Introduction to Organic Chemistry 2 ed William H. Brown

2020

20-1Copyright © 2000 by John Wiley & Sons, Inc. All rights reserved.

Introduction to Introduction to Organic Organic

ChemistryChemistry2 ed2 ed

William H. BrownWilliam H. Brown

2020


The OrganicThe OrganicChemistry ofChemistry ofMetabolismMetabolism

Chapter 20Chapter 20

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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

• We now apply this background to the study of the organic chemistry of metabolism• -oxidation of fatty acids• glycolysis

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Five Key ParticipantsFive Key Participants• Five compounds participating in these and a

great many other metabolic pathways are:• ATPATP, ADPADP, and AMPAMP are universal carriers of

phosphate groups

• NADNAD++/NADH /NADH and FAD/FADHFAD/FADH22 are coenzymes involved in oxidation/reduction of metabolic intermediates

• CoenzymeCoenzyme: a low-MW, 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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Adenoside TriphosphateAdenoside Triphosphate• ATP is the most important of the compounds

involved in the transfer of phosphate groups

a - - N glycosidebondHHHOHOOHNNNNNH2 phosphoricanhydridegroups

phosphoric ester group- -D ribofuranoseAdenine

Adenosine-O-P-O-P-O-P-O-CH2OO-OO-OO- H

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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-AMPOO-O-O +H2O-O-P-O-AMPOO- +H2PO4-Adenosine diphosphate(ADP)

Adenosine triphosphate(ATP)Phosphateacceptor

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NADNAD++/NADH/NADH• Nicotinamide adenine dinucleotide (NAD+) is a

biological oxidizing agent

a - - N glycosidebondHHHOHOOHNCNH2O+ +The plus sign on NAD represents the positive charge on this nitrogen, Nicotinamidederived ; from niacin-O-P-O-CH2OOAMPH

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NADNAD++/NADH/NADH• NAD+ is a two-electron oxidizing agent, and is reduced

to NADH

AdNCNH2O++H++2e- AdN

CNH2OHHNAD+(oxidized form)NADH(reduced form)

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NADNAD++/NADH/NADH• we will discuss two types of oxidations involving NAD+COHH CO+2H+2e-A secondary alcoholA ketoneCHO+H2OCOHO2H+2e-An aldehydeA carboxylic acid

+++

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Oxidation by NADOxidation by NAD++

NCNH2OAd+NAD+ NCNH2OAdreductionoxidationHHNADH

An electron pair is added to nitrogenCOH COHHE- B HEB

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FAD/FADHFAD/FADH22

• Flavin adenine dinucleotide (FAD) is also a biological oxidizing agent

RiboflavinO=P-O-AMPO-CH2COCCCH2NHOHOHOHHHNNNH3CH3C OHO

RibitolFlavin

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FAD/FADHFAD/FADH22• we discuss one type of oxidation involving FAD,

namely oxidation of the hydrocarbon chain of a fatty acid -CH2-CH2- -CH=CH-+2H++2e-FAD+2H++2e- FADH2Oxidation of the hydrocarbon chain:Reduction of FAD:

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Oxidation by FADOxidation by FAD

AdNNNNH3CH3C OHOEB -

EBHCCHHR1HR2 Hthe hydrocarbonchain of the fatty acid

FAD

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Oxidation by FADOxidation by FAD

AdNNNNH3CH3C OHOHHFADH2

EBHE- B

CCR1HR2 HA trans carbon-carbon double bond

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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 + 6O2CH3(CH2)14CO2H + 23O26CO2 + 6H2O16CO2 + 16H2O -3.8 -9.3 Palmitic acidGlucoseEnergy (kcal/g)

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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• Begins in the cytoplasm with formation of a

thioester• formation of the thioester is coupled with the

hydrolysis of ATP to AMP and pyrophosphate R-C-O-O+HS-CoAAMP + P2O74-ATPR-C-S-CoAOOH-Coenzyme AFatty acid(as anion)+An acyl-CoAderivative

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Activation of Fatty AcidsActivation of Fatty Acids• activation involves reaction with ATP

-O-P-O-P-O-OOO-O-intermediate with one phosphorus bonded to five groupsR-C-O-P-O-AdOOO- +PyrophosphateAn acyl-AMP(a mixed anhydride)

Ad-O-P-O-P-O-P-O-OOO-O- OO-R-C-O-OFatty acid(as anion)+ATP

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Activation of Fatty AcidsActivation of Fatty Acids• and then reaction with coenzyme ACoA-SH

R-C-S-CoAOCoenzyme AAn acyl-CoA

R-C-O-P-O-AdOOO-An acyl-AMP+ tetrahedral carbonyl additionintermediate-O-P-O-AdOO-+AMP

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-Oxidation-Oxidation• Reaction 1: oxidation of a carbon-carbon single bond

to a carbon-carbon double bondR-CH2-CH2-C-SCoAOAn acyl-CoA+FADOHCCC-SCoARH+FADH2A trans-enoyl-CoAα

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-Oxidation-Oxidation• Reaction 2: hydration of the carbon-carbon double

bond; only the R-enantiomer is formedOHCCC-SCoARH+H2OA trans-enoyl-CoA(R)-- -Hydroxyacyl CoACOHCH2-C-SCoAHRO

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-Oxidation-Oxidation• Reaction 3: oxidation of the -hydroxyl group to a

carbonyl group

(R)-- -Hydroxyacyl CoACOHCH2-C-SCoAHRO+NAD+R-C-CH2-C-SCoAO-Keto-acyl CoAO +NADH

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-Oxidation-Oxidation• Reaction 4: cleavage of the carbon chain by a reverse

Claisen condensationR-C-CH2-C-SCoAO-Keto-acyl CoAO +CoA-SH Coenzyme AR-C-SCoAOO+CH3C-SCoA -An acyl CoA-Acetyl CoA

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-Oxidation-Oxidation• mechanism of the reverse Claisen condensationR-C-CH2-C-SCoAOO

CH2=C-SCoAEnolate anion ofacetyl-CoA- S-Enz R-C-CH2-C-SCoAOS-EnzO- Tetrahedral carbonyladdition intermediateR-C-S-EnzO+An enzymethioesterO-

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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)14COHOHexadecanoic acid(Palmitic acid)+8CoA-SH7NAD+7FADAMP + P2O74-ATP

8CH3CSCoA+7NADH7FADH2OAcetyl coenzyme A

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GlycolysisGlycolysis• GlycolysisGlycolysis: a series of 10 enzyme-catalyzed

reactions by which glucose is oxidized to two molecules of pyruvate

• glycolysis is a 4-electron oxidation; it occurs in two separate 2-electron oxidation steps

C6H12O6Glucoseglycolysis ten enzyme-catalyzed steps2CH3CCO2-OPyruvate+2H+C6H12O6Glucoseglycolysis2CH3CCO2- + 6H+ + 4e-OPyruvate

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Glycolysis - Rexn 1Glycolysis - Rexn 1• Reaction 1: phosphorylation of α-D-glucose

OHOHHOHOCH2OHO+-O-P-O-P-O-AMPOO-O-Oα- -D GlucosehexokinaseMg2+OHOHHOHOCH2OPO32-OATP+-O-P-O-AMPOO-ADPα- - 6-D Glucose phosphate

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Glycolysis - Rexn 2Glycolysis - Rexn 2• Reaction 2: isomerization of glucose 6-

phosphate to fructose 6-phosphate

21HOCH2OPO32-CH2OHOOH (α)HHHO

OOHOHHOHOCH2OPO32-

α- - 6-D Glucose phosphateα- - 6-D Fructose phosphate

-phosphogluco isomerase6126

H

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Glycolysis - Rexn 2Glycolysis - Rexn 2• this isomerization is most easily seen by considering

the open-chain forms of each monosaccharide • it is one keto-enol tautomerism followed by another

Fructose 6-phosphateGlucose 6-phosphate(An enediol)21 12CHOCH2OPO32-OHHHHOOHHOHH

CCH2OPO32-OHHHOOHHOHHCHOHC

CH2OPO32-OHHOOHHOHHCH2OH

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Glycolysis - Rexn 3Glycolysis - Rexn 3• Reaction 3: phosphorylation of fructose 6-

phosphate

Fructose 6-phosphateCCH2OPO32-OHHOOHHOHHCH2OH

+ATP phospho-fructokinaseMg2+ Fructose 1,6-bisphosphateCCH2OPO32-OHHOOHHOHHCH2OPO32-

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Glycolysis - Rexn 4Glycolysis - Rexn 4• Reaction 4: cleavage of fructose 1,6-

bisphosphate to two triose phosphates

HC=OCH2OPO32-HOHCH2OPO32-OHHHO aldolaseC=O

CH2OPO32-CH2OPO32-

Fructose 1,6-bisphosphateCH2OHCC=OHOHHGlyceraldehyde3-phosphate

Dihydroxyacetonephosphate+a -hydroxylgroup

a carbonylgroup

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Glycolysis - Rexn 4Glycolysis - Rexn 4• reaction 4 is a reverse aldol reaction• an 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

HC=OCH2OPO32-HO-HCH2OPO32-OHHHO

Fructose 1,6-bisphosphate+B- HC=NHCH2OPO32-O

CH2OPO32-OHHHOH3NEnz B-Enz(-H2O)+ +

Protonated imineHH

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Glycolysis - Rexn 4Glycolysis - Rexn 4• reverse aldol reaction gives two three-carbon

fragments, one as an imine C-NHCH2OPO32-CH2OPO32-CHOHCC=OHOHHH

C=NHCH2OPO32-OCH2OPO32-OHHHOB-Enz+

Protonated imineH BEnzH

Glyceraldehyde 3-phosphateH(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=NHCH2OPO32-CH2OHEnz+ H2O

C=OCH2OPO32-CH2OH+B-H3NEnz+Protonated imineDihydroxyacetone phosphateB-C-NHCH2OPO32-CHOHBEnzH

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Glycolysis - Rexn 5Glycolysis - Rexn 5• Reaction 5: isomerization of triose phosphatesC=O CH2OPO32-CH2OHCH2OPO32- CCHOHOHGlyceraldehyde3-phosphateDihydroxyacetonephosphate

C-OHCHOHCH2OPO32-An enediolintermediate

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Glycolysis - Rexn 6 Glycolysis - Rexn 6 • Reaction 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, NAD+, is reduced to NADH

G-C-HO+H2OG-C-OHO2H+2e-NAD+H+2e- NADHA two-electron oxidationA two-electron reduction++++

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Glycolysis - Rexn 6Glycolysis - Rexn 6• We divide this reaction into three steps

• step 1: formation of a thiohemiacetalG-C-HO+HS-Enz G-C-S-EnzOHHGlyceraldehyde 3-phosphateA thiohemiacetal

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Glycolysis - Rexn 6Glycolysis - Rexn 6• step 2: oxidation of the thiohemiacetal by NAD+

G-C-S-EnzOHHNCNH2AdO+

G-C-S-EnzNCNH2AdOOHHan enzyme-bound thioester

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Glycolysis - Rexn 6 Glycolysis - Rexn 6 • step 3: conversion of the thioester to a mixed

anhydrideG-C-S-EnzO+-O-P-OHOO-G-C-O-P-OHO-Enz-SOO- A tetrahedralcarbonyl addition intermediateG-C-O-P-O-OOO-+Enz-S-1,3-Bisphosphoglycerate (a mixed anhydride)

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Glycolysis - Rexn 7Glycolysis - Rexn 7• Reaction 7: transfer of a phosphate group from

1,3-bisphosphoglycerate to ADP

+1,3-Bisphospho-glycerateCCH2OPO32-CO2-OHHCCH2OPO32-C-OPO32-OHHO

+ ATP3-Phosphoglycerate-O-P-O-AMPOO-ADPOO-

phospho-glycerate kinaseMg2+-O-P-O-P-O-AMPOO-

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Glycolysis - Rexn 8Glycolysis - Rexn 8• Reaction 8: isomerization of 3-phosphoglycerate

to 2-phosphoglycerateCCH2OPO32-CO2-OHH3-PhosphoglycerateCCH2OHCO2-OPO32-H2-Phosphoglyceratephosphoglycerate mutase

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Glycolysis - Rexn 9Glycolysis - Rexn 9• Reaction 9: dehydration of 2-phosphoglycerateCCH2OHCO2-OPO32-H2-PhosphoglycerateCCH2

CO2-OPO32-Phosphoenolpyruvate+H2OenolaseMg2+

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Glycolysis - Rexn 10Glycolysis - Rexn 10• Reaction 10: phosphate transfer to ADP

• stage 1: transfer of the phosphate groupCCH2CO2-OPO32-Phosphoenol- pyruvate+-O-P-O-P-O-AMPOO-O-OATP

-O-P-O-AMPOO-ADPC-OHCH2CO2-+ Enol of pyruvate

pyruvate kinaseMg2+

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Glycolysis - Rexn 10Glycolysis - Rexn 10• stage 2: enolization to pyruvateC-OHCH2

CO2- Enol of pyruvate

C=OCH3CO2-Pyruvate

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GlycolysisGlycolysis• Summing these 10 reactions gives the net

equation for glycolysisC6H12O6 + 2NAD+ + 2HPO42- + 2ADPGlucoseglycolysis2CH3CCO2-OPyruvate+ 2NADH + 2ATP + 2H2O + 2H+

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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 lactateCH3CCO2- + NADH + H+OPyruvateCH3CHCO2- + NAD+OHLactate

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

C6H12O6Glucose2CH3CHCO2- + 2H+OHLactate 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 ethanolCH3CH + NADH + H+OAcetaldehyde alcoholdehydrogenaseCH3CH2OH + NAD+EthanolPyruvateCH3CH + CO2OAcetaldehyde pyruvatedecarboxylaseCH3CCO2- + H+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

PyruvateCH3CSCoA + CO2 + NADHOAcetyl-CoA oxidativedecarboxylationCH3CCO2- + NAD+ + CoASHO

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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)• thiamine pyrophosphate (from thiamine, B1)• lipoic acid

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Pyruvate to Acetyl-CoAPyruvate to Acetyl-CoA

SSCH2CH2CH2CH2CO2-Lipoic acid(shown as the carboxylate anion)HNH2H3C Thiamine pyrophosphateNSHH3CCH2CH2O-P-O-P-O-OO-OO-

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End Chapter 20End Chapter 20

The Organic The Organic Chemistry of Chemistry of MetabolismMetabolism

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Introduction to Organic Chemistry 2 ed William H. Brown