StericFactorsandHydrogenBondingInfluenceHomopolysaccharideFolding

Subunitswithamoreorlessrigidstructuredictatedbycovalentbondsform3Dmacromolecular
structures
o 3Dstructuresarestabilizedbyweakinteractionswithinorbetweenmolecules(Hbonds,
hydrophobicandvanderWaalsinteractions,andelectrostaticinteractionsincharged
subunits)
o Inpolysaccharides:manyOHgroups,soHbondingissuperimportant
Polysaccharidefolding:
o Glycosidicbond:Rigidpyranoseringsconnectedbyoxygenatombridgingtwocarbon
atoms
o FreerotationaboutbothCObondsbutlimitedbysterichinderenceofsubstituents
o Useand (dihedral angles)
o Forstarchandglycogen(a14)tightlycoiledhelixstabilizedbyinterchainhydrogen
bonds
Amylose:structureisregularenoughtoallowcrystallizationanddetermination
ofstructure
6residuesperturn,60anglebetweeneachresidue
corehasdimensionsthatallowcomplexingwithiodineions
o Cellulose:
180betweeneachresidue
straight,extendedchain
AllOHgroupsareavailableforhydrogenbondingwithneighboringchains
Withseveralchainslyingsidebyside,stabilizingnetworkofinterchain
andintrachainHbondsproducesstraight,stablesupramolecularfibers
ofgreattensilestrength
Lowwatercontent:hbondingbetweencellulosemoleculessatisifies
capacity
BacterialandAlgalCellWallsContainStructuralHeteropolysaccharides
Peptidoglycan:heteropolymer
o AlternatingB14linkedNacetylglucosamineandNacetylmuramicacidresidues
o Linearpolymers
o Liesidebysideincellwall,crosslinkedbyshortpeptides
o Peptidecrosslinks:weldpolysaccharidechainsintostrongsheaththatenvelopsentire
cellandpreventscellularswelling/lysingduetoosmoticentryofwater
o Lysosyme:enzymethatkillsbacteriabyhydrolyzingB14glycosidicbondbetweenN
acetylglucosamineandNacetylmuramicacid
Agar:
o MixtureofsulfatedheteropolysaccharidesmadeupofDgalactoseandLgalactose
derivativeetherlinkedbetweenC3andC6
o Complexmixtureofpolysaccharides:samebackbonestructures,butsubstitutedto
varyingdegreeswithsulfateandpyruvate
Agarose:
o Agarcomponentwithfewestchargegroups(sulfates,pyruvates)
o Canformdoublehelixwiththreeresiduesperturn,trappingwaterwithinthecentral
cavitycanthenformgelfromintrahelicalinteractions
GlycosaminogycansareHeteropolysaccharidesoftheECM
Grounsubstance:gellikematerialinECMthatholdscellstogetherandprovidesporouspathway
fordiffusion
Glycosaminoglycans:linearpolymerscomposedofrepeatingdisaccharideunits
o oneofmonosaccharidesisalwaysNacetylglucosamineorNacetylgalactosamine
o Othermonosaccharideisnormallyauronicacid(likeDglucouronicorLiduronicacid)

Somecontainesterifiedsulategroupsthatcombinewiththecarboxylategroupsofuronic
acidtogivehighdensityofnegativechargeextendedconformationinsolution,
formingrodlikehelix
NegativeCOOHgroupsoccuronalternatesidesofthehelix
SulfatedglycosaminoglycansareattachedtoECproteinstoformproteoglycans
o Uniquetoanimalsandbacteria
o FoundinreticularECMandbasementmembrane
Hyaluronan:glycosaminoglycan:incrediblylarge
o AlternatingresiduesofDglucuronicacidandNacetylglucosamine
o Clear,highlyviscoussolutionservesaslubricantinsynovialfluidofjoints/gives
vitreoushumorofvertebrateeyeitsconsistency
o AlsoacomponentofECMofcartilageandtendonscontributestensilestrengthand
elasticityasresultofstronginteractionswithothercomponentsofmatrix
Chondroitinsulfate:
o Contributestotensilestrengthofcartilage,tendons,ligamentsandwallsofaorta
Dermatansulfate:
o Contributestopliabilityofskinandispresentinbloodvesselsandheartvalves
Keratansulfate:
o Nouronicacidandvariablesulfatecontent
o Presentincornea,cartilage,boneandhorns/hair/hoofs/nails/claws
Heparansulfate:
o Producedbyallanimalcellsancontainsvariablearrangementsofsulfatedand
nonsulfatedsugars
o Heparin:fractionatedformofheparinsulfatederivedfromleukocytes
usedtoinhibitcogulationbybindingantithrombin(proteaseinhibitor),causing
ittobindandinhibitclottingfactorthrombin
mediatedbyelectrostaticforces:heparinisHIGHLYnegative
7.3:Glycoconjugates:Proteoglycans,GlycoproteinsandGlycolipids
glycoconjugate:biologicallyactivemoleculethatisaninformationalcarbohydratejoined
covalentlytoaproteinorlipid
proteoglycan:macromoleculesofcellsurfaceorECMwithoneormoresulfated
glycosaminoglycanchainsjoinedcovalentlytoamembraneproteinorsecretedprotein
o bindthroughelectrostaticinteractionswiththenegativelychargedgroupsonthe
polysaccharide
glycoproteins:oneorseveraloligosaccharidesofvaryingcomplexityjoinedcovalentlytoa
protein
o foundonoutersurfaceofplasmamembrane,inECMandinblood
o actasspecificsitesforrecognitionbycarbohydratebindingproteinscalledlectins
Glycolipids:membranesphingolipidsinwhichhydrophilicheadgroupsareoligosaccharides
o Oligosaccharidesserveasspecificsitesforrecognitionbylectins
o Richinbrainandneurons
ProteoglycansareglycosasminoglycancontainingmacromoleculesofthecellsurfaceandECM
Actastissueorganizersandinfluencevariouscellularactivities
Basicunit:coreproteincovalentlyattachedtoglycosaminoglycanviaaSerineresidue
o Glycosaminoglycanisjoinedtoserineresidueviaatetrasaccharidebridge
o SerisgenerallyfoundinSerGlyXGlysequence
SomeareinECMandsomeareintegralmembraneproteins
Integralmembraneproteoglycans:
o Membraneheparansulfateproteoglycans:twofamilies
Syndecans:singletransmembranedomain+extracellulardomainbearing35
chainsofheparansulfate(andinsomecases,chondroitinsulfate)
o

Glypicans:attachedtomembranebylipidanchor(derivativeof
phosphatidylinositol)
Bothcanbeshedintoextracellularspace:
Proteasereleasessyndecanectodomains
Phospholipasereleasesglypicans
Nonrandomdomainstructure:
Highlysulfateddomains(NSdomains)alternatewithdomainshaving
unmodifiedGlcNAcandGlcAresidues(NacetylatedorNAdomains)
NSdomains:bindspecificallytoextracellularproteinsandsignaling
moleculestoaltertheiractivitiesthru:
o Conformationalchangeintheproteininducedbythebinding
o Abilityofadjacentdomainstobindtwodifferentproteinsand
bringintocloserproximity
o Bindingofextracellularsignalmolecules(likegrowthfactors)
toincreaselocalconcentrationsandenhanceinteractionwith
growthfactorreceptorsincellsurface
Eg.Fibroblastgrowthfactor
o NSdomainsinteract(electrostaticallyorotherwise)with
varietyofsolublemoleculesoutsidecell,maintaininghigh
localconcentrationsatthecellsurface
Proteoglycanaggregates:enormoussupramolecularassembliesofmanycoreproteinsallboundto
singlemoleculeofhyaluronan
o Aggrecan:
Aggrecancoreprotein,withserresiduesjoinedtomultiplechainsofchondroitin
sulfateandkeratinsulfatethroughtrisaccharidelinkers
Hundredsofthesethenbindsinglehyaluronate>proteoglycanaggregate
InteractsstronglywithcollageninECMofcartiliagecontributesto
thedevelopment,tensilestrengthandresiliencyofconnectivetissue
o Collagen,elastinandfibronectin:fibrousmatrixproteinsinterwovenwithproteoglycans
togiveECMstrengthandresilience
Somearehavebindingsitesforseveraldifferentmatrixmolecules(fibronectin)
Glycoproteinshavecovalentlyattachedoligosaccharides
Carbohydrateproteinconjugatesinwhichglycansaresmaller,branchedandmorestructurally
diversethantheglycosaminoglycansofproteoglycans
Carbohydrateisattachedatanomericcarbonthrough:
o aglycosidiclinktotheOHofaserineorthreonineresidue(Olinked)or
sequencesforattachmentofOlinkedchainstendtoberichinGly,ValorPro
o NglycosyllinktotheamidenitrogenofanAsnresidue(Nlinked)
SequencesforattachmentofNlinkedchainsdependsonconsensussequenceN
[P][ST]
Somehavesingleoligosaccharidechain,butmanyhavemorethanone
Mucins:secretedormembraneglycoproteinsthatcontainlargenumbersofOlinked
oligosaccharidechains
Benefitstooligosaccharideattachment:
o Veryhydrophilic:alterpolarityandsolubilityofproteinwithwhichitisconjugated
o Serveasdestinationlabelsandactinproteinqualitycontrol(taggingfordegradation)
o Chargerepulsionbetweenthemwhenmultipleareclusteredinsingleregionofprotein
favorsformationofextendedrodlikestructureinthatregion
o Bulkinessandnegativechargeprotectproteinsfromattackbyproteolyticenzymes
Glycolipidsandlipopolysaccharidesaremembranecomponents:
Gangliosides:membranelipidsofeukaryoticcellsinwhichthepolarheadgroupisacomplex
oligosaccharidecontainingasialicacidandothermonosaccharideresidues

Oligosaccharidemoeieties(likeinglycoproteins)arealmostalwaysfoundontheouterfaceofthe
plasmamembrane
Lipopolysaccharides:dominantsurfacefeatureofgramnegativebacteriasoutermembrane
o Primetargetsofvertebrateimmunesystem
o Sixfattyacidsboundtotwoglucosamineresidues(oneofwhichispointofattachment
forcomplexoligosaccharide)

7.4:CarbohydratesasInformationMolecules:TheSugarCode:
Lectinsareproteinsthatreadthesugarcodeandmediatemanybiologicalprocesses
Lectins:proteinsfoundinallorganisms
o Bindcarbswithhighspecificityandmoderatetohighaffinity
o Serveinvarietyofcellcellrecognition,signalingandadhesionprocessesandin
intracellulartargetingofnewlysynthesizedproteins
Plantlectins:foundinseeds;probablyserveasdeterrentstoinsectsandotherpredators
Animallectins:
o Somepeptidehormones:circulateinbloodandhaveoligosaccharidemoietiesthat
stronglyinfluencecirculatoryhalflife
Forexample:NlinkedoligosaccharidesofLHandthrotropinarerecognizedby
lectinsonhepatocytes,whichmediateuptakeanddestructionofthehormones
o Neu5Ac(sialicacid)situatedatendsofoligosaccharidechainsofplasmaglycoproteins
Protectproteinsfromuptakeanddegradationinliver
Responsibleforprotectingerythrocytesfromdegradation(whenremovedby
sialidase,theRBCsdisappearwithinhours)
o Selectins:plasmamembranelectinsthatmediatecellcellrecognitionandadhesion
Importantformovementofimmunecellsthroughcapillarywalls
Atinfectionsite:Pselectinonsurfaceofcapillaryendothelialcellsinteracts
withspecificoligosaccharideofglycoproteinsofcirculatingneutrophils
Slowsneutrophilsastheyadheretoandrollalongendothelialliningof
capillaries
Secondinteractionbetweenintegrinmoleculesinneutrophilplasmamembrane
andadhesionproteinonendothelialcellsurfacestopsneutrophilandallowsitto
movethroughcapillarywall
Eselectin(endothelialcell)andLselectin(neutrophil)bindcognate
oligosaccharidesonneutrophilandendothelialcell,respectively,toassistin
lymphocytehoming
o Viruses:attachtohostcellthroughinteractionswitholigosaccharidesdisplayedonhost
cellsurface
HAlectinofinfluenzavirus:essentialforviralentryandinfection
Onceenteringandreplicating,newlysynthesizedviralparticlesbudoutofthe
cell,wrappedinportionofplasmamembrane
Viralsialidasetrimsterminalsialicacidresiduefromhostcells
oligosaccharidesreleasesviralparticlesfromtheirinteractionwiththecelland
preventsaggregationwithoneanother
Antivirals:sugaranalogsthatinhibitsialidasecompetitively
LectinCarbohydrateinteractionsarehighlyspecificandoftenpolyvalent
Essentialthatoligosaccharidebeuniquesolectinrecognitionishighlyspecific
Highdensityofinformationinoligosaccharidessugarcodewithessentiallyunlimitednumberof
uniquewordssmallenoughtobereadbyasingleprotein
Lectins:incarbbindingsites,havesubtlemolecularcomplementaritythatallowsinteractiononly
withcorrectcarbcognates

AffinitybetweenoligosaccharideandlectinmaybesmallBUTlectinismultivalent(multiplecarb
bindingdomains)eacholigosaccharideonamembranesurfacecanengageoneofthelectins
CBDs,strengtheninginteractions
Generalinteractionsthatcontributetothebindingofmanycarbstotheirlectins:
o Manysugarshaveamoreandalesspolarside:morepolarsidehbondswithlectinwhile
lesspolarundergoeshydrophobicinteractionswithnonpolaraminoacidresidues
Specificinteractions:Hbondingofaminoacidstooxygenatomsofsugar

Chapter8:NucleotidesandNucleicAcids
8.1:SomeBasics
NucleotidesandNucleicAcidsHaveCharacteristicBasesandPentoses
Nucleotideshavethreecharacteristiccomponents:
o Nitrogenousbase:pyrimidineorpurinederivatives
Purines:ADENINEandGUANINE
Pyrimidines:CYTOSINEandTHYMINEorURACILinRNA

o Pentose
Numberedwithprimesigns()todistinguishfromnitrogenousbases
N1ofpyrimidinesandN9ofpurinesareboundto1carbonofpentosesugar
inNBglycosylbond(formedbycondensationofOHfrompentoseandHfrom
base)
Twokinds:
2deoxyDribose
Dribose
o Phosphate
Esterifiedto5carbon
Nucleoside:nucleotidewithoutphosphate
Nomenclature:BaseNucleosideNucleotide
o AdenineAdenosineAdenylate
o GuanineGuanosineGuanylate
o ThyminThymidineThymidylate
o CytosineCytidineCytidylate
o UracilUridineUridylate
PhosphodiesterBondsLinkSuccessiveNucleotidesinNucleicAcids
Phoaphodiesterlinkage:phosphategroupbridgesthatconnectsuccessivenucleotidesinDNA
andRNA
o 5phosphategroupofonebasewiththe3OHgroupofthenext
Covalentbackbones:alternatingphosphateandpentoseresidues
o HydrophilicOHgroupsofsugarformHbondswithwater
o Phosphategroupsarecompletelyionizedandnegativelychargedatph7
Nitrogenousbases:sidegroupsjoinedtobackboneatregularintervals
Underalkalineconditions:RNAishydrolyzedrapidlybutDNAisnot
o 2OHgroupsinRNA(absentinDNA)directlyinvolved
o Yieldscyclic2,3monophosphatenucleotidesthatthenbreakdownintoamixtureof2
and3nucleosidemonophosphates
Sequenceisalwayswrittenin53direction
Thepropertiesofnucleotidebasesaffectthethreedimensionalstructureofnucleicacids
Freepyrimidinesandpurines:weaklybasiccompoundscalledbases
AromaticwheninDNAandRNA
o Mostbondshavepartialdoublebondcharacterpyrimidinesareplanarandpurinesare
verynearlyplanarwithaslightpucker
FreepyrimidineandpurinebasesmayexistintwoormoretautomericformsdependingonpH
AllnucleotidebasesabsorbUVlight:strongabsorptionatwavelengthsnear260nm
PurineandpyrimidinebasesarehydrophobicandrelativelyinsolubleinwateratnearneutralpH
ofcell
o AtnonneutralpH:becomechargedandincreaseinsolubilityinwater
Basestacking:hydrophobicstackinginteractionsinwhichtwoormorebasesarepositionedwith
planesofringsparallelinvolvesacombinationofvanderWaalsanddipoledipoleinteractions
betweenthebasesminimizeswatercontact

 Hbondingbetweencomplementarystrandsiswhatholdsthemtogether
8.2NucleicAcidStructure
DNAisadoublehelixthatstoresgeneticinformation
A=tandG=CforallcellularDNA
A+G=T+C
WatsonandCrickmodel:
o 2helicalDNAchainswoundrighthandedlyaroundthesameaxistoformahelix
o hydeophilicbackbonesofalternatingdeoxyriboseandphosphategroupsonoutsideof
doublehelix,facingsurroundingwater
o furanoseringofdeoxyriboseisintheC2endoconformation
o nucleotidebasesarestackedwithinthedoubehelix,hydrophobicandnearlyplanar
o majorgroove+minorgroove
o 3hydrogenbondsbetweenGandCandonly2betweenAandT
o strandsrunantiparallel
o DNAduplexisheldtogetherbytwoforces:
Hydrogenbondingbetweencomplementarybasepairs
Basestackinginteractions
DNAcanoccurindifferentthreedimensionalforms
Bondrotationscanoccurinsugarphosphatebackbone
Thermalfluctuationbending,stretching,unpairingofstrands
ThreetypesofstructuralvariationinDNA:
o Differentpossibleconformationsofdeoxyribose
o Rotationaboutcontiguousbondsinphosphodeoxyribosebackbone
o FreerotationaboutC1Nglycosylbond
Purines:restrictedtosynandantiformwithrespecttodeoxyribose
Pyrimidines:restrictedtoantiformwithrespecttodeoxyribose
WatsonCrickstructure:BformofDNA(BDNA_
o MoststableforarandomsequenceDNAmoleculeunderphysiologicalconditions
o Standardpointofreference
Twostructuralvariants:
o Aform:favoredinsolutionsdevoidofwater
StillrighthandeddoublehelixBUTwiderandwith11basesperturninsteadof
10.5
Planeofbasepairstiltedabout20withrespecttohelixaxis
Deepermajorgrooveandshallowerminorgroove
ShortDNAmoleculestendtocrystallizeinAform
o Zform:sequenceswithpyrimidinesalternatingwithpurines(especiallyCandG)
Lefthandedhelicalrotation
Purinesfliptosynconformation,alternatingwithpyrimidineanti
conformation

12basepairsperturn
moreslenderandelongated
zigzagappearancetoDNAbackbone
barelyapparentmajorgrooveandnarrow/deepminorgroove
CertainDNAsequencesadoptunusualstructures
FourormoreadenosineresiduessequentiallyinonestrandbendsinDNAhelix
Palindrome:invertedrepeatswithtwofoldsymmetryovertwostrands
o Selfcomplementarywithineachstrandcanformhairpinorcruciform
Mirrorrepeat:invertedrepeatwithineachindividualstrandofDNA
o CANNOTformhairpinorcruciform

Threetofourstrandstructures:
o Triplex:CytidinepairingwithGinGCnucleotidepairorthymidinepairingwithAinAT
pair
N7,O6andN6,ofpurineshydrogenbondingoftriplexDNA
Hoogsteenpositions
NonWatsonCrickpairing:Hoogsteenpairing
Triplex:moststableatlowpHbecauseG=CCtripletrequiresprotonated
cytosine
Formmostreadilywithinlongsequencescontainingonlypyrimidinesoronly
purineswithinstrand
Eithertwopyrimidinestrandsandonepurinestrand,ortwopurine
strandsandonepyrimidinestrand
o Tetraplex:fourDNAstrands
ONLYoccursreadilyforDNAwithhighproportionofGuanosine
Gtetraplex:quitestableoverwiderangeofconditions
Orientationofstrandscanvary
MessengerRNAcodesforpolypeptidechains
mRNA:carriesgeneticinfofromDNAtoribosomes(formedviatranscription)
o InBacteriaandArchea:
monocistronic:onlycodesforonepolypeptide
polycistronic:codesfortwoormoredifferentpolypeptides
o Ineukaryotes:mostlymonocistronic
ManyRNAshavemorecomplex3Dstructures
Productoftranscription:alwayssinglestrandedRNA
o Tendstoassumerighthandedhelicalconformationdominatedbybasestacking
interactions(strongerbetweentwopurinesthanbetweenpurine+pyrimidineortwo
pyrimidines)
o BasepairingbetweenGandUisfairlycommon
Nosimple,regularsecondarystructurethatservesasareferencepoint:
o Weakinteractions,especiallybasestackinginteractions,helpstabilizeRNAstructures
o PredominantdoublestrandedstructureisanAformrighthandeddoublehelix
o Zformheliceshavebeenmadeinlaboratory
o Bformhasnotbeenobserved
o BreaksinregularAformhelixcausedbymismatchedorunmatchedbasesinoneofboth
strandsarecommonresultinbulgesorinternalloops
Hairpinloops:formbetweennearbyselfcomplementarysequences
HairpinsaremostcommontypeofsecondarystructureinRNA
Specificshortbasesequences(likeUUCG)areoftenfoundatendsofRNA
hairpinsandformparticularlytightandstableloops
o OthercontributionsmadebyHbondsthatarenotpartofstandardWatsonCrickbase
pairs:
E.g.2OHgroupofriboseHbondingwithothergroups
8.3NucleicAcidChemistry
DoubleHelicalDNAandRNACanBeDenatured
ExtremesofpHortemperaturecandenatureDNAandRNAdisruptionofHbondsbetween
pairedbasesandofbasestacking
o Separatesstrands
o Doesntbreakcovalentbonds
Renaturation:quick,onestepannealingofstrandsifstrandsarentcompletelydisconnection.
o Otherwise,twosteps:firstfindoneanother,andthenzipper
Hypochromiceffect:closeinteractionofstackedbasesinnucleicaciddecreasesUBabsorption
relativetofreenucleotidesandfurtheredwhentwocomplementarynucleicacidstrandsarepaired

Hyperchromiceffect:oppositeofhypochromiceffectcausedbyrenaturation
o Thus,candetecttransitionfromdoublestrandedDNAtosinglestrandedformby
measuringUVabsorptionat260nm
EachspeciesofDNAhascharacteristicdenaturationtemperature(meltingpoint,t m)atwhichhalf
ofDNApresentisseparated
o HighercontentofGChigherTm
o Bubbles:carefuldenaturationofweakerATsections
RNAorRNADNAduplexescanalsobedenatured
o RNAduplexoftenrequireshighertemperaturesthanDNAduplex
o RNADNAisgenerallyintermediate
NucleicAcidsfromDifferentSpeciesCanFormHybrids
CanbeusedtodetectsimilarDNAsequencesintwodifferentspeciesorwithingenomeofsingle
species
DenaturebothspeciesDNAandthenallowtoanneal
o Rateofannealingaffectedby:
Temperature
LengthandconcentrationofDNAfragment
Concentrationofsaltsinreactionmixture
Propertiesofsequenceitself
o Yieldshybridduplexes
NucleotidesandNucleicAcidsUndergoNonenzymaticTransformations
Mutations:alterationsinDNAstructurethatproducepermanentchangesinthegenetic
informationencoded
Deamination:spontaneouslossofexocyclicaminogroups
o Undertypicalcellularconditions:deaminationofcytosineuracil(inDNA):1:107
residuesin24hours
100spontaneouseventsperday
productisreadilyrecognizedasforeigninDNAstrandandisremovedbya
repairsystem
o Deaminationofadenineandguanine:1/100ththisrate
Depurination:hydrolysisofNBglycosylbondbetweenbaseandpentosetocreateDNAlesion
(APsiteorabasicsite)
o Occursathigherrateforpurinesthanforpyrimidines
o DepurinationofribonucleotidesandRNAslowerthanDNAandnotconsidered
physiologicallysignificant
o Canbeacceleratedbydiluteacid
o IncubationofDNAatpH3selectiveremovalofpurinebases,resultinginapurinicacid
Radiationpromoted:
o UVlight:
condensationoftwoadjacentpyrimidinebasestoformcycobutanepyrimidine
dimers
MostfrequentbetweenadjacentthymidineresiduesonthesameDNA
strand
Creationof64photoproduct
o Ionizingradiation(Xraysandgammarays)cancause:
ringopenings
fragmentationofbases
Breaksincovalentbackboneofnucleicacid
Chemicalreactions:
o Deaminatingagents(particularlynitrousacid(HNO2)orcompoundsthatcanbe
metabolizedtonitrousacidornitrites)
NitrousacidandBisulfite:Potentacceleratorofdeaminationofbases

Alkylatingagents
CanaltercertainbasesofDNA:
DimethylsulfatecanmethylateaguaninetoyieldO^6methylguanine
(cannotbasepairwithcytosine)
OxidativeDamage
o Hydrogenperoxide,hydroxylradicals,superoxideradicalsariseduringirradiationoras
byproductofaerobicmetabolism
o Hydroxylradicals:responsibleformostoxidativeDNAdamage
o CellshavedefensesystemtodestroyROS(catalase,superoxidedismutase)
Ifnotcaught,cancause:oxidationofdeoxyriboseandbasemoieties,strand
breaks
SomebasesofDNAaremethylated
AandCaremorefrequentlymethylatedthanGandT
ServesasdefensemechanismbymarkingownDNAwithmethylgroups
Orcanserveinmismatchrepair
ThesequencesoflongDNAstrandscanbedetermined
Electrophoresis(sangermethod)
o

8.4OtherFunctionsofNucleotides
Nucleotidescarrychemicalenergyincells:
5OHofribonucleotide+1,2or3phosphates:nucleosidemono,di,triphosphates
o threephosphatesarelabeledalpha,beta,gammabeginningwithdirectlyattachedto
ribose
o hydrolysisoftheseprovidesenergy(e.g.ATP)
Energy:
o Bondbetweenriboseandalphaphosphate:esterlinkage
Hydrolysis:14kJ/mol
o Alphabetaandbetagammalinkages:phosphoanhydrides
Hydrolysis:30kJ/mol
Adeninenucleotidesarecomponentsofmanyenzymecofactors
Adenosine:doesntdirectlyparticipateinprimaryfunction,butremovalofadenosineresultsin
drasticreductionofactivities
Mostinvolvebindingenegybetweenenzymeandcofactororsubstrate
Nucleotidebindingfold:domainthatbindsadenosine
Somenucleotidesareregulatorymolecules:
Primaryresponsefromhormonesorexternalchemicalsignal
Leadstoproductionofsecondmessengersinsidecellleadtoadaptivechangesincellinterior
o Often,secondmessengerisanucleotideformedfromATPinareactioncatalyzedby
cyclase
o E.g.cAMP(ATPcatalyzedbyadenylylcyclase)

Chapter10:Lipids
10.1:StorageLipids
Fattyacids:hydrocarbonderivativesthatarehighlyreduced
Fattyacidsarehydrocarbonderivatives
Carboxylicacidswithhydrocarbonchainsrangingfrom436carbonslong
o Insome:unbranchedandfullysaturated
o Inothers:oneormoredoublebonds
o Afew:3Crings,OHgroups,methylgroundbranches
Nomenclature:chainlength:numberofdoublebonds(^locationofdoublebonds)
o Numberingbeginsatcarboxylgroup
Mostcommonly:
o evennumberofcarbonatomsinunbranchedchainof1224carbons
o DoublebondbetweenC9andC10inmonounsaturatedfattyacids,andthen12and
15
o Almostneveralternatessingleanddoublebonds,butinsteadseparatedbymethylene
group
o Innearlyall:doubebondsarecis(transareproducedbyfermentation)
Omega3fattyacids:polyunsaturatedfattyacids(PUFAs)withdoublebondbetweenthirdand
fourthcarbonfromtheMETHYLendofchain
o Omegacarbon:methylcarbonfarthestfromCOOHgroup
o Omega6fattyacids:doublebondbetweenC6andC7
o Humans cant synthesize the required omega2 PUFA linolenic acid (ALA;
18:3(9,12,15))mustobtainindiet
From ALA humans can synthesize two other omega3 PUFAs:
eicosapentaenoic acid (EPA; 20:5(5,8,11,14,17)) and docosahexaenoic acid
(DHA;22:6(4,7,10,13,16,19))
Physicalpropertiesoffattyacids: largelydeterminedbylengthanddegreeofunsaturationof
hydrocarbonchain
o Nonpolarhydrocarbonchain:poorsolubilityoffattyacidsinwater
Longer+moresaturated>lowersolubility
COOHispolarandionizedatneutral pH accountsforslightsolubilityof
shortchainfattyacidsinwater
o Meltingpoints:
Fully saturated: free rotation around each cc bond: HC chain has great
flexibility most stable conformation = fully extended form that can pack
togethertightly
Unsaturated: cis double bond forces kink, prevents packing (weaker
interactions)
LessthermalenergyneededtodisorderthemLOWERmeltingpoints
Triacylglycerolsarefattyacidestersofglycerol:
Composedofthreefattyacidsinesterlinkagewithsingleglycerol
o Ifallthreefattyacidsaresame:simpletriacylglycerol
Namedafterfattyacidtheycontain(tripalmitin,tristearin,etc)
o Mixedtriacylgerol:contain23differentFA
Nameandpositionofeachfattyacidspecifiedinnomenclature
PolarOHofglycerolandpolarCOOHoffattyacidsboundinester
o Therefore,nonpolarandhydrophobic
o Insolubleinwater
Triacylglyercolsprovidestoredenergyandinsulation:
Typicallyformseparatephaseofmicroscopic,oilydropletsinaqueouscytosol
o Serveasdepotsofmetabolicfuel

In vertebrates: adipocytes (specialized fat cells) store large amounts of triacylglycerols as fat
droplets
Lipases:enzymesthatcatalyzethehydrolysisofstoredtriacylglycerolsreleaseFAforexportto
siteswheretheyarerequiredasfuel
Twoadvantagestousingasstoredfuels(overpolysaccharides)
o Coffattyacidsaremorereducedoxidationyieldstwiceasmuchenergy
o Triacylglycerolsarehydrophobicandunhydrated
Organismthatcarriesfatasfueldoesnothavetocarryweightofwater
Alsoserveasinsulationsometimes
Partialhydrogenationofcookingoilsproducestransfattyacids
Mostnaturalfats:complexmixturesofsimpleandmixedtriacylglycerols
o Vegetableoils:composedlargelyofunsaturatedfattyacidsliquidsatroomtemperature
o Animalfats:containmostlysaturatedwhite,greasysolids
Rancidity:exposuretooxygenoxidativecleavageofdoublebondsinunsaturatedFA
o ProducesaldehydesandCOOHacidsofshorterchainlengthandthushighervolatility
o Partialhydrogenationofcommercialvegetableoilsincreasesshelflife
Convertscisdoublebondstosinglebonds
IncreaseTmtomakemorenearlysolid
ConvertssomecisbondstotransbondsleadtohigherCVrisk
RaiselevelofLDL(bad)cholesterolandtriacylglycerolsinblood
Increasebody;sinflammatoryresponse
Waxesserveasenergystoresandwaterrepellants
Estersoflongchain(c14C36)saturatedandunsaturatedfattyacidswithlongchain(C16
C30)alcohols
Meltingpoints:generallyhigherthantriacylglycerols
Chiefstorageformofmetabolicfuelforplankton
Alsoservetolubricateandkeephairandskinwaterproof(e.g.birds)
10.2StructuralLipidsinMembranes
Membranelipidsareamphipathic
Fivegeneraltypes:
o Glycerophospholipids(twofattyacidsjoinedtoglycerol)
o Galactolipidsandsulfolipids(twofattyacidsesterifiedtoglycerolbutnophosphate)
o Archaealtetraethetlipids(twoverylongalkykchainsetherlinkedtoglycerolatboth
ends)
o Sphingolipids(singlefattyacidjoinedtofattyamine[sphingosine])
o Sterols(rigidsystemoffourfusedhydrocarbonrings
Phospholipids:glycerophopsholipidsandsomesphingolipidswherepolarheadgroupisjoinedto
hydrophobicmoietrybyphosphodiesterlinkage
Glycolipids: sphingolipids lacking phosphate but having simple sugar or complex
oligosaccharidesatpolarends
Glycerophospholipidsarederivativesofphosphatidicacid
Alsocalledphosphoglycerides
Membranelipids
Twofattyacidsesterifiedtofirstandsecondcarbonsofglycerol
Highlypolarorchargedgroupattachedthroughphosphodiesterlinkagetothethirdcarbon
o PhosphategroupbearsnegativechargeatneutralpH
Namedasderivativesofparentcompound(phosphatidicacid)accordingtopolaralcoholinhead
group
o E.g.phosphatidylcholineandphosphatidylethanolamine
Fattyacidsarevariable:givenphospholipidmayconsistofseveralmolecularspecies,eachwith
owncomplementoffattyacids

Someglycerophospholipidshaveetherlinkedfattyacids
Etherlipids:oneofthetwoacylchainsisattachedtoglycerolinether,ratherthanester,linkage
Etherlinkedchaincanbesaturated(alkyletherlipids)orcontainadoublebondbetweenC1and2
(plasmalogens)
Plateletactivatingfactor:etherlipidthatisapotentmolecularsignal
Chloroplastscontaingalactolipidsandsulfolipids
Galactolipids:oneortwogalactoseresiduesareconnectedbyglycosidiclinkagetoC3of1,2
diacylglycerol
o Localizedinthylakoidmembranesofchloroplasts
Sulfolipids:sulfonateonheadgroup(bearsnegativecharge)
Archaeacontainuniquemembranelipids
Archaeamostlyliveinextremeconditions
o Membranelipidscontaininglongchainbranchedhydrocarbonslinkedat eachendto
glycerol
o LinkagesarethroughetherbondsmuchmorestabletohydrolysisatlowpHandhigh
temperaturethanester
o Twicethelengthofphospholipidsandsphingolipids
o Glycerolmoiety:centralcarbonisinRconfigurationinArchaeaandinSconfiguration
inBacteriaandEukarya
Sphingolipidsarederivativesofsphingosine
Alsohavepolarheadgroupandtwononpolartails
Contain NO glycerol one molecule of longchain amino alcohol sphinosine or one of its
derivatives, one molecule of long chain fatty acid, and polar head group (glycosidic or
phosphodiesterlinkage)
Ceramide:structuralparentofallsphingolipids
o FattyacidattachedinamidelinkagetoNH2onC2
o Structurallysimilartoadiacylglycerol
Threesubclassesofsphingolipids:allderivativesofceramide
o Sphingomyelins:
Phosphorcholineorphosphoethanolamineaspolarheadgroup
Classifiedalongwithglycerophospholipidsasphospholipids
Resemble phosphotidylcholines in general properties and threedimensional
structure+havingnonetchargeonheadgroups
Particularlypresentinplasmamembranesofanimalcellsandinmyelin
o Glycosphingolipids:
Outerfaceofplasmamembranes
HeadgroupswithoneormoresugarsconnecteddirectlytotheOHatC1ofthe
ceramidemoiety
Donotcontainphosphate
Cerebrosides:
Singlesugarlinkedtoceramide(glucoseorgalactose)
Globosides:
Glycosphingolipidswithtwoormore sugars(usually Dglucose, D
galactoseorNacetylDgalactosamine
o Gangliosides:
Oligosaccharides as polar head groups and one or more residues of N
acetylneuraminicacid(Neu5Ac;asialicacid)attermini
sialicacidgivesnegativechargeatpH7
o distinguishesthemfromglobosides
Sphingolipidsatcellsurfacesaresitesofbiologicalrecognition
humans:atleast60diffsphingolipidsespeciallyprominentinplasmamembraneofneurons
someareclearlyrecognitionsitesoncellsurface

 carbmoietiesofcertainsphingolipids:determinehumanbloodtype
Phospholipidsandsphingolipidsaredegradedinlysosomes
mostcellscontinuallydegradeandreplacemembranelipids
foreachhydrolysablebondinglycerophospholipid:specifichydrolyticenzymeinlysosome
o PhosholipaseA:removeoneofthetwofattyacids(yieldslysophospholipid)
o Lysophospholipases:removeotherfattyacid
o PhospholipasesCandD:eachsplitoneofthephosphodiesterbondsintheheadgroup
geneticdefectinenzymesaccumulationmedicalconsequences
Sterolshavefourfusedcarbonrings:
sterolnucleus:fourfusedrings:threewith6carbonsandonewithfive
o almostplanarandrelativelyrigid
o Cholesterol:majorsterolinanimaltissues:
Amphipathic: polar head group (OH at C3) and nonpolar hydrocarbon body
(steroidnucleusandHCsidechainatC17)
o Stigmasterol:plants
o Ergosterol:fungi
BACTERIACANNOTSYNTHESIZESTEROLS
Sterolsofalleukaryotes:synthesizedfromsimplefivecarbonisoprenesubunits(likefatsoluble
vitamins)
10.3:LipidsasSignals,CofactorsandPigments
Phosphatidylinositolsandsphingosinederivativesactasintracellularsignals
Eicosanoidscarrymessagestonearbycells:
Paracrinehormones(actoncellsnearpointofhormonesynthesis)
Alldervicedfromarachidonicacid(20:4(5,8,11,14))
Threegeneralclasses:
o Prostaglandins
5Cringoriginatingfromchainofarachidonicacid
twogroups:
PGE(ethersoluble)nonpolar
PGF(phosfatebuffersoluble)
Functions:stimulatecontractionofsmoothmuscleofuterus,affectbloodflow
to specific organs, wake sleep cycle, responsiveness to epinephrine and
glucagon
Alsoelevatebodytemperatureandcauseinflammationandpain
o Thrombaxanes:
6memberringcontaininganether
producedbyplateletsandactinbloodclottingandreductionofbloodflowto
siteofclot
NSAIDS: inhibit prostaglandin H2 synthase catalyzes early step from
arachidonateprostaglandinsandthomboxanes
o Leukotrienes
Firstfoundinleukocytes
Containthreeconjugateddoublebonds
Contractionofsmoothmuscletolung(cancauseasthmaifoverproduced)
Steroidhormonescarrymessagesbetweentissues
Steroids:oxidizedderivativesofsterols
o Havesterolnucleusbutlackalkylchain
o Morepolarthancholesterol
Movethroughbloodonproteincarrierstotargettissues,wheretheyentercellsandbindtohighly
specificreceptorproteininnucleus
Effectiveatverylowconcentrationsduetohighaffinityforreceptors

Majorgroups:
o Maleandfemalesechormones
o Adrenalcortexhormones(cortisolandaldosterone)
o Steroiddrugs(prednisoneandprednisolone)
o Brassinolide(vascularplants,growthregulator)
Vascularplantsproducethousandsofvolatilesignals
Usedtoattractpollinators,repelherbivores,attractdefenders,communicatewithotherplants
VitaminsAandDarehormoneprecursors
Vitamins:compoundsessentialtohealthofanimalthatmustbeobtainedindiet
Twoclasses:
o Fatsoluble
A,D,EandK
AandDhormoneprecursors
D3:UVdrivenconversionof7dehydrocholesterolinskin
o Converted into 1,25dihydroxycholecalciferol (calcitriol) in
liverandkidney
Hormonethat regulatescalcium uptake inintestine
andcalciumlevelsinkidneyandbone
o Deficiency:defectiveboneformationandrickets
D2: same biological effect, commonly added to milk and butter as
dietarysupplement
A(retinol):functionsashormoneandvisualpigmentofvertebrateeye
o VitaminAderivativeretinoicacidregulatesgeneexpression
indevelopmentofepithelialskin
o Vitamine A derivative retinal: pigment that initiates the
response of rod and cone cells of the retina to light
producingneuronalsignaltobrain
o Invertebrates:BcarotenecanbeconvertedintovitaminA
EandKandlipidquinonesareRedoxcofactors
E:trocopherolssubstitutedaromaticring+longisoprenoidsidechain
o Hydrophobic associatewithcellmembranes,lipiddeposits
andlipoproteinsinblood
o Biologicalantioxidants
o AromaticringreactswithanddestroysROS protectunsat
FAfromoxandpreventoxdamagetomembranelipids
K:aromaticringwhichundergoescycleofoxidationandreductionin
formationofactiveprothrombin(bloodclottingfactor)
Ubiquinone(coenzymeQ)andplastoquinone:isoprenoids
o FunctionaslipophilicelectroncarriersinETC
o Bothcanacceptoneortwoelectronsandeitheroneortwo
protons
o Watersoluble
Manynaturalpigmentsarelipiddienes:
Conjugateddienes:carbonchainswithalternatingsingleanddoublebonds
o AllowsfordelocalizationofelectronscompoundscanbeexcitedbylowenergyEMR
givesvisiblecolors
Polyketides
Secondary metabolites that are not central to organisms metabolism but offer producers an
advantageinsomeecologicalniche

Chapter11:BiologicalMembranesandTransport
CompositionandArchitectureofMembranes
Eachtypeofmembranehascharacteristiclipidsandproteins
Relativeproportionsofproteinandlipidvarywithtypeofmembrane
o E.g.nerveshavemyelinmorelipid
o E.g.bacteriaandmitochondriamoreprotein
Typeoflipidsandproteinsalsovariesfrommembranetomembrane
Somemembraneproteinsarecovalentlyattachedtooneormorelipids serveashydrophobic
anchorsthatholdproteinstomembrane
Allbiologicalmembranessharesomefundamentalproperties
Impermeabletomostpolarorchargesolutesbutpermeabletononpolarcompounds
58nm(5080A)thick
appeartrilaminarincrosssection
fluidmosaicmodel
o phospholipidbilayerembeddedwithproteins(heldbyhydrophobicinteractionsbetween
membranelipidsandhydrophobicdomainsonproteins)
o proteinorientationisasymmetric:sidednessofmembrane
o moleculesarefreetomovelaterallyinplaneofmembrane
Alipidbilayeristhebasicstructuralelementofmembranes
glycerophospholipids,sphingolipids,sterols:insolubleinwater
o inwater,willspontaneouslyformlipidaggregatestominimizesurfaceareaexposedto
water
o drivingforce:increaseentropyatlipidwaterinterface
threetypesofaggregatescanform:
o micelles:sphericalstructuresthatcontainanywherefromafewdozentoafewthousand
amphipathicmolecules
favoredwhencrosssectionalareaofheadisgreaterthanthatofacylsidechain
(likefreefattyacids,lysophospholipids,detergents)
o bilayer:twolipidmonolayersformtwodimensionalsheet
favored if cross section area of head and tails are similar (like
glycerophospholipidsandsphingolipids)
relativelyunstableandspontaneouslyfoldsbackonselftoformvesicles
3nm(30A)thick
o vesicle:formedasresultofinteractionofhydrophobicedgesofbilayerwithwater
asymmetryofplasmamembrane:
o erythrocyte:cholinecontaininglipids(phosphatidylcholineandsphingomyelin)typically
found on outer leaflet while phosphatidylserine, phosphatidylethanolamine and
phosphoatidyinositolsaremorecommononinnerleaflet
Threetypesofmembraneproteinsdifferintheirassociationwiththemembrane
Integralmembraneproteins:firmlyassociatedwithlipidbilayer
o Onlyremovablebyagentsthatinterferewithhydrophobicinteractions
Peripheral membrane proteins: associate withmembrane through electrostatic interactionsand
hydrogen bonding with hydrophilic domains of integral proteins and polar head groups of
membranelipids
o Removablebyrelativelymildtreatmentsthatinterferewithelectrostaticinteractionsorh
bonds
E.g.carbonateathighpH
Amphitropicproteins:foundbothincytosolandinassociationwithmembranes
o NoncovalentinteractionwithamembraneproteinorlipidORpresenceofoneormore
lipidscovalentlyattachedtoamphitropicprotein
o Reversibleandregulatedassociation:e.g.byphosphorylation
Manymembraneproteinsspanthelipidbilayer

Localizationofproteindomansrelativetolipidbilayer:membraneproteintopology
o Determinedwithreagentsthatreactwithproteinsidechainsbutcannotcrossplasma
membranes
Glycophorin:erythrocyteglycoproteinthatspansplasmamembrane
o Aminoterminal:onoutersurface(bearscarbchains)
o Carboxylterminusinsudeofcell
o Bothterminalsarechargedorpolarandarebothhydrophilic
o Transmembranesegmentishydrophobic
Eachproteinhasspecificorientationinbilayer,givingmembranedistinctsidedness
o Glycoproteins:glycosylateddomainsareinvariablyfoundonouterface
IntegralProteinsareheldinthemembranebyhydrophobicinteractionswithlipids
Attachment of integral proteins to membrane: result of hydrophobic interactions between
membranelipidsandhydrophobicdomainsofprotein
6types:
o TypesIandII:singletransmembranehelix
AminoterminaloutsideinTypeI
AminoterminalinsideinTypeII
o TypeIII:multipletransmembranehelicesinonesinglepolypeptide
o Type IV: transmembrane domains of several polypeptides form channel through
membrane
o TypeV:heldtobilayerprimarilybycovalentlylinkedlipids
o TypeVI:havebothtransmembranehelicesandlipidanchors
Annularlipids:phospholipidmoleculesthatlieonproteinsurface,headgroupsinteractingwith
polaraminoacidresiduesatinnerandoutermembranewaterinterfacesandsidechainsassociated
withnonpolarresidues
o Formbilayershellaroundprotein
o Foundatinterfacesbetweenmonomersofmultisubunitmembraneproteinsformgrease
shell
o Embeddeddeepwithinmembraneproteinwithheadgroupwellbelowplaneofbilayer
Thetopologyofanintegralmembraneproteincansometimesbepredictedfromitsstructure
Presence of unbroken sequences of more than 20 hydropobic residuces: evidence of
transmembranedomain
Ahelicalsequenceof2025residues:justlongenoughtospanthicknessofbilayer
o Polypeptidechainsurroundedbylipidswithnowatermoleculestobondtowilltendto
formahelicesorBsheetstomaximizeintrachainhbonding
o Ifsidechainsofhelixareallnonpolar,hydrophobicinteractionswithsurroundinglipids
furtherstabilizehelix
Hydropathyindex:usedtofindregionsof20ormorehydrophobicresidues
o Overallhydrophobicityofsequenceofaminoacidsestimatedbysumminghydropathy
indicescalculatedforsuccessivesegmentsofgivensize(e.g.17,28,39)
PresenceofTyrandTrpresiduesatinterfacebetweenwaterandlipid
o Sidechainsserveasmembraneinterfaceanchors:abletointeractsimultaneouslywith
centrallipidphaseandperipheralaqueousphase
Positiveinside rule: positively charged Lys,His and Arg residues: occur more commonly on
cytoplasmicfaceofmembranes
Bbarrel:commoninbacterialmembraneproteins
o 20ormoretransmembranesegmentsformBsheetsthatlinecylinder
o stabilizedbysamefactorsasalphahelix
o porins: proteinsthat allowcertainpolarsolutestocrossoutermembraneofgram ()
bacteriahavemanystrandedBbarrelsliningpolartransmembranepassage
o moreextendedthanahelix:only79residuesneededtospanmembrane
everyotherresidueishydrophobicandinteractswithlipidbilayer

 otherresiduesmayormaynotbehydrophobic
atlipidproteininterface:aromaticsidechains
Covalentlyattachedlipidsanchorsomemembraneproteins
somemembraneproteinscontainoneormorecovalentlylinkedlipidsofoneofseveraltypes:
o longchainfattyacids
o isoprenoids
o sterols
o glycosylatedderivativesofphopsphatidylinositol(GPIs)
provideshydrophobicanchorthatinsertsintolipidbilayerandholdsproteinatmembranesurface
o strength of hydrophobic interaction between bilayer and single hydrocarbon chain
barelyenoughtoanchorproteinsecurely
mostproteinshavemorethanonelipidmoiety
otherinteractions(ionicattractionsbetweenpositiveLysandnegativelipidhead
groups)contributetostabilitiy
o integralproteins:treatmentwithalkalinecarbonatedoesnotreleasethem
however,weakerthanthatforotherintegralmembraneproteinsandreversible
11.2MembraneDynamics:
noncovalentinteractionsamonglipidsinbilayerabilitytochangeshapewithoutbecomingleaky
Acylgroupsinthebilayerinteriorareorderedtovaryingdegrees
structureandflexibilityoflipidbilayer:dependon
o kindsoflipidspresent
atphysiologicalrange:
longchainsaturatedfattyacidspacktogetherliquidorderedstate
longchainunsaturatedfattyacidshavekinksliquiddisorderedstate
shorterchainfattyacylgroups:sameeffect
o changesintemperature
belownormalphysiologicaltemp:lipidsformsemisolidgelphase
all types of motion of individual lipid molecules are strongly
constrained
bilayerisparacrystalline
above:fluid,liquiddisorderedstate
individual hydrocarbon chains of fatty acids are in constant motion
(rotationaboutcarboncarbonbondsoflongacylsidechains
interiorofbilayerismorefluidthansolid
intermediate:liquidorderedstate
lessthermalmotioninacylchains
butlateralmovementstilltakesplace
o sterolcontent:
rigidplanarstructureofsteroidnucleusreducesfreedomofneighbouringacyl
chainstomovebyrotationforceschainsintofullyextendedconformation
reducesfluidityincoreofbilayerliquidorderedphase
increasesthicknessoflipidleaflet
Transbilayermovementoflipidsrequirescatalysis
transbilayer(flipflop)diffusionofalipidmoleculesfromoneleafletofbilayertootheroccurs
slowlyifatall
o lateraldiffusion,onotherhand,isveryrapid
transbilyermovement:requiresthatpolarorchargedheadgroupleaveaqueousenvironmentand
moveintohydrophobicinteriorofbilayerlarge,positiveG
o however,necessary:
inER,glycerophospholipidsaresynthesizedoncytosolicsurface,sphingolipids
synthesizedonluminalsurfaceflipflopdiffusion

Flippases,Floppases,Scramblases:facilitatethetransbilayermovementoflipids
o Flippases:catalyzetranslocationofaminophospholipidsphosphotidylethanolamineand
phosphatidylserinefromextracellularcytosolic
Phosphatidylethanolamineandphosphatidylserine:primarilyincytosolicleaflet
Phosphatidylserine
Sphingolipidsandphosphatidylcholineinouterleaflet
AlsoactinERtomovenewlysynthesizedphospholipidsfromsiteofsynthesis
incytosolicleaflettoluminalleaflet
One ATP per molecule of phospholipid transported structurally and
functionallyrelatedtoPtypeATPases
o Floppases:phospholipidsFROMcytosolicTOextracellularleaflet
ATPdependent
MembersofABCtransporterfamily
o Scramblases:moveanymembranephospholipidacrossbilayerdownits[]gradient
NOTATPdependent
Controlledrandomizationofheadgroupcompositionontwofacesofbilayer
ActivityrisessharplywithincreaseincytosolicCa2+concentration
Results from cell activation, injury or apoptosis could trigger
apoptosisbybringingphosphatidylserinetoouterface
o Phosphatidylinositol lipids: move phosphatidylinositol lipids across lipid bilayers for
lipidsignalingandmembranetrafficking
Lipidsandproteinsdiffuselaterallyinthebilayer
Brownian motion within bilayer lipid molecules moving laterally by changing places with
neighboringlipidmolecules
o Rapid
o Tendstorandomizethepositionsofindividualmoleculesinafewseconds
FRAP:rateoffluorescencerecoveryafterphotobleaching
o Measureofrateoflateraldiffusionoflipids
Singleparticletracking:allowsonetofollowthemovementofasinglelipidmoleculeonshorter
timescale
o Movement inhibitedtosmalldiscreteregions,asthoughcorralledbyfencesthat can
occasionallybehopped(hopdiffusion)
Membraneproteins:freetodiffuselaterallyinplaneofbilayerandareinconstantmotion(also
shownbyFRAP)
o Somemembraneproteinsassociatetoformlargeaggregates(patches)onsurfaceof
cell or organelle in which individual protein molecules do not move relative to one
another
o Someareanchoredtointernalstructuresthatpreventfreediffusion
o Immobilizationmayformthefencesthatcorrallipids
SphingolipidsandCholesterolclustertogetherinmembranerafts
Glycosphingolipids(cerebrosidesandgangliosides)typicallycontainlongchainsaturatedfatty
acids
o Formtransientclustersinouterleafletthatlargeexcludeglycerophospholipids(oneunsat
fattyacyl+shortersaturatedacylgroup)
Sphingolipids:longsaturatedacylgroupscanformmorecompact,morestableassociationswith
longringsystemofcholesterolthanshorter,oftenunsatchainsofphospholipids
o Cholesterolsphingolipid microdomains in outer monolayer of plasma membrane are
slightlythickerand moreordered (lessfluid) than neighboringmicrodomains richin
phospholipids
Moredifficulttodissolvewithnonionicdetergents
Behavelikeliquidorderedsphingolipidraftsadriftonoceanoflipiddisordered
phospholipids

Enrichedintwoclassesofintegralmembraneproteins:
those anchored to membrane by two covalently attached longchain
saturatedfattyacids
GPIanchoredprotins
Lipid anchors form more stable associations with cholesterol and long acyl
groupsinraftsthanwithsurroundingphospholipids
Membraneproteinscanmoveintoandoutofraftsrapidly
Likelythatsegregationisfunctionallysignificant:forexample,getting
twoproteinsthatneedtointeracttobemorelikelytodoso
Calveolin:integralmembraneprotein
two globular domains connected by hairpin shaped hydrophobic
domain, which binds protein to cytoplasmic leaflet of plasma
membrane
threepalmitoylgroupsattachedtocarboxylterminalglobulardomain
furtheranchorittothemembrane
binds cholesterol in the membrane forces lipid bilayer to curve
inward,formingcaveolae
o unusualrats:involvebothleafletsofthebilayer(cytoplasmic
andextracellular)
implicated in variety of cellular functions (membrane trafficking,
transductionofexternalsignalsintocellularresponses
Membranecurvatureandfusionarecentraltomanybiologicalprocesses
threemechanismsforinducingmembranecurvature:
o proteinthatisintrinsicallycurvedforcesbilaryertocurvebybindingtoit
bindingenergyprovidesthedrivingforcefortheincreaseinbilayercurvature
o manysubunitsofscaffoldproteinassembleintocurvedsupramolecularcomplexesand
stabilizecurvesthatspontaneouslyforminthebilayer
o proteininsertsoneormorehydrophobichelicesintoonefaceofthebilayer,expanding
arearelativetotheotherfaceandforcingcurvature
specificfusionoftwomembranes:
o requires:
recognizeoneanother
surfaces become closely apposed (involves removal of water normally
associatedwithpolarheadgroupsoflipids)
bilayerstructuresbecomelocallydisruptedresultsinfusionofouterleafletof
eachmembrane
inreceptormediatedendocytosis:processmustbetriggeredatappropriatetime
orinresponsetoaspecificsignal
o fusionproteins:integralproteinsthatmediatefusionevents
o example:intracellularvesiclesatsynapses
involvesfamilyofSNAREs
vSNAREs:cytoplasmicfaceofintracellularvesicle
tSNAREs:targetmembranewithwhichvesiclefuses
SNAP25andNSFalsoinvolved
During fusion: vSNARE and tSNARE bind and undergo structural
change producesbundleoflongtingrodsmadeupofhelicesfrom
bothSNARESandtwohelicesfromSNAP25
o TwoSNARESinitiallyinteractattheirendsandthenzipup
into bundle of helices, pulling membranes into contact and
initiationbilayerfusion
Clostridium botulinum: protease that cleaves specific bonds in
SNARESandSNAP25

11.3SoluteTransportAcrossMembranes
PassiveTransportisFacilitatedbyMembraneProteins
Simplediffusionyouknowwhatthisis
o Membranepotential=Vmforcethatdrivessimpldiffusion
Electrochemicalgradient
o Polarorchargedsolutemustfirstgiveupinterationswithwatermoleculesinhydration
shell,thendiffusethroughlipids(nwhichitisinsoluble)energylostisregainedon
otherside
Activationbarrierexists:canbelargeenoughtopreventsimplediffusionfrom
occurring
Facilitateddiffusion:activationenergyloweredbymembraneproteins(transportersorpermeases)
o Bindsubstrateswithstereochemicalspecificitythroughmultipleweak,noncovalent
interactions
o NegativeGbindingoftheseweakinteractionscounterbalancespositiveGdehydration,
therebylowerGfortransmembranepassage
o Transporters:spanlipidbilayerseveltimes,formingtransmembranechannellinedwith
hydrophilicaminoacidsidechains
Transporterscanbegroupedintosuperfamiliesbasedonstructures
Carriers:bindsubstrateswithhighstereospecificity
o Catalyzetransportatrateswellbelowlimitsoffreediffusion
o Saturableinthesamesenseasenzyme
o Monomericproteins
o Twofamilies:
Passivetransportersimplyfacilitatediffusiondownaconcentrationgradient
Activetransportercandrivesubstratesacrossmembraneagainstconcentration
gradient
Useenergyprovideddirectlyfromchemicalreaction(primaryactive
transporters)orcouplewithsomething(secondary)
Channels:generallyallowtransmembranemovementatrateordersofmagnitudegreaterthan
carrier(approachingunhindereddiffusion)
o Showlessstereospecificitythancarriers
o Arenotsaturable
o Mostareoligomericcomplexesofseveralidenticalsubunits
Theglucosetransporteroferythrocytesmediatespassivetransport
TypeIIIintegralproteinwith12helices
Analogoustoenzyme,whereglucoseoutside=substrate,andglucoseinside=product
Glucosebindsoutsidecell,conformationalswitch,glucoseexitsinsidecell
PASSIVE:downconcentrationgradient
CanusemichaelismentenenergeticstosolveforVmax
UNIPORT:onlyonesubstrate
The chloridebicarbonate exchanger catalyzes electroneutral cotransport of anions across the plasma
membrane
COTRANSPORTSYSTEM
Anion exchange protein (AE protein) increases rate of HCO3 transport across erythrocyte
membrane
Integralproteinthatspansmembraneatleast12times
Mediatessimultaneousmovementoftwoanions:foreachHCO3ionthatmovesinonedirection,
oneClionmovesintheoppositedirection
o ELECTRONEUTRAL
o ANTIPORT:movinginoppositedirections
Symportismovinginsamedirections
Activetransportresultsinsolutemovementagainstaconcentrationorelectrochemicalgradient

Thermodynamicallyunfavorable
Takesplaceonlywhencoupletoexergonicprocess
Primaryactivetransport:soluteaccumulationcoupleddirectlytoexergonicchemicalreaction(like
ATPhydrolysis)
Secondaryactivetransport:endergonictransportofonesoluteiscoupledtoexergonicflowof
differentsolutethatwasoriginallypumpeduphillbyprimaryactivetransport
Amountofenergyneeded:calculatedbytheinitialconcentrationgradient
o Freeenergyoftransportofunchargedmoleculefromareaof[]C1to[]C2
G=G+RTln(C2/C1)
Whensoluteisanion,movementwithoutaccompanyingcounterionendergonicseparationof
positiveandnegativechargesproduceselectricalpotential
o Electrogenic
Gt=RTln(C2/C1)+ZFpsi(whereZ=chargeonion,F=Faradays,psi=
transmembraneelectricalpotentialinvolts)
PTypeATPasesundergophosphorylationduringcatalyticcycles
CationtransportersthatarereversiblyphosphorylatedbyATP
Phosphorylationforcesconformationalchangethatiscentraltomovementofthecationacrossthe
membrane
Ca2+ATPase(uniporterforCa2+ions)andNa+K+ATPasearePtype
o PlasmamembraneCa2+pump:maintainslowconcentrationofCa2+incytosolof
virtuallyallcells
Movescalciumionsoutofcell
SERCApumps:sarcoplasmicandendoplasmicreticulumcalciumpumps:PtypeATPasesclosely
relatedinstructureandmechanism
o Singlepolypeptidethatspansmembrane10times
o Threecytosolicdomainsformedbylongloopsthatconnecttransmembranehelices
Ndomain:nucleotideATPandMg2+bind
Pdomain:phosphorylatedAspresiduecharacteristicofPtypepumps
DoesnotdirectlyaffectCa2+binding
Adomain:actuatordomain(communicatesmovementofNandPdomainsto
thetwoCa2+bindingsites)
Mdomain:containstransmembranehelicesandCa2+bindingsites
o Mechanism:
E1conformation:twoCa2+bindingsitesareexposedoncytosolicsideofERor
SRandbindCa2+withhighaffinity
ATPbindingandAspphosphorylationconformationalchangefromE1E2
E2:Ca2+bindingsitesarenowexposedonluminalsideofmembraneand
affinityforCa2+isgreatlyreducedCa2+releaseintolumen
DephosphorylationreturnstoE1
FTypeATPases:reversible,ATPdrivenprotonpumps
Energycouplingfactors
Fointegralmembraneproteincomplextransmembranepathwayforprotons
FiusesenergyofATPtodriveprotonsuphillintohigherH+region
Reversiblereaction
o ProtongradientcansupplytheenergyforATPsynthesis(reversereaction)ATP
synthase
VtypeATPases
ClassofprotontransportingATPasesstructurallyandpossiblemechanisticallyrelatedtoFtype
Responsibleforacidifyingintracellularcompartmentsinmanyorganisms
Similarcomplexstructure:integraldomain(Vo)thatservesasprotonchannelandperipheral
domain(Vi)thatcontainsATPbindingsiteandATPaseactivity

ABCtransportersuseATPtodrivetheactivetransportofawidevarietyofsubstrates
Pumpaminoacids,peptides,protons,metalions,etcetcoutofcellagainst[]gradient
MDR1:multidrugtransporter:responsiblefortumorresistancetodrugs
o Broadsubstratespecificityforhydrophobiccompounds
o Pumpsdrugsoutofcellsandpreventstherapeuticeffects
o Integralmembraneproteinwith12transmembranesegmentsand2ATPbinding
domains
AllABCtransporters:twonucleotidebindingdomains(NBD)andtwotransmembranedomains
o Sometimes:allareinsinglelongpolypeptide
o Others:twosubunit,eachwith1NBDand6helices
Mostactaspumps,butatleastsomeareionchannelsATPmotors
Whencoupledwithapump,ATPdrivenmotormovessolutesagainst[]gradient
Whencoupledwithionchannel,motoropenandcloseschannel
IonGradientsprovideenergyforsecondaryactivetransport
IongradientsformedbyprimarytransportofNa+orH+canprovidedrivingforceforcotransport
ofothersolutes
Lactosetransporter(lactosepermease):protondrivencotransporter
o Singlepolypeptidechainthatfunctionsasmonomertotransportoneprotonandone
lactosemoleculeintocellwithnetaccumulationoflactose
o Lactosetransporterprovidesrouteforprotonreentry,simultaneouslycarryinglactose
intocellbysymport
o 12transmembranehelicesandconnectingloopsprotrudeintocytoplasmorperiplasmic
space
largecavityoncytoplasmicsideofmembrane,wheresubstratesbind
sidefacingoutward:closedtightly,nochannelbigenoughforlactosetoenter
o proposedmechanism:rockingmotionbetweentwodomains,drivenbysubstratebinding
andprotonmovement,alternativelyexposingsubstratingbindingdomaintocytoplasm
andperiplasm