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Crystal - Res.ku - Edu Taksnotes Biol 638 Notes CHP 16
Crystal - Res.ku - Edu Taksnotes Biol 638 Notes CHP 16
Crystal - Res.ku - Edu Taksnotes Biol 638 Notes CHP 16
Chapter-16
Pyruvate
H3C C COO
CoASH + NAD+
pyruvate
dehydrogenase
CO2 + NADH
O
COO
HO CH
L-malate
CH2
COO7
H2O
H2O
COO
CoASH
COO-
cis-Aconitate
CH
COO-
CO2
COOIsocitrate
C O
C O
COO-
CH2
CH2
NAD
C O
COO-
CO2
-Ketoglutarate
CH2
H C COO
HO C H
COO-
CH2
H C COO
CoASH
COO-
H2O
COO
CH2
S CoA
Succinyl-CoA
NADH
+ H+
COOCH2
C COO
CH2
GDP + Pi
H2O
2
7. fumarase
8. malate
dehydrogenase
Succinate CH2
CH2
Citrate
4. -ketoglutarate
dehydrogenase
5. succinyl-CoA
synthetase
6. Succinate
dehydrogenase
GTP
CH2
HO C COO
CH2
COO-
3. isocitrate
dehydrogenase
COO-
COO-
CH2
COOOxaloacetate
1. citrate
synthase
2. aconitase
Fumarate CH
HC
FAD
CoA
COO-
FADH2
COO-
Oxalosuccinate
NAD+
NADH
+ H+
Takusagawas Note
Chapter-16
-
Pyruvate generated from glycolysis is converted to acetyl-CoA before entering the citric acid
cycle.
- At the initial reaction, acetyl group from acetyl-CoA and oxaloacetate react to form citrate.
- 3NADH, FADH2 and GTP are generated from one acetyl-CoA oxidation.
- 2CO2 are released from the portion of oxaloacetate.
- At the final reaction, oxaloacetate is regenerated.
- Overall reaction in the citric acid cycle is:
3NAD+ + FAD + GDP + Pi + acetyl-CoA 3NADH + FADH2 + GTP + CoA + 2CO2
From glucose:
Glucose + 2NAD+ + 2ADP + 2Pi 2pyruvate + 2NADH + 2ATP
2pyruvate + 2NAD+ + 2CoA 2acetyl-CoA + 2NADH + 2CO2
2acetyl-CoA + 6NAD+ + 2FAD + 2GDP + 2Pi 6NADH + 2FADH2 + 2GTP + 2CoA + 4CO2
2GTP + 2ADP 2ATP + 2GDP
.
Glucose + 10NAD+ + 4ADP + 4Pi + 2FAD 10NADH + 2FADH2 + 4ATP + 6CO2
30ATP + 4ATP + 4ATP = 38ATP
2. METABOLIC SOURCES OF ACETYL-COENZYME A
- Pyruvate is converted to acetyl-CoA before entering the citric acid cycle.
- The function of coenzyme A is a carrier of acetyl and other acyl group.
- Acetyl-CoA is a high-energy compound since it has a high energy S~C bond which
releases G = -31.5 kJ/mol by hydrolysis.
Acetyl group
O
S C CH 3
-mercaptoethylamine residue
CH2
CH2
NH
C O
Adenosine-3'phosphate
CH2
CH2
NH2
NH
Pantothenic
acid residue
C O
HO C H
H3C C CH3
H2C
P O P O CH2
O-
O-
OH
-
O P O
Acetyl-coenzyme A (acetyl-CoA)
Chapter-16
Takusagawas Note
The following coenzymes and prosthetic groups are required in pyruvate dehydrogenase
multienzyme complex:
- Thiamine pyrophosphate (TPP, Fig. 16-27) decarboxylase
Chapter-16
Takusagawas Note
Chapter-16
Takusagawas Note
Takusagawas Note
Chapter-16
B:
5. Reduced E3 is reoxidized by NAD+. Initially the enzymes sulfhydryl groups (-SH) are
reoxidized by the enzyme-bound FAD, yielding FADH2, then FADH2 is reoxidized by
NAD+, producing NADH.
Takusagawas Note
Chapter-16
14
O
O
HN
N
H
Lipollysyl arm
(fully extended)
Arsenic compounds are poisonous because they covalently bind to the vicinal (adjacent) dithiols
of dihydrolipoamide.
Chapter-16
Takusagawas Note
Insulin activates
Takusagawas Note
Chapter-16
H3C C
S CoA
Acetyl-CoA
H2O
O C COO
H2C
CoA-SH
H2C C O
-
HO C COO
-
H2C
COO
COO
Citrate
Oxaloacetate
G = -32.2 kJ/mol
Reaction mechanism
1. Asp-375 acts as a base to remove a proton from the methyl group of acetyl-CoA. His-274
acts as an acid to protonate the enolate oxygen.
2. Citryl-CoA is formed in a second concerted acid-base catalysis. His-320 acts as acid, and
His-274 acts as base.
3. Citryl-CoA is hydrolyzed to citrate and CoA. This hydrolysis (G = -31.5 kJ/mol) pulls
the reaction 1 and 2.
CoASH
3
H2O
Takusagawas Note
10
Chapter-16
B. Aconitase
- catalyzes the reversible isomerization of citrate and isocitrate.
-
H2C COO
Citrate
H 2O
H2C COO
H C COO
C COO
COO
H2C COO
HO C COO
H C
H 2O
COO
HO C
COO
H
cis-Aconitate
Isocitrate
G = 13.3 kJ/mol
Reaction mechanism
- Aconitase contains a covalently bound [4Fe-4S] iron-sulfur cluster, which is required for
catalytic activity. The Fea is coordinated by the hydroxyl and the central carboxyl groups.
1. His-101 acts as an acid to eliminate -OH as water, and Ser-642 acts as a base to eliminate a
proton from C2.
2. cis-Aconitate intermediate is flipped by 180 so that C2 and C3 are exchanged their
positions.
3. The reversed acid-base catalysis is taken place to yield (2R,3S)-isocitrate.
10
Takusagawas Note
11
Chapter-16
Less acidic
Less toxic
Very toxic
H2C COO
NAD
NADH + H
H2C COO
HO C
COO
CO2
COO
-Ketoglutarate
Isocitrate
CH2
H C COO
G = -20.9 kJ/mol
There are two isozymes in mammalian cells.
1. NAD+-dependent form is in mitochondria and requires an Mn2+ or Mg2+.
2. NADP+-dependent form is in both cytosol and mitochondria.
D. -Ketoglutarate dehydrogenase
- catalyzes the oxidative decarboxylation of an -keto acid, releasing CO2, forming succinylCoA and reducing NAD+ to NADH.
+
H2C COO CoA-SH NAD
NADH
CH2
C
H2C COO
CH2
COO
S-CoA
-Ketoglutarate
Succinyl-CoA
G = -33.5 kJ/mol
11
CO2
Takusagawas Note
12
Chapter-16
3. Succinyl-CoA formation.
E3
4. Oxidation of E2.
+
5. Reduction of NAD .
E. Succinyl-CoA synthetase
- hydrolyzes the high-energy compound succinyl-CoA with the coupled synthesis of a highenergy nucleosidetriphosphate (GTP).
H2C
COO-
CH2
GDP + Pi
GTP
COO
CoA-SH
CH2
C S-CoA
CH2
-
COO
Succinate
Succinyl-CoA
G = -2.9 kJ/mol
The succinyl~CoA thioester bond energy is preserved through the formation of a series of
high-energy phosphate (~Pi). The succinate formation is as follows:
Pi
Succinyl~CoA
1
GDP~Pi (GTP)
CoASH
Succinyl~Pi
2
3
E-His~Pi
E-His
GDP
Succinate
12
E-His
Takusagawas Note
13
Chapter-16
F. Succinate dehydrogenase
- catalyzes stereospecific dehydrogenation of succinate to fumarate and produces FADH2.
-
FADH2
FAD
COO
COO
C H
H C H
H C
H C H
COO
Fumarate
COO
Succinate
G = 0 kJ/mol
The FAD in succinate dehydrogenase is covalently bound to the enzyme. Thus, FADH2
cannot be oxidized as a cofactor. FADH2 is oxidized by the electron transport chain reaction
(See Chapter-17).
For the reason, succinate dehydrogenase is the only membrane-bound citric acid cycle
enzyme. The others are dissolved in the mitochondrial matrix.
The enzyme is strongly inhibited by malonate (structural analog of succinate).
-
COO
COO
H C H
H C H
H C H
COO
COO
Malonate
Succinate
FADH2
H C H
C H
H C H
H C
Alkane
Alkene
The oxidation of alkane to alkene produces G -42 kJ/mol, whereas the FAD to FADH2
reduction requires ~42 kJ/mol (FAD + 2H+ + 2e- FADH2, E = -0.219 V = (G = 42
kJ/mol)). Thus, the oxidation of alkane to alkene is just enough to reduce FAD to FADH2,
but not enough to reduce NAD+ to NADH + H+ (G = 61 kJ/mol).
The oxidation of alcohol to aldehyde (or ketone) produces more energy than the above case.
NAD
H C H
H C OH
Alcohol
NADH + H
H C H
C O
Aldehyde or ketone
13
Takusagawas Note
14
Chapter-16
G. Fumarase
- catalyzes the hydration of fumarates double bond to form L-malate.
-
COO
H2O
COO
C H
HO C H
H C
H C H
-
COO
COO
L-Malate
Fumarate
G = -3.8 kJ/mol
H. Malate dehydrogenase
- catalyzes the oxidation of L-malates hydroxyl group to ketone in a NAD+-dependent
reaction, regenerating oxaloacetate.
-
COO
NAD
NADH + H
COO
HO C H
C O
H C H
H C H
COO
COO
L-Malate
Oxaloacetate
G = 29.7 kJ/mol
This reaction is relatively high endergonic reaction (G > 0).
However, the following two reasons, this reaction occurs.
1. [Oxaloacetate] is very low at equilibrium, i.e., RTlnKeq becomes negative where
[oxaloacetate][ NADH] < 1, i.e., lnK < 0.
Keq =
eq
[ malate] NAD +
2. The subsequent reaction (formation of citrate from oxaloacetate and acetyl-CoA) that is
highly exergonic pulls this reaction since the hydrolysis of high-energy thioester bond
of acetyl-CoA releases G = -31.5 kJ/mol energy. This is a reason why acetyl-CoA
enters the citric acid cycle.
14
Chapter-16
15
Takusagawas Note
+
CoA S C CH3 + 3H2O
2CO2 + CoA SH + 8H + 8e
2. Reduction of three NAD+ to three NADH (3-electron pairs process) and equivalent to
9ATP generation, i.e., 3NAD+ + 6H+ + 6e- 3NADH + 3H+
3. Reduction of one FAD to FADH2 (1-electron pairs process) and equivalent to 2ATP
generation, i.e., FAD + 2H+ + 2e- FADH2
4. Generation of one GTP (ATP).
Four electron pairs generated by one acetyl group oxidation are carried by 3NADH and
FADH2 to the oxidative phosphorylation pathway to generate 11ATP.
Thus, citric acid cycle generates 12ATP from one acetyl group and sends 4-electron pairs (8
electrons) to electron-transport chain, where they reduce two molecules of O2 to 4H2O, i.e.,
2O2 + 8H+ + 8e- 4H2O.
15
Chapter-16
16
Takusagawas Note
G (kJ/mol)
Negative
~0
Negative
Negative
~0
~0
~0
~0
Unlike enzymes in glycolysis and glycogen metabolism, the citric acid cycle is largely
regulated by
1. substrate availability (rate of diffusion of substrate into mitochondria)
2. product inhibition. (NADH, ATP, citrate)
3. competitive feedback inhibition by intermediates further along the cycle.
16
Chapter-16
17
Takusagawas Note
17
Takusagawas Note
18
Chapter-16
Anabolism:
Amino acids
Sugars
Fatty acids, etc.
Catabolism:
Energy yielding
materials, such
as proteins
Proteins
Nucleic acids
Lipids, etc.
18
Chapter-16
-
19
Takusagawas Note
When the citric acid cycle intermediates are transported too much as precursors, the
concentration of oxaloacetate is very low. In this case, it is necessary to replenish citric acid
cycle intermediates. The main reaction is:
- Pyruvate + CO2 + ATP + H2O oxaloacetate + ADP + Pi
The citric acid cycle is truly at the center of metabolism
- Reduced products: NADH and FADH2 are reoxidized to produce ATP.
- The citric acid intermediates are utilized in the biosynthesis of many vital cellular constituents.
19