Citric Acid Cycle

kellygorrell
Mind Map by , created over 5 years ago

Mind Map on Citric Acid Cycle, created by kellygorrell on 04/27/2014.

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kellygorrell
Created by kellygorrell over 5 years ago
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Citric Acid Cycle
1 Overview

Annotations:

  • 1. At times, fatty acid recovery 2. Provides intermediates for other reactions & pathways 3. Has a series of 8 reactions: Oxidizing acetyl group of acetyl-CoA to 2 molecules of CO2 & ocnserving energy in NADH & FADH2
  • 4. "Central hub" of all metabolism
1.1 Output

Annotations:

  • 1. 1 complete cycle yields 2 CO2, 3 NADH, 1 FADH2. 1 "high energy" compound-GTP or ATP
1.1.1 Oxidation

Annotations:

  • 1. Oxidation of acetyl coA to 2Co2 requries the transfer of 4 pairs of electrons. 2. Reduction of 3NAD+ to 3NADH accounts for 3 pairs 3. Reduction of FAD to FADH2 accounts for 4th pair 4. 11 ATP formed from these 4 electron pairs after eventual tranfer to O2
1.2 Net Reaction

Annotations:

  •  3NAD+ + FAD + GDP + P + acetyl-coA --> 3NADH + FADH2 + GTP + CoA + 2CO2
  • Oxaloacetate consumed in first and last step
1.2.1 Transport

Annotations:

  • 1. TCA occurs in mitochondria 2. All substrates including NAD+ & GDP generated in or transported into mitochondria 3. All products consumed in or transported out of mitochondria
1.3 Purpose

Annotations:

  • 1. Reduces carbon structures down to CO2 2. Produces reducing equivalents used in electron transport & subsequently reoxidized by O2
  • 3. Central pathway for recovering energy from Carbs, fatty acids, amino acids that have been broken down to acetyl-coA
1.4 Input

Annotations:

  • 1. Pyruvate & NADH are final products of glycolysis 2. Pyruvate-H+ symport moves pyruvate and H+ into mitochondria
2 Synthesis of Acetyl Co-A
2.1 Pyruvate Dehydrogenase Complex

Annotations:

  • 1. Pyruvate is catalyzed by pyruvate dehydrogenase to Acetyl Co-A
  • 2. Group of noncovalently bound associated enzyme complexes
2.1.1 Multienzyme complex

Annotations:

  • Advantages: 1. Increase reaction rate because complex minimizes distance 2. Side reactions decreased; channeling of metabolic intermediates between successive enzymes 3. Coordinately controlled
2.1.1.1 3 Enzymes

Annotations:

  • 1. Pyruvate dehydrogenase E1 2. Dihydrolipoyl transacetylase E2 3. Di hydrolipoyl dehydrogenase E3
  • 2. Core 60 units  (20 trimers) E2
2.1.1.2 5 Reactions
2.1.1.2.1 5 Cofactors

Annotations:

  • -Thiamine pyrophosphate (TPP), lipoamide, coA, FAD, NAD}
2.1.1.2.2 1st Rxn

Annotations:

  • 1. Pyruvate dehydrognease E1 requires cofactor TPP. Decarboxylates pyruvate to form hydroxyethyl TPP intermediate.
  • 2. TPP thiazolium ring can add carbonyl group and act as electron sink
2.1.1.2.3 2nd Rxn

Annotations:

  • 1. Hydroxyethyl group transferred to next enzyme dihydrolipoyl transacetylase E2. E2 contains a lipoamide group - lipoic acid linked via amide bond
  • 2. Reaction center is cyclic disulfide; reduced to yield dihydrolipoamide 3. Hydroxyethyl group derived from pyruvate attacks lipoamide disulfide with TPP eliminated
  • 4. Hydroxyethyl carbanion is oxidized to an acetyl group as the lipoamide disulfide is reduced 5. Lipoamide group on E2 is key to moving intermediate between E1 & E3
2.1.1.2.3.1 Lipoamide group

Annotations:

  • 1. Acts as long teher swinging disulfide group from E1 where it pics up hydroxyethyl group to E2 active site where hydroxyethyl group transferred forming acetyl coA
  • 3. Swings from there to E3 where reduced disulfide is reoxidized
2.1.1.2.4 3rd Rxn

Annotations:

  • 1. E2 catalyzes transesterification reaction in which acetyl-group transferred to CoA yielding acetyl-CoA and dihydrolipoamide-E2
2.1.1.2.5 4th Rxn

Annotations:

  • 1. Acetyl-CoA formed 2. Must regenerate E2 lipoamide. E3 oxidizes & completes catalytic cycle of E2 3. Oxidized E3 contains reactive Cys-Cys disulfide group & tightly bound FAD
  • 4. Oxidation of dihydrolipoamdie is disulfide interchange reaction
2.1.1.2.6 5th Rxn

Annotations:

  • 1. Reduced E3 reoxidized. Sulfhydryl groups reoxidized by FAD funneling electrons to NAD+ yielding NADH
2.1.2 Arsenic

Annotations:

  • 1. Inhibits lipoamide containing enzymes including pyruvate dehydrogenase complex and alpha-ketogluturate dehydrogenase 2. Stops respiration: TCA cycle
2.1.3 Regulation of Pyruvate Dehydrogenase Complex
2.1.3.1 1st Regulatory System

Annotations:

  • 1. Product inhibition by NADH and acetyl CoA. Drives E2 & E3 backwards 2. Competitive inhibitors with NAD and CoA binding sites
2.1.3.1.1 Conc. of NADH & Acetyl CoA

Annotations:

  • 1. High [NADH]/[NAD+] & [AcetylCo-A]/[CoA] maintains E2 in acetylated form. Ties up TPP on E1 and E2 cannot accept hydroxyethyl group
2.1.3.2 2nd Regulatory System
2.1.3.2.1 Covalent Modificiation of E1
2.1.3.2.1.1 Pyruvate Dehydrogenase Kinase
2.1.3.2.1.1.1 Activated by NADH & acetyl CoA
2.1.3.2.1.1.1.1 Inactivates enzyme + ATP
2.1.3.2.1.2 Pyruvate Dehydrogenase Phosphatase
2.1.3.2.1.2.1 Activate enzyme
2.1.3.2.1.2.1.1 When glucose increases, promotes synthesis of acety-CoA & glycogen
2.1.3.3 Other Regulators
2.1.3.3.1 Inhibit pyruvate dehydrogenase

Annotations:

  • 1. Pyruvate, ADP 2. Ca+2 (also activates phosphatase) 3. no effect from cAMP
3 1. Citrate Synthesis

Annotations:

  • 1. Catalyzes condensation of acetyl-CoA and oxaloacetate 2. Point at which carbon atoms from carbs, fatty acids, and amino acids enter cycle
  • 3. Ordered sequential. Oxaloacetate binds prior to acetyl-CoA
  • Flux: varies with [substrate] Inhibited by Citrate & succinyl-CoA
3.1 Mechanism
3.1.1 Oxaloacetate + Acetyl CoA
3.1.1.1 Rate-limiting step and hydrogen bond

Annotations:

  • 1. Enol of acetyl-CoA generated in rate-limiting step when Asp 375 (a base) removes proton from methyl group 2. His 274 forms hydrogen bond with enolate oxygen
3.1.1.1.1 Citryl-CoA + Citrate

Annotations:

  • 1. Formed in concerted acid-base catalyzed step 2. Citryl-CoA hydrolyzed to citrate and coA. 3. Free energy = -31.5 KJ/mol
3.1.1.2 Acetyl-CoA binding site

Annotations:

  • 1. By x-ray studies, know that free enzyme is dimer in"open" form 2. 2 domains form a cleft containing oxaloacetate binding site
  • 3. Oxaloacetate binds smaller domain, rotates 18 degrees. Explains enzyme's ordered sequential kinetics.
  • 4. Rotation generates acetyl-CoA binding site seals oxaloacetate binding site, excluding water
4 2. Aconitase

Annotations:

  • 1. Catalyzes reversible isomerization of citrate to isocitrate with cis-aconitate as intermediate
  • 2. Begins with dehydration. Proton & OH removed. 3. Citrate has 2 carboxymethyl groups attached to central C atom. Prochiral rather than chiral then becomes chiral
  • Flux: near EQ
4.1 Citrate --> cis-Aconitate --> Isocitrate

Annotations:

  • 1. Aconitase contains iron-sulfur cluster. [4Fe-4S] coordinates -OH group of citrate to facilitate its elimination. Iron-sulfur clusters common in redox processes
  • 2. Rehydration of double bond of cis-aconitate to isocitrate
5 3. isocitrate Dehydrogenase

Annotations:

  • 1. NAD+ dependent E catalyzes oxidative decarboxylation of isocitrate to alpha-ketoglutarate
  • 2. Inhibited by product NADH
5.1 1st CO2 & NADH

Annotations:

  • 1. This CO2 began TCA as part of oxaloacetate and not acetyl CoA 2. Requires Mn+2 and Mg+2 cofactor & catalyzes oxidation of 2nd alcohol (isocitrate) to ketone (oxalosuccinate)
  • 3. Decarboxylation of carboxyl group Beta to ketone
5.1.1 Isocitrate --> Oxalosuccinate --> Alpha-Ketoglutarate
6 4. Alpha Ketogluturate Dehydrogenase

Annotations:

  • 1. Inhibited by NADH & succinyl-CoA
6.1 2nd CO2 & NADH

Annotations:

  • 1. CO2 entered as part of oxaloacetate rather than acetyl-CoA
6.2 Resembles pyruvate dehydrogenase multienzyme complex
7 5. Succinyl-CoA Synthetase
7.1 "High-energy" cleavage

Annotations:

  • 1. Couples cleavage of "high energy" succinyl-CoA to synthesis of "high energy" GTP
  • 2. GTP normally synthesized from GDP + P. Energetically equivalent to ATP 3. Free energy = 0KJ/mol
7.1.1 Passed to GTP
7.2 3 Step Process

Annotations:

  • 1. Succinyl-CoA reacts with phosphate forming succinyl-phosphate and CoA
  • 2. Phosphoryl group transferred from succinyl phosphate to His residue on E releasing succinate
  • 3. Phosphoryl group on E transferred to GDP forming GTP
7.2.1 1 Acetyl Equivalent oxidized to

Annotations:

  • 2CO2, 2NADH, 1GTP
8 6. Succinate Dehydrogenase
8.1 Dehydrogenation of Succinate to fumarate

Annotations:

  • 1. Stereo-specific dehydrogenation of S to F 2. E strongly inhibited by malonate. Ex. of competitive inhibitor
  • 3. 1. E contains FAD covalently linked 2. General biochem reaction oxidizes alkanes to alkenes
8.1.1 Produces FADH2

Annotations:

  • 1. Reoxidized before next catalytic cycle 2. 2 electrons passed into electron transport
8.2 Only membrane-bound enzyme
8.2.1 Funnels electrons directly into electron transport
9 7. Fumarase
9.1 Hydration of Double bond to form malate

Annotations:

  • 1. Hydration proceeds via cabanion transition state. OH addition occurs before H+ addition
10 8. Malate Dehydrogenase
10.1 Final step. Regeneration of oxaloacetate

Annotations:

  • 1. OH group of malate oxidized in NAD+ dependent reaction
10.1.1 [Malate] high

Annotations:

  • 1. Delta G0 = +27 KJ/mol. 2. At EQ, [oxaloacetate] very low relative to [malate]
10.1.1.1 Endergonic RXN
10.2 Citrate Synthase

Annotations:

  • 1. Highly exergonic 2. Free deltaG0 = -31.5KJ/mol because of cleave of thioester bond of citryl CoA
10.2.1 Exergonic RXN

Annotations:

  • 1. Coupled RXNs allow citrate formation to be exergonic evan at low [oxaloacetate]. Keeps TCA working
11 Energy Production
11.1 Regulators

Annotations:

  • 1. Availability of substrates 2. Need for TCA cycle intermediates as biosynthetics precursors 3. Demand for ATP
11.2 Glycolysis Output
11.2.1 2 Pyruvate, 2NADH, 2 ATP

Annotations:

  • 1. 2 net ATP. (Produces 4ATP but 2ATP required as input)
11.2.1.1 2 Pyruvate converted to 2acetyl-CoA & 2NADH
11.2.1.1.1 TCA cycle: 3NADH, 1 FADH2, 12 ATP, 1 CO2 per turn
11.2.1.1.1.1 24 ATP from TCA cycle
11.3 1 Glucose Molecule
11.3.1 Oxidative Phosphorylation (TCA cycle + pyruvate decarboxylation+ ETC?)
11.3.1.1 8NADH + 2 FADH2+2NADH=32ATP
11.3.1.1.1 +4ATP from substrate-level phosphorylation of glycolysis & TCA
11.3.1.1.1.1 36 ATP
11.3.1.1.2 32 ATP
12 Rate controlling steps
12.1 3 enzymes likely control candidates for deltaG

Annotations:

  • 1. Citrate synthesis 2. Isocitrate dehydrogenase 3. Alpha-ketogluturate dehydrogenase
12.1.1 Most Crucial Regulators

Annotations:

  • 1. Substrates: Acetyl-CoA & Oxaloacetate 2. Product: NADH
12.1.1.1 Additional Regulators

Annotations:

  • 1. ADP: Allosteric activator of isocitrate dehydrogenase 2. ATP inhibits isocitrate dehydrogenase 3 Ca+2 activates pyruvate dehydrogenase phosphatase
12.1.1.1.1 Calcium

Annotations:

  • 1. Stimulates muscle contractions + production of ATP to fuel muscle contractions
12.2 Heart Muscle

Annotations:

  • 1. Flux proportional to O2 consumption 2. Regulated by feedback mechanisms that coordinate NADH production with energy expenditure
12.3 Muscle

Annotations:

  • 1. Muscle workload & respiration rate increases. Mitochondrial [NADH] decreases. [Oxaloacetate[ increases. Stimulates citrate synthase
13 Related Reactions

Annotations:

  • 1. Gluconeogenesis 2. Fatty Acid biosynthesis 3. Amino acid biosynthesis using oxaloacetate & Alpha-ketogluturate

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