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OrganicOrganicChemistryChemistry
William H. Brown & William H. Brown & Christopher S. FooteChristopher S. Foote
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The OrganicThe OrganicChemistry ofChemistry ofMetabolismMetabolism
Chapter 29Chapter 29
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IntroductionIntroduction We have now studied the typical reactions of the
major classes of organic compounds, and the structure and reactions of carbohydrates and lipids
Now let us apply this background to the study of the organic chemistry of metabolism
We study two key metabolic pathways• -oxidation of fatty acids• glycolysis
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Five Key ParticipantsFive Key Participants Five of the compounds participating in these and
a great many other metabolic pathways:• ATPATP, ADPADP, and AMPAMP are universal carriers of
phosphate groups
• NADNAD++/NADH/NADH and FAD/FADHFAD/FADH22 are coenzymes involved in the oxidation/reduction of metabolic intermediates
Coenzyme:Coenzyme: a low-molecular weight, nonprotein molecule or ion that binds reversibly to an enzyme, functions as a second substrate, and is regenerated by further reaction
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Adenosine TriphosphateAdenosine Triphosphate ATP is the most important compound involved in
the transfer of phosphate groups
-N-glycosidic bondHH
HO
-O-P-O-P-O-P-O-CH2
HO OH
N
N
N
N
NH2
phosphoric anhydridegroups
phosphoricester group
β-D-ribofuranose
adenine
O- O- O-
H
O O O
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Adenosine TriphosphateAdenosine Triphosphate• hydrolysis of the terminal phosphate of ATP gives
ADP and phosphate• in glycolysis, the phosphate acceptors are -OH groups
of glucose and fructose
-O-P-O-P-O-AMP H2O -O-P-O-AMP H2PO4-
O
O--O
O
-O
O+ +
ADPATP Water(a phosphate acceptor)
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Nicotinamide adenine dinucleotideNicotinamide adenine dinucleotide• a biological oxidizing agent
HH
HO
O=P-O-CH2
HO OH
N
N
N
N
NH2
HH
HO
-O-P-O-CH2
HO OH
N
CNH2
O
O
O-
O
H
H
+
a -N-glycosidic bond
nicotinamide,
adenine
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NADNAD++/NADH/NADH NAD+ is a two-electron oxidizing agent, and is
reduced to NADH
Ad
N
CNH2
+
+H+ + 2e-
Ad
N
CNH2
H H
NAD+
(oxidized form)NADH
(reduced form)
O O
:
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NADNAD++/NADH/NADH• NAD+ is involved in a variety of enzyme-catalyzed
oxidation/reduction reactions; we deal with two of these in this chapter
C
OH
H
C
O
+ 2H+ 2e-
A secondary alcohol
A ketone
C H
O
+ H2O C OH
O
2H+ 2e-
An aldehyde A carboxylic acid
+
+ +
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NADNAD++/NADH/NADH
C
O
H
H
N
C-NH2
Ad
H
enzyme- B
NAD+ NADH
N
C-NH2
Ad
H H
C
OH
enzymeB
+
reduction
oxidation
:
:
:
OO
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FAD/FADHFAD/FADH22
HH
H
H
OO=P-O-P-O-CH2
HO OH
N
N
N
N
NH2CH2
O
N
N
N
NH3C
H3C O
HO
HHOHH
OHH
OHH
O- O-
O
ribitol
flavin
adenine
adenosine
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FAD/FADHFAD/FADH22 FAD participates in several types of enzyme-
catalyzed oxidation/reduction reactions• our concern is its participation in the oxidation of a C-
C bond in a fatty acid hydrocarbon chain to a C=C bond as shown in these balanced half-reactions
-CH2-CH2- -CH=CH- + 2H+ + 2e-
FAD+ 2H+ + 2e- FADH2
Oxidation of the hydrocarbon chain:
Reduction of FAD:
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FAD oxidation of C-CFAD oxidation of C-C
Ad
N
N
N
NH3C
H3C O
HO
Ad
N
N
N
NH3C
H3C O
HOH
H
Enz B - Enz BH
EnzBH Enz- B
C C
H
H
R1
HR2
HC C
R1HR2 H
:
:
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Fatty Acids and EnergyFatty Acids and Energy Fatty acids in triglycerides are the principle
storage form of energy for most organisms• carbon chains are in a highly reduced form• the energy yield per gram of fatty acid oxidized is
greater than that per gram of carbohydrate
C6H12O6 + 6O2
CH3(CH2)14COOH + 23O2
6CO2 + 6H2O
16CO2 + 16H2O
(kJ/mol)(kJ/g)
-2870 -15.9
-38.9
Palmitic acid
Glucose
Yield of Energy
-9791
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Oxidation of Fatty AcidsOxidation of Fatty Acids There are two major stages in the oxidation of
fatty acids• activation of the free fatty acid in the cytoplasm and its
transport across the inner mitochondrial membrane• -oxidation
-Oxidation:-Oxidation: a series of four enzyme-catalyzed reactions that cleaves carbon atoms two at a time, from the carboxyl end of a fatty acids
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Activation of Fatty AcidsActivation of Fatty Acids• activation begins in the cytoplasm with formation of a
thioester between the carboxyl group of the fatty acid and the sulfhydryl group of coenzyme A
• formation of the acyl-CoA derivative is coupled with the hydrolysis of ATP to AMP and pyrophosphate
R-C-O-O
+ HS-CoA
AMP + P2O74-ATP
R-C-S-CoA
O
Coenzyme AFatty acid(as anion)
+An acyl-CoAderivative
OH-
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-Oxidation-Oxidation• Reaction 1:Reaction 1: stereospecific oxidation of a carbon-
carbon single bond to the carbonyl group
• Reaction 2:Reaction 2: regiospecific and stereospecific hydration of the carbon-carbon double bond; only the R-enantiomer is formed
R-CH2-CH2-C-SCoA
An acyl-CoA
+FAD
H
C CC-SCoA
R H
+ FADH2
A trans-enoyl-CoA
OO
+ H2O
(R)-- -Hydroxyacyl CoA
C
OH
CH2 -C-SCoAHR
OH
C CC-SCoA
R H A t -rans -enoyl CoA
O
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-Oxidation-Oxidation• Reaction 3:Reaction 3: oxidation of the -hydroxyl group
• Reaction 4:Reaction 4: cleavage of the carbon chain by a reverse Claisen condensation
(R)-- -Hydroxyacyl CoA
C
OH
CH2-C-SCoAHR
O
+ NAD+ R-C-CH2-C-SCoA
β-Ketoacyl-CoA
+ NADH
O O
+ CoA-SH
Coenzyme A
R-C-SCoA + CH3C-SCoA
An acyl-CoA Acetyl-CoA
O OR-C-CH2-C-SCoA
-Keto -acyl CoA
O O
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-Oxidation-Oxidation• mechanism of the reverse Claisen condensation
R-C-CH2-C-SCoA
CH2=C-SCoA
Enolate anion of acetyl-CoA
-S-Enz
R-C-CH2-C-SCoA
Tetrahedral carbonyladdition intermediate
R-C-S-Enz +An enzyme- thioester
O O
S-Enz
O-
O-
O
O
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-Oxidation-Oxidation• this series of reactions is then repeated on the
shortened fatty acyl chain and continues until the entire fatty acid chain is degraded to acetyl-CoA
CH3(CH2)14COH
Hexadecanoic acid (Palmitic acid)
+8CoA-SH
7NAD+
7FAD
AMP + P2O74-ATP
8CH3CSCoA +7NADH
7FADH2Acetyl coenzyme A
O
O
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GlycolysisGlycolysis Glycolysis:Glycolysis: from the Greek, glyko, sweet, and lysis, splitting• a series of 10 enzyme-catalyzed reactions by which
glucose is oxidized to two molecules of pyruvate
C6H12O6 2CH3CCOO- 6H+
Glucose
glycolysis
ten enzyme-catalyzed stepsPyruvate
+O
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Glycolysis - Rexn 1Glycolysis - Rexn 1• phosphorylation of -D-glucose
OH
OH
HOHO
CH2OHO
+ -O-P-O-P-O-AMP
-D-Glucose
hexokinase
Mg2+
OH
OH
HOHO
CH2OPO32-
O
+ -O-P-O-AMP
α-D-Glucose 6-phosphate
O-
O
O-
O
O-
O
ATP
ADP
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Glycolysis - Rexn 2Glycolysis - Rexn 2• isomerization of glucose 6-phosphate to fructose 6-
phosphate
HHO
CH2OPO32-
CH2OHO
OHH
HHO
O
OHOH
HOHO
CH2OPO32-
-D-Glucose 6-phosphate
phosphogluco-isomerase
12
6
2
(α)
1
α-D-Fructose 6-phosphate
6
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Glycolysis - Rexn 2Glycolysis - Rexn 2• this isomerization is most easily seen by considering
the open-chain forms of each monosaccharide
Fructose 6-phosphate(a 2-ketohexose phosphate)
Glucose 6-phosphate(an aldohexose phosphate)
An enediol
CHO
CH2OPO32-
OHH
HHO
OHH
OHH
C
C
CH2OPO32-
OH
HHO
OHH
OHH
H OH CH2OH
C
CH2OPO32-
O
HHO
OHH
OHH
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Glycolysis - Rexn 3Glycolysis - Rexn 3• phosphorylation of fructose 6-phosphate
Fructose 6-phosphate
+ ATP
phospho-fructokinase
Mg2+ + ADP
Fructose 1,6-bisphosphate
CH2OPO32-
C
CH2OPO32-
O
HHOOHH
OHH
CH2OH
C
CH2OPO32-
O
HHOOHH
OHH
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Glycolysis - Rexn 4Glycolysis - Rexn 4• cleavage of fructose 6-phosphate to two triose
phosphates
Fructose 1,6-bisphosphate
CH2OPO32-
C
CH2OPO32-
O
HHOOHH
OHH
aldolase
C=O
CH2OPO32-
CH2OPO32-
CH2OH
C
C=O
H OH
HGlyceraldehyde3-phosphate
Dihydroxyacetonephosphate
+
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Glycolysis - Rexn 4Glycolysis - Rexn 4• reaction 4 is a reverse aldol reaction• a key intermediate is an imine formed by the C=O
group of fructose 1,6-bisphosphate and an -NH2 group of the enzyme catalyzing this reaction
B-
H
C=NH
CH2OPO32-
O
CH2OPO32-
OH
HHOH3N Enz B-
Enz
(-H2O)
Protonated imine
HH
Fructose 1,6-bisphosphate
CH2OPO32-
C
CH2OPO32-
OHHOOHH
OHH
++
+
::
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Glycolysis - Rexn 4Glycolysis - Rexn 4• reverse aldol reaction gives two three-carbon
fragments, one as an imine
H
C=NH
CH2OPO32-
O
CH2OPO32-
OH
HHO
B-
Enz
Protonated imine
HH
+ C-NH
CH2OPO32-
CH2OPO32-
CHOH
C
C=O
H OH
H
B
Enz
H
Glyceraldehyde 3-phosphate
(enzyme-catalyzedreverse aldol
reaction) +
:
:
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Glycolysis - Rexn 4Glycolysis - Rexn 4• hydrolysis of the imine gives dihydroxyacetone
phosphate and regenerates the -NH2 group of the enzyme
:
C=NH
CH2OPO32-
CH2OH
Enz+ +H2O
C=O
CH2OPO32-
CH2OH B-
H3N Enz+
Protonated imine Dihydroxyacetone phosphate
B-
C-NH
CH2OPO32-
CHOH B
Enz
H
:
:
+
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Glycolysis - Rexn 5Glycolysis - Rexn 5• isomerization of triose phosphates
C=O
CH2OH
CH2OPO32-
C-OHCHOH
CH2OPO32- CH2OPO3
2-
C
CHO
H OH
Glyceraldehyde3-phosphate
Dihydroxyacetonephosphate
An enediolintermediate
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Glycolysis - Rexn 6 Glycolysis - Rexn 6 • oxidation of the -CHO group of glyceraldehyde 3-
phosphate• the -CHO group is oxidized to a carboxyl group• which is in turn converted to a carboxylic-phosphoric
mixed anhydride• the oxidizing agent is NAD+, which is reduced to NADH
G-C-H
O
+ H2O G-C-OH
O
2H+ 2e-
NAD+ H+ 2e- NADH
A two-electron oxidation
A two-electron reduction
++
++
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Glycolysis - Rexn 6Glycolysis - Rexn 6We divide this reaction into three stages
• stage 1: formation of a thiohemiacetal
• stage 2: oxidation of the thiohemiacetal by NAD+
G-C-H HS-Enz G-C-S-Enz
A thiohemiacetalH
OHO
+
G-C-S-Enz
OH
N
CNH2
Ad+
G-C-S-Enz
N
CNH2
Ad
H H
an enzyme-bound thioester
O O
O
H
:
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Glycolysis - Rexn 6 Glycolysis - Rexn 6 • stage 3: conversion of the thioester to a mixed
anhydride
G-C-S-Enz
O
+ - O-P-OH G-C-O-P-OH
O-
Enz-S
G-C-O-P-OHO
+ Enz-S -
1,3-Bisphosphoglycerate (a mixed anhydride)
:
:
:
O-
O
O-
O
O-
O
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Glycolysis - Rexn 7Glycolysis - Rexn 7• transfer of a phosphate group from 1,3-
bisphosphoglycerate to ADP
CH2OPO32-
C
C-OPO32-
OHH
O
O-O-P-O-AMP
ADP
Mg2+
CH2OPO32-
C
COO-
OHH
ATP
O-
-O-P-O-P-O-AMPO-
O
O-
O+
3-Phosphoglycerate
+
1,3-Bisphospho- glycerate
phospho-glycerate kinase
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Glycolysis - Rexn 8Glycolysis - Rexn 8• isomerization of 3-phosphoglycerate to 2-
phosphoglycerate
C
CH2OPO32-
COO-
OHH
3-Phosphoglycerate
C
CH2OH
COO-
OPO32-H
2-Phosphoglycerate
phosphoglycerate mutase
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Glycolysis - Rexn 9Glycolysis - Rexn 9 dehydration of 2-phosphoglycerate
C
CH2OH
COO-
OPO32-H
2-Phosphoglycerate
C
CH2
COO-
OPO32-
Phosphoenolpyruvate
+ H2OenolaseMg2+
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Glycolysis - Rexn 10Glycolysis - Rexn 10• phosphate transfer to ADP
C
COO-
OPO32-
Phosphoenol- pyruvate
C-OH
CH2
COO-
Enol of pyruvate
C=O
CH3
COO-
Pyruvate
pyruvate kinaseMg2+
ATPADPCH2
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GlycolysisGlycolysis• Summing these 10 reactions gives the net equation for
glycolysis
C6H12O6 + 2NAD+ + 2HPO42- + 2ADP
Glucose
glycolysis
2CH3CCOO-
Pyruvate
+ 2NADH + 2ATP + 2H2O
O
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Fates of PyruvateFates of Pyruvate Pyruvate does not accumulate in cells, but rather
undergoes one of three enzyme-catalyzed reactions, depending of the type of cell and its state of oxygenation• reduction to lactate• reduction to ethanol• oxidation and decarboxylation to acetyl-CoA
A key to understanding the biochemical logic behind two of these fates is to recognize that glycolysis needs a continuing supply of NAD+
• if no oxygen is present to reoxidize NADH to NAD+, then another way must be found to do it
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Lactate FermentationLactate Fermentation• in vertebrates under anaerobic conditions, the most
important pathway for the regeneration of NAD+ is reduction of pyruvate to lactate
CH3CCOO-O
+ NADH +H3O+
CH3CHCOO-
OH
+ NAD+ + H2O
Pyruvate
Lactate
lactatedehydrogenase
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Pyruvate to LactatePyruvate to Lactate• while lactate fermentation does allow glycolysis to
continue, it increases the concentration of lactate and also of H+ in muscle tissue, as seen in this balanced half-reaction
• when blood lactate reaches about 0.4 mg/100 mL, muscle tissue becomes almost completely exhausted
C6H12O6 + 2H2O 2CH3CHCOO-
OH
+ 2H3O+
Glucose Lactate
lactatefermentation
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Pyruvate to EthanolPyruvate to Ethanol Yeasts and several other organisms regenerate
NAD+ by this two step pathway• decarboxylation of pyruvate to acetaldehyde
• reduction of acetaldehyde to ethanol
Pyruvate
CH3CH + CO2
Acetaldehyde
pyruvatedecarboxylase
CH3CCO2- + H+
O O
CH3CH + NADH + H+
Acetaldehyde
alcoholdehydrogenase
CH3CH2OH + NAD+
Ethanol
O
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Pyruvate to Acetyl-CoAPyruvate to Acetyl-CoA Under aerobic conditions pyruvate undergoes
oxidative decarboxylation• the carboxylate group is converted to CO2
• the remaining two carbons are converted to the acetyl group of acetyl-CoA
CH3CCOO-O
NAD+ CoASH
CH3CSCoAO
CO2 NADH
Pyruvate
Acetyl-CoA
oxidativedecarboxylation+ +
+ +
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Pyruvate to Acetyl-CoAPyruvate to Acetyl-CoA Oxidative decarboxylation of pyruvate to acetyl-
CoA is considerably more complex than the previous equation suggests
In addition to NAD+ (from the vitamin niacin) and coenzyme A (from the vitamin pantothenic acid), it also requires• FAD (from the vitamin riboflavin)• pyridoxal phosphate (from the vitamin pyridoxine)• lipoic acid
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Pyruvate to Acetyl-CoAPyruvate to Acetyl-CoA
S S
COO-H
N
NH2
N S
O-P-O-P-O-
O
NO-
O
O-
Lipoic acid(as the carboxylate anion)Thiamine pyrophosphate
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Prob 29.21Prob 29.21Describe the type of reaction involved in this biochemical synthesis of -hydroxybutyrate.
2CH3CSCoA
OCoA-SH
Acetyl-CoA Acetoacetyl-CoA
CH3CSCoA
O
CoA-SH
1 2SCoA
O O
CH3CSCoA
O
Acetoacetate
CO2
-HydroxybutyrateNAD +
NADH
3
4
5
Acetone
( )-3- -3-S Hydroxy-methylglutaryl CoA
H+
O-
O O
O-
OH O
O
SCoA
OOH3COH
-O
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The OrganicThe Organic
Chemistry ofChemistry of
MetabolismMetabolismEnd Chapter 29End Chapter 29
