Chapter 12 (part 1)

Citric Acid Cycle

Gylcolysis

TCA Cycle

Electron Transport andOxidative phosphorylation

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

Entry into the TCA Cycle

• Pyruvate is translocated from the cytosol to the mitochondria

• Pyruvate is oxidatively decarboxylated to form acetyl-CoA

• Pyruvate dehydrogenase uses TPP, CoASH, lipoic acid, FAD and NAD+

• Acetyl-CoA then enters TCA cycle thru citrate synthase

Pyruvate Dehydrogenase

ComplexComposed of three enzymes:• pyruvate dehydrogenase (E1)

(cofactor = TPP)• Dihydrolipoamide acetyltransferase

(E2) (cofactor = Lipoamide, CoA)• Dihydrolipoamide dehydrogenase

(E3) (cofactor = FAD, NAD+)

Pyruvate Dehydrogenase

Citrate Synthase• Only step in TCA cycle that involves the

formation of a C-C bond

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

• Aconitase uses an iron-sulfur cluster to position citrate (binds –OH and carboxyl of central carbon)

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

• Rxn is metabolically irreversible

-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

Succinyl-CoA Synthetase

• A substrate-level phosphorylation • A nucleoside triphosphate is made

(ATP in plants/bacteria and GTP in animals)

• Its synthesis is driven by hydrolysis of a CoA ester

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

• Enzyme inhibited by malonate

Fumarase

• Hydration across the double bond

• trans-addition of the elements of water across the double bond

• Stereospecific reaction

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

Reduced Coenzymes Fuel ATP Production

• Acetyl-CoA + 3 NAD+ + Q + GDP + Pi +2 H20 HS-CoA + 3NADH + QH2 + GTP + 2 CO2 + 2 H+

• Isocitrate Dehydrogenase 1 NADH=2.5 ATP• -ketoglutarate dehydrogenase 1 NADH=2.5

ATP• Succinyl-CoA synthetase 1 GTP=1 ATP• Sunccinate dehydrogenase 1 QH2=1.5

ATP• Malate Dehydrogenase 1 NADH=2.5 ATP

• Total of 10 ATPs gained from oxidation of 1 Acetyl-CoA

Regulation of TCA

Cycle

Protein/amino acid

Catabolites feedInto the TCA

Cycle

Fats breakdown and feed

into the TCA Cycle

TCA Cycle provides intermediates for many biosynthetic processes

The Anaplerotic ReactionsThe "filling up" reactions

• PEP carboxylase - converts PEP to oxaloacetate

• Pyruvate carboxylase - converts pyruvate to oxaloacetate

• Malic enzyme converts pyruvate into malate

Following the carbons through

the TCA cycle

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• Rxns occur in specialized organelles

(glycoxysomes)• Plants store carbon in seeds as oil• The glyoxylate cycle allows plants to

use acetyl-CoA derived from B-oxidation of fatty acids for carbohydrate synthesis

• Animals can not do this! Acetyl-CoA is totally oxidized to CO2

• Malate used in gluconeogenesis