Goals Learn the Citric Acid Cycle sequence, enzymes, intermediates, products, and control mechanisms. Learn the different stages of cellular respiration. Know that the citric acid cycle involves the oxidation of 2-carbon units. Be familiar with the function of the pyruvate dehydrogenase complex, its reaction types, general structure, and control mechanisms. Understand how degradative reactions provide cycle intermediates. Be familiar with role of the cycle in providing biosynthetic precursors. Understand the role of anaplerotic reactions Do NOT memorize specific enzyme mechanisms
Complete Oxidation to Molecular Oxygen Glucose Note: 1 cal =4.184J C 6 H 12 O 6 + 6 O 2 6 CO 2 + 6 H 2 O G° ’=-2823 kJ mole -1 Broken down into the half reactions: C 6 H 12 O 6 + 6 H 2 O 6CO 2 + 24H + + 24 e- 6 O 2 + + 24H + + 24 e - 12 H 2 O Palmitic Acid Palmitoyl-CoA + 23O 2 + 131 P i + 131 ADP CoA + 16CO 2 + 146 H 2 O +131 ATP Palmitic Acid + 23 O 2 16 CO 2 + 16 H 2 O G°’= -9790.5 kJ mole -1 129 ADP + 129P i 129 ATP + 129 H 2 O G°’= +3941 kJ mole -1 129 ATP is the next yield since 2 ATP are needed to form palmitoyl-CoA from palmitic acid. To Form 1 ATP G°’= +30.54 kJ mole -1 = 7.3 kcal mole -1 Citric Acid Cycle
Overview of the Citric Acid Cycle Citric Acid Cycle The central metabolic hub of the cell The gateway to the aerobic metabolism for any molecule that can be converted into an acetyl group or a dicarboxylic acid.
“Products” of the Citric Acid Cycle Three (3) Hydride Ions (H - ), that is six (6) electrons are produced in the form of: 3 NADH (from isocitrate dehydrogenase, -ketoglutarate dehydrogenase, & malate dehydrogenase) 1 FADH 2 (from succinate dehydrogenase) These electron carriers donate to electron transport which in turn drives oxidative phosphorylation to produce ATP 1 GTP (or ATP)(from succinyl CoA synthetase, a substrate-level phosphorylation) 2 CO 2 (at isocitrate dehydrogenase & -ketoglutarate dehydrogenase) Citric Acid Cycle Horton 2002 Fig12.6
Berg, Tymoczko & Stryer, 2012 Fig. 17.6 Pyruvate Dehydrogenase Complex: Decarboxylation Reaction of E 1 Citric Acid Cycle / Pyruvate Dehydrogenase The charged TPP ring functions as an electron sink that acts to stabilize the transferred negative charge
Berg, Tymoczko & Stryer, 2002 Chap 17 p. 500 PDH Complex: Lipoamide Structure Citric Acid Cycle / Pyruvate Dehydrogenase
Structures and Interconversion of Lipoamide & Dihydrolipoamide Voet, Voet & Pratt 2013 Figure 17.7
Voet, Voet & Pratt 2013 Chap 17 p. 559 PDH Complex: Oxidation of the Hydroxyethyl Group and Transfer to Lipoamide Citric Acid Cycle / Pyruvate Dehydrogenase Catalyzed by pyruvate dehydrogenase component (E1). Carbanion
PDH Complex: Formation of Acetyl CoA by Transfer of Acetyl Group from Acetyllipoamide Citric Acid Cycle / Pyruvate Dehydrogenase Catalyzed by dihydrolipoyl transacetylase (E2). Voet, Voet & Pratt 2013 Chap 17 p. 559
PDH Complex: Regeneration of Oxidized Form of Lipoamide by Dihydrolipoyl Dehydrogenase Citric Acid Cycle / Pyruvate Dehydrogenase Voet, Voet & Pratt 2013 Chap 17 p. 559 Summary of Two-step Process above Berg, Tymoczko & Stryer, 2012 Chap 17
Leheninger 2000 Fig 16.7 Citric Acid Cycle Diagram: #1 1 Note that the acetyl group that enters the cycle does not give rise to the CO 2 molecules given off in the decarboxylations in ONE TURN of the cycle.
Citrate Synthase Structure OPEN CLOSED Berg, Tymoczko & Stryer Figure 17.10 Oxaloacetate binding induces the two domains to move toward each other in an 18 degree arc This forms a binding site for acetyl CoA.
Berg, Tymoczko & Stryer, 2012 Chap 17 p.504 Citric Acid Cycle: Condensation of Oxaloacetate & acetyl CoA Citric Acid Cycle Citrate synthase G = -31.4 kJ mol -1 Reaction 1
Berg, Tymoczko & Stryer, 2012 Fig. 17.11 Citric Acid Cycle: Synthesis of Citryl CoA by Citrate Synthase Citric Acid Cycle
The purpose of this reaction is to convert the citrate molecule to a secondary alcohol. Voet, Voet & Pratt, 2013 Chap 17 p.563 Citric Acid Cycle: Isomerization of Citrate by Aconitase Citric Acid Cycle Aconitase G = +8.4 kJ mol -1 G = -2.1 kJ mol -1 Reaction 2
Voet, Voet & Pratt 2013 Chap 17 p. 567 Citric Acid Cycle: Succinate Dehydrogenase R x Citric Acid Cycle Succinate dehydrogenase G = 0 kJ mol -1 Reaction 6
FAD vs NAD + Reduction In general: FAD functions biochemically to oxidize alkanes to alkenes. The oxidation of an alkane, e.g. succinate, to an alkene (fumarate) is sufficiently exergonic to reduce FAD to FADH 2 but not to reduce NAD +. NAD + oxidizes alcohols to aldehydes or ketones. Alcohol oxidation can reduce NAD + to NADH Voet, Voet & Pratt 2013 p. 567; Voet & Voet 1996 p555 Citric Acid Cycle
Voet, Voet, & Pratt 2012 Chap.. 17 p. 567 Citric Acid Cycle: Hydration of Fumarate to Malate by Fumarase Citric Acid Cycle Fumarase G = -3.8 kJ mol -1 Reaction 7 Fumarase
Control of Metabolic Flux in the Cycle Key Factors: Substrate Availability Inhibition by accumulating products Allosteric feedback inhibition of enzymes that catalyze the cycle’s early reactions. Lehninger 2000, p 587 Citric Acid Cycle Enzyme Control Points: Citrate synthase (Bacteria) Isocitrate dehydrogenase -ketoglutarate
Berg, Tymoczko & Stryer, 2012 Fig. 17.19 Control of the Citric Acid Cycle Citric Acid Cycle Voet, Voet, & Pratt 2013 Fig. 17.16
The Citric Acid Cycle and Biosynthetic Precursors Citric Acid Cycle
Anaplerotic Reactions Table ( Anaplerotic Reactions Table (most common anaplerotic reactions) Serve to replenish the citric acid cycle intermediates that are removed as biosynthetic precursors
Degradative Pathways Generating Cycle Intermediates Oxidation of odd chain fatty acids lead to the production of succinyl-CoA Breakdown of the amino acids leucine, methionine and valine also lead to succinyl CoA production Transamination and Deamination of amino acids leads to the production of -ketoglutarate and oxaloacetate.