Chemistry of Natural Products: Amino Acids, Peptides, Proteins and Enzymes

250 Pages·2022·5.953 MB·English

by  V.K. Ahluwalia, Lalita S. Kumar, Sanjiv Kumar

V. K. Ahluwalia · Lalita S. Kumar ·
Sanjiv Kumar
Chemistry of
Natural Products
Amino Acids, Peptides,
Proteins and Enzymes
Chemistry of Natural Products
· ·
V. K. Ahluwalia Lalita S. Kumar Sanjiv Kumar
Chemistry of Natural
Products
Amino Acids, Peptides, Proteins
and Enzymes
V.K.Ahluwalia LalitaS.Kumar
DepartmentofChemistry SchoolofSciences
UniversityofDelhi IndiraGandhiNationalOpenUniversity
NewDelhi,India NewDelhi,India
SanjivKumar
SchoolofSciences
IndiraGandhiNationalOpenUniversity
NewDelhi,India
ISBN978-3-030-86697-6 ISBN978-3-030-86698-3 (eBook)
https://doi.org/10.1007/978-3-030-86698-3
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Preface
The study of ‘Natural Products’ is an integral part of the undergraduate and the
postgraduate curriculum across universities in India. A need for a comprehensive
textcoveringdifferentareasofnaturalproductchemistryinreasonabledetailisfelt
bythestudentsandteachersalike.Thisbookoffersreadersjusttherightinformation
inamostconciseandarticulatemannerwithoutdilutingtheimportanceofthesubject
matter.
Thebookisdesignedfortheundergraduate(bothatpassandathonourslevels)
andthepostgraduatestudentsofchemistry.Thetextwouldbeequallyusefultothe
learnersininterdisciplinaryareaslikebiochemistry,biotechnology,etc.,andwould
provideagoodfoundationtotheonesventuringintoresearchintheareascovered
inthetext,especiallypeptidesynthesis.
Thetextisdividedintofourchapters—achaptereachdedicatedtoaminoacids,
peptides, proteins and enzymes. Chapter 1 on ‘Amino Acids’ covers nomencla-
ture,classification,stereochemistry,physicalandchemicalproperties,synthesisand
industrial applications. The important reactions have been explained with the help
ofmechanismsinvolved.
Chapter2on‘Peptides’explainstheformationandstructureofpeptidebondand
itssignificance.Thechaptergivesadetailedaccountofthesolution-phaseandsolid-
phase synthesis of peptides besides discussing the structure and function of some
biologicallyimportantpeptides.
Chapter 3 on ‘Proteins’ discusses different ways of classification and explains
theirproperties.Thestructuralorganisationofproteinshasbeencoveredinadequate
detailsincludingtheprimarystructuredetermination.
Chapter 4 on ‘Enzymes’ is a logical extension of the coverage in the first three
chapters.Itcoverstheclassification,nomenclatureandmodeofactionofenzymes
besidesadetailedaccountofthestructureandfunctionofdifferentcoenzymes.
TheauthorswishtoacknowledgeProf.J.M.KhuranaoftheUniversityofDelhi
tohavegonethroughthemanuscript.Welookforwardtocriticalcommentsfromthe
usersofthetextandwouldwelcomepointerstoerrors,omissionsandobscurities(if
any)soastoimprovethebookforfutureuse.
v
vi Preface
Lastly,theauthorsexpresstheirsincerethankstoMr.SunilSexenaandallstaff
membersofAneBooks,India,fortheirhelpandtheexcellentcooperationreceived.
NewDelhi,India V.K.Ahluwalia
LalitaS.Kumar
SanjivKumar
Contents
1 AminoAcids ................................................... 1
1.1 Introduction ............................................... 1
1.2 NomenclatureofAminoAcids ............................... 2
1.2.1 RepresentationofAminoAcids ........................ 5
1.3 ClassificationofAminoAcids ................................ 7
1.3.1 CodedorPrimaryProteinAminoAcids ................. 7
1.3.2 SecondaryandTertiaryProteinAminoAcids ............ 11
1.3.3 Non-codedorNon-proteinAminoAcids ................ 12
1.3.4 EssentialAminoAcids ................................ 13
1.4 StereochemicalAspectsofα-AminoAcids ..................... 14
1.4.1 AbsoluteConfigurationofα-AminoAcids ............... 15
1.4.2 AminoAcidswithTwoChiralCentres .................. 18
1.5 PhysicalPropertiesofα-AminoAcids ......................... 20
1.5.1 GeneralPhysicalProperties ........................... 20
1.5.2 Acid-BasePropertiesofAminoAcids ................... 20
1.5.3 SpectralPropertiesofα-AminoAcids ................... 26
1.6 ChemicalReactionsofAminoAcids .......................... 32
1.6.1 ReactionsDuetoAminoGroup ........................ 32
1.6.2 ReactionsDuetoCarboxylGroup ...................... 35
1.6.3 ReactionsDuetoBothAminoandCarboxylGroups ...... 36
1.7 IndustrialPreparationofα-AminoAcids ....................... 39
1.8 ChemicalSynthesisofα-AminoAcids ........................ 40
1.8.1 EnantiomericResolutionofα-AminoAcids .............. 51
1.8.2 AsymmetricSynthesisofα-AminoAcids ................ 53
1.9 IndustrialApplicationsofα-AminoAcids ...................... 62
2 Peptides ....................................................... 67
2.1 Introduction ............................................... 67
2.2 StructureandClassificationofPeptides ........................ 68
2.2.1 StructureofPeptideBond ............................. 68
2.2.2 ClassificationofPeptides .............................. 71
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viii Contents
2.3 NomenclatureofPeptides ................................... 71
2.3.1 RepresentationofPeptidesandPolypeptides ............. 73
2.4 PeptideSynthesis ........................................... 74
2.4.1 ProtectionofAminoGroup ............................ 77
2.4.2 ProtectionofCarboxylGroup .......................... 86
2.4.3 ProtectionofSideChains ............................. 87
2.4.4 CouplingMethods ................................... 88
2.5 Solid-PhasePeptideSynthesis ................................ 95
2.5.1 Solid-PhasePeptideSynthesisUsingt-BocProtection
(MerrifieldApproach) ................................ 98
2.5.2 Solid-PhasePeptideSynthesisUsingFmocProtection
(Sheppard’sApproach) ............................... 100
2.5.3 LimitationsofSolid-PhasePeptideSynthesis ............ 100
2.6 SomeBiologicallyImportantPeptides ......................... 102
2.6.1 Oxytocin ........................................... 103
2.6.2 Glutathione ......................................... 104
2.6.3 Insulin .............................................. 107
2.6.4 Bradykinin .......................................... 108
2.6.5 GramicidinS ........................................ 109
3 Proteins ....................................................... 113
3.1 Introduction ............................................... 113
3.2 ClassificationofProteins .................................... 114
3.2.1 ClassificationontheBasisofShapeandStructure ........ 114
3.2.2 ClassificationontheBasisofProductsofHydrolysis ...... 116
3.2.3 ClassificationontheBasisofBiologicalFunctions ........ 120
3.3 PropertiesofProteins ....................................... 121
3.3.1 MolecularWeight .................................... 121
3.3.2 AmphotericNature ................................... 122
3.3.3 Solubility ........................................... 123
3.3.4 Precipitation ........................................ 123
3.3.5 Denaturation ........................................ 125
3.3.6 ColourReactions .................................... 125
3.4 StructuralOrganisationofProteins ............................ 128
3.4.1 CovalentorPrimaryStructureofProteins ............... 130
3.4.2 ConformationalAspectsofProteins:HigherOrder
Structures ........................................... 144
4 Enzymes ...................................................... 157
4.1 Introduction ............................................... 157
4.2 NomenclatureandClassificationofEnzymes ................... 158
4.2.1 SystematicandRecommendedNames .................. 159
4.2.2 ClassificationNumbersandCodeNames ................ 159
4.3 CharacteristicsofEnzymes .................................. 166
4.3.1 CatalyticPower ...................................... 166
Contents ix
4.3.2 EnzymeSpecificity ................................... 168
4.3.3 EnzymeRegulation .................................. 170
4.4 MechanismofEnzymeAction ............................... 170
4.5 FactorsAffectingEnzymeAction ............................. 173
4.6 Chymotrypsin:AnEnzymeinAction .......................... 175
4.6.1 StructureofChymotrypsin ............................ 177
4.6.2 ImportantAminoAcidResiduesofChymotrypsin ........ 178
4.6.3 MechanismofAction ................................. 181
4.7 Cofactors(orCoenzymes) ................................... 185
4.7.1 Nicotinamide Adenine Dinucleotide (NAD+)
andNicotinamideAdenineDinucleotidePhosphate
(NADP+) ........................................... 187
4.7.2 UDP-Glucose ....................................... 190
4.7.3 FlavinMononucleotide(FMN)andFlavinAdenine
Dinucleotide(FAD) .................................. 192
4.7.4 ThiaminePyrophosphate(TPP) ........................ 195
4.7.5 Cocarboxylase ....................................... 197
4.7.6 Pyridoxal-5-Phosphate ................................ 200
4.8 EnzymesinOrganicSynthesis ................................ 205
4.8.1 EnzymaticOxidations ................................ 207
4.8.2 EnzymaticHydroxylation ............................. 209
4.8.3 EnzymaticHydrolysis ................................ 210
4.8.4 EnzymaticReductions ................................ 211
4.8.5 EnzymaticIsomerisations ............................. 212
4.8.6 PharmaceuticalApplicationsofEnzymes ................ 212
SuggestedReadings ............................................. 214
Glossary .......................................................... 215
Index ............................................................. 233
About the Authors
V.K.Ahluwalia hasworkedasprofessorofchemistry,UniversityofDelhi,Delhi
for more than three decades and taught postgraduate and M.Phil students. He has
guidedabout80studentsforM.Phil/Ph.Ddegreesandhaspublishedmorethan250
researchpapersinNationalandInternationalJournals.Hehasdeliveredanumberof
invitedlecturesinIndiaandAbroad.Prof.Ahluwaliaworkedaspost-doctoralfellow
for two years (1960-1962) and worked with Prof. Harold Shechter at the Depart-
ment of Chemistry Ohio State University, Ohio USA and for one year (1980-81)
withProfessorHerbertC.Brown,NobelLaureateattheDepartmentofChemistry,
PurdueUniversity,USA.HehasalsobeenavisitingprofessoratDr.B.R.Ambedkar
Centre for Biomedical Research University of Delhi, Delhi. Prof. Ahluwalia has
authored many books a few of which are, Reaction Mechanism, Environmental
Chemistry, Environmental Science, Environment Education, Environmental Pollu-
tionandHealthandOrganicSynthesis.HisBookonGreenChemistryisthewinner
2009Choiceaward,beingtheoutstandingacademictitle.
LalitaS.KumardidherPhDfromUniversityofDelhiintheyear1987intheareaof
SyntheticOrganicChemistry.Shehasfivepublicationstohercredit.Sheisworking
as Reader at Indira Gandhi National Open University (IGNOU), New Delhi. She
hasbeenassociatedwithdesign,developmentandmaintenanceofdistanceteaching
materialforoversixteenyears.Herareasofinterestarebiochemistry,organicreaction
mechanismandenvironmentalchemistry.
SanjivKumardidhisPhDfromUniversityofDelhiintheyear1990intheareaof
biophysicalchemistryforwhichheworkedoninteractionofpeptidesandproteins
withnuclearacids.HeisworkingasReaderatDeshbandhuCollege,Universityof
Delhi,andhasateachingexperienceofoversixteenyears.Hisareasofinterestare
biochemistry,spectroscopyandquantumchemistry.
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