* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Download Chapter 20 Notes
Biochemical cascade wikipedia , lookup
Metalloprotein wikipedia , lookup
Mitochondrion wikipedia , lookup
Photosynthetic reaction centre wikipedia , lookup
Light-dependent reactions wikipedia , lookup
Biosynthesis wikipedia , lookup
Photosynthesis wikipedia , lookup
Lactate dehydrogenase wikipedia , lookup
Fatty acid metabolism wikipedia , lookup
Fatty acid synthesis wikipedia , lookup
Adenosine triphosphate wikipedia , lookup
Biochemistry wikipedia , lookup
Evolution of metal ions in biological systems wikipedia , lookup
Electron transport chain wikipedia , lookup
Amino acid synthesis wikipedia , lookup
Microbial metabolism wikipedia , lookup
Nicotinamide adenine dinucleotide wikipedia , lookup
Glyceroneogenesis wikipedia , lookup
NADH:ubiquinone oxidoreductase (H+-translocating) wikipedia , lookup
Chapter 20 The Tricarboxylic Acid Cycle to accompany Biochemistry, 2/e by Reginald Garrett and Charles Grisham Outline • • • • • • • 20.3 Bridging Step - Pyruvate Decarboxylase 20.4 Entry - Citrate Synthase 20.5 - 20.11 All the Other Steps 20.13 Intermediates for Other Pathways 20.14 Anaplerotic Reactions 20.15 Regulation of the TCA Cycle 20.16 The Glyoxylate Cycle The TCA Cycle aka Citric Acid Cycle, Krebs Cycle • Pyruvate (actually acetate) from glycolysis is degraded to CO2 • Some ATP is produced • More NADH is made • NADH goes on to make more ATP in electron transport and oxidative phosphorylation The Chemical Logic of TCA Understand this! • TCA seems like a complicated way to oxidize acetate units to CO2 • But normal ways to cleave C-C bonds and oxidize don't work for CO2: – cleavage between Cs and to a carbonyl – an -cleavage of an -hydroxyketone The Chemical Logic of TCA Understand this! • Better to condense acetate with oxaloacetate and carry out a -cleavage - TCA combines this with oxidation to form CO2, regenerate oxaloacetate and capture all the energy as NADH and ATP! Entry into the TCA Cycle Pyruvate dehydrogenase and citrate synthase • Pyruvate is oxidatively decarboxylated to form acetyl-CoA • Pyruvate dehydrogenase uses TPP, CoASH, lipoic acid, FAD and NAD+ • Citrate synthase is classic CoA chemistry! • Know both mechanisms • NADH & succinyl-CoA are allosteric inhibitors • Note (Table 20.1) that CS has large, neg G! Aconitase Isomerization of Citrate to Isocitrate • Citrate is a poor substrate for oxidation • So aconitase isomerizes citrate to yield isocitrate which has a secondary -OH, which can be oxidized • Note the stereochemistry of the Rxn: aconitase removes the pro-R H of the pro-R arm of citrate! • Aconitase uses an iron-sulfur cluster - see Fig. 20.8 Isocitrate Dehydrogenase Oxidative decarboxylation of isocitrate to yield -ketoglutarate • Classic NAD+ chemistry (hydride removal) followed by a decarboxylation • Isocitrate dehydrogenase is a link to the electron transport pathway because it makes NADH • Know the mechanism! -Ketoglutarate Dehydrogenase A second oxidative decarboxylation • This enzyme is nearly identical to pyruvate dehydrogenase structurally and mechanistically • Five coenzymes used - TPP, CoASH, Lipoic acid, NAD+, FAD • You know the mechanism if you remember pyruvate dehydrogenase Succinyl-CoA Synthetase A substrate-level phosphorylation • A nucleoside triphosphate is made • Its synthesis is driven by hydrolysis of a CoA ester • The mechanism (Figure 20.13) involves a phosphohistidine Succinate Dehydrogenase An oxidation involving FAD • Mechanism involves hydride removal by FAD and a deprotonation • This enzyme is actually part of the electron transport pathway in the inner mitochondrial membrane • The electrons transferred from succinate to FAD (to form FADH2) are passed directly to ubiquinone (UQ) in the electron transport pathway Fumarase Hydration across the double bond • trans-addition of the elements of water across the double bond • Possible mechanisms are shown in Figure 20.18 • The actual mechanism is not known for certain Malate Dehydrogenase An NAD+-dependent oxidation • The carbon that gets oxidized is the one that received the -OH in the previous reaction • This reaction is energetically expensive Go' = +30 kJ/mol • This and the previous two reactions form a reaction triad that we will see over and over! TCA Cycle Summary One acetate through the cycle produces two CO2, one ATP, four reduced coenzymes • Make sure that you understand the equations on page 659 • A healthy exercise would be to try to derive these equations (or at least justify each term) The Fate of Carbon in TCA Study Figure 20.21 carefully! • Carboxyl C of acetate turns to CO2 only in the second turn of the cycle (following entry of acetate) • Methyl C of acetate survives two cycles completely, but half of what's left exits the cycle on each turn after that. Intermediates for Biosynthesis The TCA cycle provides several of these -Ketoglutarate is transaminated to make glutamate, which can be used to make purine nucleotides, Arg and Pro • Succinyl-CoA can be used to make porphyrins • Fumarate and oxaloacetate can be used to make several amino acids and also pyrimidine nucleotides Intermediates for Biosynthesis The TCA cycle provides several of these • Note (Fig. 20.23) that mitochondrial citrate can be exported to be a cytoplasmic source of acetyl-CoA and oxaloacetate The Anaplerotic Reactions The "filling up" reactions • PEP carboxylase - converts PEP to oxaloacetate • Pyruvate carboxylase - converts pyruvate to oxaloacetate • Malic enzyme converts pyruvate into malate • PEP carboxykinase - could have been an anaplerotic reaction, but it goes the wrong way! • CO2 binds weakly to the enzyme, but oxaloacetate binds tightly, so the reaction goes the wrong way. The Reductive TCA Cycle • The TCA cycle running backward could assimilate CO2 • This may have been the first metabolic pathway • Energy to drive it may have come from iron pyrite, which was plentiful in ancient times, and which is an ancient version of ‘iron-sulfur clusters’! Regulation of the TCA Cycle Again, 3 reactions are the key sites • Citrate synthase - ATP, NADH and succinyl-CoA inhibit • Isocitrate dehydrogenase - ATP inhibits, ADP and NAD+ activate -Ketoglutarate dehydrogenase - NADH and succinyl-CoA inhibit, AMP activates • Also note pyruvate dehydrogenase: ATP, NADH, acetyl-CoA inhibit, NAD+, CoA activate The Glyoxylate Cycle A variant of TCA for plants and bacteria • Acetate-based growth - net synthesis of carbohydrates and other intermediates from acetate - is not possible with TCA • Glyoxylate cycle offers a solution for plants and some bacteria and algae • The CO2-evolving steps are bypassed and an extra acetate is utilized • Isocitrate lyase and malate synthase are the short-circuiting enzymes Glyoxylate Cycle II • Isocitrate lyase produces glyoxylate and succinate • Malate synthase does a Claisen condensation of acetyl-CoA and the aldehyde group of glyoxylate - classic CoA chemistry! • The glyoxylate cycle helps plants grow in the dark! • Glyoxysomes borrow three reactions from mitochondria: succinate to oxaloacetate