The TCA Cycle A common metabolic pathway for glucose, aa and fatty acid 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

Entry into the TCA Cycle Pyruvate Dehydrogenase Complex Pyruvate is oxidatively decarboxylated to form acetyl-CoA Pyruvate dehydrogenase uses TPP, CoASH, lipoic acid, FAD and NAD+ Pyruvate dehydrogenase (E1) (丙酮酸脱氢酶) Dihydrolipoyl transacetylase (E2) (二氢硫辛酰转乙酰基酶) Dihydrolipoyl dehydrogenase (E3) (二氢硫辛酰脱氢酶)

Pyruvate Dehydrogenase Complex Pyruvate Acetyl-CoA Pyruvate Dehydrogenase Complex

Pyruvate dehydrogenase complex consists of three enzymes

Arsenic Compounds Are Poisonous in part because They Sequester Lipoamide

① Condensation

Citrate Synthase Formation of citrate Another example for the induced fit model OAA, the first substrate to bind to the enzyme, induce a large conformational change, creating a binding site for the second substrate, acetyl-CoA. When citroyl-CoA forms on the enzyme surface, another conformational change brings the side of a crucial Asp residue into position to cleavage the thioester. This mechanism decreases the likelihood of premature and unproductive cleavage of the thioester bond of acetyl-CoA

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

② Dehydration and hygration

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!

③ Oxidative decarboxylation

③ Oxidative decarboxylation

 -Ketoglutarate Dehydrogenase Complex 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 Another target for arsenic compounds

④ Oxidative decarboxylation

Succinyl-CoA Synthetase A substrate-level phosphorylation A nucleoside triphosphate is made Its synthesis is driven by hydrolysis of a CoA ester The mechanism involves a phosphohistidine

Succinate Dehydrogenase An oxidation involving FAD 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 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!

The Fate of Carbon in TCA 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.

TCA Cycle Summary Total rxn: Acetyl-CoA+3NAD＋+FAD+GDP+Pi+2H2O→2CO2+3NADH+FADH2+GTP+2H＋+CoA One Acetyl-CoA through the cycle produces two CO2, one ATP, four reduced coenzymes Two H2Os are used as substrates Absolutely depends on O2

Function of the TCA Cycle Produces More ATPs As a source of biosynthetic precursors A common final metabolic pathway for glucose, aas and fatty acids Some Immediates act as effectors to regulate other metabolic pathways Produces CO2

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