BioChem Final Part 2

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BioChem Final Part 2
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2011-04-19 15:02:23
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BioChemistry
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For Biochem final
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  1. Name the reactant and product, and any co factors: aconitase?
  2. Name the reactant and product, and any cofactors for isocitrate dehydrogenase?
  3. Name the reactant product and any cofactos for alpha-ketoglutarate dehydrogenase.
    • Part of TCA cycle
  4. Show the step in TCA cycle of substrate-level phosphorylation.
    • Nucleotide diphosphate kinase leads to ATP production from GTP.
  5. Name the products, reactants, and cofactors involved in succinate dehydrogenase.
  6. You hydrate furmate to form what molecule?
    • Malate
  7. Name the products, reactants, and cofactors for enzyme malate dehydrogenase.
  8. What is the main regulating enzyme for the TCA cycle?
    • PDH
  9. What happens to PDH in a state of starvation?
    PDH Kinase increases, which deactivates PDH. This shuts down gylcolysis and prevents oxidation of pyruvate to CO2.
  10. In what cell types are PDH Kinase activated?
    Activated in tumor cells.
  11. In what type of cells are PDH Phosphatase activated
    • Activated in insulin cells in liver adipose.
    • Inactivated by NADH.
  12. Isocitrate dehydrogenase and alpha-ketoglutarate dehydrogenase are inhibited by what?
    • Inhibited by increase in ATP and increase in NADH.
    • This means that there is an increase in citrate, which inhibits PFK (shuts off gylcolysis).
  13. What are the reactions that replenish OAA?
    • pyruvate carboxylase
    • PEPCKase (cofactor GDP and CO2 added)
  14. What is the reaction that replenishes malate?
    • Reverse reaction:
  15. What is oxidative phosporylation?
    • It is the syntheiss of ATP powered by re-oxidation of NADH or FADH2.
    • Major source of ATP synthesis.
  16. Where does oxidative phosphorylation take place?
    In the mitochondria matrix and inner mitochondria membrane.
  17. What are the two phases of oxidative phosphorylation?
    • Oxidative phase: refers to NADH and FADH2 oxidized to H2O.
    • Phosphorylation phase: refers to ATP synthesis
  18. What is redox potiental mean?
    Is the measure of how strongly compound wants an electron.
  19. Define what an oxidizing agent and reducing agent is.
    • Oxidizing agent: accept electrons and are reduced in a redox reaction.
    • Reducing agent: donates electrons and is oxidized in a redox reaction.
  20. The tendency for a reactant to be oxidized or reduced is found through its reducation potiental E. Write the equation that shows the relation of delta G and delta E to show the spontaneous direction of a reaction.
    deltaG^o= -nF(deltaE^o)
  21. What is Faraday's constant value?
    96,500 J/Vxmol
  22. How do you calculate delta E^o?
    delta E^o= oxidizing agent - reducing agent
  23. What is a rough drawing of the electron transport chain look like?
    • Remember that in the intermembrane fatty acyl dehydrogenase and glycerophosphate dehydrogenase donate 2e- to UQ/UQH2 through FADH2.
  24. What are the four electron enterance points in electron transport chain?
    • Complex I: NADH CoQ reductase
    • Complex II: Succinate Dehydrogenase, and succinate-CoQ reductase
    • Fatty acyl dehydrogenase
    • Glycerophosphate dehydrogenase
  25. What is the reaction of quinone to quniol (which shows the transfer of electrons to CoQ)?
  26. What is the involvment of Fe in complex I of the electron transport chain? Can Fe-S form clusters?
    • Fe Center is Fe II tranfered to Fe III
    • Fe-S forms clusters of cubes.
  27. Are electrons in contact during electron chain transport?
    • No. Electrons hop from one site to another. Hopping rate is inversely proportional to distances (depends on environment).
    • Electrons transfer fast and further in protein.
  28. How many H+ are transferred per NADH across the membrane? Show the breakdown of complexes.
    • Complex I: 4 H+
    • Complex II: 0 H+
    • Complex III: 2 H+
    • Complex IV: 4 H+
    • Total: 10 H+ transferred.
    • This generates about 1 pH unit gradient across the inner membrane.
  29. What is the enzyme between complex III and IV that leads to O2 reducation in complex IV?
    • Cytochrome C. oxidase.
    • This leads to 1/2 O2 -> H2O
  30. What does the Chemiosmotic theory state?
    • This was developed by Peter Mitchell.
    • This describes ATP synthesis by way of H+ coupling. This usually involves F1F0 ATPase.
  31. What is the protein structure of F1F0 ATPase?
  32. What is the conformational Coupling Model?
    • Paul Boyer created it.
    • H+ enters through the a,b subunits. This causes C subunit to rotate.
    • Sigma causes ATPase to rotate in one direction..
    • Have three forms: L, T, and O.
  33. What is the ATPase mechnism look like?
    • L= low affinity for ADP
    • T= high affinity for ATP
    • O= open structure; waiting for ADP + Pi to come in.
  34. What are the inhibitors for each complex?
    • Complex I: rotenone (plant defense molecule), and demerol (anti-depressent).
    • Complex II: carboxin (herbicide)
    • Complex III: antimycin (fungal defense)
    • Complex IV: well-known posions= CO, N3, CN (block e- transport to O2)
  35. What is the function of uncouplers to ATPase?
    Uncouplers are compounds that dissipate H+ gradient prior to F1F0 ATPase.
  36. What are examples of uncouplers in ATPase?
    • Aspirin: reduces ATP yeild from e- transport.
    • Native uncouplers are: thermogenin, and UCP 1, 2, and 3.
  37. ATP/ADP translocase is what type of enzyme, and what is its role?
    • It is an antiporter.
    • Leads ADP in intermembrane space into matrix; ATP in matrix into intermembrance space (ims).
    • This also affects the membrane potiental.
  38. What are the ATP yields for NADH and FADH2?
    • NADH= 3 ATP (2.5 experimentally)
    • FADH2= 2 ATP (1.5 experimentally)
  39. What is the Pentose Phosphate Pathway?
    • PPP uses glucose to generate reducin equivalents for anabolic reactions.
    • Convert glucose in the ribose for nucleic acids.
  40. What is anabolism?
    It is the set of metabolic pathways that construct molecules from smaller units. Requires energy.
  41. What is catabolism?
    It is the set of pathways that break down molecules into smaller units and release energy.
  42. Where does PPP take place?
    • Adipose tissue; mammary tissue.
    • testes
    • red blood cells
    • liver
    • cytoplasm
  43. What are the two phases of Pentose Phosphate Pathway?
    • Oxidative
    • Non-oxidative
  44. What are the oxidative reactions?
    • 1. glucose-6-phosphate dehydrogenase
    • 2. gluconolactonase
    • 3. 6-phosphogluconate dehydrogenase
    • 4. phosphopentose isomerase
  45. What is the product, reactant, and cofactors for glucose-6-phosphate dehydrogenase?
  46. What is the product, reactant, and cofactors for gluconolactonase?
  47. What is the product, reactant, and cofactors for enzyme 6-phosphogluconate dehydrogenase?
  48. What is the product reactant, and cofactors for enzyme phosphopentose isomerase?
  49. What is the net reaction for PPP oxidative phase?
    G6P (2NADP+) -> (2NADPH + H+) R5P + CO2
  50. What is the positive of oxidative PPP? negative?
    • Positive- cell needs lots of NADPH and ribose.
    • Negative- We need more NADPH, so what we do with excess R5P?
  51. What are the non-oxidative PPP enzymes used?
    • 1. phosphopentose epimerase
    • 2. transketolase
    • 3. SU7P + G3P -> E4P + F6P
    • 4. transketolase
  52. What is the committed step of Pentose Phosphate Pathway?
    Gylcose-6-Phosphate dehydrogenase (G6PDH) by NADP+
  53. What does lots of ribose do?
    Need lots of ribose to make DNA. Especially in rapidly divind cells.
  54. What happens to PPP when no NADPH there?
    • G6P to F6P to F-1,6-bP to DHAP and G3P.
    • DHAP, G3P, and F6P can be made into ribose.
    • Ribose then produce more DNA, RNA, and ATP.
  55. What happens if you have lots of NADPH but no ribose?
    • G6P forms Ru5P and CO2. Converts to R5P which then can convert to F6P and G3P.
    • These make G6P through gluconeogenesis.
    • 1 G6P makes 12 NADPH + 6 CO2 and is active in adipocytes.

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