Chapter 17 The citric acid cycle (The t ri c arboxylic a cid cycle; The Krebs cycle)
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Transcript of Chapter 17 The citric acid cycle (The t ri c arboxylic a cid cycle; The Krebs cycle)
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Chapter 17 The citric acid cycle(The tricarboxylic acid cycle; The Krebs cycle)
– the final common pathway for the oxidation of fuel molecules
– an important source of precursors, storage fuels and building blocks
– to harvest high energy electrons from carbon fuels, via the aerobic processing
– take place inside mitochondria
Acetyl CoA
oxaloacetate
succinate
3 hydride
8 electrons (3 NADH, 1 FADH2)
oxidative phosphorylation
Roundabouts, or traffic circles, function as hubs to facilitate traffic flow.
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Coenzyme A: a carrier of acyl group
thioester
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2 m in length
0.5 m in diameter
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The function of TCA cycle– the harvesting of high energy electrons from carbon fuels
No large amount of ATP generation
No oxygen as a reactant (p. 490)
Cellular respiration
TCA + OP
90% energy production in aerobic cells
Substrate-level phosphorylation
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§ 17.1 The link between glycolysis and the TCA
cyclepyruvate + CoA + NAD+ acetyl CoA + CO2 + NADH
a specific pyruvate carrier embedded in membrane
decarboxylation and high-transfer-potential e-
Pyruvate dehydrogenase complex
In mitochondria matrix
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Pyruvate dehydrogenase complex (4~10 103 kd)–– increase the overall reaction rate and minimize side
reactions
CoA, NAD+
+ Lys
Catalytic cofactors
Stoichiometric cofactors
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Reactions of the pyruvate dehydrogenase complex
firstorder
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E1
C3 or C4 of Glc
NAD+ NADH
Derived by decarboxylation
thiazole ringp.
C C
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Decarboxylation:
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Decarboxylation:
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Lipoyl-lysine arm of lipoamide
Oxidation:
oxidized reduced
E2
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E2
Activated acyl groups carrier
Dihydrolipoyl transacetylase
Dihydrolipoyl dehydrogenase E3
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Nelson
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Substrate channeling:
all enzymes and coenzymes are clustered, allowing the intermediates
to react quickly without diffusing away from the surface of the enzyme
complex.
Nelson
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Citrate synthase:OAA + acetyl CoA + H2O citrate + CoA + H+
¤ synthase: two units are jointed without the direct participation of ATP
¤ OAA binds first, induced a structure rearrangement, followed by acetyl CoA
¤ citryl CoA formation, thioester hydrolysis
¤ CoA leaves the enzyme, followed by citrate, return to the original conformation
Side effects p. 440
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Aconitasecitrate cis-aconitate isocitrate
An interchange of hydrogen atom and hydroxyl group
dehydration hydration
isomerase
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Aconitase
¤ an iron-sulfur protein, or nonheme iron protein
¤ 4Fe-4S-3Cys, 1Fe binds to the carboxylate and hydroxyl groups of citrate
¤ the availability of iron in the cell (02)
An inhibitor of aconitase
(2003) NTU
Fluoroacetate (Garrette, p. 573)
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Isocitrate dehydrogenase
isocitrate + NAD+ -ketoglutarate +CO2 + NADH
the determining rate of TCA cycle
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-ketoglutarate dehydrogenaseis homologous to the pyruvate dehydrogenase
complex
Pyruvate + CoA + NAD+ acetyl CoA + CO2 + NADH
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Succinyl CoA synthetase (succinate thiokinase)
The only substrate-level phosphorylation in TCA cycle
Thioester bond cleavage coupled to GDP phosphorylation
E. coli enzyme uses either GDP or ADP as the phosphoryl-group acceptor
Plants use ADP as the phosphoryl-group acceptor
Nucleoside diphosphokinase: GTP + ADP GDP + ATP adenylate kinase
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The committed point of TCA cycle– the allosteric enzymes
Citrate synthase (in many bacteria), inhibit by ATP
Key sites:
Isocitrate dehydrogenase
-ketoglutarate dehydrogenase
Citrate can be transported to the cytoplasm,
inhibit glycolysis (phosphofructokinase)
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The source of biosynthetic precursors
gluconeogenesis
Pyruvate carboxylase
Anaplerotic reaction
Acetyl CoA synthetase p. 495
(bacteria and plants, and humans)
high / low energy charge
Acetate + CoA + ATP
+ AMP + PPi
p. 460/493
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Glyoxylate cycle (in glyoxysomes of oil-rich seeds)
Bypass two decarboxylation steps of TCA cycle
isocitrate lyase and malate synthase (in bacteria and plants)
2 acetyl CoA + NAD+ + 2H2O succinate + 2 CoA + NADH + 2H+
TCA, gluconeogenesis
(to power seeding growth)
Metabolic versatility
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ICL and MLS have as targets for therapeutic drugs to treat
some bacterial and fungal infections
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The Glyoxylate cycle— In plants, certain invertebrates, and some microorganisms acetate can serve both as an energy-rich fuel and as a source of phosphoenolpyruvate for carbohydrate synthesis
— the enzymes are sequestered in the membrane-bound organelles,
glyoxysomes, which are specialized peroxisomes
— glyoxysomes develop in lipid-rich seeds during germination
— glyoxysomes also contain all the enzymes needed for the degradation
of fatty acids
Nelson (05)
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Beriberi
¤ a neurologic and cardiovascular disorder
nervous system relies on Glc as its only fuel
¤ a dietary deficiency of thiamine (vitamin B1)
¤ inactivated thiamine-related enzymes
eg., pyruvate dehydrogenase, -ketoglutarate dehydrogenase,
transketolase (a diagnostic indicator of red cells)
¤ limbs pain, musculature weakness, skin sensation disorder, heart enlargement, cardiac output inadequate
¤ similar symptoms for an organism is exposed to mercury or arsenite
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Arsenite(AsO33-) poisoning
– high affinity for neighboring sulfhydryls
Dihydrollipoyl transacetylase -mercaptoethanol
Dithiothreitol (DTT)
Arsenate (AsO43-)
– lead to central nervous system pathologies
Mad as a hatter: HgNO3
-amylase
As2O3
(antidote)
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Arsenate (AsO43-)
glyceraldehyde 3-phosphate + Pi + NAD+
1,3-bisphosphoglycerate + NADH + H+
1-arseno-3-phosphoglycerate
Ch.16 EX. 13
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Citric acid/Citrate/citrate synthase:
— three negatively charged carboxyl groups
— a tart or fruity flavor
— a plasticizer and foam inhibitor in some resins preparation, as a mordant
to brighten colors, and as an antioxidant to preserve the flavors of foods
— industrial production: Aspergillus niger, beet molasses as carbon
source
— a good chelator of metal ions
— released into soil in some plants
— alleviate the toxicity of Al3+ in acidic soil
— highly expressed bacterial citrate synthase in plants
Nelson (05)
nitrate malate oxalate
phosphate citrate
strawberry red 0.764 1.356 0.343 0.661 10.303
strawberry green 1.098 1.774 0.421 0.696 13.030
loquat 0 4.271 0.034 0.110 0
mg/g FW
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Citric acid cycle:
an amphibolic pathway, both catabolic and anabolic processes
Nelson (05)
?
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Regeneration of OAA
¤ Succinate dehydrogenase: isoalloxazine ring of FAD
¤ Fumarase: a stereospecific trans addition, L-isomer malate formation
¤ Malate dehydrogenase: a significantly positive free energy
¤ a metabolic motif: 2 oxidation, 1 hydration,
methylene group (CH2) carbonyl group (CO)
More energy is extracted in the form of FADH2 and NADH
L-
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Succinate dehydrogenase
¤ the free-energy change is insufficient to reduce NAD+
¤ an iron-sulfur protein, contains three kinds: 2Fe-2S, 3Fe-4S, 4Fe-4S
¤ is embedded in the inner mitochondrial membrane, directly associated with the electron-transport chain
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1953 Nobel
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2nd run **
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Alexander (1948)
an asymmetric enzyme which attacks a symmetrical
compound can distinguish between its identical groups.
Ex. 11 and 12
p. 500 oxaloacetate
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Only under aerobic conditionsMetabolon: the enzymes are physically associated with one another to facilitate substrate channeling between active sites.
Acetyl CoA + 3 NAD+ + FAD + GDP + Pi + 2 H2O 2 CO2 + 3 NADH + FADH2 + GTP + 2 H+ + CoA
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Irreversible step
TCA
energy generation
p. 490
O2 does not participate directly in
the TCA cycle. However, the cycle operates only under aerobic conditions.
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Regulation of pyruvate dehydrogenase complex
¤ allosteric inhibitors: acetyl CoA (for E2), NADH (for E3)
¤ reversible phosphorylation (for E1): energy charge, biosynthetic intermediates
¤ [Ca2+] cyto [Ca2+] mito activate phosphatase
epinephrine (liver), [Ca2+] (p. 388) insulin (liver and adipose tissue), in fed state: glucose pyruvate acetyl CoA fatty acid synthesis
A phosphatase deficiency: Glc lactic acid, unremitting lactic acidosis, central nervous system malfunction
The kinase is associated with the E2
The phosphatase is stimulated by Ca2+
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At rest As exercise begins
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§ 16.3 Regulation of the citric acid cycle
Allosteric effectors
Covalent modification
Nelson (05)
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p. 499 coupling rxs.
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96
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98T
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98C
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揭開砒霜於白血病治療中的運作機制
作者:駐法科技組 97.05.09
摘要砒霜是治療某種罕見白血病十分有效的成份。位於 Saint Louis 醫院附設大學血液學研究院( Institut Universitaire d'Hématologie ,混合機構分屬法國國家科學研究中心 [CNRS] 與巴黎第七大學)的研究員已經證實砒霜在罕見白血病治療中的機制。這些研究結果應該會讓我們進一步了解這類疾病的治療,進而找出更為有效的醫療策略。這項最新的研究成果由抗癌陣線所支持,同時已刊載於 2008 年 4 月 13 日自然細胞生物學( Nature cell biology )的線上期刊中。本文毒藥砒霜於醫界之運用已有三千多年的歷史。目前,砒霜在急性骨髓性白血病 ( leucémie aiguë promyélocytaire )治療中經常可見。這種類型白血病的發展特徵在於骨髓性白血病( PML )蛋白質與 RARA 蛋白質的融合。 PML-RARA 蛋白質的融合就足以產稱白血病細胞。由 Huges de Thé 教授所率領的研究團隊首度發現砒霜會引起小泛素( SUMO )蛋白質的固定( fixation )。 SUMO 是一種肽,負責調節 PML-RARA 蛋白質間的互動。但這類複合體的降解( degradation )機制尚未解密,因為 SUMO 一般而言可以對抗蛋白質的降解。
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法國研究員日前在降解機制中成功辨識 RNF4 酶。這種酶在經由砒霜修飾後的 PML-RARA 蛋白質形式的降解與辨識過程中,扮演著關鍵的角色。它會固定這個複合體( PML/RARA-SUMO )上的另一個泛素( ubiquitine )酶,而這種已知的酶將會引發其所接合的蛋白質降解。之後,泛素將針對 PML/RARA-SUMO 蛋白質進行修飾。
這種由 SUMO 所引發並由泛素執行的降解管道的存在已經可以透過酵母( levure )的遺傳研究來預測,然而迄今尚未成功辨識出任何底物( substrat ,或譯為受質)。目前的研究結果或許可以進一步了解這類疾病的治療,進而擬出更為有效的醫療策略。
參考資料:Arsenic degrades PML or PML-RARA through a SUMO-triggered RNF4/ubiquitin-mediated pathway, Lallemand-Breitenbach, V., Jeanne, M., Benhenda, S., Nasr, R., Lei, M., Peres, L., Zhou, J., Zhu, J., Raught, B., and de The, H., Nature Cell Biology, en ligne le 13 avril 2008