Biomolecules lecture notes

carbohydrates,amino acids,proteins,lipids,proteins, vitamins and porphyrins

1. Biomolecules
Carbohydrates,Proteins,lipids,Nucleic
acids,VitaminsandPorphyrins.
LecturenotesforBScstudentsofBiologicalSciences
2020
SH/BT/GSc/CTA
[Typethecompanyname]
4/21/2020

2. 1
BIOMOLECULES SH/BT/GSC/CTA 1/1/2018Biomolecules
Carbohydrates,Proteins,lipids,Nucleic
acids,VitaminsandPorphyrins.
SH/BT/GSc/CTA
[COMPANYNAME]

3. 2
BIOMOLECULES SH/BT/GSC/CTA Module3Biomolecules
CarbohydratesStructureandBiologicalFunctions
Definition,basicstructureandstereoisomericformsofcarbohydrates
 
WhatareCarbohydrates?:
 
Carbohydratesaredefinedaspolyhydroxyaldehydeorketonewithempiricalformula(CH2O)n.,
thesimplestbeingglyceraldehydeordihydroxyacetone.Carbohydratesincludesugars,starches,
celluloseandmanyothercompoundsfoundinlivingorganisms.
 
Whataresaccharides?:
 
• SaccharideisatermderivedfromtheLatinforsugar(origin="sweetsand”).Theterm
carbohydrateismostcommoninbiochemistrywhereitisasynonymof saccharide.
• Carbohydratesareoftenclassifiedaccordingtothenumberofsaccharideunitstheycontain.
Theyaredividedintofourchemicalgroupings:monosaccharides,disaccharides,
oligosaccharidesandploysaccharides.
• Intheirbasicform,carbohydratesaresimplesugarsormonosaccharides.Thesesimplesugars
cancombinewitheachothertoformmorecomplexcarbohydrates.Thecombinationoftwo
simplesugarsisadisaccharide.Carbohydratescomprisingof2-10monosaccharideunitsare
calledoligosaccharides,andthosewithalargernumberarecalledpolysaccharides.
 
BasicStructure
• Thesaccharidesencounteredinlivingsytemsaregenerallybuiltofmonosaccharideswith
generalformula(CH2O)n wherenisthreeormore.
• AtypicalmonosaccharidehasthestructureH-(CHOH)x (C=O)-(CHOH)y -H,containinga
ketonicfunctionalgrouporH-(C=O)-(CHOH)x -H,containinganaldehydicfunctionalgroup.It
hashydroxylgroupsoneachcarbonatom,excludingthefunctionalgroupcarbonatom.
• Glucose,fructose,ribose,deoxyriboseandglyceraldehydearemostcommonlyoccurring
monosacchridesinthelivingsystems.
• Itisimportanttonotethattherearemanychemicalsthatmayhavethesameformulabutare
notconsideredtobemonosaccharides(e.g.,formaldehydeCH2Oandinositol(CH2O)6.

4. 3
BIOMOLECULES SH/BT/GSC/CTA  
Studyofcarbohydratesnecessitatestheconceptofisomerism:
 
• Twobroadcategoriesforisomericformsare:
(i)Structuralisomers.
(ii)Stereoisomers.
• Thestructuralisomersaredefinedasisomershavingsamemoleculeformulabutdifferent
structures.
• Thestereoisomershavesamemolecularandstructuralformulabutdifferinconfigurationi.e.
arrangementofatomsinspace.
• Stereoisomersarefurthersubgroupedintoopticalisomersandgeometricalisomers. 
• Opticalisomerismaremorerelevantincarbohydratechemistry.
• Opticalisomerismstemsfromthepresenceofchiralcentre(asymmetriccarbonatom).Chiral
centerreferstothecarbonatomhavingfourdifferentgroupsattachedtoit.Thisleadstotwo
possibilitiesbywhichatomscanbearrangedasshowninfigurebelow:

5. 4
BIOMOLECULES SH/BT/GSC/CTA  
• Incaseofcarbohydrates,D-glyceraldehydeisusedasreferencecompound.
• D-representsthehydroxylgrouponrighthandside,whereasL-representshydroxylgroupon
thelefthandside.Thesetwoformsreflectmirrorimageofeachother’sandcalled enantiomers.
Thestereoisomerswhicharenotenantiomersaretermedas distereoisomers.
Inthefigureabove,IandII,IIIandIVareenantiomerswhereasI,III,IVandII,III,IVarerelatedas
diastereomers.
• Enantiomershavesamephysicalpropertieslikemeltingpoint,boilingpoint,solubilityinvarious
solventsbuttheyrotateplanepolarizedlightinoppositedirections.Thosewhichrotateplane
polarizedlightinclockwisedirectionarecalled dextrorotatory (representedby+)andthose
whichrotateinanticlockwisedirectionarecalled levorotatory(representedby-).ThusD-
Glucosecanexistasbothdextrorotatory(+)andLevorotatory(-).
• Van’tHoffformulaof2nworksgivesthenumbersofpossibleopticalisomers,wherenisthe
numberofchiralcarbon.Atriosewillhavetwoopticalisomersandatetrosewillhavefour.
• D-GlucoseandD-MannosehavedifferentconfigurationonlyatC-2carbon.Such
carbohydrateswhichdifferinconfigurationonlyatonecarbonatomaredesignated
as epimers ofeachother
ClassificationsofMonosaccharides
 

6. 5
BIOMOLECULES SH/BT/GSC/CTA SimpleCarbohydrates:
 
• Thesearemadeupofasinglebasicsugar.Simplecarbohydratesareresponsibleforthe
sweettasteinourfood.Fruitsugar,tablesugarorcornsugarareallsimplesugars.On
consumption,thesesugarsaredirectlyabsorbedinthebloodandgenerallyusedforenergy
requirementsofthebody.
• Glucoseprovidesinstantenergyandreachesdifferentpartsofthebodyviablood,by
beingquicklymetabolized.
• Simplesugarsareoccurinplentyinnaturalfoodslikefruits,vegetables,milkandmilk
products.Additionally,honey,molasses,cornandmaplesyruparealsorichsourcesof
simplesugars.
 
Monosaccharides:
 
• 'Mono'referstosingle.
• Thesearethebasiccompoundsconsistingofcarbon,hydrogenandoxygenintheratio
1:2:1havingtheempericalformulaof(CH2O)n.
• Monosaccharidesaresweettotaste,colourlesscrystallinesolids,freelysolubleinwater
butinsolubleinnonpolarsolvents.
• Glucose,fructoseandgalactosearetypesofmonosaccharides.
 
Basicstructureofmonosaccharides:
 
• Anunbranchedsinglebondedcarbonchainprovidesbackboneformonosaccharides.
• Oneofthecarbonatomisdoublybondedtoanoxygenatomresultinginformationofa
carbonylgroup.
• Themonosaccharidesmaybeanaldehyde(carbonylgroupplacedattheendofthe
carbonchain)andisreferredtoasan ALDOSE oraketone(whenthecarbonylgroupis
placedatanyotherpositioninthechain)andisreferredtoasa KETOSE.
• Forexample,GlyceraldehydeisanaldosewhileDihydroxyacteoneisaketose.
• Monosaccharidescontaining3,4,5,6or7carbonatoms,intheirbackbonearecalledtriose,
tetroses,pentoses,hexosesandheptosesrespectively.
• Foraldehydicorketonicmonosaccharides,theyarethusdesignatedasaldotriose
(aldehyde+triose)andketotriose(Ketone+triose)respectively.
• Likewise,aldopentoses,ketopentoses;aldohexoses,ketohexoses;aldoheptosesand
ketoheptosesalsoexist.

7. 6
BIOMOLECULES SH/BT/GSC/CTA • Forexample,GlyceraldehydeisanaldotrisewhileDihydroxyacteoneisaketotrise.
 
Chainandringforms:structureandfunctionsofmajormonosaccharides
 
ChainandRingforms:
 
• Manysimplesugarscanexistinachainformoraringform.
• Theopen-chainformofamonosaccharideoftencoexistswithaclosedringformwherethe
aldehyde/ketoniccarbonylgroupcarbon(C=O)andhydroxylgroup(-OH)reactforminga
hemiacetalwithanewC-O-Cbridge.Fiveandsix-memberedringsarefavouredoverotherring
sizesbecauseoftheirlowangleandeclipsingstrain.
• Thecyclicstructuresaretermed furanose(five-membered)or pyranose(six-membered),the
nomenclaturebeingderivedonthebasisoftheirrelationshiptocommonheterocyclic
compoundsfuranandpyran.
 

8. 7
BIOMOLECULES SH/BT/GSC/CTA • Thecyclicpyranoseformsofvariousmonosaccharidesdrawninaflatprojectionareknownas
a Haworthformula aftertheBritishchemist,NormanHarworth.TheseHaworthformulasmake
itconvenientfordisplayingstereochemicalrelationships,butdonotrepresentthetrueshapeof
themolecules.
 
• Theglucoseringformiscreatedwhentheoxygenoncarbonnumber5linkswiththecarbon
comprisingthecarbonylgroup(carbonnumber1)andtransfersitshydrogentothecarbonyl
oxygentocreateahydroxylgroup.Therearrangementproducesalphaglucosewhenthe
hydroxylgroupisontheoppositesideofthe -CH2OH group,or beta glucose whenthehydroxyl
groupisonthesamesideasthe -CH2OH group.
 Isomers,suchasthese,whichdifferonlyintheirconfigurationabouttheircarbonylcarbonatom
arecalledanomers.
• Ketosessimilarlyformhemi-ketalringleadingtofuranoselikestructure.Hence,ketosesare
oftendesignatedinfuranosewhereasthealdosesinpyranoseform.
 
Propertiesofmonosaccharides:
 
• Simplemonosaccharidesarereducingagentsbecauseoftheirabilitytoreducepotential
oxidisingagentslikeCu
2+
 andhydrogenperoxide.Theyarethuscalled"reducingsugars".
• ThisreactionformsthebasisofBendict’stestforqualitativeanalysisofsimplesugars.
 
• Glucose,the"bloodsugar“andanimmediatesourceofenergyforcellularrespiration.
 

9. 8
BIOMOLECULES SH/BT/GSC/CTA Disaccharides:
 
• Whentwomonosaccharidesbondtogetherbyacondensationreaction,therebyreleasinga
moleculeofwater,adisaccharideisformed.Thetwomonosaccharideunitsarelinked
by glycosidicbond inαorβanomericcarbon.
• Commonlyavailabledisaccahridesaresucrose,maltoseandlactose.
• Disaccharidescannotbeabsorbedthroughthewallofthesmallintestineintothebloodstream.
Theyarethereforehydrolyzedtorespectivemonosaccharidesbycarbohydarespresentinsmall
intestine,specificallysucraseorinvertase,maltaseandlactase(β-galactosidase).
 
MajorDisaccharides:
 
Sucrose:
• Majorcarbohydratepresentincanesugar,commonlycalledtablesugar.
• Glucose+fructosearelinkedbyα(1-->1)glycosidicbonds.
 

10. 9
BIOMOLECULES SH/BT/GSC/CTA sucroseisnotareducingsugarduetotheabsenceoffreeanomericcarbonfrombothglucose
orfructoseunits.
• Animalsareunabletoabsorbsucroseassuchintothebloodstream.
• EnzymeSucrase,alsoknownasinvertasecatalyseshydrolysisofsucroseintoD-glucoseand
D-fructoseintheintestine,wherefromtheyarereadilyabsorbedintobloodstream.
 
Lactose:
 
• Amajorsugarinmilkandmilkproducts.
• Glucose+galactoseunitslinkedbyα(1-->4)glycosidicbonds.
 
Availabilityoffreecarbonylgrouponglucoseresiduemakesitareducingdisaccharide.
• EnzymeLactasecatalyzesthehydrolysisofthisdisaccharideduringdigestionprocessin
animals.
• LackofthisenzymesleadsaclinicalconditionreferredasLactoseintolerance.Thesubjectin
suchcasesareunabletometabolizelactose,becauseofalactasedeficiency.
 
Maltose:
 
• Simplestsugar;presentinbarleymaltandalsoaproductofstarchdigestion.
• Glucose+glucoselinkedbyα(1-->4)glycosidicbonds.

11. 10
BIOMOLECULES SH/BT/GSC/CTA  
Maltoseisareducingsugarbecauseofthepresenceofafreecarbonylgroupwhichmaybe
oxidizedtothefreeacid.
• MaltoseishydrolyzedtotwomoleculesofD-glucosebytheintestinalenzymemaltase,which
specificallycleavestheα(1-->4).bond.
 
Cellobiose:
Themoleculeisderivedfromthecondensationoftwoglucosemoleculeslinkedinaβ(1-->4)
fashion.Itcanbeobtainedbyenzymaticoracidichydrolysisofcelluloseandcelluloserich
materialssuchascotton,juteorpaper.
Oligosaccharides:
 
• Carbohydrateshavingmorethantwooruptotenmonosaccharideunitsaretermedas
oligosaccharides.Raffinoseandstachyosearetwomajorexamplesofoligosaccharideswhich
consistofrepetitivechainsoffructose,galactoseandglucose.
Raffinoseisatrisaccharidewidelyfoundinlegumesandvegetableslikebeans,peas,soy,
cabbage,brusselssprouts,andbroccoli.Here,galactoseisbondedtosucroseviaaα(1-->6)
glycosidiclinkage.HumansareunabletodigestsuchsaccharidesThusundigestedsaccharides
arethusfermentedbycolonicbacteriaresultingintoflatulenceformation.
 

12. 11
BIOMOLECULES SH/BT/GSC/CTA  
Polysaccharides:
 
• Polysaccharidesarepolymericcarbohydratestructures,formedofrepeatingunits(eithermono
-ordi-saccharides)joinedtogetherbyglycosidicbonds.
• PolysaccharideshaveageneralformulaofCx(H2O)y wherexisusuallyalargenumberbetween
200and2500.
• Thesestructuresareoftenlinear,butmaycontainvariousdegreesofbranching.
• Theymaybeamorphousoreveninsolubleinwater.
Basedonthemonosccharideunits,polysaccharidesarebroadlyputintotwocategories:
• Homopolysaccharides:
Ifthepolysaccharidesconsistsofonlyonetypeofmonosaccharideunits,thesearecalled
homopolysaccharides.Commonexampleofhomopolysaccharideisstarchwhichcomprisesof
onlyD-glucoseunits.
• Heteropolysaccharides: Whenmorethanonetypeofmonosaccharidesarepresentina
polysaccharide,theyarecalledheteropolysaccharidese.g.pectin(polymerofgalactouranicacid
anditsmethylatedester).
 

13. 12
BIOMOLECULES SH/BT/GSC/CTA Majorstoragepolysaccharides:
 
Starch: 
• Starchconstitutesthemostpredominantstoragepolysaccharideinnatureandisa
characteristicstoragesugarofallplantcells.
• Thisisabundantintubers,likepotatoesandcornseeds.
• Starchisapolymerofglucoseandcontainstwotypesofglucosepolymersnamely:
(a) Amylose: Amyloseconsistsoflinear,unbranchedchainsofseveralhundredD-glucose
residues.Theglucoseresiduesarelinkedbyα(1-->4)glycosidicbondbetweentheirC1andC4
carbonatoms.Molecularweightofsuchchainsmayextendupto50000.
(b)Amylopectin: Amylopectindiffersfromamyloseinbeinghighlybranched.Thetotalnumberof
glucoseresiduesinamoleculeofamylopectinmayrunintoseveralthousands.Branchingtakesplace
withα(1-->6)bondsoccurringevery24to30glucoseunits.
Starchcanbetransformedintomanycommercialproductsbyhydrolysisusingacidsor
enzymesascatalysts.
• Producedbythehydrolysisofstarch, dextrins aremixturesofpolymersofD-glucoseunits
linkedbyα(1-->4)orα(1-->6)glycosidicbonds.Thesearelowinmolecularweight.When
producedbyheat,thesearetermedaspyrodextrins.
• Partialhydrolysisofstarchresultsinalesssweetoralmostflavourless Maltodextrin.These
areeasilydigestableandhenceactasasourceofreadilyavailableenergy.Thesecanbeeasily
derivedfromanystarch.

14. 13
BIOMOLECULES SH/BT/GSC/CTA • Syrups,suchascornsyrupmadearemadefromhydrolysisofcornstarch. Cornsyrupsolids,
aremildlysweetsemi-crystallineorpowderyamorphousproducts.Thelatterarenotreadily
digestedbutpartiallyfermentedbyintestinalbacteria.
• HighFructoseCornSyrup(HFCS) isanotherderivativeofcornsyrupwhichisassweetas
sugarandisoftenusedinsoftdrinks.
• Whenstarchismodifiedbyanymechanicalorchemicaltreatments,theresultingproduct
is Modifiedstarch.
• Hydrogenatedglucosesyrup(HGS) isproducedbyhydrolyzingstarch,followedbyits
hydrogenation.Theresultingsyrupisusedtoproducesugaralcoholsaswellashydrogenated
oligo-andpolysaccharides.
• Polydextrose (poly-D-glucose)isahighly-branchedandsyntheticpolymer.Itisknownto
possessmanytypesofglycosidiclinkageswhicharegenerateduponheatingdextrose.
 
Glycogen:
 
• Glycogenisthemainstoragepolysaccharideinanimalcells,acounterpartofstarchinplant
cells.
• Glycogen,isalsoabranchedpolysaccharideofDglucosemonomerunitsbondedviaα(1-->4)
glycosidiclinkage.Theα(1-->6)branchesinglycogenareshorterandmorefrequentand
extensivethanthoseinamylopectin.Theoverallstructureismorecompacthere.
 
• Theglucosechainsareorganizedglobularlyoriginatingfromapairofmoleculesof
glycogenin,aproteinwithamolecularweightof38,000atthecoreofthestructure.
• Glycogeniseasilyconvertedbacktoglucosetoprovideenergy. 
• Bothglycogenandstarcharehydrolysedinthedigestivetractbyα-amylasespresentin
thesalivaandpancreaticjuicewhicharesecretedintothedigestivetract.
• α-amylaseshydrolyseα(1-->4)glycosidiclinkageoftheouterbranchesofglycogenand
amylopectinresultinginD-glucose,maltoseandaresistantcorenamedas“limitdextrin”.
• α-amylasescannotfurtherhydrolyselimitdextrinsbecauseoftheirinabilitytocleaveα(1
-->6)linkages.This,however,isachievedbya“debranching”enzyme,α(1-->6)glucosidase
actingonthebranchlinkages.
• Togetherα-amylaseandα(1-->6)glucosidasecompletelydegradeglycogenandstarch
(amylopectin). 
• β-Amylasehydrolysesalternateα(1-->4)glycosidiclinkagesyieldingmostlymaltose
withverylittleglucose.
 
Cellulose:

15. 14
BIOMOLECULES SH/BT/GSC/CTA  
• Celluloseisthemajorstructuralpolysaccharide,predominantinthecellwalloftheplants.
Celluloseisfoundincellwallsofstalks,stems,trunks,woodyportionsofplanttissues.
• Likestarch,cellulosealsocomprisesofglucoseasmonomerunitswhicharelinkedbyβ
(1-->4)glycosidicbondsinalinearfashion.Theabsenceofsidechainsallowscellulose
moleculestolieclosetogetherandformarigidstructures.
 
 Thebasicstructuraldifferencebetweencelluloseandstarchorglycogenisthatincellulose,the
glucosemonomerunitsarelinkedbyβ(1-->4)glycosidiclinkagewhileinamylose,amylopectin
orglycogentheglycosidiclinkagesareα(1-->4).
• Onaccountofthisstructuraldifference,themainchainsinglycogenorstarchassumeacoiled
andhelicalconformationleadingtoformationofdensegranules.Themainchainsofcellulose,
ontheotherhandtakeupanextendedconformationandallowlateralaggregationtoform
insolublefibrils.
• Cellulosearehydrolyzedtoitsconstituentglucoseunitsbymicroorganismsthatinhabitthe
digestivetractoftermitesandruminants.TheintestinaltractoftermitesharborsTriconympha,a
parasiticmicroorganismthatsecretesenzymecellulasewhichisacellulosehydrolysing
enzyme.
• Celluloseismostlyunavailableasfoodforvertebratessincetheycannotbe
digested/hydrolysedbyanyenzymeinthem(exceptcattleandruminantanimals).Thedigestive
systemofcattleandruminantanimalslikesheep,goats,camelsetcisthusabundantwith
microorganismsthatsecretecellulasetodegradecellulosetoglucoseunits.
 
Functionofstarchandcellulose:
 
• Theprecisefunctionsofthisclassofbiomoleculesinthecellsareinnumerable.
• Carbohydratesarethesourceofenergy(~4Kcal/g)inmostdiets.Potato,rice,wheat,andcorn
aremajorsourcesofstarchinthehumandietwhichprovidebulkofthecalories.
• Celluloseisthemajorconstituentofcellwall.Wood,cottonandpaperareformsofcellulose.
• Carbohydratealsoformsthepartofsomeglycoproteins.
Hemicellulose:

16. 15
BIOMOLECULES SH/BT/GSC/CTA  
• Theterm"hemicellulose"appliestothepolysaccharidecomponentsofplantcellwalls
otherthancellulose.Thisisapolysaccharideintheplantcellwallswhichisextractableby
dilutealkalinesolutions.
• Hemicellulosescomprisealmostone-thirdofthecarbohydratesinwoodyplanttissue.
Thisisalsofoundinfruit,plantstems,andgrainhulls.
• Thechemicalstructureofhemicellulosesconsistoflongchainsofavarietyofpentoses,
hexoses,andtheircorrespondinguronicacids.
• Althoughundigestible,hemicellulosescanbefermentedbyyeastsandbacteria.The
polysaccharidesyieldingpentosesonhydrolysisarecalledpentosans.Xylanismajor
exampleofapentosanconsistingofD-xyloseunitswithβ(1-->4)linkages.
 
Dextran:
 
• Dextranisapolysaccharidewhereinthemainchainsareformedbyα(1-->6)glycosidic
linkagesandthesidebranchesareattachedbyα(1-->3)orα(1-->4)linkages.
• Dextranisanoralbacterialproductthatadherestotheteeth,creatingafilmcalledplaque.
• Itisalsousedcommerciallyinconfections,inlacquers,asfoodadditives,andasplasma
volumeexpanders.
 
• Someplantsstorecarbohydratesintheformof inulin.Inulins,alsocalledfructans,are
polymersconsistingoffructoseunitsthathaveaterminalglucose.
• Thesearepresentinmanyvegetablesandfruits,includingonions,leeks,garlic,bananas,

17. 16
BIOMOLECULES SH/BT/GSC/CTA asparagus,chicory,andJerusalemartichokes.
• Oligofructose hasthesamestructureasinulin,butthechainsconsistof10orfewer
fructoseunits.
• Oligofructosehasapproximately30to50%ofthesweetnessoftablesugar.Inulinand
oligofructosearenondigestiblebyhumanintestinalenzymes,butarefermentedbycolonic
microorganisms.
• Oligofructoseareoftenaddedtoprobioticdairyproductslikeyoghurt.Theyareconsumed
bybeneficialintestinalbacteriawhichtherebymultiplyfaster.Suchbacteriaareimportant
fordigestionandtheimmunesystem. 
• Inulinandoligofructoseareusedtoreplacefatorsugarinfoodslikeicecream,dairy
products,confectionsandbakedgoods.
 
Pectin:
 
• Pectinisapolysaccharidethatactsasabindingmaterialforthecellwallsofplant
tissues.Lemonsandorangescontainsapproximately30%pectin.
• Pectinisthemethylatedesterofpolygalacturonicacid,whichconsistsofchainsof300to
1000galacturonicacidunitsjoinedwithα(1-->4)linkages.
• Pectinisanimportantingredientoffruitpreserves,jellies,andjams.
 
 
Peptidoglycans:
 
• Thisisanimportantpolymerfoundinthebacterialplasmamembrane.Itconsistsof
polysaccharideandpeptidechainsinastrongmolecularnetwork.
• Peptidoglycan,alsoknownas murein,consistsofalternatingresiduesofβ(1-->4)linked
N-acetylglucosamineandN-acetylmuramicacid.Apeptidechainofthreetofiveamino
acidsisattachedtotheN-acetylmuramicacid.Thepeptidechaincanbecross-linkedtothe
peptidechainofanotherstrandformingathreedimensionalnetwork.Peptidoglycanserves
thefunctionalroleofprovidingstructuralstrengthandrigiditytothebacterialcellwall.
 

18. 17
BIOMOLECULES SH/BT/GSC/CTA Aminoacids,peptideandproteins
Aminoacids-buildingblocksofproteins
 
• Proteinsareoneofthemostimportantclassofbiomoleculeswhichplaypivotalrolesinawide
arrayofcellularactivities.
• Proteinsareconstitutedbyaminoacids,asmonomericunitorbuildingblocks.Atypicalamino
acidhastheamino,carboxylmoietiesand"R"group(alsocalledassidechain).
 
Aminoacids:
 
• Whendissolvedinwater,aminoacidsexistsinsolutionasdipolarioncalled"zwitterion".Itcan
actasanacid(protondonor)orabase(protonacceptor).Becauseofthisdualnature,theyare
oftencalledasampholytes. 
• Aminoacidsintheproteinarelinkedbypeptidebonds.Thus,twoaminoacidsjoinedby
peptidebondarecalleddi-peptide,three-tripeptide,four-tetrapeptide.Thelongerchainiscalled
polypeptide.Proteinsaremadeofsingleormorepolypeptidechains.
 

19. 18
BIOMOLECULES SH/BT/GSC/CTA • Therearetwentydifferentkindofaminoacidsfoundinbiologicalsystemsbesidesome
unusualaminoacids.ThenatureofR-groupvariesfromaminoacidtoaminoacid.
• EachfunctionalgroupofaminoacidhasafixedpKavalue.pKavaluesofaminoacidside
chainsplayanimportantroleindefiningthepH-dependentcharacteristicsofaprotein.Thus,the
ionizationstateofaminoacidswillbepHdependent.
• Eachaminoacidhasastandardthreeletterandoneletterabbreviationswhichareused
insteadoffullname.
 
FunctionalgroupsandpKavaluesofdifferentaminoacids 

20. 19
BIOMOLECULES SH/BT/GSC/CTA Non-AromaticAminoAcidswithHydroxylR-Groups:
 
AminoAcidswithSulfur-ContainingR-Groups:
AcidicAminoAcidsandtheirAmides:

21. 20
BIOMOLECULES SH/BT/GSC/CTA BasicAminoAcids:
 
AminoAcidswithAromaticRings:
IminoAcids:
 Allaminoacidsexceptglycine(R=H)arechiral,existinginDandLform.However,alltheamino
acidsinbiologicalsystemexistsintheL-configuration,where"L"impliesthattheaminoacid
confirmationsimilartoL-glyceraldehyde.
Propertiesofaminoacids:
 
• Thepropertiesofeachaminoacidaremainlydictatedbythesidechain,whichcanvaryinsize,
shape,charge,reactivityandabilitytohydrogenbond.Theaminoacidsaregroupedaccordingto
thepropertiesoftheirsidechains:
1.Aminoacidswithnon-polarorhydrophobicRgroup:- 
• Aliphatic:Thefirstsixaminoacids,glycine(GLY,G),alanine(ALA,A),Methionine(Met,M),
valine(VAL,V)leucine(LEU,L),andisoleucine(ILE,I),proline(PRO)andarealiphaticinnature.
Glycineissmallest.Glycineandalaninearetoosmalltohaveahydrophobiceffect.Methionine
issulphurcontainingaminoacid.Valine,leucineandisoleucineareconsiderablyhydrophobic.
• Aromatic:Phenylalanine(PHE,F),tryptophan(TRP,Y)andtyrosine(TYR,W)arearomaticin

22. 21
BIOMOLECULES SH/BT/GSC/CTA nature.Thesecontainaromaticsidechain.Theyarespecificallyabsorbsat280nmthusform
thebasisofquantitativeestimationofproteinbyultraViolet(UV)method.
2.AminoacidswithpolarbutunchargedRgroup:
• Thesearesulfurcontaining,namelycysteine(CYS,C),twohydroxyl-containingserine(SERS)
threonine(THR,T)andamidecontainingAspargine(ASN,N)andglutamine(GLN,Q).
• Onetypicaliminoacid,Proline(PRO,P)isalsofoundinthiscategory.Becauseofitscyclic
structure,itleadstobendingofproteinchain.Prolineisanimineandusualinthatitsnitrogen
atompresentassecondary.
• Cysteineisinvolvedinintermoleculardisulfidebond(calledcystine)withothercysteineofthe
polypeptidechain.Thesedisulphidebondsaretheonlycovalentbondbesidepeptidebondin
theproteinandimpartstabilitytotheprotein.
• SerandThrhavesidechainswhichcanhydrogenbondtowaterortoothergroupson
neighbouringmacromolecules.AsnandGlnareamideofacidicaminoacids-asparticand
glutamicacid.
3.Polarpositivelychargedaminoacids:
• Aminoacidslysine(LYS,K),arginine(ARG,R)andhistidine(HIS,H)areconsideredbasic
hydrophilic,sincetheycontainbasicsidechaingroupsthatwillhaveapositivechargeatpH7.4.
4.Polarnegativelychargedaminoacids:
• Asparticacid(ASP,D)andglutamicacid(GLU,E)areconsideredacidichydrophilic,sincethey
containacidicsidechaingroupsthatwillhaveanegativechargeatpH7.4.
Peptidebonds:
 
• Proteinchainsareheldtogetherbypeptidebonds,whicharesimplyamidelinkagesbetween
alphaaminoandcarboxylicgroupofneighbouringaminoacids.Aminoacidslinked,through
peptidebonds,formspolypeptide.TheirmolecularweightsareexpressedinDaltons,(1Daltonis
equalto1atomicmassunit).
• Eachpeptidechainhastwofreeends,theaminoterminusorN-terminal,whichisontheleft,
andthecarboxylterminusorC-terminal,whichisontheright.Thepeptidechainsisrepresented
fromN-terminaltoC-terminalandthesequenceofaminoacidiswritteninthreeletter
abbreviationse.g.N-Met-Ser-Tyr-Cys-Val-Lys-Ala-C.
• Thepeptidebonditselfisrigid,andthusisnotfreetorotate.Thisrigidityleadstoonlya
definitepossibleconformationtoproteinstructure.
 

23. 22
BIOMOLECULES SH/BT/GSC/CTA Inapeptidebond,allthesixatomwithintheplanehavefixedbondlengthandangles.Thesebondare
α-carbontocarbonylcarboncalledψ;imidenitrogentoα-carboncalledφandtheC-Nbond.
• BasedonthesterichindranceofRgroups,aconstraintisposedonrotationofC-CandC-N,
limitingthevalueofψandφ.Thisallowsonlyafixedsecondarystructure(helixorsheetetc)
accordingtheaminoacidresidues(Rgroup)andtheirsequence.
• Basedonψandφvalues,thestructurecanbepredictedbyRamcahandran’splot.
 
Somebiologicallyimportantpeptides:
 
1.Glutathione -atripeptidewhichpreventsoxidativedamagetoRBC.
2.Vesopressinandoxytocins -anonapeptide;hormonescausingriseinbloodpressureby
constrictingtheperipheralbloodvessels;andcontractionofsmoothmuscles,respectively.

24. 23
BIOMOLECULES SH/BT/GSC/CTA 3.Gramicidin -acirculardecapeptideusedasanantibiotic.
4.Aspartame -atripeptidewidelyusedasanartificialsweetener.
Assayofaminoacids
Thereactionbetweenalpha-aminoacidandninhydrininvolvedinthedevelopmentofcolorare
describedbythefollowingfivemechanisticsteps:
alpha-aminoacid+ninhydrin--->reducedninhydrin+alpha-aminoacid+H2O
alpha-aminoacid+H2O--->alpha-ketoacid+NH3
alpha-ketoacid+NH3--->aldehyde+CO2
Step(1)isanoxidativedeaminationreactionthatremovestwohydrogenfromthealpha-aminoacid
toyieldanalpha-iminoacid.Simultaneously,theoriginalninhydrinisreducedandlosesanoxygen
atomwiththeformationofawatermolecule.
InStep(2),theNHgroupinthealpha-iminoacidisrapidlyhydrolyzedtoformanalpha-ketoacidwith
theproductionofanammoniamolecule.Thisalpha-ketoacidfurtherundergoesdecarboxylation
reactionofStep(3)
Underaheatedconditiontoformanaldehydethathasonelesscarbonatomthantheoriginalamino
acid.Acarbondioxidemoleculeisproducedhere.Thesefirstthreestepsproducethereduced
ninhydrinandammoniathatarerequiredfortheproductionofcolorinthelasttwoSteps(4)and(5).
Theoverallreactionfortheabovereactionsissimply(slightlyinaccurately)expressedinReaction
(6)asfollows:
alpha-aminoacid+2ninhydrin--->CO2+aldehyde+finalcomplex(BlUE)+3H2O
Insummary,ninhydrin,whichisoriginallyyellow,reactswithaminoacidandturnsdeeppurple.Itis
thispurplecolorthatisdetectedinthismethod.
Ninhydrinwillreactwithafreealpha-aminogroup,NH2-C-COOH.Thisgroupiscontainedinallamino
acids,peptides,orproteins.Whereas,thedecarboxylationreactionwillproceedforafreeamino
acid,itwillnothappenforpeptidesandproteins.Thus,theoreticallyonlyaminoacidswillleadtothe
colordevelopment.However,oneshouldalwayscheckoutthepossibleinterferencefrompeptides
andproteinsbyperformingblanktestsespeciallywhensuchsolutionsarereadilyavailable.For
example,onecansimplyaddtheninhydrinreagenttoasolutionofonlyproteinsandseeifthereis
anycolordevelopment.Thereisnoexcuseforfailingtoperformsuchavitaltestwhenthesample
mixturecontainsbothproteinsandaminoacids.Therearealsoreportsthatchemicalcompounds
otherthanaminoacidsalsoyieldpositiveresults.
Thistestcanbeusedroutinelyforthedetectionofglycineintheabsenceofotherinterfering
species.Althoughthisisafastandsensitivetestforthepresenceofalpha-aminoacids,becauseof
thenonselectivity,itcannotbeusedtoanalyzetherelativeindividualcontentsofamixtureof
differentaminoacids.Furthermore,thecolorintensitydevelopedisdependentonthetypeofamino
acid.Finally,itdoesnotreactwithtertiaryoraromaticamines.
Notethatsinceninhydrinisastrongoxidizingagent,propercautionshouldbeexercisedinhandling
thiscompound.Itisespeciallypotentattheelevatedtemperatureunderwhichthereactioniscarried

25. 24
BIOMOLECULES SH/BT/GSC/CTA out.Theninhydrinreagentwillstaintheskinblueandcannotbeimmediatelywashedoffcompletely
ifitcomesincontactwiththeskin.However,asinanyotherstainontheskin,thecolorwillgradually
ruboffafteraboutaday.
Proteinsarenitrogenousorganiccompoundsofhighmolecularweightwhichplayavitalorprime
roleinlivingorganisms.Theyaremadeupof20standarda-aminoacids.
Functionsofproteins:
 
Proteinscarryoutmostdiverseandpossiblythelargestvolumesofcellularfunctions.Someofthe
keyfunctionsaresummarizedasbelow:
• Biocatalysis-Almostallthebiologicalreactionsarecatalyzedbytheenzymes.Thesearesubstrate
specificandcarryoutreactionsatveryhighratesundermildphysiologicalconditions.Several
thousandenzymeshavebeenidentifiedtodate.
• Membraneareconstituteoflipoproteinandsomeproteinsareintegralpartofmembrane.
Receptorsfoundonthemembranearealsoproteininnature.
• Transportandstorageproteins-smallmoleculesareoftencarriedbyproteinsinthephysiological
settinge.g.haemoglobinisresponsibleforthetransportofoxygentotissues.
• Musclearemadeupofproteinsandtheircontractionisdonebyactinandmyosinprotein.
• Mechanicalsupport-skinandbonearestrengthenedbytheproteincollagen.
• Antibodiesofimmunesystemareproteinstructures.
ClassificationofProteins:
Proteinsareclassifiedbasedupon:
(1)Theirsolubilityand(2)Theirstructuralcomplexity.

26. 25
BIOMOLECULES SH/BT/GSC/CTA A.ClassificationBaseduponSolubility:
Onthebasisoftheirsolubilityinwater,proteinsareclassifiedinto:
1.Fibrousproteins:
Theseareinsolubleinwater.Theyincludethestructuralproteins.Theyhavesupportivefunction
(e.g.,collagen)and/orprotectivefunction(e.g.,hairkeratinandfibrin).
2.Globularproteins:
Theyaresolubleinwater.Theyincludethefunctionalproteins,e.g.,enzymes,hemoglobin,etc.
B.ClassificationBaseduponStructuralComplexity:
Onthebasisoftheirstructuralcomplexitytheyarefurtherdividedinto:
(1)Simple
(2)Conjugatedand
(3)Derivedproteins.
1.Simpleproteins:
Proteinswhicharemadeupofaminoacidsonlyareknownassimpleproteins.
Theyarefurthersub-dividedinto:
(a) Albumins:
Theyarewatersoluble,heatcoagulableandareprecipitatedonfullsaturationwithammonium
sulphate,e.g.,serumalbumin,lactalbuminandovalbumin.
(b) Globulins:
Theyareinsolubleinwater,butsolubleindilutesaltsolutions.Theyareheatcoagulableand
precipitateonhalf-saturationwithammoniumsulphate,e.g.,serumglobulinandovo-globulin.
(c) Glutelins:
Theyareinsolubleinwaterandneutralsolvents.Solubleindiluteacidsandalkalies.Theyare
coagulatedbyheat,e.g.,glutelinofwheat.
(d) Prolamines:
Waterinsolublebutsolublein70%alcohol,e.g.,gliadinofwheat,proteinsofcorn,barley,etc.
(e) Histones:
Watersoluble,basicinnatureduetothepresenceofarginineandlysine,foundinnucleus.Theyhelp
inDNApackaginginthecell.Theyformtheproteinmoietyofnucleoprotein.
(f) Protamine’s:
Watersoluble,basicinnature,not-heatcoagulable.Foundinspermcells,hencecomponentof
spermnucleoprotein.
(g) Globin’s:
Theyarewatersoluble,non-heatcoagulable.e.g.,globinofhaemoglobin.
(h) scleroproteins:

27. 26
BIOMOLECULES SH/BT/GSC/CTA Insolubleinallneutralsolvents,diluteacidsoralkalies,e.g.,keratinofhairandproteinsofboneand
cartilage.
2. Conjugatedproteins:
Proteinswhicharemadeupofaminoacidsandanon-aminoacid/proteinsubstancecalledthe
prostheticgroupareknownasconjugatedproteins.
Thevarioustypesofconjugatedproteinsare:
(a) Chromoproteins:
Herethenon-proteinpartisacolouredcompoundinadditiontotheproteinpart.Ex.Haemoglobin
hashemeastheprostheticgroupandcytochromesalsohaveheme.
(b) Nucleoproteins:
Theseproteinsareboundtonucleicacids,e.g.,chromatin(histones+nucleicacids).
(c) Glycoproteins:
Whenasmallamountofcarbohydrateisattachedtoaproteinitisknownasglycoproteins,e.g.,
mucinofsaliva.(Note:Glycoproteinshavemajoramountsofproteinandsomeamountof
carbohydratesandproteoglycanscontainmajoramountsofcarbohydratesandlittleamountof
proteins).
(d) Phosphoprotein:
Phosphoricacidispresentwiththeprotein.Ex.Milkcaseinandeggyolk(vitellin).
(e) Lipoproteins:
Proteinsincombinationwithlipids,e.g.,LDL,HDL.
(f) Metalloproteins:
Theycontainmetalioninadditiontotheaminoacids,e.g.,hemoglobin(iron),ceruloplasmin
(copper).
3. Derivedproteins:
Theyaretheproteinsoflowmolecularweightproducedfromlargemolecularweightproteinsbythe
actionofheat,enzymesorchemicalagents.
Proteins→Proteans→Proteoses→Peptones→Peptides→Aminoacids
Proteinconformation/structure
 
• Thespatialarrangementofatomsinaproteiniscalleditsconformation. 
• Thepossibleconformationsofaproteinincludeanystructuralstatethatcanbeachievedwithout
breakingcovalentbonds.Achangeinconformationcouldoccur,forexample,byrotationabout
singlebonds.Ofthenumerousconformationsthataretheoreticallypossibleinaproteincontaining
hundredsofpeptidebonds,oneor(morecommonly)afewgenerallypredominateunderbiological
conditions.
• Theneedformultiplestableconformationsreflectsthechangesthatmustoccurinmostproteins
astheybindtoothermoleculesorcatalyzereactions.

28. 27
BIOMOLECULES SH/BT/GSC/CTA • Theconformationsexistingunderagivensetofconditionsareusuallytheonesthatare
thermodynamicallythemoststable,havingthelowestGibbsfreeenergy(G).Proteinsinanyoftheir
functional,foldedconformationsarecallednativeproteins.
 
Structure:
 
• Proteinshaveatotaloffourlevelsofstructures.
• Primarystructure.
• Secondarystructure.
• Tertiarystructure.
• Quaternarystructure.
 
• Primarystructure:-
• Thesimpleaminoacidsequenceofaproteiniscalledasitsprimarystructure.
• Sincethepossiblewayofarrangementofthechainwilldependonthesequenceofaminoacid
residuesleadingtoproperproteinfolding,theprimarystructuredictatethreedimensionalstructure
oftheproteins.

29. 28
BIOMOLECULES SH/BT/GSC/CTA Secondarystructure:-
• Thisdefinestheinteractionofcloselylocatedaminoacidsinachain.Twomaintypesofsecondary
structuresobservedintheproteinsarehelices(αhelices)andpleatedsheets(βpleatedsheets).
• Alphahelixisahelicalstructurearoundanaxis.
• Thisiscoiledinclockwise(righthanded)manner.Ithasanaverageof3.6aminoacidsperturn.
Pleasewriteotherdimensionstoo. 
• Thereare3.6residueperturnwithinafixpitchof5.4
0
A
• Thustheriseperresiduecomeouttobe1.5
0
A.Inatypicalα-helixφvaluerangesfrom113to
132
0
 andψfrom123to136
0
.

30. 29
BIOMOLECULES SH/BT/GSC/CTA  
Thereasonastowhyalphahelicesformmorereadilyinproteinsthananyotherpossible
conformationsisthatthesearrangementsmakeoptimaluseofinternalhydrogenbondstoattain
stability.Thehelixisstabilizedbyhydrogenbondingbetweenthecarbonylofeachfirstaminoacid
ofthechaintotheNHoftheaminoacidfourresiduesaway.Allmainchainaminoandcarboxyl
groupsarethushydrogenbonded,andtheRgroupsstickoutfromthestructureinaspiral
arrangement.
Betapleatedsheet iscomposedoftwoormorestraightchainsthatarehydrogenbondedsideby
side.Iftheaminoterminiareonthesameendofeachchain,thesheetistermedparallel,andifthe
chainsrunintheoppositedirection(aminoterminalonoppositeends),thesheetistermed
antiparallel.
Pleatedsheetsmaybeformedfromasinglechainifitcontainsabetaturn,whichformsahairpin
loopstructure.Oftenaprolinecanbefoundinabetaturn,sinceitplacesa"kink"inthechain.
GlycineandAlaarepredominantaminoacidsinbetasheet.
 
• Tertiarystructure:- referstothearrangementofaminoacidsinthespacei.e.inthreedimensional
form.
• Distinctaminoacidarebroughtcloserinchainarefurtherlinkedby:
-polar-polarinteraction,
-hydrophobicinteraction,

31. 30
BIOMOLECULES SH/BT/GSC/CTA -ionicinteraction,
-disulfidebonds,
-VanderWaalsforces.
-hydrogenbonds.
• Hydrophobicaminoacids:- areburiedinsidethecoreofproteinandchargedandpolargroupare
locatedonthesurfacewhichtendtoclusterandexcludewater.Thisallowsaproteintohavegreater
watersolubility.
• Quaternarystructure:- Ifproteinconsistsofmorethanonepolypeptidechains,theirassociation
witheachother–impliestheQuaternarystructure.
 
• Accordinglyproteinaretermedasdimeric(whereinonechainisreferredasmonomericunit),
trimericoroligomeric.Ifthechainsaresimilari.e.havesameaminoacidsequencethesearecalled
homomericorheteromericifchainsaredifferent.
• Proteinshavealsobeenputintotwomajorgroups:
(a) Fibrousproteins,havingpolypeptidechainsarrangedinlongstrandsorsheets.
(b) Globularproteins,havingpolypeptidechainsfoldedintoasphericalorglobularshape.
• Thetwogroupsare structurallydistinct: fibrousproteinsusuallyconsistlargelyofasingletypeof
secondarystructure;globularproteinsoftencontainseveraltypesofsecondarystructuree.ga-
keratinsarepredominantlyalphahelixwhereassilkproteinsarebeta–sheets.
• Thetwogroupsdiffer functionally inthatthestructuresthatprovidestructure,support,shape,and
externalprotectiontovertebratesaremadeoffibrousproteins,whereasmostenzymesand
regulatoryproteinsareglobularproteins.
 
ProteinAssaymethods

32. 31
BIOMOLECULES SH/BT/GSC/CTA Introduction
Proteinassaysareoneofthemostwidelyusedmethodsinlifescienceresearch.Estimationof
proteinconcentrationisnecessaryinproteinpurification,electrophoresis,cellbiology,molecular
biologyandotherresearchapplications.Althoughthereareawidevarietyofproteinassays
available,noneoftheassayscanbeusedwithoutfirstconsideringtheirsuitabilityforthe
application.Eachassayhasitsownadvantagesandlimitationsandoftenitisnecessarytoobtain
morethanonetypeofproteinassayforresearchapplications.
DyeBindingAssays(Bradford)thedyebindingproteinassayisbasedonthebindingofprotein
moleculestoCoomassiedyeunderacidicconditions.Thebindingofproteintothedyeresultsin
spectralshift,thecolorshiftsfrombrown(Amax=465nm)toblue(Amax=610nm).Thechangein
colordensityisreadat595nmandisproportionaltoproteinconcentration.Thebasicaminoacids,
arginine,lysineandhistidineplayaroleintheformationofdye-proteincomplexescolor.Small
proteinslessthan3kDaandaminoacidsgenerallydonotproducecolorchanges.CB™andCB-X™
proteinassaysaredyebindingproteinassays.SPN™andSPN™-htpproteinassaysarespincolumn
formatdyebindingassays
CopperIonBasedAssays(Lowry&BCA)
Inthecopperionbasedproteinassays,theproteinsolutionismixedwithanalkalinesolutionof
coppersalt.Underalkalineconditions,cupricions(Cu2+)chelatewiththepeptidebondsresultingin
reductionofcupric(Cu2+)tocuprousions(Cu+).Ifthealkalinecopperisinexcessovertheamount
ofpeptidebonds,someofthecupricions(Cu2+)willremainunboundtothepeptidebondsandare
availablefordetection(Figure1).Proteinassaysbasedoncopperionscanbedividedintotwo
groups,assaysthatdetectreducedcuprousions(Cu+)andassaysthatdetecttheunboundcupric
(Cu2+)ions.Thecuprousionsaredetectedeitherwithbicinchoninicacid(BCA)orFolinReagent
(phosphomolybdic/phosphotungsticacid)asintheproteinassaysbasedonLowrymethod.
Cuprousions(Cu+)reductionofFolinReagentproducesabluecolorthatcanbereadat650-750nm.
Theamountofcolorproducedisproportionaltotheamountofpeptidebonds,i.e.sizeaswellasthe
amountofprotein/peptide.
Thepresenceoftyrosine,tryptophan,cysteine,histidineandasparginineinproteincontributesto
additionalreducingpotentialandenhancestheamountofcolorproduced.Hence,theamountof
bluecolorproducedisdependentonthecompositionofproteinmolecules.Thereactionofcuprous
ions(Cu+)withthebicinchoninicacidandcolorproductionissimilartothatofFolinReagent.Inthe
assaysbasedonthedetectionofunboundcupricions,theproteinsolutionismixedwithanamount
ofalkalinecopperthatisinexcessovertheamountofpeptidebond.Theunchelatedcupricionsare
detectedwithacolor-producingreagentthatreactswithcupricions.Theamountofcolorproduced
isinverselyproportionaltotheamountofpeptidebond
ProteinAssay
ProteinAssayIntroductionProteinassaysareoneofthemostwidelyusedmethodsinlifescience
research.Estimationofproteinconcentrationisnecessaryinproteinpurification,electrophoresis,
cellbiology,molecularbiologyandotherresearchapplications.Althoughthereareawidevarietyof
proteinassaysavailable,noneoftheassayscanbeusedwithoutfirstconsideringtheirsuitabilityfor
theapplication.Eachassayhasitsownadvantagesandlimitationsandoftenitisnecessaryto
obtainmorethanonetypeofproteinassayforresearchapplications.Thisguideisdesignedtohelp
researchersselectthemostappropriateassayfortheirapplication.G-Biosciencesoffersassays
thatareenhancementsofdyebindingproteinassays(Bradford),proteinassaysbasedoncopper

33. 32
BIOMOLECULES SH/BT/GSC/CTA ions(Lowry),oranovelteststripandspotapplicationassay.
DyeBindingAssays(Bradford)
ThedyebindingproteinassayisbasedonthebindingofproteinmoleculestoCoomassiedyeunder
acidicconditions.Thebindingofproteintothedyeresultsinspectralshift,thecolorshiftsfrom
brown(Amax=465nm)toblue(Amax=610nm).Thechangeincolordensityisreadat595nmandis
proportionaltoproteinconcentration.Thebasicaminoacids,arginine,lysineandhistidineplayarole
intheformationofdye-proteincomplexescolor.Smallproteinslessthan3kDaandaminoacids
generallydonotproducecolorchanges.CB™andCB-X™proteinassaysaredyebindingprotein
assays.SPN™andSPN™-htpproteinassaysarespincolumnformatdyebindingassays.CopperIon
BasedAssays(Lowry&BCA)Inthecopperionbasedproteinassays,theproteinsolutionismixed
withanalkalinesolutionofcoppersalt.Underalkalineconditions,cupricions(Cu2+)chelatewith
thepeptidebondsresultinginreductionofcupric(Cu2+)tocuprousions(Cu+).Ifthealkaline
copperisinexcessovertheamountofpeptidebonds,someofthecupricions(Cu2+)willremain
unboundtothepeptidebondsandareavailablefordetection(Figure1).Proteinassaysbasedon
copperionscanbedividedintotwogroups,assaysthatdetectreducedcuprousions(Cu+)and
assaysthatdetecttheunboundcupric(Cu2+)ions.Thecuprousionsaredetectedeitherwith
bicinchoninicacid(BCA)orFolinReagent(phosphomolybdic/phosphotungsticacid)asinthe
proteinassaysbasedonLowrymethod.Cuprousions(Cu+)reductionofFolinReagentproducesa
bluecolorthatcanbereadat650-750nm.Theamountofcolorproducedisproportionaltothe
amountofpeptidebonds,i.e.sizeaswellastheamountofprotein/peptide.
Thepresenceoftyrosine,tryptophan,cysteine,histidineandasparginineinproteincontributesto
additionalreducingpotentialandenhancestheamountofcolorproduced.Hence,theamountof
bluecolorproducedisdependentonthecompositionofproteinmolecules.Thereactionofcuprous
ions(Cu+)withthebicinchoninicacidandcolorproductionissimilartothatofFolinReagent.Inthe
assaysbasedonthedetectionofunboundcupricions,theproteinsolutionismixedwithanamount
ofalkalinecopperthatisinexcessovertheamountofpeptidebond.Theunchelatedcupricionsare
detectedwithacolor-producingreagentthatreactswithcupricions.Theamountofcolorproduced
isinverselyproportionaltotheamountofpeptidebond.
 
Commontotalproteinassays.
assay absorption mechanism detection
limit
advantages disadvantages
UVabsorption280nm
tyrosineand
tryptophan
absorption
0.1-100
ug/ml
smallsample
volume,rapid,
lowcost
incompatiblewith
detergentsand
denaturating
agents,high
variability
Bicinchoninic
acid
562nm
copperreduction
(Cu
2+
 toCu
1+
),
BCAreaction
withCu
1+
20-2000
ug/ml
compatiblewith
detergentsand
denaturating
agents,low
variability
loworno
compatibilitywith
reducingagents
Bradfordor
Coomassie
470nm
complex
formation
20-2000
ug/ml
compatiblewith
reducingagents,
incompatiblewith
detergents

34. 33
BIOMOLECULES SH/BT/GSC/CTA brilliantblue
between
Coomassie
brilliantbluedye
andproteins
rapid
Lowry 750nm
copperreduction
byproteins,Folin
-Ciocalteu
reductionbythe
copper-protein
complex
10-1000
ug/ml
highsensitivity
andprecision
incompatiblewith
detergentsand
reducingagents,
longprocedure
StructureandFunctionsofLipids
Definition,nomenclatureandfunctionoflipids
 
Whatarelipids?:
 
• Lipidsareoneamongthefourmajorbiomoleculesoflivingsystems.
• Bydefinition,thesearetheclassofbiomoleculeswhichareinsolubleorsparinglysolublein
aqueoussolutionsandsolubleinorganicsolvents.
• Fattyacidsaremajorconstituentsoflipids.Fattyacidsaremonocarboxylicacidcontaining
short/long-chainhydrocarbonmolecules.Someimportantfattyacidsareenlistedbelow.
• Thenumberingofcarbonsinfattyacidsbeginswiththecarbonofthecarboxylategroup.Fatty
acidrepresentedbythetotalnumberofcarbonse.g.,palmiticacida16-carbonfattyacid
CH3(CH2)14COOHisdesignatedasC16.
• ItiscustomarytowriteitasC16:0wherezerorepresentthatthereisnodoublebondinthe
fattyacid).Ifthereisonedoublebond,thenitwillbewrittenasC:16:1
 
 
Typesoffattyacids:
 

35. 34
BIOMOLECULES SH/BT/GSC/CTA • Saturatedfattyacids:
Allsetsofexamplesintheprevioustablewerefattyacidsthatcontainednocarbon-carbon
doublebonds.Thesearecalledsaturatedfattyacids.Saturatedfattyacidshavingshortcarbon
chainareliquidatroomtemperature,whereaslongcarbonchainfattyacidsaresolid.
• Unsaturatedfattyacids:
Thesehavecarbon-carbondoublebondsinbetween,thusleadingtounsatuaration.The
representationsforthesefattyacidsconsistsofthenumberofcarbonatoms,followedbythe
numberdoublebondandtheplaceofunsaturation.Theplaceofunsaturationinafattyacidis
indicatedbythesymbol(Δ)andthenumberofthefirstcarbonofthedoublebondinsuperscript
form.Thusoleicacida16-carbonfattyacidwithonesiteofunsaturationbetweencarbons9
and10,andwillberepresentedbyC16:1Δ
9
.
Biologicalfunctionsoflipids:
 
Lipidsperformandareinvolvedinvarietyofimportantcellularfunctions.However,followingare
someofthemajorphysiologicalfunctionsattributedtolipids:
• Energysourceinanimals,insects,birdsandhighlipidseedse.g.triacylglycerols.
• Activatorsofenzymesnamelyglucose-6-phosphatase,stearoylCoAdesaturase,
monooxygenaseswhichareimportantmitochondrialenzymes.
• Someofthelipidsderivativesserveasvitaminsandhormonese.g.Prostaglandins.
• Arachidonicacidisthespecificprecursorforallprostaglandinsandleukotrienes.Itisboundas
anacylmoietytothe2positionofanumberofphospholipidsandthisisinactiveasasubstrate.
UponreleasebytheactionofphospholpiaseA2,thefreearachidonicacidisconvertedbya
cyclooxygenasetoformtwoveryprostaglandinderivatives,prostacyclinI2,anactive
physiologicalvasodilatorandThromboxaneA2,anactivevasoconstrictor.
• Essentialcomponentsofbiologicalmembranese.g.shingolipidsandglycoloipids.
• Aslipoproteinsinproteinmodificationandrecognitions.

36. 35
BIOMOLECULES SH/BT/GSC/CTA • Componentsoftheelectrontransportsystemintheinnermembraneofmitochondria.
Structureandfunctionofvariousclassesoflipids
 
Classificationoflipids:
 
Lipidsaregenerallyclassifiedintofollowingsevengroups:
1.Acylglycerols.
2.Phosholipids.
3.Sphingolipids.
4.Glycolipids.
5.Alkylglycerylethers.
6.Terpenoids.
7.Wax
 
1.Acylglycerols:
 
• ThesearealsocalledasTriacylglyceridesorneutrallipids,beingcomposedofaglycerol
backbone,inwhicheachalcoholicgroupisesterifiedbyfattyacids.
• FollowingisthetypicaltriglyceridestructureinwhichfattyacidsareindicatedbyR.These
aremostcommonlyoccurringformoflipidsincell,storedinadiposeorfatdepot.Their
functionistoserveasmajorenergysource.
 
2.Phospholipids:
 
• Theyarethemajorcomponentofmembrane.
• Thebasicstructureofphospholipidsisverysimilartothatofthetriacylglyceridesexcept

37. 36
BIOMOLECULES SH/BT/GSC/CTA thatCarbon-3(Sn3),oftheglycerolbackboneisesterifiedbyphosphoricacid.
• Thisbasicphospholipidsiscalled phosphatidicacid.Phosphotidicacidhavefurther
substitutionas–Xshowninadjoiningfigure.
• Phospholipidsareamphipathicinnatureduetopresenceofbothhydrophilic/charged
substitution(PO4-andXatSn-3)andhydrophobicfattyacidchainsatSn1andSn2.
 
Differenttypesofphospholipids:
 
• Severaldifferenttypesofphosopholipidsareformedbyfurtherattachmentofdifferentgroups
(X)atPhosphatidicacidSn-3phosphoricacid.
• Somerepresentativeexamplesare:
X=Ethanolamine,thephospholipidiscalledphosphatidylethanolamine.
X=Choline--->phosphatidylcholine,alsocalledlecithins.
X=Serine--->phosphatidylserine.
X=Glycerol--->phosphatidylglycerol.
X=myo-inositol--->phosphatidylinositol.
X=diphosphatidylglycerol--->cardiolipins.
Theirpresenceandfunctionshavebeenbrieflyenumeratedinthefollowingslide.
 

38. 37
BIOMOLECULES SH/BT/GSC/CTA 3.Sphingolipids:
 
• Sphingolipidsarecomposedofabackboneofsphingosine,whichisderivedfromglycerol.
• Thestructureofsphingosineisshownbelow:
 

39. 38
BIOMOLECULES SH/BT/GSC/CTA  Sphingolipidsarepredominantlypresentinthemyelinsheathofnervefibers.
 
Someoftheimportantsphingolipidsare:
• Ceramides:– Inthiscase,thesphingosineisN-acetylatedatCH2OHbyavarietyoffattyacids
generatingdifferenttypesofceramides.
• Sphingomyelin:- ItisanabundantsphingolipidinwhichCH2OHisesterifiedbyphosphoricacidand
cholineinsteadoffattyacid.
• Glycosphingolipids othermajorclassofsphingolipidsaregeneratedbysubstitutionof
carbohydratesatCH2OH.CerbrosidesandGangliosidesaremajorclassesofglycosphingolipids.
• Cerebrosides:- Itisalsocalledgalactocerebrosidesbecausegalactoseisthecarbohydratepresent
init.
• Gangliosides:- Italsocontainssialicacid.
4.Glycolipids:
 
• Theyarecarbohydratecontainingderivativeoftriglycerides.Galactoseisthepredominant
carbohydratepresentinglycolipids.Sn-3monogalactosylgalactosyldiacylglycerolandSn-3di
galactosyldiacylglycerolarecommonlypresentinmembranestructuresespeciallyinthechloroplast
membrane.
• Arepresentativestructureofglycolipidisgivenbelow:
 
 
5.Glycerolethers:
 
• Thesealsocalledplasmalogens.
• StructurallytheycontaineitheranO-alkyl(-O-CH2-)orO-alkenylether(-O-CH=CH-)speciesatC-1
(Sn1)ofglycerol.AbasicO-alkenyletherspeciesisshownintheadjoiningpicture:
 
 
• Oneofthephysiologicallyimportantalkyletherplasmalogensisplateletactivatingfactor(PAF)
whichisacholineplasmalogeninwhichtheC-2(sn2)positionofglycerolisesterifiedwithanacetyl
groupinsteadofalongchainfattyacid.PAFmediateshypersensitivityandacuteinflammatory
reactions.
 
6.TerpenoidsandSterols:
 
• Theseareverydistinctgroupoflipidscomposedofthemonomerrepeatingunitscalled“isoprenoid
units”.Steroids,carotenoids,rubberandterpenesfallinthisclassoflipids.
 

40. 39
BIOMOLECULES SH/BT/GSC/CTA  
• Terpenesarethechiefconstituentsoftheessentialoils,balsams,resins,waxes,andrubber.Plant
terpenoidsareknownfortheiraromaticqualities.Theyplayimportantpartintraditionalherbal
remediesandareunderstudyforantibacterial,andpharmaceuticalapplications.
• The steroidsandsterols inanimalsarebiologicallyproducedfromterpenoidprecursors.
• Structureofβ-caroteneandcholesterol,fewamongimportantcompoundofthisclassareshown
below:
 
7.Waxes:
 
Theseareclassoflipidsfoundasprotectivecoatingonfruitsandleavesorsecretedbyinsects.
Chemicallythesearecomplexmixtureoflongchainalkanesandderivativesofsecondaryalcoholand
ketones.
 
Lipoproteins:
 
• A lipoprotein isacomplex assemblycontainingboth proteins and lipids bondedcovalentlyornon-
covalentlytotheproteins.Enzymes,transporters,structuralproteins, antigens,adhesinsand
toxins arelipoproteins.Foreg:HDL(highdensitylipoprotein),LDL(lowdensitylipoprotein).The
lipoproteinparticleiscomposedofanoutershellofphospholipid,whichmakesitwatersoluble;acore
offatsandasurfaceapoproteinmoleculethatallowsrecognitionbythetissuesanduptakeofthe
particle.
• Thegeneralstructureofalipoproteinisgivenbelow:
 
 
• Thelipoproteinparticleiscomposedofanoutershellofphospholipid,whichmakesitwatersoluble;
acoreoffatsandasurfaceapoproteinmoleculethatallowsrecognitionbythetissuesanduptakeof
theparticle.
 
Classificationandfunctionsoflipoproteins:
 
Themajorfunctionoflipoproteinparticlesistotransportlipids(fats)(suchastriacylglycerol)around
thebodyintheblood.Lipoproteinsmaybeclassifiedonthebasisoftheirdensity.Theymaybe
categorisedas:
• Chylomicron(lowestindensity) whichcarrytriglyceridesfromtheintestinetotheadiposetissue.
• VLDL (verylowdensitylipoprotein);carry(newlyynthesised) triacylglycerol fromthelivertoadipose
tissue.

41. 40
BIOMOLECULES SH/BT/GSC/CTA • IDL(intermediatedensitylipoprotein);internediatebetweenLDLandVLDL.
• LDL(lowdensitylipoprotein);carrycholesterolfromthelivertocell/tissuesofthebody.
• HDL(highdensitylipoprotein);carrycholesterolfromthebodytissuesbacktotheliver.
StructureandFunctionsofNucleicAcids
Nucleicacidsasgeneticmaterial
Whatarenucleicacids?:
 
• Nucleicacidsarethemostimportantbiomoleculesofthecellsformingverybasisofcentral
dogmaoflife. 
• Mostimportantly,thenucleicacids:deoxyribonucleicacid(DNA)andribonucleicacid(RNA),
arethemolecularrepositoriesofgeneticinformations.DNAisthemastermoleculeresponsible
forheredity.Theabilitytostoreandtransmitgeneticinformationfromonegenerationtothenext
isafundamentalconditionforlife.
• Thestructureofeveryprotein,andultimatelyofeverybiomoleculeandcellularcomponent,isa
productofinformationprogrammedintothenucleotidesequenceofacell’sDNA.Thisway
nucleicacidgovernsthefunctionsandphysiologyofthecells.
• Nucleotidesaremonomericunitorbuildingblocksofnucleicacids.
 
FunctionsofNucleicacid:
 
• TheconceptofCentralDogmaexplainsthefunctionsofnucleicacidinnutshellasbelow:
 
 
• DNAisverybasisoflife.Itisthemastermoleculeresponsibleforhereditaryandgenetic
materialofthecellcarryingalltheinformations.
• Itisabletoreplicatesitselfduringcelldivisionandtheprocesscalledreplication.
• ItsynthesisesacomplementarymessengerRNAwhichisresponsibleforcarryingthe

42. 41
BIOMOLECULES SH/BT/GSC/CTA informationforproteinsynthesis.
• Italsoregulatesproteinsynthesis.
DNAContent of Organisms:
 
• The overall DNA contained inone cell is called a genome. 
• Prokaryoticcells contain one moleculeofDNA, while humansomaticcells contain
46 molecules of DNA per nucleus. 
• The somaticcells of eukaryotes commonly havetwo sets of genes
derived from both parents, andthese cells are called diploids. 
• Cells thathave only one set of genes are called haploids.Forexample,
most prokaryotes are haploids. 
• DNAcontentgreatlyvariesamongorganisms.Generally,DNAcontentpercellislargerin
eukaryotesthaninprokaryotes. 
• Humansomaticcellscontainapproximately1,000timesasmuchDNAasthoseofE.coli
(perhaploid).Fordiploidcells,theamountpercellis6pg. 
• Althoughitmaygenerallybeseenthatamongeukaryotes,thehigheranorganism,the
moreDNAcontent,therecanbevariationsamongorganismsofthesamegroup. 

43. 42
BIOMOLECULES SH/BT/GSC/CTA • Forexample,amongvertebrates,suchvariationsmaybeseeninfishandamphibians,with
somespecieshavingmoreDNAcontentthanhumans. 
• SomehigherplantspeciesalsohavemoreDNAthanhumans.
 
 
Buildingblocksofnucleicacids
 
Thenitrogenousbases:
 
• PurinesandPyrimidinesaretwotypesofbaseswhichoccurinnucleicacids.
 
Therearefivemajorbasesfoundincells.Thederivativesofpurineare
called adenine and guanine,whilethoseofpyrimidineare
called thymine, cytosine and uracil.
• Thecommonabbreviationsusedforthesefivebasesare,A,G,T,CandU.DNAcontainsA,
G,CandT,whereasRNAcontainsA,G,CandUbases.
 
Structureofnitrogenousbases:

44. 43
BIOMOLECULES SH/BT/GSC/CTA  Sugar: Riboseand2-deoxyribosearethetwosugarsfoundinRNAandDNArespectively.
TherecurringdeoxyribonucleotideunitsofDNAcontain2-deoxy-D-ribose,andthe
ribonucleotideunitsofRNAcontainD-ribose.Innucleotides,thesearefoundintheir
furanose(closedfive-memberedring)form.
 
Phosphoricacid getsattachedtoC-5OHgroupofthesugar.
 

45. 44
BIOMOLECULES SH/BT/GSC/CTA • Thebaseandsugararecalled “nucleoside”.Thebondbetweenthemiscalledthebeta
-glycosidiclinkage.Thepositionofattachmentisshownbelow.Examplesof
nucleosidesincludecytidine,uridine,adenosine,guanosine,thymidine.
 
Nucleotides arecomposedofthreecomponentsnamelynitrogenousbases,pentosesugar
andphosphategroup.Thephosphateisattachedto5’CH2OHgroupofsugarpartof
nucleoside.Atypicalnucleotideisshownbelow:
Thebaseofanucleotideisjoinedcovalently(atN-1ofpyrimidinesandN-9ofpurines)inan
N—glycosylbondtothe1carbonofthepentose,andthephosphateisesterifiedtothe5
carbon.TheN-glycosylbondisformedbyremovalofawatermolecule.
 
 
• Thebaseofanucleotideisjoinedcovalently(atN-1ofpyrimidinesandN-9ofpurines)in
anN—glycosylbondtothe1carbonofthepentose,andthephosphateisesterifiedtothe5
carbon.TheN-glycosylbondisformedbyremovalofawatermolecule.
 
Polynucleotides:
 
• Polynucleotides areformedbyjoiningofnucleotidesbyphosphodiesterlinkages.
• Thebondformationtakesplacebetweenthealcoholofa5'-phosphateofonenucleotide
andthe3'-hydroxylofthenext,resultingintoaphosphodiesterbond.
 
 
• DNAandRNAarepolynucleotides.

46. 45
BIOMOLECULES SH/BT/GSC/CTA InDNAandRNAthenucleotidesarearrangedinlinearwayandproceedsinthe5'---->3'
direction.Acommonrepresentationofploynucleotideforexamplecanbeseenasbelow:
5'pApTpGpCOH3'
 
 
 
DNA-structure,propertiesandfunction
 
StructureofDNA:
 
• ThediscoveryofDNAstructureisoneofthehallmarkofthemodernmolecularbiology.
• BasedontheassumptionsofChargoffandutilizingX-raydiffractiondata,obtainedfrom
crystalsofDNAbyRosalindFranklinandMauriceWilkins,JamesWatsonandFrancisCrick
proposedamodelforthestructureofDNAin1953.
• TheyestablishedthatDNAhasadoublehelicalstructurecomprisingoftwocomplementary

47. 46
BIOMOLECULES SH/BT/GSC/CTA antiparallelpolynucleotidestrands,woundaroundeachotherinarightwarddirection.
• Thebackboneofthehelixissugar-phosphateandthebasesareintheinteriorofthehelixand
extendedat90
0
perpendiculartotheaxisofthehelix.Basesfromoppositehelixpairwitheach
other.Purinesformbasepairswithpyrimideneasathumbrule-AwillpairwithT,andCwithG.
Accordingtothispattern,knownasWatson-Crickbase-pairing.
SpecificfeaturesofDNAstructure:
 
• Itisdoublehelicalstructure.Onepolynucleotidechainformsonestrand.Twosuchstrandsform
doublehelix.
• Chainhassugarphosphatebackboneandthebasesarearrangedperpendiculartothechain.
• Twostrandsareantiparalleltoeachother:onein5'--->3'directionandtheotherinthe3'--->5'
direction.
• AandT;andGandCoccurascomplementaryandformbasepairwithcorresponding
complementarybaseinoppositestrand.

48. 47
BIOMOLECULES SH/BT/GSC/CTA • Oneturnofthehelixis36Aand10basepairsarefoundperturnwithriseof3.6A.
• Onthesurfaceofdoublehelixtwodeepgroovesarefoundwhicharecalledmajorand minor
grooves.
• Helixisrighthandedalongtheaxis.
 
Thebasespairsarehydrogenbondswitheachotherandimpartstabilitytothestructure.Thebase-
pairscomposedofGandCcontainthreeH-bonds,whereasthoseofAandTcontaintwoH-bonds.For
thisreasonG-Cbase-pairsarestrongerthanA-Tbase-pairs.TheoutcomewillbethatDNAhaving
moreGCbasepairswillbemorestablethantheonehavingmoreATpairs.
 
Basesarestackedovereachotherinthedoublehelix.
• HydrophobicinteractionsbetweenstackedbasesalsostabilizetheDNA.
• Thesugarphosphatebackboneofeachstrandisnegativelycharged(duetophosphategroup(pKa
beingneartozero).ThesechargesarestabilizedbyMg
2+
.
 
 
VariousconformationsofDNA:
 
• OneofthepropertiesoftheDNAisthatitshowsconformationalflexibility,andcouldexistin
alternativestructuralforms.TheWatson-CrickstructureistheB-formDNAorB-DNA.
• TheBfromisthemoststablestructureforarandomsequenceDNAmoleculeunderphysiological
conditionsandistherefore“thestandardpointofreferenceinanystudyofthepropertiesof
DNA”.TheB-DNApredominatesinthecell.
• TherearetwootherstructuralvariantsofDNAthathavebeenwellcharacterizedincrystal

49. 48
BIOMOLECULES SH/BT/GSC/CTA structures.TheyaretheA-DNAandZ-DNA.TheseDNAvariantsdifferintheirhelicalsense,diameter,
basepairsperhelicalturn,helixriseperbasepair,basetiltnormaltothehelixaxis,sugarpucker
conformation,andglycosylbondconformation.
 
StructureofRNA:
 
UnlikeDNA,RNAaresinglestrandedpolynucleotide.Itcontainsuracilbaseinsteadofthymine,
thusfourbasesofRNAareA,U,GandC.TherearethreetypesofRNApresentinthecell: 
• MessengerRNA. 
• TransferRNA. 
• RibosomalRNA.
 
MessengerRNA:
 
• MessengerRNAaredesignatedasm-RNA. 
• m-RNAdoesnotcontainveryorganizedsecondarystructure. 
• Thepolypeptideislinearingeneral,exceptacquiringhairpinstructureatsomeplacesduetothe
basepairingbetweencomplementarybasepairsofthechain.MessengerRNAisgeneratedinthe
nucleusasthecomplementarycopyofDNAstrand,byaprocesscalledtranscription. 
• ItcarriesthegeneticinformationoftheDNAtobeusedforproteinsynthesis.

50. 49
BIOMOLECULES SH/BT/GSC/CTA  
TransferRNA:
 
• Designatedast-RNA.Theyhavewelldefinedcloverleafstructureasshowninfigure.Ithasfour
arms,whicharedesignatedasDihydrouridine(DHU),anticodon,pseudouridine(TΨC)armsandone
smalloptionalarm.3’ofthet-RNAhasconservedsequenceCCAatwhichspecificaminoacidis
attached.
 
Itactsasadaptermolecule.Anticodonslocatedatanticodonarmformcomplementarybase
pairswithcodonduringproteinsynthesisprocess.Thustheroleoft-RNAistotransferamino
acidforproteinsynthesis.
 
 
RibosomalRNA:
 
• Designatedasr-RNA. 
• Inthecytoplasm,ribosomalRNAandproteincombinetoformanucleoproteincalleda
ribosome.TheribosomebindsmRNAandcarriesoutproteinsynthesis. 
SeveralribosomesmaybeattachedtoasinglemRNAatanytime.
 

51. 50
BIOMOLECULES SH/BT/GSC/CTA MicroRNAs:
 
• MicroRNAs(miRNA)aresingle-strandedRNAmoleculesof21-23nucleotideslength.miRNAsare
post-transcriptionalregulatorsthatbindtocomplementarysequencesonmRNAtranscriptsleading
torepressionoftranslationorgenesilencing. 
• miRNAsareencodedbygenestranscribedfromDNAbutnottranslatedintoprotein(non-coding
RNA); 
• Theyareprocessedfromprimarytranscriptsknownaspri-miRNAtoshortstem-loopstructures
calledpre-miRNAandfinallytofunctionalmiRNA. 
• ThemainfunctionofmaturemiRNAmoleculesappearstobeinregulationofgeneexpression. This
effectwasfirstdescribedin1993fortheworm C.elegans byVictorAmbrosandhisgroup.Since2002,
miRNAshavebeenconfirmedinvarious plants and animalsforeg. C.elegans andthe

52. 51
BIOMOLECULES SH/BT/GSC/CTA plant Arabidopsisthaliana. 
• Thehumangenomeencodesover1000miRNAsandabundantlyfoundinmanyhumancelltypes.
 
Short-interferingRNAs:
 
Short-interferingRNAs (siRNAs)foundinplantsarefunctionalinpreventingthetranscription
of viral RNA.ThesiRNAisdouble-strandedbutthemechanismofactionissimilartothatofmiRNA.
siRNAsarealsousedtoregulatecellulargenes.
 
Double-strandedRNA:
 
Double-strandedRNA(dsRNA)referstoRNAwithtwocomplementarystrands.dsRNAformsthe
geneticmaterialofsomeviruses(double-strandedRNAviruses).Double-strandedRNAsuchasviral
RNAorsiRNAareknowntobeabletotriggerRNAinterferenceineukaryotes.RNAcanalsoactas
carriersofgeneticinformation. 
• Forexample,genomesofRNAvirusesarecomposedofRNAthatencodesforanumberofproteins.
Theviralgenomeisreplicatedbysomeofthoseproteins. 
• Similarly,viroidsareanothergroupofpathogens,consistingonlyofRNA.Theydonotencodeforany
proteinandarereplicatedbypolymerasebelongingtothehostplantcell.
 
 
VitaminsandCoenzymes
Definitionandroleofvitamins
Whatarevitamins?
 
• Thename “vitamin” issourcedfrom "vitalamines" sinceitwasoriginallythoughtthatthese
substanceswereallamines.
• Vitaminsareaclassoforganiccompoundsthatareimportantfornormalgrowthandnutrition;
requiredin smallquantities inthedietbecausetheycannotbesynthesizedbythebody.Theseare
thereforeessentialnutrientsforlivingsystem. 
• Vitaminsparticipateinregulationoftheenergy-producingprocesses. Withtheexceptionofvitamin
DandK,vitaminscannotbesynthesizedbythehumanbodyandmustbeobtainedfromthediet.
 
TypesofVitamins :
 
Vitaminscanbebroadlyclassifiedintotwomaincategories:
Water-solublevitaminsand 
Fat-solublevitamins. 

53. 52
BIOMOLECULES SH/BT/GSC/CTA • Water-solublevitamins:
Asthenamesuggests,thesevitaminsarewatersolubleandcan’tbestoredinthebody.Theseare
eliminatedinurine.Wethereforeneedacontinuoussupplyofthemindiets.Thewater-soluble
vitaminsaretheB-complexgroupandvitaminC.ExamplesofwatersolublevitaminsareThiamin
(vitaminB1),Riboflavin(vitaminB2),Niacin,VitaminB6,Folate,VitaminB12,Biotin,Pantothenicacid
andVitaminC.
• Fat-solublevitamins:
Thefat-solublevitaminsdifferfromthewatersolubleonesinthatthesearestoredinthebody.Fat-
solublevitaminsincludethegroupofvitaminsA,D,EandK.Theyaresolubleinfatandareabsorbed
bythebodyfromtheintestinaltractbytheuseofbileacidsfromtheliver.Oncethesevitaminsare
absorbed,thebodystorestheminbodyfat.Whenneeded,thebodyutilizesthemoutofstoragetobe
used.
Fatsolublevitaminsshouldnotbeconsumedinexcesssinceanexcesscanresultinsideeffectslike
irritability,weightloss,nausea,headache,diarrheaetc. 
 
Roleofvitamins:
 
• Individualvitaminslikethiamine,riboflavin,nicotinicacid,pentothenicacid,pyridoxine,lipoicacid,
biotin,folicacid,ascorbicacidhavespecificfunctionsoftheirown.
• Asagroup,theyareinvolvedingrowth,maintenanceofhealthandregulationofcellularprocess. 
• Theyalsoplayaroleinmetabolism,enablingthebodytouseessentialnutrientssuchas
carbohydrates,fats,proteinsandminerals. 
• Vitaminsareimportantforaregularandnormalappetite,digestion,andresistanceagainstdiseases
andinfections.
• Theyhaveseveraltherapeuticandmedicinaleffects.
VITAMINS
Vitaminsareorganiccompoundsrequiredbythebodyinsmallamountsformetabolism,toprotect
health,andforpropergrowthinchildren.Vitaminsalsoassistintheformationofhormones,blood
cells,nervous-systemchemicals,andgeneticmaterial.Theygenerallyactascatalysts,combining
withproteinstocreatemetabolicallyactiveenzymesthatinturnproducehundredsofimportant
chemicalreactionsthroughoutthebody.Withoutvitamins,manyofthesereactionswouldslowdown
orcease.
CHEMICALCOMPOSITION:
Vitaminsareorganiccompoundsofdifferentchemicalnature.Thesearealcohols,aldehyde,organic
acids,theirderivativesornucleotidederivatives.
CLASSIFICATIONOFVITAMINS:
Vitaminsareclassifiedaccordingtotheirabilitytobeabsorbedinfatorwater.
1.FatSolubleVitamins:Theseareoilyandhydrophobiccompounds.Thesearestoredintheliverand

54. 53
BIOMOLECULES SH/BT/GSC/CTA arenotexcretedoutofthebody.Bilesaltsandfatsarerequiredfortheirabsorption.VitaminA,D,E
andKarefatsolublevitamins.Becausethesevitaminscanbestored,theirexcessiveintakemay
havetoxiceffectandcanresultinHypervitaminosis.
2.WaterSolubleVitamins:VitaminBcomplexandvitaminCarewatersoluble.Theyarecompounds
ofcarbon,hydrogen,oxygenandnitrogen.Theyarenotstoredinthebodythereforetheyrequired
dailyinsmallamount.
FATSOLUBLEVITAMIN
1.VITAMINA:
VitaminAisapaleyellowprimaryalcoholderivedfromcarotene.
ItincludesRetinol(alcoholicform),Retinal(Aldehydeform)andRetinoicacid(acidicform).
Source:•Inanimalform,vitaminAisfoundinmilk,butter,cheese,eggyolk,liver,andfish-liver
oil.•Inplantsourceitobtainedfromvegetablesascarrots,broccoli,squash,spinach,kale,and
sweetpotatoes.
PhysiologicalSignificance:•AllthreeformsofvitaminAarenecessaryforpropergrowth,
reproduction,vision,differentiationandmaintenanceofepithelialcells.
•VitaminAacceleratesnormalformationofboneandteeth.
•Retinoicacidisneededforglycoproteinsynthesis.
DeficiencyofVitaminA:•Anearlydeficiencysymptomisnightblindness(difficultyinadapting
todarkness).•Othersymptomsareexcessiveskindryness•Lackofmucousmembrane
secretion,causingweaknesstoresistbacterialattack
•Drynessoftheeyesduetoamalfunctioningofthetearglands.
HypervitaminosisofVitaminA:ExcessvitaminAcaninterferewithgrowth,stopmenstruation,
damageredbloodcorpuscles,andcauseskinrashes,headaches,nausea,andjaundice.
2.VITAMIND(CalciferolorAntirachiticVitamin):
Source:VitaminD2VitaminD3•VitaminDisobtainedfromeggyolk,codliveroilandliveroil
fromotherfishes.•Itisalsomanufacturedinthebodywhensterols,whicharecommonly
foundinmanyfoods,migratetotheskinandbecomeirradiated.
PhysiologicalSignificance:•Thisvitaminisnecessaryfornormalboneformationandfor
retentionofcalciumandphosphorusinthebody.•Italsoprotectstheteethandbonesagainst
theeffectsoflowcalciumintakebymakingmoreeffectiveuseofcalciumandphosphorus.•It
decreasespHinthelowerintestine.
Deficiency:•VitaminDdeficiencyproducesricketsinchildrenandOsteomalaciainadult.
•Ricketsischaracterizedbyabnormitiesoftheribcageandskullandbybowlegs,dueto
failureofthebodytoabsorbcalciumandphosphorus.
•Osteomalaciaischaracterizedbysoftnessofpelvicgirdle,ribsandfemoralbones.
HypervitaminosisofVitaminD:
•BecausevitaminDisfat-solubleandstoredinthebody,excessiveconsumptioncancause
vitaminpoisoning,kidneydamage,lethargy,andlossofappetite.
3.VITAMINE(TocopherolorFertilityVitamin):
Source:•Itisfoundinvegetableoils,wheatgerm,liver,andleafygreenvegetables.•Theyare

55. 54
BIOMOLECULES SH/BT/GSC/CTA alsopresentinlittleamountinmeat,milkandeggs.
PhysiologicalSignificance:•VitaminEactsasantioxidants.Theyplaysomeroleinformingred
bloodcellsandmuscleandothertissuesandinpreventingtheoxidationofvitaminAandfats.
•Itisalsoassociatedwithcellmaturationanddifferentiation.
Deficiency:•DeficiencyofvitaminEcausessterilityinbothmaleandfemales.•Itcauses
musculardystrophy.•Inchildrenitcauseshaemolysis,creatinuria.
4.VITAMINK(PhylloquinoneorAntihemorragicVitaminorCoagulationVitamin):
VitaminKisacomplexunsaturatedhydrocarbonfoundintwoformsVitaminK1
(Phylloquinone)andVitaminK2(Menaquinone).VitaminK1-Phylloquinone
Source:
•TherichestsourcesofvitaminKarealfalfa,fishlivers,leafygreenvegetables,eggyolks,
soybeanoil,andliver.•Itisalsoproducedbybacteriainhumanintestinethereforenodietary
supplementisneeded.Physiological
Significance:
•Thisvitaminisnecessarymainlyforthecoagulationofblood.
•Itaidsinformingprothrombin,anenzymeneededtoproducefibrinforbloodclotting.•Acts
asaninducerforthesynthesisofRNA.
•Itisalsorequiredfortheabsorptionoffat.
Deficiency:
•DigestivedisturbancesmayleadtodefectiveabsorptionofvitaminKandhencetomild
disordersinbloodclotting.HypervitaminosisofVitaminK:
•AdministrationoflargedosesofvitaminKproduceshaemolyticanemiaandjaundicein
infantsbecauseofbreakdownofRBCs.
WATERSOLUBLEVITAMIN
KnownalsoasvitaminBcomplex,thesearefragile,water-solublesubstances,severalof
whichareparticularlyimportanttocarbohydratemetabolism.
TheyincludeVitaminB1(Thiamine),VitaminB2(Riboflavin),VitaminB3(NiacinorNicotinic
Acid),VitaminB6(Pyridoxine),VitaminB12(Cobalamin)etc.
5.VITAMINB1(Thiamine):VitaminB1(ThiamineChloride)Thiamine,orvitaminB1,acolorless,
crystallinesubstance.Itisreadilysolubleinwaterandslightlyinethylalcohol.
Source:•VitaminB1isabundantlyfoundingerminatingseeds,un-milledcereals,beans,
orangejuice,tomato,egg,meat,fish,organmeats(liver,heart,andkidney),leafygreen
vegetables,nuts,andlegumes.Physiological
Significance:•Actsasacatalystincarbohydratemetabolism,enablingpyruvicacidtobe
absorbedandcarbohydratestoreleasetheirenergy.
•Thiaminealsoplaysaroleinthesynthesisofnerve-regulatingsubstances.
Deficiency:•Deficiencyinthiaminecausesberiberi,whichischaracterizedbymuscular
weakness,swellingoftheheart,andlegcramps.

56. 55
BIOMOLECULES SH/BT/GSC/CTA 6.VITAMINB2(Riboflavin):VitaminB2(Riboflavin)
Source:•Thebestsourcesofriboflavinareliver,milk,meat,darkgreenvegetables,wholegrain
andenrichedcereals,pasta,bread,andmushrooms.
PhysiologicalSignificance:•Itisessentialforcarbohydratemetabolism.Enzymecontaining
riboflaviniscalledFlavoproteins.•Itactsascoenzymeforenzymecatalyzingoxidation-
reductionreaction.Deficiency:•ItsdeficiencycausesGlossitis(inflammationoftongue).•
Lackofthiaminecausesskinlesions,especiallyaroundthenoseandlips,andsensitivityto
light.
7.VITAMINB3(NiacinorNicotinicAcid):VitaminB3(Niacinamide)
Source:•Thebestsourcesofniacinareliver,poultry,meat,cannedtunaandsalmon,whole
grainandenrichedcereals,driedbeansandpeas,andnuts.•Thebodyalsomakesniacinfrom
theaminoacidtryptophan
PhysiologicalSignificance:•Nicotinicacidisessentialforthenormalfunctioningofskin,
intestinaltractandthenervoussystem.•VitaminB3worksasacoenzymeinthereleaseof
energyfromnutrients.
Deficiency:•Adeficiencyofniacincausespellagra,thefirstsymptomofwhichisasunburn
likeeruptionthatbreaksoutwheretheskinisexposedtosunlight.•Latersymptomsareared
andswollentongue,diarrhea,mentalconfusion,irritability,and,whenthecentralnervous
systemisaffected,depressionandmentaldisturbances.
8.PANTOTHENICACIDorVITAMINB5:VitaminB5(PantothenicAcid)
Source:•Itsmainsourcesareliver,milk,meat,eggs,wheatgerm,wheatbran,potatoes,sweet
potatoes,tomatoes,cabbage,cauliflowerandbroccoli.Fruitandothervegetablesalsohave
pantothenicacid.
PhysiologicalSignificance:•Pantothenicacidisessentialforgrowthofinfantsandchildren,•
Itplaysamajorroleinthemetabolismofproteins,carbohydrates,andfats.Deficiency:•Its
deficiencycausesnausea,vomiting,gastrointestinaldisorders,impropergrowthandfattyliver.
9.VITAMINB6(Pyridoxine):VitaminB6(Pyridoxal)
ChemicalStructureSource:•Thebestsourcesofpyridoxinearewhole(butnotenriched)
grains,cereals,bread,liver,avocadoes,spinach,greenbeans,andbananas.•Itisalsofoundin
milk,eggs,fish,chicken,beaf,porkandliver.PhysiologicalSignificance:•Pyridoxine,orvitamin
B6,isnecessaryfortheabsorptionandmetabolismofaminoacids.•Italsoplaysrolesinthe
useoffatsinthebodyandintheformationofredbloodcells.Deficiency:•Pyridoxine
deficiencyischaracterizedbyskindisorders,cracksatthemouthcorners,smoothtongue,
convulsions,dizziness,nausea,anemia,andkidneystones.
10.VITAMINb7(Biotin):VitaminB7(Biotin)Biotinisalsoknownas“anti-eggwhiteinjury
factor”orasH-factor.Source:•Biotinoccursincombinedstateasbiocytin.Itisfoundinyeast,
liver,kidney,milkandmolasses.PhysiologicalSignificance:•Biotinservesasprostheticgroup
formanyenzymeswhichcatalyzefixationofCO2intoorganicmolecules.•Ithelpsin
synthesisoffattyacids.Deficiency:•Itsdeficiencycausedthedestructionofintestinal
bacteria.•Itleadstonauseaandmuscularpain.
11.VITAMINB9orMorBc(FolicAcid):VitaminMorFolicAcidSource:•Folicacidisfoundin
yeast,liverandkidney.•Fishmeatandgreenleafyvegetables,milkandfruitsalsoprovidefolic

57. 56
BIOMOLECULES SH/BT/GSC/CTA acid.PhysiologicalSignificance:•Folicacidactsasacoenzymeandhelpinsynthesisof
purinesandthymineduringDNAsynthesis.•Ithelpsinformationandmaturationofredblood
cells.Deficiency:•Folicaciddeficiencygivesrisetomegaloblasticanemia.•Thepatient
suffersfromretardedgrowth,weakness,infertility,inadequatelactationinfemalesand
gastrointestinaldisorders.
12.VITAMINB12(Cynocobalamin):VitaminB12orCobalamin,orAnti-PerniciousAnaemic
Factor(APA),oneofthemostrecentlyisolatedvitamins.
Source:•Cobalaminisobtainedonlyfromanimalsources—liver,kidneys,meat,fish,eggs,and
milk.VegetariansareadvisedtotakevitaminB12supplements.
PhysiologicalSignificance:•Itisnecessaryinminuteamountsfortheformationof
nucleoproteins,proteins,andredbloodcells.•Itisnecessaryforthefunctioningofthe
nervoussystem.•Itstimulatestheappetiteofthesubject.
Deficiency:•DuetoitsdeficiencyPerniciousAnemiaresultswhichischaracterizedby
symptomsofineffectiveproductionofredbloodcells,faultymyelin(nervesheath)synthesis,
andlossofepithelium(membranelining)oftheintestinaltract.
13.LIPOICACID:•LipoicacidisaSulphurcontainingfattyacid.Itiswidelydistributedin
naturalfoods.Lipoicacidfunctionsasacoenzymeinoxidativedecarboxylationofpyruvicacid
andα-ketoglutaricacid.Itsdeficiencydisordershavenotbeenrecorded.
14.INOSITOLSource:•Yeast,meat,milk,nuts,fruits,vegetablesandgrainscontainsInositol.
PhysiologicalSignificance:•Itincreasesperistalsisofsmallintestine,increasetherateof
contractionofheartmuscles.Deficiency:•Deficiencysymptomsincluderetardedgrowth,
failureoflactation,andlossofhairoverthebody(alopecia)etc.
15.CHOLINE:
Source:•Cholineisfoundinliver,eggyolk,meat,cereals,rice,milk,fruitsandvegetables.
PhysiologicalSignificance:•Acetylcholineisachemicalmediatorofparasympathetic
activitiesandotheractivitiesofnervoussystem.•Itpreventsaccumulationoffatintheliver.
Deficiency:•Itsdeficiencycausesfattyliver,slippedtendondiseasesetc.
16.VITAMINC(AscorbicAcidorAntiscorbuticVitamin):
VitaminC-AscorbicAcidSource:•SourcesofvitaminCincludecitrusfruits,fresh
strawberries,cantaloupe,pineapple,andguava.•GoodvegetablesourcesareBroccoli,
Brusselssprouts,Tomatoes,Spinach,Kale,GreenPeppers,Cabbage,andTurnips.
Physiological
Significance:•VitaminCisimportantintheformationandmaintenanceofcollagen,theproteinthat
supportsmanybodystructuresandplaysamajorroleintheformationofbonesandteeth.•Italso
enhancestheabsorptionofironfromfoodsofvegetableorigin.•Theconnectivetissuefibrilsand
collagenaresynthesizedwiththehelpofvitaminC.•Itplayimportantroleinwoundrepair.•It
protectsbodyagainststress.
Deficiency:•Thiswell-knownScurvyistheclassicmanifestationofsevereascorbicaciddeficiency.
Itssymptomsarelossofthecementingactionofcollagenandincludehemorrhageswhichleadto
looseningofteethandcellularchangesinthelongbonesofchildren.
Summaryofvitaminsoffatsolubleandwatersolublevitamins

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BIOMOLECULES SH/BT/GSC/CTA

59. 58
BIOMOLECULES SH/BT/GSC/CTA

60. 59
BIOMOLECULES SH/BT/GSC/CTA Porphyrin
PorphyrinnucleusPorphyrinsarehighlycolouredcyclictetrapyrrolicpigmentsformedbythelinkage
offourpyrroleringsthroughmethene(–HC=)bridges(Fig.1).Thebasicstructureofatetrapyrroleis
fourpyrroleringssurroundingacentralmetalatom.Porphyrinsare22pelectronsystemswhosemain
conjugationpathwaycontains18pelectrons,whichexplainsthearomaticnaturefromwhichthe
intensecolourassociatedwiththemstems.
Theporphyrinsrepresentthemostwidespreadofalltheprostheticgroupsfoundinnature.They
mediateaspectrumofcriticalfunctionsinavarietyofbiologicalsystemsrangingfromelectron
transfer,oxygentransport,photosyntheticenergytransductionandconversionofcarbondioxideinto
fuel.Inaddition,porphyrinsinwhichthemacrocycleisoxidized,i.e.cationradicals,areimportant

61. 60
BIOMOLECULES SH/BT/GSC/CTA intermediatesinthecatalyticcyclesofhemeproteinsandinphotosyntheticprocesses.Theseare
aptlytermedas‘pigmentsoflife’.Commonexamplesofimportantporphyrinsincludehemeand
cytochrome(withchelatediron),chlorophyll(withchelatedmagnesium),coenzymeB12(with
chelatednickel).Thus,theparentformofthesetetrapyrrolicmacrocycleshasacommonporphin
nucleus
Porphyrinnucleus
ClassificationofporphyrinsTheporphyrinsarenamedandclassifiedonthebasisoftheirside-chain
substituentgroups.Incaseofnaturalporphyrins,varioussidechainsaresubstitutedfortheeight
hydrogenatomsintheporphinnucleus.Thus,thenaturallyoccurringporphyrinsinclude:&TypeI&
TypeIII
MetalloporphyrinsoccurringinnatureTheporphyrinscontainingthemetalatomarecalled
metalloproteins.Theporphyrinshaveacharacteristicpropertyofformationofcomplexeswithmetal
ionsboundtothenitrogenatomofthepyrrolerings.Variousexamplesofmetalloproteinsoccurring
innatureare:™Ironcontainingporphyrins:Hemeproteins(hemoglobin,myoglobin,cytochrome,
enzymescatalaseandperoxidase)™Magnesiumcontainingporphyrin:Chlorophyll™Cobalt
containingporphyrins:VitaminB12HemeproteinsHemesareadiversegroupoftetrapyrrole
pigments.HemesarepresentastheprostheticgroupofbothHaemoglobin(Hb)andMyoglobin(Mb)
alongwithotherglobinproteins.Hemeisresponsibleforthecharacteristicredcolourandisthesite
atwhicheachglobinmonomerbindsonemoleculeofO2.Hemeisalsorequiredbythecytochromes
(includingthoseinvolvedintherespiratoryandphotosyntheticelectrontransport)andthe
cytochromeP450thatisusedindetoxificationreactions.Someenzymes,includingcatalaseand
peroxidase,alsocontainheme.Inalltheseproteins,thefunctionofthehemeiseithertobindand
releasealigandtoitscentralironatom,orfortheironatomtoundergoachangeinoxidationstate,
releasingoracceptinganelectronforparticipationinaredoxreaction.Theheterocyclicringsystem
ofhemeisaporphyrinderivative(protoporphyrinIX)andconsistsoffourpyrroleringslinkedby
methenebridges.Besides,itformsachelatecomplexwithFe(II),calledprotohemeormoresimply
hemeprostheticgroup.AsimilarcomplexwithFe(III)iscalledheminorhematin.Inheme,thisFe2+
bondswithfournitrogenatomsinthecenteroftheprotoporphyrinringformingasquare-planar
complex,andtheremainingfifthandsixthcoordinationpositionsofironareperpendiculartothe
planeoftheporphinringoneitherside.Whenthefifthandsixthpositionsofironareoccupied,the
resultingstructureisahemochromeorhemochromogen.Thestructureofhemeprostheticgroup(Fe-
protoporphyrinIX)

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BIOMOLECULES SH/BT/GSC/CTA StructureofHaem
Inmammals,hemeissynthesizedprimarily(85%ofbody’shemegroups)inimmatureerythrocytes
(erythroblasts)withtheremainderoccurringintheliver.Fig.8outlinesthesynthesisofhemefromδ-
amino-levulinicacid(ALA).
Haemoglobin(Hb):Hbisamemberofthefamilyofpigmentscalledtetrapyrroles.Itisaoxygen
bindingallosterichemeproteinandthehemegroupisresponsibleforthedeepred-browncolourof
Hb.Hbisaheterotetramer,α2β2containingtwotypesofsubunits,αandβ
Eachofthefoursubunitsofhaemoglobin(Hb)noncovalentlybindsasinglehemegroup.
Three-dimensionalstructureofhaemoglobinTheαandβsubunitsarestructurallyandevolutionarily
relatedtoeachotherandtotheMb,themonomericoxygen-bindingproteinofmuscle.Closetowhere
theO2bindstothehemegroupinHb,isahistidineresidue,thedistalhistidine(HisE7).
Thisservestwoveryimportantfunctions.First,itpreventshemegroupsonneighboringHbmolecules
comingincontactwithoneanotherandoxidizingtotheFe3+stateinwhichtheycannolongerbind
O2.Second,itpreventscarbonmonoxide(CO)bindingwiththemostfavourableconfigurationtothe
Fe2+,therebyloweringtheaffinityofhemeforCO.ThisisimportantbecauseonceCOhasbound
irreversiblytotheheme,theproteincannolongerbindO2.Intheglobins(HbandMb),fourpyrrole
nitrogensoccupytheonetofourpositionsofiron,thefifthpositionisoccupiedbyanimidazolegroup
ofahistidineresidue,theproximalhistidine,whichlieseighthresiduesalonghelixFofhaemoglobin
(HisF8).Thesixthpositioniseitherunoccupied(deoxyHbanddeoxyMb)oroccupiedbyoxygen
(oxyHbandoxyMb)orotherligands,suchascarbonmonoxide.InbothHbandMb,theironatom
normallyremainsintheFe(II)(ferrous)oxidationstatewhetherornotthehemeisoxygenated(binds
O2).
Thus,althoughtheoxygen-bindingsiteinHbandMbisonlyasmallpartofwholeprotein,the
polypeptidechainmodulatesthefunctionofthehemeprostheticgroup.Althoughmanyinvertebrate
specieshavehaemoglobin-basedoxygentransportsystems,othersproduceoneoftwoalternative
typesofO2-bindingproteins:(i)Haemocyanin,acoppercontainingproteinthatisblueincomplex
withoxygenandcolorlessotherwise;(ii)Haemerythrin,anon-hemeFe-containingproteinthatis
burgundycolouredincomplexwithoxygenandcolorlessotherwise.

63. 62
BIOMOLECULES SH/BT/GSC/CTA STRUCTUREOFHAEMOGLOBIN
Cytochromes(Cyt):
In1925,Keilingavethename‘cytochrome’toagroupofintracellular,electron-transferring
hemoproteinscontainingiron-porphyringroups.Thesearefoundonlyinaerobiccells.Someare
locatedintheinnermitochondrialmembrane,wheretheyactsequentiallytocarryelectrons
originatingfromvariousdehydrogenasesystemstowardmolecularoxygen.
CytochromeP450isfoundinendoplasmicreticulum,whereitplaysaroleinspecialized
hydroxylationreactions.AllcytochromesundergoreversibleFe(II)-Fe(III)valencechangesduring
theircatalyticcycles.Dependingonthenatureofthehemeprostheticgroups,(viz.sidechainsof
theirporphyrinsetc.),thecytochromesfallintodifferentgroups-a,b,candd.
Cytochromea:Hemegroupcontainsaformylsidechain.
Cytochromeb:Hasprotohemeprostheticgroup,whichisnon-covalentlyboundtoprotein.
Cytochromec:Hascovalentlinkagesbetweenthehemesidechainsandtheprotein.
Cytochromed:Hemegroupcontainsadihydro-porphyrin(chlorin).
Incaseofacytochromehavingtwodifferenthemegroupsattachedtoaspecificprotein,bothhemes
maybeindicated,e.g.,‘cytochromebc’.Theuseofunprimeditaliclettersimpliesthatnotonlyare
fourofthecoordinateplacesoftheironattachedtothefournitrogenatomsoftheporphyrin,butalso
positionsfiveandsixareattachedtogroupsintheprotein.Forexample,incytochromec,oneofthe
placesisoccupiedbyahistidineandtheotherbyamethionineresidueintheprotein.Wherethe
hemeisnotinthistypeofstructure,aprimeisused,e.g.,cytochromec’.Thewellestablished
cytochromesareidentifiedbysubscriptnumeralsattachedtotheletterindicatingthegroup,e.g.,
cytochromec3.
Thereducedformsofcytochromesshowamarkedabsorptioninthevisiblerange.Hence,some
cytochromesaregivennamesbasedonthewavelength(innm)oftheα-bandofthereducedform,
e.g.,cytochromec-554etc.[Theabsorptionspectrumofatypicalsinglecytochromeinthereduced
formshowsthreemainbandsinthevisibleregion:thesearecalled,indecreasingorderof
wavelength,theα-,β-andγ-bands].
Thereducedformscannotbeoxidizedbymolecularoxygen,withtheexceptionoftheterminal
cytochromesofmitochondrialrespiration,namely,cytochromea3orcytochromescoxidase,which
alsocontainstightlyboundcopper.Inthemitochondriaofhigheranimals,wheretherespiratorychain
hasbeenmostthoroughlystudied,atleastfivedifferentcytochromeshavebeenidentifiedinthe
innermembrane:cytochromesb,c1,c,aanda3.Atleastoneofthese,cytochromesb,occursintwo
ormoreforms.Inadditiontocytochromesfoundonlyintheinnermembraneofmitochondria,
anothertype,cytochromesb5,occursintheendoplasmicreticulum.Innearlyallthecytochromes,
unlikeglobins,thefifthandsixthpositionsoftheironareoccupiedbytheRgroupsofspecificamino
acidresiduesofproteins.Thesecytochromesthereforecannotbindwithligandslikeoxygen,carbon
monoxideorcyanide;animportantexceptioniscytochromesa3,whichnormallybindsoxygeninits

64. 63
BIOMOLECULES SH/BT/GSC/CTA biologicalfunction.
Chlorophyll
Chlorophyllsaretheessentialcomponentsforphotosynthesisandoccurinchloroplastsasgreen
pigmentsinallphotosyntheticplanttissues.
Theseareimportantintheenergyproducingmechanismsofphotosynthesis.LikeHb,itisamember
ofthefamilyofpigmentscalledtetrapyrroles.Chemically,eachchlorophyllmoleculecontainsa
porphyrin(tetrapyrrole)nucleuswithachelatedmagnesiumatomatthecenterandalongchain
hydrocarbon(phytyl)sidechainattachedthroughacarboxylicacidgroup.
Thereareatleastfivetypesofchlorophyllsinplants.Chlorophyll‘a’and‘b’occurinhigherplants,
fernsandmosses.Chlorophyll‘c’,‘d’and‘e’areonlyfoundinalgaeandincertainbacteria.
ThestructureofchlorophyllaandbisshowninFig.
Theyshareacommonfunctioninalloftheseorganismstoactaslight-harvestingandreactioncenter
pigmentsinphotosynthesis.Thisfunctionisachievedbyanumberofmodificationstothebasic
tetrapyrrolestructure.
Theseinclude:Theinsertionofmagnesiumasthecentralmetalion.Theadditionofafifthringto
thetetrapyrrolestructure.Lossofadoublebondfromoneormoreofthepyrrolerings.
Bindingofonespecificsidechaintoalongfat-likemoleculecalledphytol.Thesechangesgive
chlorophyllsandbacteriochlorophyllsanumberofusefulproperties.Forexample,chlorophyllsare
membranebound,absorblightatlongerwavelengthsthan11hemeandareabletorespondto
excitationbylight.Inthisway,chlorophyllscanacceptandreleaselightenergyanddrive
photosyntheticelectrontransport.