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chapter 3 The Molecules of Cells

Objectives
Introduction Explain how spider silk is produced. Describe the special properties of spider silk that help spiders capture prey. Introduction to Organic Compounds and Their Polymers 3.1 Explain why carbon is unparalleled in its ability to form large, diverse molecules. 3.1 3.2 Define organic compounds, hydrocarbons, a carbon skeleton, and an isomer. Describe the properties of and distinguish between the four functional groups of organic molecules. List the four classes of macromolecules, explain the relationship between monomers and polymers, and compare the processes of dehydration synthesis and hydrolysis.

3.3

Carbohydrates 3.43.7 Describe the structures, functions, properties, and types of carbohydrate molecules. Lipids 3.83.10 Proteins 3.113.18 3.19

Describe the structures, functions, properties, and types of lipid molecules.

Describe the structures, functions, properties, and types of proteins. Describe the major achievements of Linus Pauling.

Nucleic Acids 3.20 Compare the structures and functions of DNA and RNA.

Key Terms
organic compound hydrocarbon carbon skeleton isomer functional group hydrophilic hydroxyl group carbonyl group carboxyl group carboxylic acid amino group amine macromolecule polymer monomer dehydration synthesis hydrolysis carbohydrate monosaccharide disaccharide polysaccharide starch glycogen cellulose

lipid hydrophobic fat triglyceride unsaturated saturated phospholipid wax steroid anabolic steroid

protein enzyme amino acid peptide bond polypeptide denaturation primary structure secondary structure alpha helix pleated sheet

tertiary structure quaternary structure nucleic acid deoxyribonucleic acid (DNA) ribonucleic acid (RNA) gene nucleotide phosphate group nitrogenous base double helix

Word Roots
carb- = coal (carboxyl group: a functional group present in organic acids, consisting of a carbon atom double-bonded to an oxygen atom) di- = two (disaccharide: two monosaccharides joined together ) glyco- = sweet (glycogen: a polysaccharide sugar used to store energy in animals) hydro- = water (hydrocarbon: an organic molecule consisting only of carbon and hydrogen) iso- = equal (isomer: one of several organic compounds with the same molecular formula but different structures and therefore different properties) macro- = large (macromolecule: a large molecule) mono- = single; -sacchar = sugar (monosaccharide: simplest type of sugar) poly- = many (polysaccharide: many monosaccharides joined together) tri- = three (triacylglycerol: three fatty acids linked to one glycerol molecule)

Lecture Outline
Introduction SpiderSilk:StrongerThanSteel A. Lifesbeautyandpropertiesbegintoemergeatthemacromolecularlevel. B. Thecentraltopicofthischapterishowsmallermolecularunitsareassembledinto largerones. C. Figure3.0isagoodstartingexampleofmacromolecularstructureandfunction. I. IntroductiontoOrganicCompoundsandTheirPolymers Module3.1 Lifesmoleculardiversityisbasedonthepropertiesofcarbon. A. Organiccompoundscontainatleastonecarbonatom(Figure3.1).

B. Carbonhas4electronsintheoutershell;thereforecarbonhasastrongtendencytofill theshellto8byformingcovalentbondswithotheratoms,particularlyhydrogen, oxygen,andnitrogen.The4electronsintheoutermostshellofcarbonallowittoform complexstructures(e.g.,long,branchedchains,ringstructures).Thisisamajorreason whycarbonisthestructuralbackboneoforganiccompounds.Acompoundcomposed onlyofcarbonandhydrogeniscalledahydrocarbon.

Review:Covalentbonds(Module2.8). NOTE:Atthispointyoumightwanttoasktheclassifanyofthemhaveeverseenthe episodeoftheoriginalStarTrekinwhichtheHorta,asiliconbasedlifeform,appeared;ask ifsiliconbasedlifemakeschemicalsense. C. PointoutthedoublebondinFigure3.1,explainingthatitrepresents4sharedelectrons. NOTE:Althoughthetopicisnotintroducedhere,youmightmentionthattriplebonds whichoccurinmolecularnitrogen,amongotherplacesarerepresentedbythreelines(6 sharedelectrons). C. Thewaybondingoccursamongatomsinmoleculesdeterminesanoverallshape. D. Isomersaremoleculeswiththesamenumbersofeachatombutwithdifferentstructural arrangementsoftheatoms. Module3.2 Functionalgroupshelpdeterminethepropertiesoforganiccompounds. A. Functionalgroupsaregenerallyattachedtothecarbonbackboneofdifferent macromoleculesandexhibitpredictablechemicalproperties. B. Functionalgroupsaretheatomsofanorganiccompounddirectlyparticipatingin chemicalreactions. C. GooverFigure3.2,discussingafewoftheexamples. D. Allofthesefunctionalgroupshavepolarcharacteristics.Therefore,mostofthe moleculestheyarefoundonarepolarmolecules. Module3.3 Cellsmakeahugenumberoflargemoleculesfromasmallsetofsmallmolecules. A. Monomersarethefundamentalmolecularunit.Polymersaremacromoleculesmadeby linkingmanyofthesamekindoffundamentalunits. B. Typesofreactions(notethatwaterisinvolvedinboth;Figure3.3A,B):dehydration synthesismoleculessynthesizedbylossofawatermoleculebetweenreacting

monomers,themostcommonwayorganicpolymersaresynthesized;hydrolysis literally,breakingapartwithwaterhemostcommonwayorganicpolymersare degraded. C. Thestudyofmolecularreactionsinlivingsystemsisabroadtopicthatwillbeatheme throughoutthecourse.Thetworeactionsreviewedinthismoduleareonesinvolvedin theformationofmolecularstructuresintroducedintheremainingmodules. D. Lifeschemicalreactionsoccurinparticularintracellularandextracellularenvironments andundercontrolledconditions. E. Preview:Chapter4willdiscussthecellularframeworkonwhichandinwhichmolecular reactionsoccur. F. Preview:Chapters57discussmetabolism,i.e.,cellularreactionsinvolvingenergy uptake,storage,andrelease. II.Carbohydrates Module3.4 Monosaccharidesarethesimplestcarbohydrates. NOTE:Thewordcarbohydrateindicatesthatthesecompoundsaremadeofcarbon(carbo,C) andwater(hydrate,H2O).Thisisreiteratedinthegeneralformula(CH2O)nfor monosaccharides.

A. Showexamplesoftheisomersglucoseandfructose(Figure3.4B). B. Thesuffixoseindicatesthatthemoleculeisasugar.

C. Insolution,manymonosaccharidesformringshapedmolecules(Figure3.4C). D. Preview:Thebasicrolesofsimplesugarsareasfueltodowork,asrawmaterialfor carbonbackbones,andasthemonomersfromwhichdisaccharidesandpolysaccharides aresynthesized. Module3.5 Cellslinksinglesugarstoformdisaccharides. A. Twomonosaccharidesareputtogethertoformadisaccharideviaaglycosidicbond (Figure3.5). B. Disaccharideformationisanexampleofdehydrationsynthesis(Module3.3). C. Themostcommondisaccharideissucrose(tablesugar),whichiscomposedofglucose andfructose.

Module3.6 Connection:Howsweetissweet? A. Therearefourwelldocumentedtastereceptorsonthetongue:bitter,salty,sour,andsweet. B. Humansperceiveasweettastewhenachemicalbindstothesweetreceptoronthe tongue.Thechemicalcanbeasugarorotherchemicalslikeaspartame. C. Thestrongerthebindingbyachemicaltothesweetreceptor,thesweeterthechemicalis perceivedtobe.Fructoseisconsidered4timessweeterthansucrose. D. Preview:Thediscussioninthismodulecontinueswithadditionalmaterialonnutritionin Chapter21. Module3.7 Polysaccharidesarelongchainsofsugarunits. A. Differentorganismsusemonosaccharides,suchasglucose,tobuildseveraldifferent polymers:starch,glycogen,andcellulose(Figure3.7). NOTE:Hydrogenatomsandfunctionalgroupsarenotshowninthefigure. B. Eachofthesemoleculesissynthesizedbydehydrationsynthesis,buttherearesubtle differencesinthecovalentbondsthatleadtodifferentoverallstructuresandfunctions. Review:Covalentbonds(Module2.8). C. Starchisusedforlongtermenergystorageonlyinplants.Starchmoleculesarehelical andmaybeeitherunbranchedorbranched.Animalscanhydrolyzethispolymerto obtainglucose. NOTE:Theunbranchedformofstarchiscalledamylose.Thebranchedformiscalled amylopectin.Starchesrichinamylopectinretainwaterandareoftenusedinfrozenfoods. Thiscanalsobeusedtoillustratetheconventionusedfornamingenzymesthestarch amyloseisbrokendownbytheenzymeamylase. D. Glycogenhasthesamekindofbondbetweenmonomersasstarch,butitishighlybranched. Glycogenalsoisusedforlongtermenergystorage,butonlyinanimals.Animalscan hydrolyzethispolymertoobtainglucose. E. Cellulosehasadifferentkindofbondbetweenmonomers,forminglinearpolymersthatare crosslinkedbyhydrogenbondswithotherlinearchains.Celluloseistheprincipal structuralmoleculeinthecellwallsofplantsandalgae.Sinceanimalscannothydrolyzethis polymertoobtainglucose(onlycertainbacteria,protozoans,andfungican)itisreferredto asafiber. III. Lipids Module3.8Lipidsincludefats,whicharemostlyenergystoragemolecules.

A. Inlipids,carbonandhydrogenpredominate;thereisverylittleoxygen.General molecularformulaforfattyacid:(CH2)n. B. Diversetypesoflipidshavedifferentroles,butallaremoreorlesshydrophobic.

C. Fatsarepolymersoffattyacids(usuallythree)andoneglycerolmolecule,formedby dehydrationsynthesisreactions,andarecalledtriglyceridesortriacylglycerides(Figure 3.8B,C). D. Saturatedfattyacidshavenodoublebondsbetweencarbons(thecarbonsare saturatedwithhydrogenatoms).Themolecularbackbonesareflexibleandtendto ballupintotightglobules.Saturatedfatslikebutterandlardaresolidatroom temperature. E. Unsaturatedfatsmayincludeseveraldoublebondsbetweencarbons.Thiscausesthe moleculestobelessflexibleandtheydonotpackintosolidglobules.Unsaturatedfats likeoliveoilandcornoilareliquidatroomtemperature. F. Mostplantfatsareunsaturated,whereasanimalfatsarericherinsaturatedfats. Preview:Therearetwotypesofunsaturatedfats(Chapter21).Polyunsaturatedfats includetheessentialfattyacids.Monounsaturatedfats(inmoderation),contraryto thegeneralreputationoffat,havecardiovascularbenefits.Omegafatsinfisharea goodexampleofahealthyfat. NOTE:Byhydrogenatingunsaturatedoils,thedoublebondsareremovedandthe moleculesbecomemoresolidatroomtemperature.Thesestructurallymodified (trans)fatsareasdetrimentalastheirnaturallysaturatedcounterpartsinleadingto atheroscleroticplaques. Module3.9 Phospholipids,waxes,andsteroidsarelipidswithavarietyoffunctions. A. Phospholipidsareamajorcomponentofcellmembranes,buthavetwofattyacid moleculesinsteadofthreeandaphosphategroup. B. Waxesareeffectivehydrophobiccoatingsformedbymanyorganisms(insects,plants, evenhumans)towardoffwater.Theyconsistofasinglefattyacidlinkedtoanalcohol. C. Steroidsarelipidswithbackbonesbentintorings.Cholesterolisanimportantsteroid formedbyanimals(Figure3.9;noticethatthediagramomitscarbonsandhydrogensateach intersectionintheringsandjustshowsthebackboneshape).Amongotherthings, cholesterolistheprecursortobileacidsthatfunctionsinthedigestionoffatsandasstarting materialforthesynthesisoffemaleandmalesexhormones.

NOTE:Despiteitsreputation,cholesterolplaysmanyvitalrolesinthebody. C. Preview:Thestructuralrolesofphospholipidcontainingmembranesareintroducedin Chapter4,oncellstructure;theirmolecularstructureandfunctionarediscussedin Chapter5,withothertopicsrelatingtocellularwork.Likefats,theyarepolymersof fattyacidsandglycerol,butincludeaPO4groupinplaceofonefattyacid.Thisgives themtheuniquepropertyofhavingahydrophobictailandahydrophilichead.

Module3.10 Connection:Anabolicsteroidsandrelatedsubstancesposehealthrisks. A. Anabolicsteroidsaresyntheticandnaturalvariantsofthemalehormonetestosterone,which, amongotherroles,causesthebuildupofmuscleandbonemassduringpubertyinmen. NOTE:Sincecollegeagebodybuildersmaybetemptedtousesteroids,youmightwantto pointoutsomeofthemedicalproblemssuchusecouldleadto,includingproblemssuchas: testicularatrophy,livercancer,breastdevelopmentinmales,masculinizationoffemales, andantisocialbehavior. IV. Proteins Module3.11Proteinsareessentialtothestructuresandactivitiesoflife. A. Proteinsareconstructedfromaminoacids. B. Thestructureoftheproteindeterminesitsfunction. C. Thesevenmajorclassesofproteinare: 1. Structural:hair,cellcytoskeleton 2. Contractile:aspartofmuscleandothermotilecells,producemovement 3. Storage:sourcesofaminoacids,suchaseggwhite 4. Defense:antibodies,membraneproteins,complementproteins 5. Transport:hemoglobin,membraneproteins 6. Signaling:hormones,membraneproteins 7. Enzymatic:decreasetherateofabiochemicalreactionmuchlikeachemicalcatalyst Module3.12 Proteinsaremadefromjust20kindsofaminoacids. A. Aminoacidsarecharacterizedbyhavinganalphacarbonatomcovalentlybondedto onehydrogen,oneaminogroup(NH2),onecarboxylgroup(COOH),andonefunctional groupsymbolizedbyanR(Figure3.12A). Review:Covalentbonds(Module2.8).

B. Eachnaturallyoccurringaminoacidhasoneof20functionalgroups(Figure3.12B), whichdeterminesthechemicalcharacteristicsofeachaminoacid. Module3.13 Aminoacidscanbelinkedbypeptidebonds. A. Organismsuseaminoacidsasthemonomertobuildpolypeptidesbydehydration synthesis.Thebondbetweeneachaminoacidiscalledapeptidebond(Figure3.13). B. Proteinpeptidebondscanbebrokendownbyhydrolysis,toreleasefreeaminoacids. C. Polypeptidesarefromseveraltooverathousandaminoacidslongandthespecific sequencedeterminesthefunctionoftheprotein(apolypeptidewithmorethan20amino acidsisclassifiedasaprotein). NOTE:AddareversearrowtoFigure3.13andlabelitHydrolysis. Module3.14 Overview:Aproteinsspecificshapedeterminesitsfunction. A. Longpolypeptidechainsincludenumerousandvariousaminoacids. B. Thefinalstructureofaprotein,andthusitspotentialrole,dependsonthewaythese long,linearmoleculesfoldup. C. Eachsequenceofaminoacidsfoldsinadifferentwayspontaneously(Figure3.14A). D. Changesinheat,ionicstrength,salinity,andsooncancauseproteinstounfold(thisis calleddenaturation). E. ThefourlevelsofstructureareshownintheproteintransthyretininFigures3.153.18. NOTE:Ateachlevelinthediagrams,detailsarehiddentoshowtheessential structureaddedatthatlevel. Module3.15Aproteinsprimarystructureisitsaminoacidsequence. A. Transthyretinisfoundinbloodandisimportantinthetransportofathyroidhormone andvitaminA. B. Threeletterabbreviationsrepresentaminoacids;eachaminoacidisinapreciseorderin thechain(Figure3.15). C. Intransthyretin,therearefourpolypeptidechains,eachwith127aminoacids. D. Changesintheprimarystructureofaprotein(theaminoacidsequence)canaffectits overallstructureandthusitsabilitytofunction.

Module3.16 Secondarystructureispolypeptidecoilingorfoldingproducedbyhydrogenbonding. A. HydrogenbondsoccurbetweenNHandC=Ogroupsofaminoacidsinsequence alongeachpolypeptidechain. Review:Hydrogenbonds(Module2.10). B. Dependingonwherethegroupsarerelativetooneanother,thesecondarystructure takestheshapeofanalphahelixorapleatedsheet(Figure3.16). C. TheRgroupsusuallydonotplayaroleinsecondarystructureandarenotdiagrammed. NOTE:Diagrammingthesecondarystructuresofproteinsusescylinders,flatarrows,and linestorepresenthelicalregions,betapleatedsheets,andnonhydrogenbondedregions (alsocalledrandomcoils),respectively. Module3.17Tertiarystructureistheoverallshapeofapolypeptide. A. TertiarystructureresultsfromtheclusteringofhydrophobicandhydrophilicRgroups andbondformation(hydrogenandionic)betweencertainRgroupsalongthecoilsand pleats(Figure3.17).Animportantandoftenoverlookedcovalentbondthatmaintains tertiarystructureisthedisulfidebondthatformsbetweentwocysteineaminoacids. B. Intransthyretin,thetertiaryshapeisessentiallyglobular.

Module3.18 Quaternarystructureistherelationshipamongmultiplepolypeptidesofaprotein. A. Many(butnotall)proteinsconsistofmorethanoneprimarychain. B. Transthyretinconsistsoffourchains,eachidentical(Figure3.18).Otherproteinsmight haveallchainsdifferentorbeadditionallycomplexedwithotheratomsormolecules. Anothergoodexampleofaproteinwithquaternarystructureishemoglobin:4subunits (2+2)and4hemeprostheticgroups. NOTE:Quaternarybondingislargelybypolarandhydrophobicinteraction. Module3.19 TalkingAboutScience:LinusPaulingcontributedtoourunderstandingofthechemistry oflife. A. Dr.Paulingfeltthattherewasvalueinreductionismwhenstudyingbiologyinan attempttoanswerquestionsaboutwholeorganisms. B. Hewasthefirsttodescribethecoiledandpleatedsheetsecondarystructureofprotein andthefirsttodescribethestructureofhemoglobinandtheabnormalformfoundinthe redbloodcellsofthosewithsicklecelldisease.

C. Laterinhislife,PaulingwasmostnotedforhisworkontheroleofvitaminCin maintaininghealth,whichhasnotbeensubstantiated. D. Paulingalsohadalifelonginterestinthebiologyofaging. E. Asaremanyscientists,Paulingwaspoliticallyactive,beinganadvocateforabanonthe testingofnuclearweapons. V.NucleicAcids Module3.20Nucleicacidsareinformationrichpolymersofnucleotides. A. Nucleotidesarecomplexmoleculescomposedofthreefunctionalparts(Figure3.20A, B):phosphategroup,fivecarbonsugar(deoxyriboseinDNA;riboseinRNA), nitrogenousbase. B. Therearefivebasictypesofnitrogenousbases:A,T,G,CinDNAandA,U,G,Cin RNA(Figure10.2B,C). NOTE:DNAnucleotidesequencesencodetheinformationrequiredforproductionofthe primarystructureofproteins;suchsequencesarecalledgenes(Modules10.7and10.8). C. Nucleotidemonomersjoinbydehydrationsynthesisbetweenthenucleotideparts (phosphatetosugar)toformpolynucleotideswithalinearstructureofsugarphosphate repeats(Figures3.20A,B;Figure10.2A). D. Hydrogenbondingbetweennitrogenousbases(AtoTandGtoC)causesthefinal structureofthenucleicacid. Preview:Themechanismsbywhichthesestructuresdeterminegeneexpressionare discussedinChapters10and11. E. InDNA,twolinearchainsareheldtogetherinanantiparalleldoublehelix(Figure 3.20C). F. InRNA,onelinearchainmaybewrappedarounditselfinplaces,formingoneofthree typesofRNA:transferRNA(tRNA),ribosomalRNA(rRNA),ormessengerRNA(mRNA). SeeChapter10forstructuraldetails.

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