The TCA CycleThe TCA CycleA 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 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 SynthaseCitrate 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

AconitaseAconitase• 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 DehydrogenaseIsocitrate Dehydrogenase• Oxidative decarboxylation of isocitrate to y

ield -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 Comp-Ketoglutarate Dehydrogenase Complexlex

• 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 SynthetaseSuccinyl-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 DehydrogenaseSuccinate 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

FumaraseFumarase

• 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 DehydrogenaseMalate 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 TCAThe 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 CycleFunction 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 CycleThe Glyoxylate Cycle• A variant of TCA for plants and bacteria Acetate-based growth - net synthesis of carbohy

drates 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 IIGlyoxylate Cycle IIIsocitrate lyase produces glyoxylate and succin

ate Malate synthase does a Claisen condensation o

f 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