Citric Acid Cycle

glycogen → glucose → pyruvate → acetyl coenzyme A → CO2

full pathway

24

complete oxidation of glucose → CO₂ removes ___ electrons

4

glycolysis removes __ electrons as NADH

4

2 pyruvate → 2 acetate removes __ electrons as NADH

16

2 acetyl coenzyme A → 4 CO₂ removes __ electrons (6 NADH + 2 FADH₂)

mitochondria

where pyruvate is oxidatively decarboxylated to acetyl coenzyme A

pyruvate dehydrogenase complex

• multi-enzyme complex that catalyzes oxidative decarboxylation of pyruvate → acetyl coenzyme A

• pyruvate + NAD⁺ + CoA → Acetyl CoA +CO₂ + NADH

three enzymes that make up the pyruvate dehydrogenase (PDH) complex

• pyruvate dehydrogenase (E1)

• dihydrolipoamide acetyltransferase (E2)

• dihydrolipoamide dehydrogenase (E3)

five coenzymes that make up pyruvate dehydrogenase (PDH) complex

• vitamin B1

• FAD/FADH₂ vitamin B2

• NAD/NADH₂ vitamin B3

• coenzyme A vitamin B5

• lipoic acid

thiamine pyrophosphate (TPP)

• bound to E1

• decarboxylates pyruvate

• vitamin B1

lipoic acid

• linked to E2

• replaces TPP on carbanion

coenzyme A

• substrate for E2

• replaces lipoamide on acetyl group

• vitamin B5

pyruvate dehydrogenase (E1)

decarboxylates pyruvate → hydroxyethyl-TPP carbanion

pyruvate dehydrogenase (E1)

gets TPP back and replaces it with lipoamide

dihydrolipoamide transacetylase (E2)

gets lipoamide back and replaces it with CoA

dihydrolipoamide dehydrogenase (E3)

uses lipoamide to reduce FAD → FADH₂

dihydrolipoamide dehydrogenase (E3)

uses FADH₂ to reduce NAD+ → NADH + FAD

FAD

• bound to E3

• gets reduced to FADH₂ by lipoamide

• vitamin B2

NAD+

• substrate for E3

• gets reduced to NADH by FADH₂

• vitamin B3

citrate synthase

• acetyl CoA + oxaloacetate → citrate

• initiates krebs cycle

• larger negative delta G (highly regulated)

inhibitors for citrate synthase

NADH and succinyl-CoA

aconitase

• isomerizes citrate → isocitrate

• isocitrate has secondary -OH which is more easily oxidized

• uses iron-sulfur cluster

fluoroacetate

• trojan horse inhibitor that blocks citric acid cycle

• does not affect any of the isolated enzymes

• aconitase is inhibited by fluorocitrate which is formed from fluoroacetate

isocitrate dehydrogenase

• catalyzes first oxidative decarboxylation of isocitrate → alpha-Ketoglutarate

• uses NAD+ to remove hydride → then removes CO2

• negative delta G, high regulation

alpha-ketoglutarate dehydrogenase

• catalyzes second decarboxylation of alpha-ketoglutarate → succinyl-CoA

• nearly identical to pyruvate dehydrogenase

Succinyl-CoA synthetase

• substrate-level phosphorylation

• makes GTP because succinyl-CoA is high energy

• hydrolysis of succinyl-CoA to succinate

succinate dehydrogenase

• stereospecific dehydrogenation

• succinate → fumarate (C=C)

• uses FAD → FADH₂

• has 3 types of Fe-S centers

fumarase

• trans-hydration of fumarate → L-malate

• add H and OH on opposite side of double bond and make it single

malate dehydrogenase

• oxidizes L-malate → oxaloacetate

• uses NAD+ → NADH

• large, positive delta G (coupled with favorable citrate synthase reaction)

net reaction of citric acid cycle

3 NAD⁺ + FAD + GDP + P_i + acetyl-CoA → 3NADH + FADH₂ + GTP + CoA + 2CO₂

glycolysis yield

• 2 ATP

• 2 NADH → 6ATP

• total = 8 ATP

pyruvate dehydrogenase yield

2 NADH → 6ATP

citric acid cycle yield

• 2 × 3NADH → 18 ATP

• 2 × 1FADH₂ → 4 ATP

• 2 × 1GTP → 2 ATP

• total = 24 ATP

32

“actual” ATP yield from one glucose

citrate synthase, isocitrate dehydrogenase, alpha-ketoglutarate dehydrogenase

irreversible enzymes of citric acid cycle

citrate synthase inhibitors

ATP, NADH, succinyl-CoA

isocitrate dehydrogenase inhibitors

ATP, NADH

isocitrate dehydrogenase activator

ADP

alpha-ketoglutarate dehydrogenase inhibitors

NADH, succinyl-CoA

alpha-ketoglutarate dehydrogenase activator

AMP

pyruvate dehydrogenase inhibitors

ATP, NADH, acetyl-CoA

pyruvate dehydrogenase activators

NAD⁺, CoA

anaplerotic reactions

reactions that replenish intermediates of citric acid cycle

cataplerotic reactions

reactions that use up intermediates of citric acid cycle

glyoxylate cycle

• use extra acetate as only carbon source rather than glucose/carbohydrates

• bypasses CO₂ producing steps of citric acid cycle to conserve carbon

• helps plants grow in the dark

all 20 amino acids

can be made from the intermediates of citric acid cycle

pyruvate carboxylase

• catalyzes reaction of pyruvate → oxaloacetate

• uses CO2 and ATP

• anaplerotic reaction

PEP (phosphoenolpyruvate) carboxylase

• catalyzes reaction of phosphoenolpyruvate (PEP) → oxaloacetate

• uses H2O, CO2 and releases P_i

• anaplerotic reactions

malic enzyme

• catalyzes reaction of pyruvate → L-malate

• uses NADPH + H⁺ + CO₂

• forms NADP⁺

• anaplerotic reaction

isocitrate lyase and malate synthase

short-circuiting enzymes of glyoxylate cycle

glyoxysomes and mitochondria

specialized organelles where glyoxylate cycle occurs

isocitrate lyase

• converts isocitrate → succinate (used for citric acid cycle in mitochondria) and glyoxylate

• glyoxylate cycle short-circuiting enzyme

malate synthase

uses glyoxylate and acetyl-CoA to from malate

acetate (from fatty acids)

seeds are a rich source of ______

lipids

many seeds like peanuts, soyabeans, castor beans are rich in ____

2

glyoxylate cycle consumes __ molecules of acetyl CoA per cycle

4

glyoxylate cycle produces ___ carbon units instead of 1 carbon units (CO2)