17.nitrogen Compounds Lecture Notes

HwaChongInstitution2013
17 NitrogenCompounds
17NitrogenCompounds
CONTENT
Introduction
1.1
Amines
1.2
Amides
Nomenclature
2.1
Amines
2.2
Amides
PhysicalProperties
3.1
Smell
3.2
BoilingPoint
3.3
Solubility
Basicity
4.1
Amines
4.2
Phenylamines
4.3
SubstitutedPhenylamines
4.4
Amides
SynthesisofAminesandAmides
5.1
Amines
5.2
Amides
ChemicalReactionsofAminesandAmides
6.1
Amines
6.2
Amides
Aminoacids
7.1
Generalfeaturesofaminoacids
7.2
AcidBasebehaviour
7.3
Electrophoresis
7.4
Physicalpropertiesofaminoacids
7.5
Peptidebondformation
7.6
Featuresofapolypeptidechain
Proteins
HydrolysisofProteins
8.1
8.2
HierarchyofProteinstructure
8.3
FunctionsofProteins
8.4
DenaturationofProteins
Independent
Learning
subtopic
Independent
Learning
subtopic
Independent
Learning
subtopic
TanCS/ChengML/ColinLoy/WeeCS
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17NitrogenCompounds
LEARNINGOUTCOMES
Candidatesshouldbeableto:
(a) describe the formation of ethylamine (by nitrile reduction) and of phenylamine (by the reduction of
nitrobenzene)
(b) explainthebasicityofamines
(c) explaintherelativebasicitiesofammonia,ethylamineandphenylamineintermsoftheirstructures
(d) describethereactionofphenylaminewithaqueousbromine
(e) describetheformationofamidesfromthereactionbetweenRNH2andR'COCl
(f) describeamidehydrolysisontreatmentwithaqueousalkalioracid
(g) describetheacid/basepropertiesofaminoacidsandtheformationofzwitterions
(h) describetheformationofpeptide(amide)bondsbetweenaminoacidsand,hence,explainproteinformation
(i) listthemajorfunctionsofproteinsinthebody
(j) describethehydrolysisofproteins
(k) explainthetermprimarystructureofproteins
(l) recognisethatthetwentyaminoacidsthatmakeupalltheproteinsinthebodyareaminoacidswiththe
general formula RCH(NH2)CO2H, and be able to interpret the properties of amino acids in terms of the
natureoftheRgroup
(m) describe the secondary structure of proteins: helix and pleated sheet and the stabilisation of these
structuresbyhydrogenbonding
(n) statetheimportanceofthetertiaryproteinstructureandexplainthestabilisationofthetertiarystructure
withregardtotheRgroupsintheaminoacidresidues(ioniclinkages,disulfidebridges,hydrogenbondsand
vanderWaalsforces)
(o) describe
(i)
thequaternarystructureofproteins
(ii)
theproteincomponentsofhaemoglobin
(p) explaindenaturationofproteinsbyheavymetalions,extremesoftemperatureandpHchanges
(q) apply the knowledge of the loss and formation of secondary and tertiary structures to interpret common
everydayphenomena
REFERENCES
1.
2.
PeterCann&PeterHughes(2002).ChemistryforAdvancedLevel.
JohnMcMurry(2004).OrganicChemistry.Brooks/Cole.
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17NitrogenCompounds
INTRODUCTION
1.1
Amines
Amines are nitrogencontaining compounds that can be derived from the inorganic compound ammonia, NH3, in
whichoneormorehydrogenatomsarereplacedbyorganicgroups,suchasalkylorarylgroups.
Organicnitrogencompoundscanbeclassifiedintogroupsthatshowsimilarchemicalproperties,assummarisedinthe
tablebelow:
Primaryamines
Secondaryamines
Tertiaryamines
Quaternary
ammoniumions
R'''
Description
Exampleofaliphatic
amine
Exampleof
phenylamines&
derivatives
(inwhichthe
nitrogenatomis
directlyattachedto
thebenzenering)
H N R
H
H N R
R'
oneoftheHatoms
inammoniahasbeen
replacedbyanalkyl
orarylgroup
twooftheHatoms
inammoniahave
beenreplacedbyan
alkylorarylgroup
CH3CH2NH2
ethylamine
CH3CH2NHCH3
Nmethylethylamine
NH2
phenylamine
CH3
Nmethylphenylamine
R''
N R
R'
N
R'
allthreeoftheH
atomsinammonia
havebeenreplaced
byanalkyloraryl
group
(CH3)3N
trimethylamine
CH3
R''
CH3
amonopositively
chargedioninwhich
thereare4alkylor
arylgroupsattached
totheNatom
(CH3)4N+
Tetramethyl
ammoniumion
N(CH3)3
N,N,N
N,N
trimethylphenylam
dimethylphenylamine
moniumion
1.2
Amides
The simplest amides are carboxylic acid derivatives, where the OH group has been replaced by an NH2 group.
SubstitutedamidescanhaveoneortwoalkylgroupsinplaceofthehydrogenatomsnormallyattachedtotheNatom.
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17NitrogenCompounds
NOMENCLATURE
2.1
Amines
Simpleaminesarenamedbyaddingthesuffixaminetothenameofthelongestalkylgroupthatisattachedtothe
nitrogenatom.
The longest carbon chain containing the amine group is considered the parent structure. Number the alkane chain
beginningattheendnearertheaminegroup.
Note:Analternativewayofnamingaminesistoreplacethefinaleinthenameoftheparentcompoundwiththe
suffixamine.
Insecondaryandtertiaryamines,substituentgroupsonthenitrogenatomareidentifiedbyacapitalN.
Ifthereisafunctionalgroupofhigherpriority,theNH2groupcanbeconsideredasanaminosubstituent.
2.2
Amides
PrimaryamideswithanunsubstitutedNH2grouparenamedbyreplacingtheoicacidoftheparentcarboxylicacid
withamide.
Ifthenitrogenatomisfurthersubstituted,thepositionofthesubstituentgroupsisidentifiedbyacapitalN.
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17NitrogenCompounds
Exercise1
Namethefollowingcompoundsandindicatewhetheritisaprimary,secondaryortertiaryamine:
NH2
(a)
Cl
(b)
(c)
(d)
PHYSICALPROPERTIES
3.1
Smell(*INDEPENDENTLEARNINGSUBTOPIC*)
Thealiphaticaminesoflowermolecularweighthaveacharacteristicpungentsmellwhereasthehighermembershave
strong fishy odours. Sometimes even foul smelling is an understatement, and two of the amines produced in
decayingflesharenamedcadaverineandputresine.
3.2
BoilingPoint(*INDEPENDENTLEARNINGSUBTOPIC*)
Amongisomericamines,primaryamineshavethehighestboilingpoints,andtertiaryaminesthelowest.Sincetertiary
amines have no NH bond, they are unable to form hydrogen bonds. Consequently, their molecules are held
together by weaker permanent dipole permanent dipole interaction which requires less energy to overcome as
comparedtostrongerhydrogenbondsbetweenmoleculesofprimaryandsecondaryamines.
Primaryamine
Compound
Mr
CH3CH2CH2NH2 59
Boilingpoint/oC
Intermolecularforces
50
hydrogenbonding
Secondaryamine CH3CH2NHCH3
59
34
hydrogenbonding
Tertiaryamine
59
permanentdipolepermanentdipoleinteraction
(CH3)3N
Formoleculeswithsimilarsizeofelectroncloud,amineshavehigherboilingpointthanalkanesbutlowerboilingpoint
thanalcohols.
Compound
Functionalgroup
Mr
Boilingpoint/oC
CH3CH3
Alkane
30
89
CH3NH2
Amine
31
CH3OH
Alcohol
32
65
Methylamine,becauseitcanparticipateinintermolecularhydrogenbonding,hasaconsiderablyhigherboilingpoint
thanethane,anonpolaralkaneinwhichthemoleculesareheldtogetherbyweakerdispersionforces.However,its
boiling point is lower than that of methanol, since the NH bond is less polar than the OH bond. Hence, the
intermolecular hydrogenbonds in alcohols are stronger than those between amine molecules and require more
energytoovercome.
69
17NitrogenCompounds
Amidesarewhitecrystallinesolidsatroomtemperature,apartfrommethanamide,whichisaliquid.Amidescanform
extensiveintermolecularhydrogenbondsasaresultofthepolarnatureoftheNHbond,andthesehydrogenbonds
resultinrelativelyhighmeltingandboilingpoints.
3.3
Solubility(*INDEPENDENTLEARNINGSUBTOPIC*)
Loweraliphaticamines(fewerthansixorsevencarbonatoms)arereadilysolubleinwaterduetotheirabilitytoform
stronghydrogenbondswithwatermolecules.
Phenylamines and higher molecular weight amines are virtually insoluble in water because they contain large
hydrocarbonskeletonswhicharenonpolar.Theydodissolve,though,inorganicsolvents,e.g.benzene.
Foramides,theirabilitytoformextensivehydrogenbondswithwateralsomeansthatsimpleamidesareverysoluble
inwater.
BASICITY
Aminesareweakbases.Whentheyaredissolvedinwater,anequilibriumisestablishedinwhichthewaterdonatesa
hydrogeniontotheamine.Theextenttowhichthisreactionoccursisameasureoftheaminesbasicity.
RNH2+H2ORNH3++OH
Kb
[RNH3 ][OH ]
andpK b lgKb
[RNH2 ]
ThelargertheKbvalues,thegreateritsbasicity;thesmallerthepKb,thestrongerthebase.
Tocomparethebasicityoftwocompounds,keepinmindthefollowing:
AnyfactorthatincreasestheelectrondensityontheNatomincreasesanaminesbasicity.
Anyfactorthatstabilisestheconjugateacidformedincreasesanaminesbasicity.
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17NitrogenCompounds
4.1
Amines
Aliphaticaminesaremorebasicthanammoniabecausealkylgroupsareelectrondonatinginnature;theyincreasethe
electron density on nitrogen atom, making the lone pair of electrons more available to form a dative bond with a
proton.
Therefore,
pKb:3.283.354.74
Note: Based on the above reasoning, tertiary amines are expected to be the strongest bases, followed by
secondary then primary amines. However, tertiary amines (pKb 4.21) are not as basic as expected as their
resulting conjugate acids are not as effectively solvated through hydrogen bonding by the surrounding water
moleculesascomparedtoconjugateacidsofprimaryandsecondaryamines.
4.2
Phenylamines
Phenylamines are considerably less basic than ammonia. This is because for phenylamine, the electron pair on
nitrogenisdelocalizedintothebenzenering.Thisdecreasestheelectrondensityonthenitrogenatom,makingthe
lonepairofelectronslessavailabletoformadativebondwithaproton.
Anextendeddelocalizedringispresentinphenylamines:
Therefore:
pKb:3.35
4.74
9.40
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17NitrogenCompounds
4.3
SubstitutedPhenylamines
Theyaremoreorlessbasicthanphenylaminedependingonthenatureofthesubstituent.
Electrondonatinggroupsincreaseelectrondensityonthebenzenering,makingthelonepaironnitrogenatommore
availablefordonationtoanacid.Hencethesesubstitutedphenylaminesaremorebasicthanphenylamine.
Electronwithdrawing groups decrease electron density on the benzene ring, making the lone pair on nitrogen less
availablefordonationtoanacid.Hence,thesesubstitutedphenylaminesarelessbasicthanphenylamine.
Therefore,
4.4
pKb:
8.92
9.40
13.0
Amides
Unlikeamines,amides,giveneutralsolutionsinwater.Thelonepaironthenitrogenatominamidesisinaporbital,
andcanoverlapwiththeorbitaloftheadjacentcarbonylgroup.Thedelocalisationofthelonepaironthenitrogen
atomovertheC=Obondreducestheelectrondensityonthenitrogenatomsuchthatthelonepairofelectronsonthe
nitrogenatomisnotavailableforreactionwithanacid.Thisdelocalisationofthelonepaironthenitrogenatomalso
confersconsiderabledoublebondcharactertothecarbonnitrogenbond,resultinginrestrictedrotationaboutit.
Therefore,
pKb: 3.35
4.74
9.40
14.50
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17NitrogenCompounds
Exercise2
Arrangethefollowingcompoundsinorderofincreasingbasicity:
SYNTHESISOFAMINESANDAMIDES
5.1
Amines(*INDEPENDENTLEARNINGSUBTOPIC*)
5.1.1 FromNucleophilicSubstitutionofHalogenoalkanes
Whenahalogenoalkaneisheatedwithconcentratedammoniaunderpressure(usingasealedtube),inthepresence
ofethanolassolvent,anamineisformed.Undertheseconditions,NH3behavesasanucleophileanddisplacesthe
halidetoformthecorrespondingprimaryamine.
R X
R NH2
Reagents&Conditions:
EthanolicconcentratedNH3,heatinasealedtube
Comment:
The use of excess NH3 helps to prevent further substitution,
favouringtheformationofaprimaryamine.
Amines themselves also have a lone pair of electrons on the nitrogen atom and, like NH3, they can also behave as
nucleophiles.Ifthehalogenoalkaneisinexcess,furthersubstitutionoccurs.Theyreactwithhalogenoalkanestoform
secondary,tertiaryaminesandquaternaryammoniumions.
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17NitrogenCompounds
Mechanismofnucleophilicsubstitutionofhalogenoalkaneswithammoniaoramines
WithNH3asthenucleophile:
Withaprimary,secondaryortertiaryamineasthenucleophile:
5.1.2 FromReductionofNitriles
Amines can be formed from the reduction of organic nitriles. In the process, the CN triple bond is broken and
becomessaturated.
Reagents&Conditions: LiAlH4 indryether ORH2(g)/Ni,hightemp,highpressure

Comment:
LiAlH4 is a very powerful reducing agent which works by

providingahydrideion,H.Heatingshouldbeavoidedsoas
topreventexplosions.
74
17NitrogenCompounds
5.1.3
FromReductionofNitrobenzene
Phenylamine can be prepared by reduction of aromatic nitrocompounds using tin and excess concentrated
hydrochloric acid. The product appears as a salt, C6H5NH3+Cl, and excess NaOH(aq) is added to liberate the free
phenylamine.
NO2
NH2
1. Sn / excess conc. HCl, heat
+
6[H]
2. NaOH(aq)
2H2O
Reagents&Conditions: 1.SninexcessconcentratedHCl/heatunderreflux
2.dil.NaOH(aq)
Comment:AqueousNaOH(astrongbase)isaddedtoliberatetheamine.
Note:Aliphaticnitrocompoundscannotbereducedusingthesamereducingagent.
5.2
Amides(*INDEPENDENTLEARNINGSUBTOPIC*)
5.2.1 FromAcylchlorides
Simpleamidesarepreparedbyreactionofanacylchloridewithammonia.Nsubstitutedamidescanalsobemadeby
reactionofanacylchloridewithaprimaryorsecondaryamine.
Reagents &Conditions:
Ammonia or primary amines or secondary amines (in

excess),roomtemperature
Noreactionwithtertiaryamines(Why?)
Comment:
Note:Carboxylicacidscannotbeusedinthepreparationofamides.Thisisbecausetheyreactwithamines/ammonia
inanacidbasereactioninstead.
E.g.
CH3CO2H+NH3CH3CO2NH4+
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17NitrogenCompounds
Exercise3
Givethereagentsandconditionsthatyouwoulduseinthefollowingconversions:
(a)
(b)
(c)
CHEMICALREACTIONSOFAMINESANDAMIDES
6.1 Amines
Thechemistryofaminesisdominatedbythelonepairofelectronsonnitrogenatom.Theycanbehave:
asLewisbases(donatingthelonepairtoaH+ion)
asgoodnucleophiles(beingabletoattackatthepartialpositiveendofapolarizedbond)
as excellent ligands (with transition metals) to be covered under Topic 20 Introduction to Transition
Elements
6.1.1 Reactionwithacids(asabase)
Amines(bothaliphaticandphenylamines)reactwithacids(mineralorcarboxylicacids)toformsalts.
Reagents&Conditions: Mineralacids(HClorH2SO4)orcarboxylicacids,
roomtemperature
Comment:
Thesaltsaresolubleinaqueoussolution.Onevaporatingthissolution,
thesolidsaltscanbeobtainedaswhitecrystallinesolids.
76
17NitrogenCompounds
Because the salts are ionic, they are soluble in water but insoluble in organic solvents. Thus an amine can be
separatedfromotherorganiccompoundsbyconvertingittoawatersolubleammoniumsaltbyanacidbasereaction.
Theaminescanberegeneratedfromtheircorrespondingsaltsbyusingstrongbases,suchasNaOH(aq).
6.1.2 Reactionwithhalogenoalkanes(asanucleophile)
Primary, secondary and tertiary amines can react with halogenoalkanes to form secondary amines, tertiary amines
andquaternaryammoniumsaltsrespectively.
Reagents&Conditions:
Halogenoalkane,heatinasealedtube
Comment:
Topreventmultiplesubstitutions,excessamineisused.
77
17NitrogenCompounds
6.1.3 Reactionwithacylchlorides(asanucleophile)
Primaryandsecondaryamines(bothaliphaticandphenylamines)reactwithacidchloridestoformamides.
H N
R'
H
R
H N
R'
R''
Cl
O
C
Cl
O
R'
R''
HCl
C
NHR
O
C
NRR'
HCl
Reagents&Conditions: Acylchlorides,roomtemperature
Comment:
TertiaryaminesdonotcontainareplaceableHatomontheN,sothey
areincapableofformingamides.
Note:Tomakeamides,carboxylicacidscannotbeusedinsteadofacidchlorides.(Why?)
Foryourinformation
Mechanismofnucleophilicacylsubstitutioninformingamidesfromacidchloridesandamines
O
C +
CH3CH2NH2
amine
CH3CH2
acidchloride
C
CH3CH2NH
amide
Cl
Cl
+HCl
CH3CH2
N
H
R
H
Cl
78
17NitrogenCompounds
6.1.4 Reactionwithbromine(forphenylaminesonly)
Aliphaticaminesdonotreactwithbromine.However,phenylaminereactsveryquicklywithaqueousbromineviaan
electrophilicsubstitutionmechanismtoformawhiteprecipitate.
Reagents&Conditions: Aqueousbromine,roomtemperature
Observations: Yelloworangesolutiondecolourise;whitepptformed
Comments:
NoLewisacidcatalyst(halogencarrier)isrequiredforthisreaction,unlike
brominationofbenzene(whichrequiresAlCl3orFeCl3).NH2groupis2,4
directing.
Explanation:
Likephenol,thelonepairofelectronsontheNH2groupisdelocalisedintothe
benzenering,theelectrondensityintheringisgreatlyincreased,makingit
muchmoresusceptibletoelectrophilicattackthanbenzene.Hence,the
presenceoftheNH2grouphighlyactivatesthebenzeneringtowards
electrophilicsubstitutionandnocatalystisrequired.
Exercise4
Describeasimplechemicaltesttodistinguishbetweenphenylamineandphenylmethylamine.
Statetheobservationsineachcase.
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17NitrogenCompounds
6.2
Amides
Unlikeamines,thelonepaironthenitrogenatominamidesisinaporbitalthatcanoverlapwiththeorbitalofthe
adjacent carbonyl group. Thus, the electron density on the nitrogen atom is reduced, making it unable to act as a
nucleophileandtoundergonucleophilicreactionslikeamines.
The delocalization also gives good stability to amides and makes them the least reactive of the carboxylic acid
derivatives.
6.2.1 Reactionwithacidsorbases
Amides can be hydrolysed by aqueous acids (e.g. dil H2SO4) or aqueous bases (e.g. dil NaOH) when heated under
refluxtoyieldthecarboxylicacidorsaltrespectively.
O4
dil
t
hea
H 2S
NH4+
NH3
OH
C
dil
Na
hea OH
t
NH2
O
R
C
O-
Reagents&Conditions: Diluteacidsorbases,heat
Observation:
Ammoniawillbeproducediftheprimaryamidesundergoalkalinehydrolysis.
Note:Forsubstitutedamides,aminesareformedinstead.
Comment:
Althoughtheexactsamebondiscleavedinbothacidandalkalinehydrolysis,the
actualproductsofhydrolysisdependonthepHoftheenvironment.
Exercise5
Writebalancedequationsforthehydrolysisofthefollowingamidesinthegivenconditions:
(i)acidichydrolysis;and(ii)alkalinehydrolysis.
(a)
(b)
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17NitrogenCompounds
Resolvingconfusionaboutthetermhydrolysis
Whatishydrolysis?
Hydrolysisisreactioninwhichamoleculeissplitintotwobytheactionofwater.ThereactionisoftencatalysedbyH+
orOH.
Example:Acidhydrolysisofamide
Mechanismofacidhydrolysisofamide(notinsyllabus)
+
H actsasthecatalystwhileH2Oactsasthenucleophilethatcausestheamidetosplitintotwo.Inthefirststep,the
C=O group of the amide is protonated which makes the carbonyl carbon more electron deficient and hence more
susceptibletoattackbythewaternucleophile.H+thatisregeneratedistransferredtothebasicNH3toformNH4+.
BasehydrolysisofamidesfollowsasimilarmechanismbutOHionactsasthenucleophileinsteadofH2O.Theresultis
similarenoughthatitisstillclassifiedashydrolysis.
Whereelsehaveweseenthetermhydrolysisandwhatdoesitmean?
Hydrolysisreactions
Effectofhydrolysis
Reagents&Conditions
substitutingahalogenatombya
OHgroup.CXbondisbroken.
hydrolysisofahalogenoalkane:
hydrolysisofanacidchloride:
AqueousNaOH,heatwithreflux
ToprovidetheOHnucleophilefor
nucleophilicsubstitution.
substitutingthehalogenatomby Asacidchloridesareveryreactive,
aOHgrouptoformacarboxylic H2Oalonecanhydrolysetheacid
chlorideatroomtemperature.
acid.CClbondisbroken.
hydrolysisofanester:
splittinguptheesterbybreaking diluteacidsorbases,heatwith
reflux
theCObond
Productsdependonmediumused.
hydrolysisofanorganicnitrile:
splittinguptheCNtriplebond
diluteacidsorbases,heatwith
reflux
hydrolysisofanamide:
splittinguptheamideby
breakingtheCNbond
diluteacidsorbases,heat
hydrolysisofaproteinorpolypeptide:
splittinguptheproteinintoits
componentaminoacidsby
breakingthepeptidebonds
diluteacidsorbases,prolonged
heating
Foodforthought:Isthereactionofalkenewithsteamconsideredhydrolysis?
81
17NitrogenCompounds
AminoAcids
Aminoacidscontainbothanacidiccarboxylgroup(CO2H)andabasicaminogroup(NH2).Naturallyoccurringamino
acidsareaminoacidswheretheaminogroupisbondedtothecarbon.Thecarbonisthecarbonatomdirectly
attachedtothecarboxylicacidfunctionalgroup.Itdoesnotincludethecarbonthatispartofthecarboxylgroup.The
generalformulaofanaminoacidisasfollows:
6.1
Generalfeaturesofaminoacids
Amino acids are the building blocks for all the proteins in the human body. The table on page 20 shows the 20
naturallyoccurringaminoacids.These20aminoacidshavecommonnamesandtheirnamescanberepresented
byeitheraoneletterorathreeletterabbreviationasshowninthetable.
The20aminoacidshavesimilarstructureanddifferonlyintheidentityoftheRgroupbondedtothecarbon.The
Rgroupiscalledthesidechainoftheaminoacid.
Thesimplestaminoacid,calledglycine,hasR=H.Thesidechainoftheotheraminoacidscanbeasimplealkyl
group,oritcanhaveadditionalfunctionalgroupssuchasOH,SH,CO2HorNH2.Exceptforglycine,allother
aminoacidsarechiral.
Exercise6
Whichofthefollowingareaminoacids?
CH2CH3
(i)
NH2CH2CO2H
(ii)
H2N
C
CH2
H
CO2H
CH2CH2CHNH2
(iii)
CO2H
CO2H
7.2
AcidBasebehaviour
Aminoacidscanundergoanintramolecularacidbasereaction,andexistasdipolarionscalledzwitterions.
DependingonthepHofthemedium,itcanexistintwootherforms:
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17NitrogenCompounds
The pH at which the overall net charge on the amino acid is zero is called the isoelectric point. This isoelectric pH
dependsonthenatureofthesidechain,R.
Aminoacid
Alanine
Lysine
Asparticacid
Structure
Natureofsidechain
Isoelectricpoint
neutral
basic
acidic
6.01
9.74
2.77
Exercise7
Draw the structure of the major species of lysine that can exist in aqueous solution of various pH. Start with the
speciesinasolutionofverylowpHandconsiderthechangeinstructureaspHincreases.Henceidentifythemajor
speciesthatexistsatisoelectricpoint.
7.3 Electrophoresis
Since amino acids are charged at certain pH values, we can use an electric field to separate them. This process is
knownaselectrophoresis.
Astreakoftheaminoacidmixtureisplacedinthecentreofapieceoffilterpaperwetwithabuffersolution.Two
electrodesareplacedincontactwiththeedgesofthepaperandanelectricpotentialisappliedacrosstheelectrodes.
Positivelycharged(cationic)aminoacidsareattractedtothenegativeelectrode(thecathode),andnegativelycharged
(anionic)aminoacidsareattractedtothepositiveelectrode(theanode).Anaminoacidatitsisoelectricpointhasno
netcharge,soitdoesnotmove.
Thedistancethatanaminoacidmigratesinagiventimeisproportionaltoitschargeandinverselyproportionaltoits
mass:
distancemigrated
charge
mass
83
17NitrogenCompounds
The20naturallyoccurringaminoacids
Foryourinformation
Essentialaminoacidscannotbesynthesizedinthehumanbodyandareobtainedfromfoodintake.
84
17NitrogenCompounds
Exercise8
Consider glutamic acid (isoelectric point = 3.22). What pH would you use to separate the mixture of glutamic acid,
asparticacidandalanineviaelectrophoresis?
Indicatethemotionoftheaminoacidsontheelectrophoresisplate.
7.4
Physicalpropertiesofaminoacids
Theformationofzwitterionsgivesaminoacidssomeunusualproperties:
Amino acids are crystalline solids with high melting points. This is due to strong electrostatic forces of
attractionbetweenthedipolarzwitterionsinthesolidlatticestructure.
Amino acids are more soluble in water than in organic solvents. This is due to the strong iondipole
interactionbetweenthezwitterionsandwatermolecules.
7.5 Peptidebondformation
Anamidelinkagebetweenaminoacidsiscalledapeptidebond:
PeptidebondsareformedfromthecondensationreactionbetweentheCO2HandtheNH2groupsontwoamino
acids through the elimination of a watermolecule. In this manner, any number ofamino acids can be bonded in a
continuouschain.
Adipeptideistheresultof2aminoacidunitscondensingtogether,whileatripeptideresultsfrom3unitsdoing
so,andsoonandsoforth.
Molecules containing up to about 50 amino acid residues are called polypeptides (or polyamides). Anything
largerisclassifiedasaproteinmolecule.
Note: In the lab, the reaction

between a carboxylic acid and an
aminewouldresultinsaltformation,
butlivingorganismsemployenzymes
toformpeptidebonds.
85
17NitrogenCompounds
7.6 Featuresofapolypeptidechain
The backbone is the main chain of the polypeptide which includes everything except the sidechains. The
sequenceispeptidebondcarbonpeptidebondcarbonetc
ThesidechainsaretheRgroupsofeachaminoacidresidue.
Amino acid residues: When a polypeptide is formed, the original amino acids can still be recognised by their
sidechains(theRgroups).However,becausetheyhavebeencondensedtogether,theynolongerpossessfree
aminoandcarboxylicacidgroups,sotheycannotbereferredtoasaminoacids.Instead,theyarecalledamino
acidresidues.
Thepeptidebondsresultfromthecondensationbetweenadjacentaminoacids.
NandCtermini:Ateachendofthepolypeptidechain,therewillbeoneuncondensed(orfree)aminogroup
and one uncondensed carboxylic acid group. These are referred to as the Nterminus and Cterminus
respectively.
Convention:polypeptidechainsarealwayswrittenfromNterminus(ontheleft)toCterminus.
Exercise9
Considerthepolypeptidechainbelow,and:
(i) labelthecarbonsandcirclethesidechains;
(ii) usingthelistonpage20,statethesequenceofaminoacidresiduesusingthe3letterabbreviation.
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17NitrogenCompounds
PROTEINS
Proteinsareformedwhenalargenumberofaminoacidsarecondensedtogethertoformalongpolypeptidechain.
They are a type of biopolymer produced by living organisms. Proteins serve as structural materials (keratin in hair,
nails, horns and feathers), muscle fibres, basic materials in enzymes (pepsin, tyrosine, rennin, etc) and hormones
(insulin,adrenaline,etc).
CharacteristicsofProteins:
Theyarenaturallyoccurringpolypeptidesofmolecularweightgreaterthan5000.
Theycanhaveover105aminoacidresiduesalllinkedbypeptidebonds.
8.1
HydrolysisofProteins
Proteins can by hydrolysed into their constituent amino acids either by an appropriate enzyme or heating in the
presenceofadiluteacidoralkaliforseveralhoursinthelaboratory.
Exercise10
Aspartameisthenameforanartificialsweetenerusedasasugarsubstituteinmanyfoodsandbeverages.
DrawthestructuralformulaeofalltheorganicproductsobtainedwhenaspartameisheatedwithdiluteH2SO4.
87
17NitrogenCompounds
8.2
HierarchyofProteinstructure
Proteinshavethreeorfourlevelsofstructuralorganizationandcomplexity.
Structure
Description
Primary
Thesequenceofaminoacidresiduesinthepolypeptidechain.
Secondary
The regular arrangement of sections of the polypeptide chain. Common repeating

structuralpatternsinproteinsarehelicesandpleatedsheets
Tertiary
The overall threedimensional shape of a protein formed by folding of the

polypeptidechain.
The characteristics manner in which the individually folded polypeptide subunits

Quaternary aregrouped.
(Applicabletoproteinswithmorethanonepolypeptidechain/subunit)
88
17NitrogenCompounds
8.2.1 PrimaryStructure
The primary structure of a protein is the sequence of the amino acid residues in the polypeptide chain(s) of the
protein.
Example:Humaninsulinisaproteinmadeupoftwopolypeptidechains
Usingthreeletterabbreviationsforeachaminoacidresidue,theprimarysequenceofthetwopolypeptidechainsin
humaninsulinwouldlooklikethis:
8.2.2 SecondaryStructure
Thesecondarystructureofaproteinistheregulararrangementofsectionsofthepolypeptidechains.Thetwomost
common secondary structures are the helix and the pleated sheet. These structures are both stabilised by
hydrogenbonds.
ThehydrogenbondsareformedbetweenthelonepaironOatomofC=ObondofapeptidelinkageandHatomof
NHbondofanotherpeptidelinkageinthepolypeptidebackbone.
[Contrast: Tertiary structure of proteins may also be stabilised by hydrogen bonds, but these are formed between
atomsofthesidechains(Rgroups).]
O
C
N
H
hydrogen bond
O
C
N
H
Note:Sectionsofapolypeptidethatarenotarrangedinaregularpatternhavenosecondarystructure,andsaidtobe
arrangedinarandomcoil.
89
17NitrogenCompounds
(i)
Helix
The helix forms when a peptide chain twists into a righthanded or clockwise spiral. The backbone of the
polypeptidechainisstabilisedbyhydrogenbonds.Fourimportantfeaturesofthehelixareasfollows:
Eachturnofthehelixhas3.6aminoacidresidues.
The NH and C=O bonds point along the axis of the helix. All C=O bonds
pointinonedirectionandallNHbondspointintheoppositedirection.
The C=O group of one amino acid residue is hydrogen bonded to an NH

group four amino acid residues farther along the chain. Thus, hydrogen
bondingoccursbetweentwoaminoacidresiduesinthesamechain.Note,
too,thatthehydrogenbondsareparalleltotheaxisofthehelix.
TheRgroupsoftheaminoacidresiduesextendoutwardfromthecoreof
thehelix.
[thenatureofthesesidechainswilldeterminethefoldingofthechaininto
thetertiarystructureoftheprotein]
Howtodrawasimplehelix:
Note: N of NH should be on the

backpartofthehelixlikethatofC
oftheC=Obond.
90
17NitrogenCompounds
(ii) pleatedsheet
Thepleatedsheetsecondarystructureformswhentwoormoresectionsofthepeptidechain,calledstrands,lineup
sidebyside.Allpleatedsheetshavethefollowingcharacteristics:
TheC=OandNHbondslieintheplaneofthesheet.
HydrogenbondingoftenoccursbetweenNHandC=Ogroupsofnearbyaminoacidresidues.
TheRgroupsareorientedaboveandbelowtheplaneofthesheet,alternatingalongagivenstrand.
Thepeptidestrandsofpleatedsheetscanbeorientedintwodifferentways:
(themorecommonofthetwoistheantiparallelconfiguration)
A3dimensionalrepresentation:
91
17NitrogenCompounds
8.2.3TertiaryStructure
The tertiary structure of a protein is the overall threedimensional shape of a protein formed by folding of the
polypeptidechain.Thefoldingisduetointeractionsbetweenthesidechains(Rgroups)oftheaminoacidresidues.
vanderWaals
forces
Thereare4waysinwhichsidechainscaninteracttoformthetertiarystructureofaprotein:
1) Hydrogenbonding: The tertiary structureof a proteincan be stabilised byhydrogen bonds formed between
sidechainsofaminoacidsresiduescontainingOHorNHgroupssuchSerandLys.
2) Electrostaticattractions:(ioniclinkages/saltbridges)Thetertiarystructureofaproteincanalsobestabilizedby
electrostatic forces of attraction between amino acid side chains of opposite charge, such as the NH3+ side
chainofLysandtheCO2sidechainofAsp.
3) vanderWaalsforces:Proteinsoftenfoldsothatthenonpolarsidechainsofthecertainaminoacids(Ala,Val,
Leu,Ile,Pro,Met,PheandTrp)areburiedwithintheprotein,wheretheycaninteractthroughvanderWaals
forcestoformhydrophobicpockets.ThevanderWaalsforcesbetweenthesenonpolarsidechainsstabilize
the3Dstructureoftheprotein.
4) Disulfide (SS) bridges: If the folding of a protein brings two cysteine residues together, the two SH side
chainscanbeoxidizedtoformacovalentSSbond.Thesedisulfidebondscrosslinkthepolypeptidechain(s).
92
17NitrogenCompounds
8.2.4 QuaternaryStructure
Quaternarystructureappliestoproteinsthatconsistofmorethanonepolypeptidechainandtheindividualchainsare
called subunits. The characteristics manner in which the individually folded polypeptide subunits are grouped is
knownasthequaternarystructure.Thequaternarystructureofproteinsismaintainedbythesameinteractionsthat
areresponsiblefortertiarystructure.
Note:Itisthetertiaryandquaternarystructuresofproteinthatultimatelydetermineitsfunction.
Haemoglobin
HaemoglobinisaproteinfoundinredbloodcellsandittransportsO2inmammalianblood,takingitfromthe
lungsanddeliveringittotissuesaroundthebody.
It has a quaternary structure, made up of four polypeptide subunits; two chains and two chains, each
withanassociatedheme(haem)group.The4subunitsareheldtogetherbythesametypeofinteractions
thatstabilisethetertiarystructure.
Thechainsconsistof
146aminoacidresidueseach
Thechainsconsistof
141aminoacidresidueseach
Each heme group consists of a central Fe2+ ion which can bind reversibly with one O2 molecule via dative
bond.Thus,eachhaemoglobinisabletocarryamaximumoffouroxygenmolecules.
TheFe2+ionisheldinplaceby4nitrogenatomsinthecentreofthehemering.Itisalsofirmlybondedtoone
of the amino acid residues in the protein below the ring. A 6th position is either a H2O molecule in
deoxyhaemoglobinoranO2moleculeinoxyhaemoglobin.Thisgivesrisetoanoctahedralstructurearound
thecentralFe2+ion.
Hbprotein
II
hemegroup
93
8.3
17NitrogenCompounds
FunctionsofProteins(*INDEPENDENTLEARNINGSUBTOPIC*)
Proteinsareessentialforlifeinalllivingorganismsandhavemanybiologicalfunctionsinthebody:
Enzymesaremadeupofproteinsandactasbiologicalcatalysts.
Antibodiesarespecificproteinmoleculesproducedbyspecializedcellsoftheimmunesysteminresponseto
foreignantigens.
Transportproteinscarrymaterialsfromoneplacetoanotherinthebody.
Regulatoryproteinscontrolmanyaspectsofcellfunction,includingmetabolismandreproduction.
Structuralproteinsprovidemechanicalsupporttolargeanimalsandprovidethemwiththeiroutercoverings.
Movement proteins are necessary for all forms of movement. Our muscles, including the most important
muscle,theheart,contractandexpandthroughtheinteractionofactinandmyosinproteins.
Nutrientproteinsserveassourcesofaminoacidsforembryosorinfants.Eggalbuminandcaseininmilkare
examplesofnutrientstorageproteins.
DenaturationofProteins(*INDEPENDENTLEARNINGSUBTOPIC*)
8.4
Proteinsarefragilemoleculesthatareremarkablysensitivetochangesintheirenvironment.
Denaturationisaprocesswhereby:
thehighlyorganizedstructureofnativeproteinsisdisrupted.
thequaternary,tertiaryandsecondaryproteinstructurebreaksdownresultingintheproteinunfoldingto
givearandomlycoiledpolypeptide.
theaminoacidsequence(primarystructure)oftheproteinremainsunaffected.
Sincethespecific3Dconformationisaltered,denaturationofproteinsisaccompaniedby:
thelossoftheirbiologicalactivity
changesintheirphysicalandchemicalproperties,suchas:
(a)
decreaseinsolubility
(b)
irreversibleformationofgels
(c)
highersusceptibilitytoenzymehydrolysis
Thesechangesarealmostalwaysirreversible.
94
17NitrogenCompounds
8.4.1 FactorsleadingtoProteinDenaturation
Manyfactorscancausedenaturation:
(i)
Heat
Excessive heat results in strong molecular vibrations that agitate the polypeptide chains enough to overcome the
weakerinteractionsthatstabilizeproteinconformation,i.e.hydrogenbondsandvanderWaalsforces.Theprotein
structurebecomesdisorganizedandtheproteinisdenatured.
At this point, coagulation can take place as the unfolded protein molecules can get entangled more easily and
aggregatetoformasolid.
Mostglobularproteinsundergoirreversibledenaturationwhenheatedabove6070 oC(e.g.cookingofaneggby
frying.Noticethattheeggdoesnotgobacktobeinguncookedevenwhenlefttocool).
(ii)
ChangesinpH
Changing the pH will protonate or deprotonate the ionic R groups and

hence, will result in disruption of the electrostatic attractions which are
involvedinthemaintenanceoftheproteinsconformation.
AtacertainpH,theproteinwillbeisoelectric,i.e.whenthepolypeptidehas
anequalnumberofpositiveandnegativecharges.Whenproteinshaveno
netsurfacecharge,theynolongerrepeloneanotherandtheythustendto
coagulateandprecipitateoutofsolution.(e.g.curdlingofmilkinacidicpH)
(iii) MechanicalAgitation
Stirring, whipping or shaking can disrupt the weaker interactions that
maintain protein conformation (e.g. whipping egg whites produces a stiff
meringue).
95
17NitrogenCompounds
(iv) Oxidizing and Reducing Agents can either create or disrupt disulfide (SS) bonds that
maintain protein conformation, thereby altering its shape. (e.g. the perming of hair uses
reducingagenttobreakdisulfidebridgesandmakehairsoft,followedbyanoxidizingagentto
formnewdisulfidebondstoholdhairinthenewposition.
(v) Detergents that make the nonpolar amino acid side chains soluble and thereby destroy the hydrophobic
interactions,causingtheproteinchaintounfold.
(vi) HeavyMetalsinterferewiththesaltbridgesformedbetweentheionicsidechainsoftheaminoacidresidues,
resultinginlossofconformation.HeavymetalionsmayalsoreactwithSHgroupstoformprecipitates.
Ananalogytohelpinunderstandingthedifferencebetweendenaturationandhydrolysis
Imagine a protein to be like a pasta strand that is twisted and coiled into a 3D shape. This 3D
shape is what allows it to fit in certain receptors in the body (like hormones), or to stretch and
contract(likemuscles),etc.
Denaturing the protein would be analogous to uncoiling or untwisting some parts of the pasta
strand. This alters the 3D conformation of the protein and therefore causes it, in most cases, to
lose its function. But note that the strand itself is still intact similarly, denaturation does not
usuallyaffecttheprimarystructureofaprotein.
Ifweconsiderinsteadhydrolysingtheprotein,itwouldbeanalogoustocuttingour
pasta strand into smaller pieces. Of course, this most definitely destroys the 3D
structure of the protein. In fact, it even goes all the way to destroy the primary
structureoftheprotein.
hydrolysis
polypeptidechain
peptidefragments
96
17NitrogenCompounds
Exercise11
Therearefourtypesofsidechain(orRgroup)interactionswhichholdthetertiarystructureofaproteininitsshape.
Completethefollowingtableabouttheseinteractions.Youwillneedtorefertopage20forthestructureoftheamino
acidsidechains.
(iii)IdentifywhichtypeofRgroupinteractionisdestroyedbyeachfactor:
(i)TypeofR
group
interactions
whichholdthe
tertiarystructure
ofproteins
together:
(ii)Drawthe
structureofanR
groupthatwould
interactinsucha
waydescribedin
(i)(includingthe
nameofthe
aminoacid
residueitis
from).
(1)Cu2+,
Ag+,Hg+
(2)heat
(3)
extreme
pH
changes
covalentdisulfide
bridges
e.g.
(phenylalanineside
chain)
Theseinteractions
arenotaffectedby
thepresenceofheavy
metalions.
Theseinteractions
arenotdisruptedby
extremepHchanges
becausethereareno
favourable
interactionsbetween
thenonpolarR
groupsinvolvedand
H+orOHions.
Theseinteractions
involvecovalentSS
bondswhichare
relativelystrong.
Hencetheyarenot
usuallydestroyedby
regularheating.(They
maybedestroyed
withsufficientheat
energy)
97
17NitrogenCompounds
SelfReview
Completethefollowingflowchartbyfillingintheappropriatereagentsandconditionsabovethesolidarrows.Draw
thestructureoftheorganicproductsformedintheboxes.
98

17.nitrogen Compounds Lecture Notes

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HwaChongInstitution2013

Reagents&Conditions: LiAlH4 indryether ORH2(g)/Ni,hightemp,highpressure

LiAlH4 is a very powerful reducing agent which works by

Ammonia or primary amines or secondary amines (in

Note: In the lab, the reaction

The regular arrangement of sections of the polypeptide chain. Common repeating

The overall threedimensional shape of a protein formed by folding of the

The characteristics manner in which the individually folded polypeptide subunits

The C=O group of one amino acid residue is hydrogen bonded to an NH

Note: N of NH should be on the

Changing the pH will protonate or deprotonate the ionic R groups and

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