Exam 4 Long Questions Flashcards
Describe the structure of the pyruvate dehydrogenase complex and how it contributes to efficient function (describe relative locations of enzymes and relevant cofactors).
The three enzymes of the pyruvate dehydrogenase complex are structurally integrated and the lipoamide arm allows rapid movement of substrates and products from one active site of the complex to another. There is a transacetylase core (E2), a pyruvate dehydrogenase component (E1), and the dihydrolipoyl dehydrogenase (E3).
Describe the regulation of the pyruvate dehydrogenase complex and how misregulation contributes to disease.
Key site of regulation is in E1.
Phosphorylation: A kinase phosphorylates and inactivates E1. Phosphatase removes the phosphate and activates E1.
Energy Charge: ATP, acetyl CoA, and NADH inhibit the complex. ADP and pyruvate stimulate the complex.
Misregulation of the pyruvate dehydrogenase complex could lead to a misregulation of the CAC.
Describe the mechanism for citrate synthase and explain why it is important for preventing unwanted reactions.
Oxaloacetate binding by citrate synthase induces structural changes that lead to the formation of the acetyl CoA binding site. Creation of citric CoA causes a structural change that will complete active site formation. Citryl CoA is cleaved to make citrate and coenzyme A. Prevents reactions like the mistaken cleavage of acetyl-CoA
Describe how defects in the CAC contribute to aerobic glycolysis and the activity of HIF-1
Lactic acidosis and build up of intermediates lead to neurological defects and problems with muscle development.
In deficiencies of succinate dehydrogenase and fumarate lead to aerobic glycolysis. HIF-1 up regulates glycolysis and blood vessel development.
Describe the Q-cycle mechanism for complex III
First Half: 2 electrons of a bound QH2 are transferred to cytochrome c and to a bound Q in a second binding site to form the semiquinone radical anion Q- which dissociates and enters the Q pool.
Second Half: A second QH2 also gives up its electron, one to a second molecule of cytochrome c and the other to reduce Q- to QH2. Results in the uptake of two protons from the matrix.
4 protons are pumped out of the mitochondria and 2 are removed from the matrix.
Describe the relative contributions of each of the following to the proton gradient across the membrane: NADH produced from the citric acid cycle, FADH2 produced from the citric acid cycle and NADH produced from glycolysis.
NADH from glycolysis in the Muscle cells: Glycerol shuttle (not a proton pump) moves electrons to QH2.
NADH from glycolysis in the Liver Cells: Malate aspartate shuttle (not a proton pump) moves electrons and they then behave like the NADH from the CAC.
NADH from the CAC: electrons go through complex 1 (proton pump) and then QH2
FADH2: Electrons go from complex 2 (not a proton pump) to QH2
After QH2, all of the electrons will move to Complex 3 (proton pump) then cytochrome c then Complex 4 (proton pump)
Describe the experiment that demonstrated gamma subunit rotation is required for ATP synthesis by the F1 portion of ATP synthase.
Using cloned alpha3beta3gamma subunits, with the beta subunits tagged with a histidine that attached it to a nickel-coated slide, and using another fluorescent tag linked to the g subunit, the rotation could be observed using a fluorescent microscope.
Explain the mechanism for coupling the energy from the proton gradient to ATP synthesis by ATP synthase.
F0 mechanism: composed of two subunits a and c positioned in the membrane. Protons enter the half channel of subunit a in the intermembrane space but can only go half way through; the only way to the matrix is by using the aspartate of subunit c. The protonated c subunit rotates and the donates a proton to the adjacent bottom half channel of subunit a. The deprotonated subunit c can now accept a proton from the top half of subunit a. The rotary proton transfer causes the rotation of the gamma unit of F1 of ATP Synthase.
Describe the process of glycogen synthesis. Include all necessary enzymes and components.
- Preparation of glucose monomer units to UDP-Glucose.
- Priming the glycogen core by glycogenin and addition of α-1,4 linkages by glycogen
synthase. - Forming branch points by transferring chains of α-1,4 linkages to another part of the
glycogen molecule and forming an α-1,6 linkage.
Describe the coordinated regulation of glycogen degradation and glycogen synthesis under each of the following conditions: after a meal and in response to glucagon.
After a meal: Glycogen synthesis is required. Protein phosphatase 1 stimulates glycogen synthesis.
In response to glucagon: Protein kinase A inhibits glycogen synthesis????
Describe the two phases of the pentose phosphate pathway and what each phase contributes to metabolism.
Oxidative Phase that generates NADPH: G6P to Ribulose 5-Phosphate + CO2 + 2NAPH. The key enzyme is glucose 6-phosphate dehydrogenase that is used in the first step. Lactonase and 6-phosphogluconate dehydrogenase is also used.
Non-oxidative Phase that interconverts phosphorylated sugars: 3 C5 sugars to 2 C6 sugars (F6P) and 1 C3 sugar (GAP). Uses a transketolase to transfer 2C subunits and a transaldolase to transfer 3C subunits.
Describe the relationship of the pentose phosphate pathway and managing oxidative stress
Glutathione helps to prevent damage by reactive oxygen species generated in the course of metabolism. NADPH generated by the pentose phosphate pathway is required to maintain adequate levels of reduced glutathione. Oxidized glutathione is converted into reduced glutathione by NADPH.
