of pyruvate.
Lipoate has two thiol groups that can undergo reversible oxidation to a disulfide bond. Lipoate can serve both as an electron carrier and as an acyl carrier. Lipoate is a PDH complex and is composed of three subunits: (E1) Pyruvate Dehydrogonase, (E2) dehydrolipoyl transacetylas, (E3) dihydrolipoyl dehydrogenase.
The concentration of oxaloacetate in the cell is normally low. What factor in citrate synthase reaction prevents this from hindering the operation of the cycle?
Oxaloacetate is continually removed by the citrate synthase reaction, which is highly exergonic, so concentrations are kept low. The largely negative delta G value prevents this from hindering the operation of the cycle.
What are the advantages to the cell of substrate channeling?
Substrate channeling ensures efficient passage of the product of one enzyme reaction to the next enzyme in the pathway. By doing so it provides a more rapid and efficient metabolic pathway along with protecting the intermediate from being consumed by competing reactions catalyzed by other enzymes.
What are the roles of the citric acid cycle? Where in eukaryotes do these reactions take place?
TCA cycle finishes the sugar hydrolysis that was started in glycolysis and fuels the production of ATP. It also converts citrate into oxaloacetate and release's two CO2 molecules. It also provides intermediates that are used to build amino acids and other molecules such as NAPH FADH2 which are electron carriers that bring the electrons to the electron transport chain which fuels the production of ATP. These reactions take place in the matrix of the mitochondria.
Why is a process as complex as the citric acid cycle actually an economical way for cells to do their metabolic business?
The TCA cylce is the hub of intermediate metabolism. The 4 and 5 carbon products of many catabolic pathways feed into the TCA cycle as a source of fuel. Also, under certain metabolic conditions the intermediates of the TCA cycle are drawn out of the pathway and serve as precursors to a variety of other biosynthetic pathways. The TCA cycle is amphibolic, meaning it serves both catabolic and anabolic purposes. The TCA cycle is not confined to the oxidation of acetate. Even though it is not the shortest pathway from acetate to CO2 it confered the greatest biological advantage.
What is the net energy yield per molecule of glucose for the combined reactions of glycolysis, the pyruvate dehydrogenase reaction and the citric acid cycle?
The net energy yield from the combined reactions of glycolysis, the pyruvate dehydrogenase reaction and the TCA cycle is on average in typical cellular conditions 32 - 36 ATP molecules. The physical reactions only generate 4 ATP molecules; the other 28-32 ATP molecules are generated from NADH and FADH2 indirectly via ATPase.
The oxidative decarboxylation of pyruvate is a highly exergonic reaction. How is energy released by this reaction conserved?
The transfer of electrons from NADH to oxygen generates 2.5 molecules of ATP per pair of electrons. The complex cannot reattach radioactivity labeled CO2 to acetyl-CoA to yield carboxyl-labeled pyruvate.
Why are citrate synthase, isocitrate dehydrogenase, and a-ketoglutarate dehydrogenase good candidates for regulatory enzymes?
They are good candidates for regulatory enzymes because their reactions are thermodynamically favorable (not at equilibrium). These enzymes govern the substrate availability rate through the cycle inhibition by accumulating products and allosteric feedback inhibition of the enzymes that are cayalyzed in the preliminary steps of the cycle.
The hydration of fumarate to malate is readily reversible, with a DG'o = -3.8 kJ/mol. Why do you think it proceeds in the direction of malate formation in vivo?
This enzyme is very stereospecific and catalyzes hydration of the trans double bond of fumarate but not the cis double bond of maleate (the cis isomer of fumarate). in the reverse direction, fumarase is equally as steriospecific but its product, d-maleate, is not a substrate. The product of the trans double bond of fumarate is l-maleate, which is why it proceeds in this direction in vivo. From this conclusion, the l form is preferred over the d form, and causes the reaction to proceed. **as the products of the reaction are consumed, the equilibrium pushes for more product. High standard free energies of some of the steps are able to push other steps with low standard free energies to occur**
What is the net equation for one turn of the citric acid cycle?
acetyl CoA + 3 NAD + FAD + ADP + HPO4-2 -----> 2 CO2 + CoA + 3 NADH+ + FADH+ + ATP
