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Krebs Cycle and other Fun Stuff

Sean Lim 5 questions

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Questions in this quiz (5)

  1. 1Fill in your favorite thing about Biochemistry: points of regulation! Type all the molecules/processes that hinder progression to the next step on the left in the RED column, and type all the molecules/processes that encourage progression to the next step on the right in the GREEN column. Good luck! You'll need it.

    Also, within each red and green column, column one is allosteric regulation by substrate, column two is any modifying enzyme, and column three is any active site regulation by substrate. The substrate priorities from top to bottom is smaller to larger molecules (i.e: ATP derivatives, NADH derivatives, and then larger molecules). The priorities from left to right within the enzyme regulation column is listed similarly. Don't put any substrates (like pyruvate under PDH) because you should know them by now :)    Image for question 1
    1. APDH Phosphatase
    2. BPDH Kinase
    3. CCa2+
    4. DInsulin
    5. EATP
    6. FNADH
    7. GAcetyl CoA
    8. HNAD+
    9. INADH
    10. JAcetyl CoA
    11. KADP
    12. LH2O
    13. MADP
    14. NATP
    15. ONADH
    16. PATP
    17. QNADH
    18. RSuccinyl CoA
    19. SGDP
    20. TNAD+
    21. UNAD+
    22. VNAD+
    23. WH2O
    24. XFe-S
    25. YFAD
    26. ZFAD
  2. 2Follow the electron in the Light Reaction in Rhodopseudomonas!

    Special Pigment Pair: [blank_start]P960[blank_end]
    1st Electron Acceptor: [blank_start]Bacteriochlorophyll b[blank_end]
    2nd Electron Acceptor: [blank_start]Bacteriopheophytin[blank_end] (this does not have an [blank_start]Mg[blank_end] cofactor)
    Immobile [blank_start]Quinone A[blank_end] becomes a Semiquinone
    Fully reduced QH2 ([blank_start]Quninone B[blank_end])
    [blank_start]Cytochrome bc1 Complex[blank_end]: pumps [blank_start]2[blank_end] H+ into the Periplasm
    Completes the Cycle: [blank_start]Cytochrome C[blank_end] (has a [blank_start]Heme[blank_end] group)
    Its purpose is to neutralize the charge left behind in [blank_start]P960[blank_end] by photoinduced charge separation.
    1. AP960
    2. BBacteriochlorophyll b
    3. CBacteriopheophytin
    4. DMg
    5. EQuinone A
    6. FQuinone B
    7. GCytochrome bc1 Complex
    8. H2
    9. ICytochrome C
    10. JHeme
    11. KP960
  3. 3Follow the electron in the light reaction of a plant!

    [blank_start]Oxygen Evolving Complex[blank_end] (4 photons to oxidize 2 H2O, held by [blank_start]Mn4+[blank_end] clusters)
    Special Pigment Pair: [blank_start]P680[blank_end] (PSII)
    1st Electron Acceptor: [blank_start]Pheophytin[blank_end]
    Immobile Quinone: [blank_start]Plastoquinone[blank_end] (can become QH2)
    [blank_start]Cytochrome bf Complex[blank_end] (pumps 2H+ per photon)
    1 Electron Carrier: [blank_start]Plastocyanin[blank_end] (soluble and faces thylakoid lumen, has reducible Cu2+)
    Special Pigment Pair: [blank_start]P700[blank_end]
    1st Electron Acceptor: [blank_start]Chlorophyll A0[blank_end]
    Immobile Quinone [blank_start]A1[blank_end]
    1 Electron Carrier: [blank_start]Ferredoxin[blank_end] (can also reduce [blank_start]Thioredoxin[blank_end], which activates [blank_start]Calvin Cycle[blank_end] enzymes)
    [blank_start]Ferredoxin NADP Reductase[blank_end] (stepwise reduction of [blank_start]FAD[blank_end] to [blank_start]FADH2[blank_end] 1 electron at a time)
    Converts [blank_start]NADP+[blank_end] to [blank_start]NADPH[blank_end] per 2 electrons

    Notes:
    If no [blank_start]NADP+[blank_end] is available, the electrons can go from [blank_start]Ferredoxin[blank_end] to the [blank_start]Cytochrome bf Complex[blank_end] (pumps 2H+ per photon).
    The net charge between the stroma and thylakoid lumen is balanced by [blank_start]Mg2+[blank_end] ions, which flow [blank_start]out[blank_end] as H+ flows [blank_start]in[blank_end].

    1. AOxygen Evolving Complex
    2. BMn4+
    3. CP680
    4. DPheophytin
    5. EPlastoquinone
    6. FCytochrome bf Complex
    7. GPlastocyanin
    8. HP700
    9. IChlorophyll A0
    10. JThioredoxin
    11. KCalvin Cycle
    12. LFerredoxin
    13. MA1
    14. NFerredoxin NADP Reductase
    15. OFAD
    16. PFADH2
    17. QNADP+
    18. RNADPH
    19. SNADP+
    20. TFerredoxin
    21. UCytochrome bf Complex
    22. VMg2+
    23. Wout
    24. Xin
  4. 4Let's start off this final with a bang! Fill in the blanks for what happens at the start of each important process.

    [blank_start]Calvin Cycle[blank_end]:
    [blank_start]Rubisco[blank_end] first [blank_start]dehydrogenates[blank_end] Ru-1,5BP. It follows this up with a [blank_start]carboxylation[blank_end] reaction. Then, the resulting unstable 6 carbon compound is [blank_start]hydrolyzed[blank_end] into [blank_start]3-Phosphoglycerate[blank_end]. This 3 carbon molecule is built into hexose using first [blank_start]ATP[blank_end] then [blank_start]NADPH[blank_end].

    [blank_start]Pentose Phosphate Pathway[blank_end]:
    [blank_start]Glycerol 6-Phosphate[blank_end] first gets [blank_start]dehydrogenated[blank_end], producing [blank_start]NADPH[blank_end]. Then, the lactone gets opened. The product gets [blank_start]dehydrogenated[blank_end] again, producing [blank_start]NADPH[blank_end] and [blank_start]CO2[blank_end]. This 5 carbon ketose is turned into a different 5 carbon ketose or a 5 carbon aldose by [blank_start]Phosphopentose Isomerase[blank_end] or [blank_start]Phosphopentose Epimerase[blank_end], respectively.

    [blank_start]Beta-Keto Oxidation[blank_end]:
    [blank_start]Acyl CoA Synthetase[blank_end] attaches a [blank_start]CoA[blank_end] group onto the fatty acid chain. This requires [blank_start]2[blank_end] ATP because AMP is the byproduct. The molecule then must be associated with [blank_start]Carnitine[blank_end], which utilizes a [blank_start]translocase[blank_end] to dump the molecule into the [blank_start]Mitochondria[blank_end].
    1. Adehydrogenates
    2. Bcarboxylation
    3. CRubisco
    4. Dhydrolyzed
    5. EATP
    6. FNADPH
    7. GCalvin Cycle
    8. HPentose Phosphate Pathway
    9. IGlucose 6-Phosphate
    10. Jdehydrogenated
    11. KNADPH
    12. Ldehydrogenated
    13. MNADPH
    14. NCO2
    15. OPhosphopentose Epimerase
    16. PPhosphopentose Isomerase
    17. QBeta-Keto Oxidation
    18. RAcyl CoA Synthetase
    19. SCoA
    20. T2
    21. UCarnitine
    22. Vtranslocase
    23. WMitochondria
    24. X3-Phosphoglycerate
  5. 5[blank_start]Pyruvate[blank_end] first gets converted by [blank_start]PDH[blank_end] into [blank_start]Acetyl CoA[blank_end], leaving behind a [blank_start]CO2[blank_end] and generating [blank_start]NADH[blank_end]. Recall, our 3 carbon sugar comes in as a pair from [blank_start]glycolysis[blank_end]. Then, [blank_start]Acetyl CoA[blank_end] combines with [blank_start]Oxaloacetate[blank_end] (which is the first to bind due to [blank_start]ordered kinetics[blank_end]) to form [blank_start]Citroyl CoA[blank_end] which is held firm by [blank_start]Citrate Synthase[blank_end]. What drives the 6 carbon sugar to formation is the [blank_start]Thioester[blank_end] bond. Several [blank_start]Histidine[blank_end] and [blank_start]Aspartic[blank_end] Acid residues assist in activating each species for [blank_start]Enol[blank_end] attack. Only when [blank_start]Citroyl CoA[blank_end] is produced, [blank_start]Hydrolysis[blank_end] occurs, and [blank_start]Citrate[blank_end] leaves. [blank_start]Aconitase[blank_end] converts that into [blank_start]Isocitrate[blank_end] via a [blank_start]Dehydration[blank_end] and [blank_start]Hydration[blank_end] reaction. Several [blank_start]Fe-S[blank_end] prosthetic groups are used to attract the carboxylate groups for the catalyzation. [blank_start]Isocitrate Dehydrogenase[blank_end] then produces [blank_start]Alpha-Ketoglutarate[blank_end], and [blank_start]NADH[blank_end] first is generated then [blank_start]CO2[blank_end] falls off. [blank_start]Alpha-Ketoglutarate Dehydrogenase[blank_end] follows up this transformation with another [blank_start]CO2[blank_end] and [blank_start]NADH[blank_end] production, very similar to PDH's mechanism, and creating [blank_start]Succinyl CoA[blank_end]. We still have the [blank_start]2[blank_end] carbons from Acetyl CoA. [blank_start]Succinyl CoA Synthetase[blank_end] forms [blank_start]Succinate[blank_end] using a [blank_start]Phosphate[blank_end] from solution to displace the CoA. This [blank_start]Phosphate[blank_end] is then grabbed by a [blank_start]Histidine[blank_end] residue and transferred to a waiting [blank_start]GDP[blank_end] group. Then, [blank_start]Succinate Dehydrogenase[blank_end], located on the Mitochondrial [blank_start]Inner[blank_end] Membrane, facilitates in the oxidation reaction for generation of [blank_start]Fumarate[blank_end]. In the process, [blank_start]FADH2[blank_end] is produced. [blank_start]Fumarase[blank_end] is the enzyme that produces [blank_start]Malate[blank_end], utilizing a [blank_start]Hydration[blank_end] reaction, which then can be converted back into [blank_start]Oxaloacetate[blank_end] by [blank_start]Malate Dehydrogenase[blank_end], producing [blank_start]NADH[blank_end], which is the only reaction that has a [blank_start]Positive[blank_end] Delta G value. The disappearance of [blank_start]Oxaloacetate[blank_end] is the driving force for the reaction.
    1. APyruvate
    2. BPDH
    3. CAcetyl CoA
    4. DCO2
    5. ENADH
    6. Fglycolysis
    7. GAcetyl CoA
    8. HOxaloacetate
    9. Iordered kinetics
    10. JCitroyl CoA
    11. KCitrate Synthase
    12. LThioester
    13. MHistidine
    14. NAspartic
    15. OEnol
    16. PCitroyl CoA
    17. QHydrolysis
    18. RCitrate
    19. SAconitase
    20. TIsocitrate
    21. UDehydration
    22. VHydration
    23. WFe-S
    24. XIsocitrate Dehydrogenase
    25. YAlpha-Ketoglutarate
    26. ZNADH
    27. AACO2
    28. ABAlpha-Ketoglutarate Dehydrogenase
    29. ACCO2
    30. ADNADH
    31. AESuccinyl CoA
    32. AF2
    33. AGSuccinyl CoA Synthetase
    34. AHSuccinate
    35. AIPhosphate
    36. AJPhosphate
    37. AKHistidine
    38. ALGDP
    39. AMSuccinate Dehydrogenase
    40. ANInner
    41. AOFumarate
    42. APFADH2
    43. AQFumarase
    44. ARMalate
    45. ASHydration
    46. ATOxaloacetate
    47. AUMalate Dehydrogenase
    48. AVNADH
    49. AWPositive
    50. AXOxaloacetate

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Description
Quiz on Krebs Cycle and other Fun Stuff, created by Sean Lim on 02/05/2016.
Author
Sean Lim
Language
English
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