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Note Set 12 1

CITRIC ACID CYCLE (AKA TCA CYCLE, KREB'S CYCLE)

2nd pathway involved in the complete aerobic oxidation of to CO2 and H2O

Focus: 1. Conversion of pyruvate to acetylCoA

an obligatory step in the aerobic oxidation of glucose

2. The reactions of the TCA cycle

a catalytic process by which acetylCoA is degraded to CO2 and H2O with accompanying reduction of NAD+ to NADH

3. Regulation of the TCA cycle

4. Anabolic function of the TCA cycle

GENERAL CONSIDERATIONS 1. lactate formation from glucose has a DG°' = -47 kcal/mol; the complete oxidation of glucose to CO2 and H2O has a DG = -686 kcal/mol

•aerobic organisms trap this extra energy in the form of ATP

the yield of ATP is about 19 times greater than in

2. the aerobic oxidation of glucose involves 3 separate enzymatic pathways:

glycolysis

TCA cycle

terminal respiratory chain

3. the TCA cycle functions mainly to oxidize acetylCoA formed from pyruvate to CO2 and H2O

this oxidation process is coupled to the reduction of NAD+ to NADH

4. all the of the TCA cycle except one are located in the matrix compartment of the mitochondria

all except 1 are soluble

HISTORICAL BACKGROUND 1. main outline of the cycle was worked out in a relatively short period of time (1935- 1937) Note Set 12 2

2. a key finding by A. Szent-Gyorgi was that addition of malate or oxaloacetate to muscle homogenates catalyzes the uptake of oxygen in amounts greater than expected from the amount of acid added (acid = , ...etc)

•he postulated the following sequence:

succinate--->fumerate--->malate--->oxaloacetate

•during the same period Martius and Knoop showed the following reactions:

citrate--->a -ketoglutarate--->succinate

3. the complete cycle was detailed by Krebs:

•the key observations were:

stimulation of glucose oxidation by di- and tricarboxylic acids, eg: pyruvate, succinate, citrate

inhibition of oxidation of pyruvate by malonate, an inhibitor of succinate

formation of citrate from "a substance derived from pyruvate" and oxaloacetate

in a malonate poisoned system, the oxidation of pyruvate could be relieved by addition of large amounts of oxaloacetate

4. even though almost all the reactions of the TCA cycle were known by 1937, the mechanism by which pyruvate and oxaloacetate react to form citrate was not elucidated until 1950, mainly through the work of Reed

SYNTHESIS OF Acetyl CoA FROM OF PYRUVATE

oxaloacetate reacts with acetylCoA

formed by an oxidative decarboxylation of pyruvate

very important to TCA cycle, although not part of the cycle itself

1. Synthesis of adetyl CoA from pyruvate is catalyzed by the complex, a multiprotein complex

MW 7 x 107

2. overall reaction:

pyruvate + CoA + NAD+ ----->acetylCoA + CO2 + NADH + H+ Note Set 12 3

DG°' = -8 kcal/mol

3. components of the complex:

•24 units of pyruvate dehydrogenase (TPP coenzyme, TPP = pyrophosphate))

•24 units of dihydrolipoyl transacetylase

covalently bound

linked through a peptide bond with the e -amino group of a lys

•12 units of dihydrolipoyl dehydrogenase (NAD+ coenzyme)

•complex also contains 6 units of pyruvate dehydrogenase kinase and 2 units of phosphatase

catalyze the and dephosphorylation of a on pyruvate dehydrogenase (PDH)

important for regulation

4. regulation of the complex

•if [ATP] is high, and Mg++ is low, and NADH is high, the kinase phosphorylates the ser on PDH and the enzyme is inactivated

•if [ATP] is low, and Mg++ and Ca++ are present, the phosphatase removes the Pi from ser and this activates the enzyme

•Therefore:

When the intracellular pool of ATP/NADH is high, activity of the complex is suppressed

When the ATP pool is low, and Mg++ (and/or Ca++ ) are high, the complex is activated and pyruvate utilization is increased

Note that hormones can activate PDH by increasing Ca++ release into the and/or mitos

REACTIONS OF THE TCA CYCLE •cyclic process involving participation of 8 enzymes

•all localized in the mitochondria Note Set 12 4

with the exception of , which is membrane bound, remaining 7 enzymes are soluble proteins present in the matrix compartment of the mitos

•it is an autocatalytic process in which 2 C's of are put in and 2 C's are oxidized to 2 CO2's in one turn of the cycle

•there are 4 oxidation steps

•3 result in the reduction of NAD+ to NADH

•1 of FAD to FADH2

•there is one substrate level phosphorylation step resulting in the esterification of GDP and Pi

OVERALL REACTION:

CH3-C-SCoA + 3NAD+ + FAD + GDP + Pi + 2H2O -----> 2CO2 + CoA(SH) + 3NADH + 3H+ + FADH2 + GTP

DETAILED REACTIONS:

1. formation of citrate

•citrate (6C) is formed from oxaloacetate (4C) and acetyl CoA (2C)

•catalyzed by citrate (condensing enzyme)

•exergonic reaction

DG°' = - 7.7 kcal/mol

followed by a

•proceeds at expense of energy of hydrolysis of the thioester bond of acetyl CoA

•citryl CoA is formed as an intermediate

•rate of reaction depends on [acetyl CoA] and [oxaloacetate]

•inhibited by succinyl CoA and ATP

•important control step in the cycle

2 and 3. isomerization of citrate to form isocitrate Note Set 12 5

•catalyzed by

•iron-sulfer (nonheme iron protein)

•equilibrium mixture consists of 93% citrate and 7% isocitrate

•1st step is a dehydration

DG°' = + 2 kcal/mol

•2nd step is a hydration

DG°' = - 0.5 kcal/mol

•overall, an H and an OH switch positions

4. formation of a -ketoglutarate from isocitrate

•catalyzed by (NAD+ dependent)

•oxidative decarboxylation

DG°' = - 2 kcal/mol

•isocitrate is oxidized to oxalosuccinate

•NAD+ is reduced to NADH

•oxalosuccinate is decarboxylated to a -Ketogluterate (a -KG)

decarboxylation step requires Mg++

in the absence of divalent metal oxalosuccinate accumulates

•isocitrate dehydrogenase shows allosteric control with ADP

ADP activates

ATP and NADH inhibit

KM for isocitrate decreases as a function of increasing [ADP]

5. formation of succinyl CoA from a -ketoglutarate

•the 2nd oxidative decarboxylation

•catalyzed by the -ketoglutarate dehydrogenase complex Note Set 12 6

similar to the pyruvate dehydrogenase complex

mechanism is similar, but no kinase or phosphatase regulation

DG°' = - 7.2 kcal/mol

MW = 2.7 x 106

•consists of 3 enzymes

a -KG dehydrogenase (TPP)

dihydrolipoyl transsuccinylase (lipoic acid)

dihydrolipoyl dehydrogenase (FAD)

6. formation of succinate

•catalyzed by succinyl CoA synthetase

DG°' = - 0.8 kcal/mol

•substrate level phosphorylation

GDP is phosphorylated to GTP

only step that directly yields a high energy P bond

•energy of hydrolysis of the thioester bond (DG°' = -7.5 kcal/mol) is conserved in the form of the terminal P of GTP

•mechanism involves a phosphorylated enzyme intermediate (hisP)

7. succinate is oxidized to fumarate

•succinate dehydrogenase

DG°' » 0

•contains covalently bound FAD

FAD gets reduced to FADH2

DG°' not enough to reduce NAD+ because 2 Hs that are attached to Cs are removed…this requires a lot of energy

• contains iron-sulfer protein (will be discussed in connection with electron transport) Note Set 12 7

•membrane bound

8. fumarate is converted to L-malate

•by

DG = - 0.9 kcal/mol

•trans addition of water to fumarate yielding L-malate

9. oxaloacetate is regenerated by oxidation of L-malate

DG°' = + 7.1 kcal/mol

•NAD+ is reduced to NADH

•inhibited by oxaloacetate

•even though reaction is endergonic, products are rapidly removed and reaction proceeds in forward direction

REGULATION OF THE TCA CYCLE 1. Modulators of enzyme activity

•includes ADP, ATP NADH, citrate, succinyl CoA, metals, etc.

•most important is probably the relative concentration of ATP and ADP

at high ATP/ADP forward flux is inhibited

at low ATP/ADP forward flux is stimulated

•enzymes regulated by ATP and ADP:

Pyruvate Dehydrogenase Complex: phosphorylation by kinase to inactive form occurs at high ATP/ADP

Citrate synthase is inhibited by ATP

Isocitrate dehydrogenase is stimulated by ADP

2. Respiratory Control

•forward flux of cycle depends on availability of NAD+

•NAD+ depends on rate of reoxidation of NADH Note Set 12 8

•oxidation of NADH is under respiratory control

rate is high when ATP/ADP is low

•oxidation of succinate is also under respiratory control

ENERGETICS •ATP yield in aerobic utilization of glucose:

NADH ATP FADH2 glycolysis Glucose à 2 pyruvate 2 2 0

PDH complex 2 pyruvateà 2 acetyl CoA 2 0 0

TCA cycle 2 acetyl CoA à 4 CO2 6 2 GTP 2

•in the terminal respiratory chain:

the oxidation of each NADH is coupled to the synthesis of about 3 ATP

the oxidation of FADH2 is coupled to the synthesis of about 2 ATP

GTP can transfer its g to ADP to form ATP catalyzed by nucleoside diphosphate kinase

total ATP yield is thus about 38 ATP's formed/mol of glucose oxidized

•glucose à CO2 + H2O

DG°' = - 686 kcal/mol

net yield of ATP = about 38

•conservation of energy = 38 x 7.3 = 277 kcal/mol

•efficiency = 277/686 = 40%

ANAPLEROTIC REACTIONS

1. In addition to its catabolic function, TCA cycle also provides important intermediates in ()

•a number of amino acids are made from TCA cycle intermediates

2. Reactions that replenish TCA cycle intermediates:

reaction Note Set 12 9

oxaloacetate can be made from pyruvate

[oxaloacetate] is usually low because Keq of favors formation of citrate

if [oxaloacetate] gets too low, it is replenished by of pyruvate catalyzed by pyruvate carboxylase

pyruvate carboxylase is a biotin enzyme

pyruvate carboxylase is an allosteric enzyme that is stimulated by high [acetyl CoA]

•malic enzyme

pyruvate + CO2 + NADPH + H+ ----> L-malate + NADP+

GLYOXYLATE CYCLE

An anabolic variant of cycle

1. plant cells (and some ) can carry out net synthesis of from

•crucial to develpoment of seeds

energy stored as triacylglycerols

•vegetable oils we use: mixtures of triacylglycerols from seeds

•when seeds germinate, triacylglycerol broken down, converted to sugars

energy and raw material for growth

2. glyoxylate cycle allows net synthesis of carbohydrate from acetyl CoA

•2 main fates of acetyl CoA are oxidation thru TCA, and synthesis of fatty acids

•acetyl CoA cannot be converted to pyruvate

PDH complx reaction is irreversible

acetyl CoA can be converted to oxalo., but 2 C's lost as CO2 in process, so it is not net synthesis

3. glyoxylate cycle converts 2 acetyl units, as acetyl CoA, to succinate

•uses some TCA cycle enzymes Note Set 12 10

•bypasses 2 reactions where C is lost

IDH and a KGDH

•2nd mole of acetyl CoA brought in at bypass

•each turn of cycle brings in 2 2C units and results in net synthesis of 1 4C unit (succinate)

•succinate transported to mito where it is converted to oxaloactate via TCA

•acetate can be used as C source via glyoxylate cycle:

1st converted to acetyl CoA by acetate thiokinase

acetate + CoA-SH + ATP ----> acetyl CoA + AMP + PPi

4. glyoxylate cycle and also some of the b oxidation of FAs (fatty acids) takes place in glyoxysomes

b oxidation generates the acetyl CoA for glyoxylate cycle

5. reactions:

•acetyl CoA à isocitrate as in TCA

enzymes are isozymes of TCA enzymes, specialized for glyoxylate cycle

then:

•isocitrate cleaved to succinate and glyoxylate by

succ goes to TCA in mitos

•glyoxylate accepts acetate from another acetyl CoA to form malate: catalyzed by

•malate then to oxaloactate for another turn by isozyme of malate dehydrogenase PENTOSE PHOSPHATE PATHWAY

1. an alternative pathway for carbohydrate oxidation

•also called hexose monophosphate shunt

•operates to varying extents in different cells and tissues Note Set 12 11

-primarily anabolic

-under some conditions can oxidize glucose completely to CO2

2. 2 primary functions:

•to provide NADPH for reductive biosynthesis

•to provide -5-P for and nucleic acid biosyn.

•additional function:

-metabolizes dietary pentose sugars from digestion of nucleic acids

3. NADPH

•same as NADH, but w/ 2' P on one of the ribose groups

•metabolically different:

-NAD+/NADH pair function w/enzymes that oxidize substrates

-NADP+/NADPH pair function with enzxymes that reduce substrates

•use: for example, for and biosynthesis

-adrenal gland, , adipose , mammary gland have high PP pathway activity

-also is ultimate e- source for reduction of ribonucleotides to deoxyribonuccleotides, so rapidly growing tissue has high PP pathway enzymes

4. PP pathway located in

A. Oxidative Phase

•generation of reducing power as NADPH

1. conversion of glucose-6-P to ribulose-5-P Note Set 12 12

-1st and 3rd are oxidative reactions

•1st: glucose-6-P dehydrogenase

glu 6-P to 6-phosphogluconolactone

•converted to 6-phosphogluconate by lactonase

•converted to ribulose-5-P by 6-phosphogluconate dehydrogenase

CO2 lost

2. net result:

•2 mol of NADPH

•1 mol pentose phosphate

•lose 1 CO2

B. Nonoxidative Phase

•fates of pentose tailored to metabolic needs

1. next ribulose-5-P converted to ribose-5-P by phosphopentose isomerase

•enediol intermediate

-like triose-P isomerase and phosphoglucoisomerase

•primary functions of pathway now fullfilled

NADPH and ribose-5-P

2. balanced equation for pathway so far: glucose-6-P + 2NADP+ à ribose-5-P + CO2 + 2NADPH + 2H+ Note Set 12 13

3. many cells need the NADPH, but don't need all the ribose-5-P

•so there are ways to catabolize the extra ribose-5-P in a series of sugar phosphate transformations

•net result:

3 5C sugar-P's converted to 2 6C sugar-P's and 1 3C sugar-P

-the 3C sugar-P is glyceraldehyde-3-P and it enters glycolysis

-the hexoses can be catabolized either by recycling through the PP pathway or entering glycolysis

4. 3 enzymes involved in conversions: phosphopentose epimerase (PPE) transketolase (TK) transaldolase (TA)

•PPE converts ribulose-5-P to xylulose-5-P (its epimer)

•x-5-P reacts w/ ribose-5-P to form glyceraldehyde-3-P and 7C sugar-P sedoheptulose-7-P

-E is TK

-now must get rid of sed-7-P

•sed-7-P + glycer-3-P form -6-P + erythrose-4-P

-E is TA

-net so far: 2 5C-sugarPs converted to 1 6C and 1 4C Note Set 12 14

-now get rid of erythrose:

•x-5-P + erythrose-4-P form glyceraldehyde-3-P and fructose-6-P

-E is TK

•so far, input of 3 pentose P's required: 2 in 1st TK reaction, 1 in 2nd TK reaction

•so considering these 3 pass through oxidative phase, pathway to this point is:

-oxidative phase:

3 glucose-6-P + 6NADP+ à 3 pentose-5-P + 6NADPH + 6H+ + 3CO2

-plus rearrangement of nonoxidative phase:

3 pentose-5-P ••> 2 F-6-P + G-3-P

-overall:

3 glucose-6-P + 6NADP+ ••> 2 F-6-P + G-3-P3 + 6NADPH + 6H+ + 3CO2

•alternatively, can write equation for complete oxidation of 1 mol of hexose to CO2

6 hexose-6-P + 12NADP à 5 hexose-6-P + 6CO2 + 12NADPH + 12H+

C. fate of sugarP's depends on metabolic needs of cell

1. nucleotide biosynthesis needed: ribose-5-P and NADPH generated

2. NADPH needed for other reductive biosynthesis, don't need :

G-3-P and F-6-P converted back to glu-6-P for reentry into PP pathway so more NADPH can be made

3. Energy needed along with the NADPH: Note Set 12 15

F-6-P and G-3-P go thru glycolysis and TCA

•completely oxidized to CO2 and H2O

•ATP generated

4. unlikely that any one of these modes operates exclusively in any one cell

•each cell has multiple metabolic needs

D. human genetic disorders involving PP pathway enzymes

1. deficiency of glucose-6-P dehydrogenase

•causes hemolytic anemia (massive destruction of red cells) when person under (peroxides generated)

•peroxides normally inactivated via reduction by ()

•also, Hb Fe kept in Fe+2 state by glutathione

•glutathione made frm cys, gly and g glu

•oxidized glutathione is reduced by glutathione reductase

-requires NADPH

•PP pathway only source of NADPH in red cell

•mutant E abt 10% activity of wt

-OK until lots of peroxides show up

-then methemoglobin accumulates, changes structure of cell, membrane weakens, cells rupture

*antimalarial Note Set 12 16

2. Wernicke-Korsakoff syndrome

•mental disorder and loss of memory and partial paralysis

-from thiamine def. in affected people

•TK has 10 fold lower affinity for thiamine

-other TPP E's not affected

3. both diseases illustrate interplay between genetics and environment in onset of disease

•symptoms become apparent only after some kind of moderate stress that does not affect normal individuals