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Biochemistry:CarbonandMacromolecules

CarbonTheBackboneofBiologicalMolecules

Althoughcellsare7095%water,therestconsistsmostlyofcarbonbasedcompounds.

Carbonisunparalleledinitsabilitytoformlarge,complex,anddiversemolecules.

Carbonaccountsforthediversityofbiologicalmoleculesandhasmadepossiblethegreat
diversityoflivingthings.
Proteins,DNA,carbohydrates,andothermoleculesthatdistinguishlivingmatterfrom
inorganicmaterialareallcomposedofcarbonatomsbondedtoeachotherandtoatomsof
otherelements.
Theseotherelementscommonlyincludehydrogen(H),oxygen(O),nitrogen(N),sulfur
(S),andphosphorus(P).

Organicchemistryisthestudyofcarboncompounds
Thestudyofcarboncompounds,organicchemistry,dealswithanycompoundwith
carbon(organiccompounds).
Organiccompoundscanrangefromsimplemolecules,suchasCO 2orCH4,tocomplex
moleculessuchasproteins,whichmayweighmorethan100,000daltons.
Theoverallpercentagesofthemajorelementsoflife(C,H,O,N,S,andP)arequite
uniformfromoneorganismtoanother.
However,becauseofcarbonsversatility,thesefewelementscanbecombinedtobuild
aninexhaustiblevarietyoforganicmolecules.

Carbonatomscanformdiversemoleculesbybondingtofourotheratoms
Withatotalof6electrons,acarbonatomhas2inthefirstelectronshelland4inthe
secondshell.
Carbonhaslittletendencytoformionicbondsbylosingorgaining4electronsto
completeitsvalenceshell.
Instead,carbonusuallycompletesitsvalenceshellbysharingelectronswithotheratoms
infourcovalentbonds.

Thistetravalencebycarbonmakeslarge,complexmoleculespossible.

Whencarbonformscovalentbondswithfourotheratoms,theyarearrangedatthe
cornersofanimaginarytetrahedronwithbondanglesof109.5.
Inmoleculeswithmultiplecarbons,everycarbonbondedtofourotheratomshasa
tetrahedralshape.
However,whentwocarbonatomsarejoinedbyadoublebond,allbondsaroundthose
carbonsareinthesameplaneandhaveaflat,threedimensionalstructure.

Thethreedimensionalshapeofanorganicmoleculedeterminesitsfunction.

Theelectronconfigurationofcarbonmakesitcapableofformingcovalentbondswith
manydifferentelements.
Thevalencesofcarbonanditspartnerscanbeviewedasthebuildingcodethatgoverns
thearchitectureoforganicmolecules.
Lecture Outline for Campbell/Reece Biology, 7th Edition, Pearson Education, Inc.

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Incarbondioxide,onecarbonatomformstwodoublebondswithtwodifferentoxygen
atoms.
Inthestructuralformula,O=C=O,eachlinerepresentsapairofsharedelectrons.This
arrangementcompletesthevalenceshellsofallatomsinthemolecule.
WhileCO2canbeclassifiedaseitherorganicorinorganic,itsimportancetotheliving
worldisclear.
CO2isthesourceofcarbonforallorganicmoleculesfoundinorganisms.Itisusually
fixedintoorganicmoleculesbytheprocessofphotosynthesis.
Urea,CO(NH2)2,isanothersimpleorganicmoleculeinwhicheachatomformscovalent
bondstocompleteitsvalenceshell.
Variationincarbonskeletonscontributestothediversityoforganicmolecules.

Carbonchainsformtheskeletonsofmostorganicmolecules.

Theskeletonsvaryinlengthandmaybestraight,branched,orarrangedinclosedrings.

Thecarbonskeletonsmayincludedoublebonds.

Atomsofotherelementscanbebondedtotheatomsofthecarbonskeleton.

Hydrocarbonsareorganicmoleculesthatconsistofonlycarbonandhydrogenatoms.

Hydrocarbonsarethemajorcomponentofpetroleum,afossilfuelthatconsistsofthe
partiallydecomposedremainsoforganismsthatlivedmillionsofyearsago.
Fatsarebiologicalmoleculesthathavelonghydrocarbontailsattachedtoa
nonhydrocarboncomponent.
Petroleumandfatarehydrophobiccompoundsthatcannotdissolveinwaterbecauseof
theirmanynonpolarcarbontohydrogenbonds.
Isomersarecompoundsthathavethesamemolecularformulabutdifferentstructures
and,therefore,differentchemicalproperties.
Forexample,butaneandisobutanehavethesamemolecularformula,C 4H10,butbutane
hasastraightskeletonandisobutanehasabranchedskeleton.

Enantiomersaremoleculesthataremirrorimagesofeachother.

Enantiomersarepossiblewhenfourdifferentatomsorgroupsofatomsarebondedtoa
carbon.
Inthiscase,thefourgroupscanbearrangedinspaceintwodifferentwaysthataremirror
images.

Theyarelikelefthandedandrighthandedversionsofthemolecule.

Usuallyoneisbiologicallyactive,whiletheotherisinactive.

Evensubtlestructuraldifferencesintwoenantiomershaveimportantfunctional
significancebecauseofemergentpropertiesfromspecificarrangementsofatoms.
Oneenantiomerofthedrugthalidomidereducedmorningsickness,thedesiredeffect,but
theotherisomercausedseverebirthdefects.
TheLdopaisomerisaneffectivetreatmentofParkinsonsdisease,buttheDdopa
isomerisinactive.

Lecture Outline for Campbell/Reece Biology, 7th Edition, Pearson Education, Inc.

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Functionalgroupsarethepartsofmoleculesinvolvedinchemicalreactions
Thecomponentsoforganicmoleculesthataremostcommonlyinvolvedinchemical
reactionsareknownasfunctionalgroups.
Ifweconsiderhydrocarbonstobethesimplestorganicmolecules,wecanview
functionalgroupsasattachmentsthatreplaceoneormoreofthehydrogenatomsbondedto
thecarbonskeletonofthehydrocarbon.

Eachfunctionalgroupbehavesconsistentlyfromoneorganicmoleculetoanother.

Thenumberandarrangementoffunctionalgroupshelpgiveeachmoleculeitsunique
properties.
Asanexample,thebasicstructureoftestosterone(amalesexhormone)andestradiol(a
femalesexhormone)isthesame.
Botharesteroidswithfourfusedcarbonrings,buttheydifferinthefunctionalgroups
attachedtotherings.

Thesefunctionalgroupsinteractwithdifferenttargetsinthebody.

Therearesixfunctionalgroupsthataremostimportanttothechemistryoflife:hydroxyl,
carbonyl,carboxyl,amino,sulfhydryl,andphosphategroups.

Allarehydrophilicandincreasethesolubilityoforganiccompoundsinwater.

Inahydroxylgroup(OH),ahydrogenatomformsapolarcovalentbondwithan
oxygenatom,whichformsapolarcovalentbondtothecarbonskeleton.
Becauseofthesepolarcovalentbonds,hydroxylgroupsincreasethesolubilityoforganic
molecules.
Organiccompoundswithhydroxylgroupsarealcohols,andtheirnamestypicallyendin
ol.
Acarbonylgroup(>CO)consistsofanoxygenatomjoinedtothecarbonskeletonbya
doublebond.

Ifthecarbonylgroupisontheendoftheskeleton,thecompoundisanaldehyde.

Ifthecarbonylgroupiswithinthecarbonskeleton,thenthecompoundisaketone.

Isomerswithaldehydesversusketoneshavedifferentproperties.

Acarboxylgroup(COOH)consistsofacarbonatomwithadoublebondtoanoxygen
atomandasinglebondtotheoxygenofahydroxylgroup.

Compoundswithcarboxylgroupsarecarboxylicacids.

Acarboxylgroupactsasanacidbecausethecombinedelectronegativitiesofthetwo
adjacentoxygenatomsincreasethedissociationofhydrogenasanion(H +).
Anaminogroup(NH2)consistsofanitrogenatombondedtotwohydrogenatomsand
thecarbonskeleton.

Organiccompoundswithaminogroupsareamines.

Theaminogroupactsasabasebecausetheaminogroupcanpickupahydrogenion(H +)
fromthesolution.

Aminoacids,thebuildingblocksofproteins,haveaminoandcarboxylgroups.

Asulfhydrylgroup(SH)consistsofasulfuratombondedtoahydrogenatomandto
thebackbone.
Lecture Outline for Campbell/Reece Biology, 7th Edition, Pearson Education, Inc.

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Thisgroupresemblesahydroxylgroupinshape.

Organicmoleculeswithsulfhydrylgroupsarethiols.

Twosulfhydrylgroupscaninteracttohelpstabilizethestructureofproteins.

Aphosphategroup(OPO32)consistsofaphosphorusatomboundtofouroxygen
atoms(threewithsinglebondsandonewithadoublebond).

Aphosphategroupconnectstothecarbonbackboneviaoneofitsoxygenatoms.

Phosphategroupsareanionswithtwonegativecharges,astwoprotonshavedissociated
fromtheoxygenatoms.

Onefunctionofphosphategroupsistotransferenergybetweenorganicmolecules.

Adenosinetriphosphate,orATP,istheprimaryenergytransferringmoleculeinliving
cells.

BiochemistryTheMoleculesofLife

Withincells,smallorganicmoleculesarejoinedtogethertoformlargermolecules.

Theselargemacromoleculesmayconsistofthousandsofcovalentlybondedatomsand
weighmorethan100,000daltons.
Thefourmajorclassesofmacromoleculesarecarbohydrates,lipids,proteins,andnucleic
acids.

Mostmacromoleculesarepolymers,builtfrommonomers
Threeofthefourclassesofmacromoleculescarbohydrates,proteins,andnucleicacids
formchainlikemoleculescalledpolymers.
Apolymerisalongmoleculeconsistingofmanysimilaroridenticalbuildingblocks
linkedbycovalentbonds.
Therepeatedunitsaresmallmoleculescalledmonomers.
Someofthemoleculesthatserveasmonomershaveotherfunctionsoftheirown.
Thechemicalmechanismsthatcellsusetomakeandbreakpolymersaresimilarforall
classesofmacromolecules.
Monomersareconnectedbycovalentbondsthatformthroughthelossofawater
molecule.Thisreactioniscalledacondensationreactionordehydrationreaction.
Whenabondformsbetweentwomonomers,eachmonomercontributespartofthewater
moleculethatislost.Onemonomerprovidesahydroxylgroup(OH),whiletheother
providesahydrogen(H).
Cellsinvestenergytocarryoutdehydrationreactions.
Theprocessisaidedbyenzymes.
Thecovalentbondsconnectingmonomersinapolymeraredisassembledbyhydrolysis,
areactionthatiseffectivelythereverseofdehydration.
Inhydrolysis,bondsarebrokenbytheadditionofwatermolecules.Ahydrogenatom
attachestoonemonomer,andahydroxylgroupattachestotheadjacentmonomer.
Ourfoodistakeninasorganicpolymersthataretoolargeforourcellstoabsorb.Within
thedigestivetract,variousenzymesdirecthydrolysisofspecificpolymers.Theresulting
monomersareabsorbedbythecellsliningthegutandtransportedtothebloodstreamfor
distributiontobodycells.
Lecture Outline for Campbell/Reece Biology, 7th Edition, Pearson Education, Inc.

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Thebodycellsthenusedehydrationreactiontoassemblethemonomersintonew
polymersthatcarryoutfunctionsspecifictotheparticularcelltype.

Animmensevarietyofpolymerscanbebuiltfromasmallsetofmonomers.

Eachcellhasthousandsofdifferentkindsofmacromolecules.
Thesemoleculesvaryamongcellsofthesameindividual.Theyvarymoreamong
unrelatedindividualsofaspecies,andevenmorebetweenspecies.

Thisdiversitycomesfromvariouscombinationsofthe4050commonmonomersand
someothersthatoccurrarely.
Thesemonomerscanbeconnectedinagreatmanycombinations,justasthe26lettersin
thealphabetcanbeusedtocreateagreatdiversityofwords.

Carbohydratesserveasfuelandbuildingmaterial

Carbohydratesincludesugarsandtheirpolymers.

Thesimplestcarbohydratesaremonosaccharides,orsimplesugars.

Disaccharides,ordoublesugars,consistoftwomonosaccharidesjoinedbya
condensationreaction.

Polysaccharidesarepolymersofmanymonosaccharides.

Sugars,thesmallestcarbohydrates,serveasfuelandasourceofcarbon.
Monosaccharidesgenerallyhavemolecularformulasthataresomemultipleoftheunit
CH2O.
Forexample,glucosehastheformulaC6H12O6.

Monosaccharideshaveacarbonylgroup(>C=O)andmultiplehydroxylgroups(OH).
Dependingonthelocationofthecarbonylgroup,thesugarisanaldoseoraketose.
Mostnamesforsugarsendinose.
Glucose,analdose,andfructose,aketose,arestructuralisomers.

Monosaccharidesarealsoclassifiedbythenumberofcarbonsinthecarbonskeleton.
Glucoseandothersixcarbonsugarsarehexoses.
Fivecarbonbackbonesarepentoses;threecarbonsugarsaretrioses.

Monosaccharides,particularlyglucose,areamajorfuelforcellularwork.

Theyalsofunctionastherawmaterialforthesynthesisofothermonomers,suchas
aminoacidsandfattyacids.

Whileoftendrawnasalinearskeleton,monosaccharidesinaqueoussolutionsformrings.

Twomonosaccharidescanjoinwithaglycosidiclinkagetoformadisaccharidevia
dehydration.
Maltose,maltsugar,isformedbyjoiningtwoglucosemolecules.
Sucrose,tablesugar,isformedbyjoiningglucoseandfructose.Sucroseisthemajor
transportformofsugarsinplants.
Lactose,milksugar,isformedbyjoiningglucoseandgalactose.
Polysaccharides,thepolymersofsugars,havestorageandstructuralroles.
Polysaccharidesarepolymersofhundredstothousandsofmonosaccharidesjoinedby
glycosidiclinkages.
Lecture Outline for Campbell/Reece Biology, 7th Edition, Pearson Education, Inc.

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Somepolysaccharidesserveforstorageandarehydrolyzedassugarsareneeded.

Otherpolysaccharidesserveasbuildingmaterialsforthecellorthewholeorganism.

Starchisastoragepolysaccharidecomposedentirelyofglucosemonomers.
Mostofthesemonomersarejoinedby14linkages(number1carbontonumber4
carbon)betweentheglucosemolecules.
Thesimplestformofstarch,amylose,isunbranchedandformsahelix.
Branchedformssuchasamylopectinaremorecomplex.

Plantsstoresurplusglucoseasstarchgranuleswithinplastids,includingchloroplasts,and
withdrawitasneededforenergyorcarbon.
Animalsthatfeedonplants,especiallypartsrichinstarch,havedigestiveenzymesthat
canhydrolyzestarchtoglucose.

Animalsstoreglucoseinapolysaccharidecalledglycogen.
Glycogenishighlybranchedlikeamylopectin.
Humansandothervertebratesstoreadayssupplyofglycogenintheliverandmuscles.

Celluloseisamajorcomponentofthetoughwallofplantcells.
Plantsproducealmostonehundredbilliontonsofcelluloseperyear.Itisthemost
abundantorganiccompoundonEarth.

Likestarch,celluloseisapolymerofglucose.However,theglycosidiclinkagesinthese
twopolymersdiffer.
Thedifferenceisbasedonthefactthatthereareactuallytwoslightlydifferentring
structuresforglucose.
Thesetworingformsdifferinwhetherthehydroxylgroupattachedtothenumber1
carbonisfixedabove(betaglucose)orbelow(alphaglucose)theplaneofthering.

Starchisapolysaccharideofalphaglucosemonomers.

Celluloseisapolysaccharideofbetaglucosemonomers,makingeveryotherglucose
monomerupsidedownwithrespecttoitsneighbors.
Thedifferingglycosidiclinksinstarchandcellulosegivethetwomoleculesdistinct
threedimensionalshapes.
Whilepolymersbuiltwithalphaglucoseformhelicalstructures,polymersbuiltwithbeta
glucoseformstraightstructures.
Theenzymesthatdigeststarchbyhydrolyzingitsalphalinkagescannothydrolyzethe
betalinkagesincellulose.
Celluloseinhumanfoodpassesthroughthedigestivetractandiseliminatedinfecesas
insolublefiber.
Asittravelsthroughthedigestivetract,celluloseabradestheintestinalwallsand
stimulatesthesecretionofmucus,aidinginthepassageoffood.
Somemicrobescandigestcellulosetoitsglucosemonomersthroughtheuseofcellulase
enzymes.
Manyeukaryoticherbivores,fromcowstotermites,havesymbioticrelationshipswith
cellulolyticmicrobes,providingthemicrobeandthehostanimalaccesstoarichsourceof
energy.
Somefungicanalsodigestcellulose.
Anotherimportantstructuralpolysaccharideischitin,usedintheexoskeletonsof
arthropods(includinginsects,spiders,andcrustaceans).

Lecture Outline for Campbell/Reece Biology, 7th Edition, Pearson Education, Inc.

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Chitinissimilartocellulose,exceptthatitcontainsanitrogencontainingappendageon
eachglucosemonomer.
Purechitinisleatherybutcanbehardenedbytheadditionofcalciumcarbonate.

Chitinalsoprovidesstructuralsupportforthecellwallsofmanyfungi.

Lipidsareadiversegroupofhydrophobicmolecules

Unlikeothermacromolecules,lipidsdonotformpolymers.

Theunifyingfeatureoflipidsisthattheyallhavelittleornoaffinityforwater.

Thisisbecausetheyconsistmostlyofhydrocarbons,whichformnonpolarcovalent
bonds.

Lipidsarehighlydiverseinformandfunction.

Fatsstorelargeamountsofenergy.
Althoughfatsarenotstrictlypolymers,theyarelargemoleculesassembledfromsmaller
moleculesbydehydrationreactions.

Afatisconstructedfromtwokindsofsmallermolecules:glycerolandfattyacids.
Glycerolisathreecarbonalcoholwithahydroxylgroupattachedtoeachcarbon.
Afattyacidconsistsofacarboxylgroupattachedtoalongcarbonskeleton,often16to
18carbonslong.
ThemanynonpolarCHbondsinthelonghydrocarbonskeletonmakefats
hydrophobic.
Fatsseparatefromwaterbecausethewatermoleculeshydrogenbondtooneanotherand
excludethefats.

Inafat,threefattyacidsarejoinedtoglycerolbyanesterlinkage,creatinga
triacylglycerol,ortriglyceride.

Thethreefattyacidsinafatcanbethesameordifferent.

Fattyacidsmayvaryinlength(numberofcarbons)andinthenumberandlocationsof
doublebonds.
Ifthefattyacidhasnocarboncarbondoublebonds,thenthemoleculeisasaturated
fattyacid,saturatedwithhydrogensateverypossibleposition.
Ifthefattyacidhasoneormorecarboncarbondoublebondsformedbytheremovalof
hydrogenatomsfromthecarbonskeleton,thenthemoleculeisanunsaturatedfatty
acid.
Asaturatedfattyacidisastraightchain,butanunsaturatedfattyacidhasakinkwherever
thereisadoublebond.

Fatsmadefromsaturatedfattyacidsaresaturatedfats.
Mostanimalfatsaresaturated.
Saturatedfatsaresolidatroomtemperature.

Fatsmadefromunsaturatedfattyacidsareunsaturatedfats.
Plantandfishfatsareliquidatroomtemperatureandareknownasoils.
Thekinkscausedbythedoublebondspreventthemoleculesfrompackingtightlyenough
tosolidifyatroomtemperature.
Thephrasehydrogenatedvegetableoilsonfoodlabelsmeansthatunsaturatedfatshave
beensyntheticallyconvertedtosaturatedfatsbytheadditionofhydrogen.

Lecture Outline for Campbell/Reece Biology, 7th Edition, Pearson Education, Inc.

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Peanutbutterandmargarinearehydrogenatedtopreventlipidsfromseparatingoutasoil.
Adietrichinsaturatedfatsmaycontributetocardiovasculardisease(atherosclerosis)
throughplaquedeposits.
Theprocessofhydrogenatingvegetableoilsproducessaturatedfatsandalsounsaturated
fatswithtransdoublebonds.Thesetransfatmoleculescontributemorethansaturated
fatstoatherosclerosis.
Themajorfunctionoffatsisenergystorage.
Agramoffatstoresmorethantwiceasmuchenergyasagramofapolysaccharidesuch
asstarch.
Becauseplantsareimmobile,theycanfunctionwithbulkyenergystorageintheformof
starch.Plantsuseoilswhendispersalandcompactstorageisimportant,asinseeds.
Animalsmustcarrytheirenergystoreswiththemandbenefitfromhavingamore
compactfuelreservoiroffat.
Humansandothermammalsstorefatsaslongtermenergyreservesinadiposecellsthat
swellandshrinkasfatisdepositedorwithdrawnfromstorage.

Adiposetissuealsofunctionstocushionvitalorgans,suchasthekidneys.

Alayeroffatcanalsofunctionasinsulation.
Thissubcutaneouslayerisespeciallythickinwhales,seals,andmostothermarine
mammals.

Phospholipidsaremajorcomponentsofcellmembranes.
Phospholipidshavetwofattyacidsattachedtoglycerolandaphosphategroupatthe
thirdposition.
Thephosphategroupcarriesanegativecharge.
Additionalsmallergroupsmaybeattachedtothephosphategrouptoformavarietyof
phospholipids.

Theinteractionofphospholipidswithwateriscomplex.
Thefattyacidtailsarehydrophobic,butthephosphategroupanditsattachmentsforma
hydrophilichead.

Whenphospholipidsareaddedtowater,theyselfassembleintoassemblageswiththe
hydrophobictailspointingtowardtheinterior.
Thistypeofstructureiscalledamicelle.

Phospholipidsarearrangedasabilayeratthesurfaceofacell.
Again,thehydrophilicheadsareontheoutsideofthebilayer,incontactwiththeaqueous
solution,andthehydrophobictailspointtowardtheinteriorofthebilayer.
Thephospholipidbilayerformsabarrierbetweenthecellandtheexternalenvironment.
Phospholipidsarethemajorcomponentofallcellmembranes.

Steroidsincludecholesterolandcertainhormones.

Steroidsarelipidswithacarbonskeletonconsistingoffourfusedrings.

Differentsteroidsarecreatedbyvaryingfunctionalgroupsattachedtotherings.

Cholesterol,animportantsteroid,isacomponentinanimalcellmembranes.

Cholesterolisalsotheprecursorfromwhichallothersteroidsaresynthesized.
Manyoftheseothersteroidsarehormones,includingthevertebratesexhormones.

Lecture Outline for Campbell/Reece Biology, 7th Edition, Pearson Education, Inc.

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Whilecholesterolisanessentialmoleculeinanimals,highlevelsofcholesterolinthe
bloodmaycontributetocardiovasculardisease.
Bothsaturatedfatsandtransfatsexerttheirnegativeimpactonhealthbyaffecting
cholesterollevels.

Proteinshavemanystructures,resultinginawiderangeoffunctions
Proteinsaccountformorethan50%ofthedrymassofmostcells.Theyareinstrumental
inalmosteverythingthatanorganismdoes.
Proteinfunctionsincludestructuralsupport,storage,transport,cellularsignaling,
movement,anddefenseagainstforeignsubstances.
Mostimportant,proteinenzymesfunctionascatalystsincells,regulatingmetabolismby
selectivelyacceleratingchemicalreactionswithoutbeingconsumed.
Humanshavetensofthousandsofdifferentproteins,eachwithaspecificstructureand
function.

Proteinsarethemoststructurallycomplexmoleculesknown.
Eachtypeofproteinhasacomplexthreedimensionalshapeorconformation.

Allproteinpolymersareconstructedfromthesamesetof20aminoacidmonomers.

Polymersofproteinsarecalledpolypeptides.

Aproteinconsistsofoneormorepolypeptidesfoldedandcoiledintoaspecific
conformation.
Aminoacidsarethemonomersfromwhichproteinsareconstructed.

Aminoacidsareorganicmoleculeswithbothcarboxylandaminogroups.

Atthecenterofanaminoacidisanasymmetriccarbonatomcalledthealphacarbon.

Fourcomponentsareattachedtothealphacarbon:ahydrogenatom,acarboxylgroup,an
aminogroup,andavariableRgroup(orsidechain).
DifferentRgroupscharacterizethe20differentaminoacids.
Rgroupsmaybeassimpleasahydrogenatom(asintheaminoacidglycine),oritmay
beacarbonskeletonwithvariousfunctionalgroupsattached(asinglutamine).
ThephysicalandchemicalpropertiesoftheRgroupdeterminetheuniquecharacteristics
ofaparticularaminoacid.
OnegroupofaminoacidshashydrophobicRgroups.
AnothergroupofaminoacidshaspolarRgroupsthatarehydrophilic.
Athirdgroupofaminoacidsincludesthosewithfunctionalgroupsthatarecharged
(ionized)atcellularpH.
SomeacidicRgroupsarenegativeinchargeduetothepresenceofacarboxylgroup.
BasicRgroupshaveaminogroupsthatarepositiveincharge.
Notethatallaminoacidshavecarboxylandaminogroups.Thetermsacidicandbasicin
thiscontextreferonlytothesegroupsintheRgroups.
Aminoacidsarejoinedtogetherwhenadehydrationreactionremovesahydroxylgroup
fromthecarboxylendofoneaminoacidandahydrogenfromtheaminogroupofanother.
Theresultingcovalentbondiscalledapeptidebond.

Repeatingtheprocessoverandovercreatesapolypeptidechain.

Lecture Outline for Campbell/Reece Biology, 7th Edition, Pearson Education, Inc.

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Atoneendisanaminoacidwithafreeaminogroup(theNterminus)andattheotheris
anaminoacidwithafreecarboxylgroup(theCterminus).

Polypeptidesrangeinsizefromafewmonomerstothousands.

Eachpolypeptidehasauniquelinearsequenceofaminoacids.

Proteinconformationdeterminesproteinfunction.
Afunctionalproteinconsistsofoneormorepolypeptidesthathavebeentwisted,folded,
andcoiledintoauniqueshape.
Itistheorderofaminoacidsthatdetermineswhatthethreedimensionalconformationof
theproteinwillbe.

Aproteinsspecificconformationdeterminesitsfunction.

Whenacellsynthesizesapolypeptide,thechaingenerallyfoldsspontaneouslytoassume
thefunctionalconformationforthatprotein.
Thefoldingisreinforcedbyavarietyofbondsbetweenpartsofthechain,whichinturn
dependonthesequenceofaminoacids.
Manyproteinsareglobular,whileothersarefibrousinshape.
Inalmosteverycase,thefunctionofaproteindependsonitsabilitytorecognizeand
bindtosomeothermolecule.
Forexample,anantibodybindstoaparticularforeignsubstance.
Anenzymerecognizesandbindstoaspecificsubstrate,facilitatingachemicalreaction.
Naturalsignalmoleculescalledendorphinsbindtospecificreceptorproteinsonthe
surfaceofbraincellsinhumans,producingeuphoriaandrelievingpain.
Morphine,heroin,andotheropiatedrugsmimicendorphinsbecausetheyaresimilarin
shapeandcanbindtothebrainsendorphinreceptors.
Thefunctionofaproteinisanemergentpropertyresultingfromitsspecificmolecular
order.
Threelevelsofstructureprimary,secondary,andtertiarystructuresorganizethe
foldingwithinasinglepolypeptide.

Quaternarystructureariseswhentwoormorepolypeptidesjointoformaprotein.

Theprimarystructureofaproteinisitsuniquesequenceofaminoacids.
Lysozyme,anenzymethatattacksbacteria,consistsof129aminoacids.
Thepreciseprimarystructureofaproteinisdeterminedbyinheritedgeneticinformation.

Evenaslightchangeinprimarystructurecanaffectaproteinsconformationandability
tofunction.
Thesubstitutionofoneaminoacid(valine)forthenormalone(glutamicacid)ata
particularpositionintheprimarystructureofhemoglobin,theproteinthatcarriesoxygen
inredbloodcells,cancausesicklecelldisease,aninheritedblooddisorder.
Theabnormalhemoglobinscrystallize,deformingtheredbloodcellsintoasickleshape
andcloggingcapillaries.

Mostproteinshavesegmentsoftheirpolypeptidechainsrepeatedlycoiledorfolded.

Thesecoilsandfoldsarereferredtoassecondarystructureandresultfromhydrogen
bondsbetweentherepeatingconstituentsofthepolypeptidebackbone.
Theweaklypositivehydrogenatomattachedtothenitrogenatomhasanaffinityforthe
oxygenatomofanearbypeptidebond.

Lecture Outline for Campbell/Reece Biology, 7th Edition, Pearson Education, Inc.

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Eachhydrogenbondisweak,butthesumofmanyhydrogenbondsstabilizesthe
structureofpartoftheprotein.

Typicalsecondarystructuresarecoils(analphahelix)orfolds(betapleatedsheets).

Thestructuralpropertiesofsilkareduetobetapleatedsheets.
Thepresenceofsomanyhydrogenbondsmakeseachsilkfiberstrongerthanasteel
strandofthesameweight.

TertiarystructureisdeterminedbyinteractionsamongvariousRgroups.
Theseinteractionsincludehydrogenbondsbetweenpolarand/orchargedareas,ionic
bondsbetweenchargedRgroups,andhydrophobicinteractionsandvanderWaals
interactionsamonghydrophobicRgroups.
Whilethesethreeinteractionsarerelativelyweak,strongcovalentbondscalleddisulfide
bridgesthatformbetweenthesulfhydrylgroups(SH)oftwocysteinemonomersactto
rivetpartsoftheproteintogether.

Quaternarystructureresultsfromtheaggregationoftwoormorepolypeptidesubunits.
Collagenisafibrousproteinofthreepolypeptidesthataresupercoiledlikearope.
Thisprovidesstructuralstrengthforcollagensroleinconnectivetissue.
Hemoglobinisaglobularproteinwithquaternarystructure.
Itconsistsoffourpolypeptidesubunits:twoalphaandtwobetachains.
Bothtypesofsubunitsconsistprimarilyofalphahelicalsecondarystructure.
Eachsubunithasanonpeptidehemecomponentwithanironatomthatbindsoxygen.

Whatarethekeyfactorsdeterminingproteinconformation?

Apolypeptidechainofagivenaminoacidsequencecanspontaneouslyarrangeitselfinto
a3Dshapedeterminedandmaintainedbytheinteractionsresponsibleforsecondaryand
tertiarystructure.
Thefoldingoccursastheproteinisbeingsynthesizedwithinthecell.
However,proteinconformationalsodependsonthephysicalandchemicalconditionsof
theproteinsenvironment.
AlterationsinpH,saltconcentration,temperature,orotherfactorscanunravelor
denatureaprotein.
Theseforcesdisruptthehydrogenbonds,ionicbonds,anddisulfidebridgesthatmaintain
theproteinsshape.
Denaturationcanalsobecausedbyheat,whichdisruptstheweakinteractionsthat
stabilizeconformation.
Thisexplainswhyextremelyhighfeverscanbefatal.Proteinsinthebloodbecome
denaturedbythehighbodytemperatures.
Someproteinscanreturntotheirfunctionalshapeafterdenaturation,butotherscannot,
especiallyinthecrowdedenvironmentofthecell.
Biochemistsnowknowtheaminoacidsequencesofmorethan875,000proteinsandthe
3Dshapesofabout7,000.
Nevertheless,itisstilldifficulttopredicttheconformationofaproteinfromitsprimary
structurealone.
Mostproteinsappeartoundergoseveralintermediatestagesbeforereachingtheir
matureconfiguration.
Lecture Outline for Campbell/Reece Biology, 7th Edition, Pearson Education, Inc.

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Nucleicacidsstoreandtransmithereditaryinformation
Theaminoacidsequenceofapolypeptideisprogrammedbyaunitofinheritanceknown
asagene.

AgeneconsistsofDNA,apolymerknownasanucleicacid.

Therearetwotypesofnucleicacids:RNAandDNA.
Therearetwotypesofnucleicacids:ribonucleicacid(RNA)anddeoxyribonucleicacid
(DNA).
Thesearethemoleculesthatallowlivingorganismstoreproducetheircomplex
componentsfromgenerationtogeneration.

DNAprovidesdirectionsforitsownreplication.

DNAalsodirectsRNAsynthesisand,throughRNA,controlsproteinsynthesis.

OrganismsinheritDNAfromtheirparents.
EachDNAmoleculeisverylong,consistingofhundredstothousandsofgenes.
Beforeacellreproducesitselfbydividing,itsDNAiscopied.Thecopiesarethenpassed
tothenextgenerationofcells.

WhileDNAencodestheinformationthatprogramsallthecellsactivities,itisnot
directlyinvolvedinthedaytodayoperationsofthecell.
ProteinsareresponsibleforimplementingtheinstructionscontainedinDNA.
EachgenealongaDNAmoleculedirectsthesynthesisofaspecifictypeofmessenger
RNAmolecule(mRNA).
ThemRNAmoleculeinteractswiththecellsproteinsynthesizingmachinerytodirect
theorderingofaminoacidsinapolypeptide.

TheflowofgeneticinformationisfromDNA>RNA>protein.

Proteinsynthesisoccursoncellularstructurescalledribosomes.

Ineukaryotes,DNAislocatedinthenucleus,butmostribosomesareinthecytoplasm.
mRNAfunctionsasanintermediary,movinginformationanddirectionsfromthenucleusto
thecytoplasm.
ProkaryoteslacknucleibutstilluseRNAasanintermediarytocarryamessagefrom
DNAtotheribosomes.
Anucleicacidstrandisapolymerofnucleotides.

Nucleicacidsarepolymersmadeofnucleotidemonomers.

Eachnucleotideconsistsofthreeparts:anitrogenousbase,apentosesugar,anda
phosphategroup.
Thenitrogenbasesareringsofcarbonandnitrogenthatcomeintwotypes:purinesand
pyrimidines.
Pyrimidineshaveasinglesixmemberedring.
Therearethreedifferentpyrimidines:cytosine(C),thymine(T),anduracil(U).
Purineshaveasixmemberedringjoinedtoafivememberedring.
Thetwopurinesareadenine(A)andguanine(G).
ThepentosejoinedtothenitrogenbaseisriboseinnucleotidesofRNAanddeoxyribose
inDNA.
Lecture Outline for Campbell/Reece Biology, 7th Edition, Pearson Education, Inc.

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Theonlydifferencebetweenthesugarsisthelackofanoxygenatomoncarbontwoin
deoxyribose.
Becausetheatomsinboththenitrogenousbaseandthesugararenumbered,thesugar
atomshaveaprimeafterthenumbertodistinguishthem.
Thus,thesecondcarboninthesugarringisthe2(2prime)carbonandthecarbonthat
sticksupfromtheringisthe5carbon.
Thecombinationofapentoseandanitrogenousbaseisanucleoside.

Theadditionofaphosphategroupcreatesanucleosidemonophosphateornucleotide.

Polynucleotidesaresynthesizedwhenadjacentnucleotidesarejoinedbycovalentbonds
calledphosphodiesterlinkagesthatformbetweentheOHgrouponthe3ofonenucleotide
andthephosphateonthe5carbonofthenext.
Thiscreatesarepeatingbackboneofsugarphosphateunits,withappendagesconsisting
ofthenitrogenousbases.

Thetwofreeendsofthepolymeraredistinct.
Oneendhasaphosphateattachedtoa5carbon;thisisthe5end.
Theotherendhasahydroxylgroupona3carbon;thisisthe3end.

ThesequenceofbasesalongaDNAormRNApolymerisuniqueforeachgene.
Becausegenesarenormallyhundredstothousandsofnucleotideslong,thenumberof
possiblebasecombinationsisvirtuallylimitless.

Thelinearorderofbasesinagenespecifiestheorderofaminoacidstheprimary
structureofaprotein,whichinturndeterminesthreedimensionalconformationand
function.
InheritanceisbasedonreplicationoftheDNAdoublehelix.

AnRNAmoleculeisasinglepolynucleotidechain.

DNAmoleculeshavetwopolynucleotidestrandsthatspiralaroundanimaginaryaxisto
formadoublehelix.
ThedoublehelixwasfirstproposedasthestructureofDNAin1953byJamesWatson
andFrancisCrick.
Thesugarphosphatebackbonesofthetwopolynucleotidesareontheoutsideofthe
helix.
Thetwobackbonesruninopposite5>3directionsfromeachother,anarrangement
referredtoasantiparallel.
Pairsofnitrogenousbases,onefromeachstrand,connectthepolynucleotidechainswith
hydrogenbonds.

MostDNAmoleculeshavethousandstomillionsofbasepairs.

Becauseoftheirshapes,onlysomebasesarecompatiblewitheachother.
Adenine(A)alwayspairswiththymine(T)andguanine(G)withcytosine(C).

Withthesebasepairingrules,ifweknowthesequenceofbasesononestrand,weknow
thesequenceontheoppositestrand.
Thetwostrandsarecomplementary.
ATP(adenosinetriphosphate)moleculesconsistofanitrogenousbasecalledadenine,a
5carbonsugar(ribose),andthreemoleculesofphosphoricacid(phosphate)linkedtogether
bytwopyrophosphatebondstoformatriphosphategroup.
Lecture Outline for Campbell/Reece Biology, 7th Edition, Pearson Education, Inc.

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Thepyrophosphatebondsarecalledhighenergybondsbecauseagreatdealoffree
energyinthebondsisliberatedwhenATPishydrolyzedtoadenosinediphosphate(ADP)
andinorganicphosphate.

Lecture Outline for Campbell/Reece Biology, 7th Edition, Pearson Education, Inc.

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