Karp Ch 2 细胞学英文版 第二章.docx

Karp Ch 2 细胞学英文版 第二章.docx

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KarpCh2细胞学英文版第二章

Chapter2

TheChemicalBasisOfLife

Objectives

▪Defineandexplainthechemicalprinciplesthatformthebasisofthechemistryoflife.

▪Clarifytheprincipleofchemicalbonding（covalentandnoncovalentbonds）.

▪Explainionization.

▪Describethechemistryofwateranditsrelationshiptobiologicalchemistryandcellbiology.

▪Explainthechemistryofhydrophobicandhydrophilicmolecules.

▪Defineandexplainacids,bases,pH,andbuffersforyourstudents.

▪Familiarizestudentswiththestructureandfunctionofthefourmajorgroupsofbiologicalmacromolecules.

▪Getstudentstoappreciatethesimilaritiesofanddifferencesbetweenthemacromolecules.

▪Explaintheimportanceofpolymerizationtotheproductionofmacromolecules.

▪Emphasizetheimportanceofshapeinbiologicalchemistry.

LectureOutline

CovalentBonds

I.Molecularatomsarejoinedtogetherbycovalentbondsinwhichelectronpairsaresharedbetweenatoms

A.Formationgovernedbythebasicprinciplethatatomsaremoststablewithafullouterelectronshell

1.Thenumberofbondsformedisdeterminedbythenumberofelectronsneededtofilloutershell

2.Bondformationaccompaniedbyenergyrelease

3.Reabsorptionofenergybybondbreaksit;C-C,C-HorC-Ocovalentbondsrequire80-100kcal/moletobreak–thisenergyisquitelargesothesebondsarestableundermostconditions

B.Atomscanbejoinedbybondsinwhich>1pairofelectronsareshared-if2pairsshared->doublebond（O2）;if3pairsshared->triplebond（N2）

C.Typeofbondcandeterminemolecularshape-atomsjoinedbysinglebondcanrotaterelativetooneanother;double&triplebondscannot

II.Electronegativityandunequalorequalsharingofelectrons

A.Whenatomssharingelectronsarethesame,electronsaresharedequally

B.Ifatomssharingelectronsaredifferent,oneusuallyattractselectronsmore（nucleusmorepositivelycharged）

1.Electronslocatedclosertoatomwithgreaterattractiveforce（themoreelectronegativeone）

C.Electronegativityofanatomdependsontwofactors

1.Numberofpositivechargesinnucleus（moreprotons->moreelectronegative）

2.Distanceofouterelectronsfromnucleus（greaterdistance->lesselectronegative）

D.OandNatomsarethemostelectronegativeonescommonlypresentinbiologicalmolecules

III.Polarandnon-polarmolecules

A.Water-O-Hbondsinwaterarepolarized（oneatom[O]partiallynegative;theother[H]partiallypositive）;itisapolarmolecule–suchmoleculeshaveanasymmetricchargedistribution

B.Biologicallyimportantpolarmoleculeshaveoneormoreelectronegativeatoms-usuallyO,N,Sand/orP）

C.Moleculeswithoutelectronegativeatoms&polarbonds（thoseconsistingofC&H）arenonpolar

D.Presenceofstronglypolarizedbondsisofutmostimportindeterminingmolecularreactivity

1.Moleculeswithoutelectronegativeatoms（waxes&fats）arerelativelyinert

2.Moleculeswithelectronegativeatomstendtobemorereactive

3.Manyinterestingbiologicalmolecules（proteins,phospholipids）havebothpolar&nonpolarregions&behaveverydifferently

IV.Ionization-someatomsaresostronglyelectronegativethattheycancaptureelectronsfromanotheratomduringachemicalreaction

A.Sodium（Na;silvercoloredmetal）&chlorine（Cl;toxicgas）-mixthem;togetherformtablesalt

1.SingleelectroninNaoutershellmigratestoelectron-deficientchlorineatom

2.Eachatombecomescharged（ion）:

Cl-（anion）andNa+（cation）;togetherformcrystal

B.IonslikeNa+andCl-arerelativelystablebecauseoffilledoutershell

C.Adifferentelectronarrangementinatomproduceshighlyreactivespecies（freeradical）

NoncovalentBonds

I.Noncovalentbondsgoverninteractionsbetweenmoleculesordifferentpartsofalargebiologicalmolecule;suchbondsaretypicallyweakerlinkages

A.Dependonattractiveforcesbetweenpositively&negativelychargedregionswithinsamemoleculeorontwoadjacentmolecules;usuallyweakerthancovalentbondswhicharestrong

1.Individualonesareoftenweak（~1-5kcal/mole）;thusreadilybroken&reformed

2.Whenmanyofthemactinconcert（DNA,protein,etc.）,attractiveforcesaddup&providestructurewithconsiderablestability

B.Noncovalentbondsmediatethedynamicinteractionsamongmoleculeswithinthecell

II.Typesofnoncovalentbonds:

Ionicbonds（orsaltbridges）

A.Ionicbonds-resultfromtransferofelectron（s）from1atomtoanotherleadingtoatomswithpositive&negativechargesthatattracteachother;canholdmoleculestogether（DNA-protein）

1.Incrystal,strong;inwater,ionssurroundedbywater,preventsattractionbetweenthem

2.Bondsbetweenfreeionsnotimportantincellsbecausecellsaremostlywater

3.Weakionicbondsbetweenoppositelychargedgroupsoflargemoleculemuchmoreimportant

4.Ionicbondsincellgenerallyweak（~3kcal/mole）duetowater

5.Deepinproteincorewherewaterexcluded,theycanbeinfluential

B.Hydrogen（H）bonds-hydrophilic（water-loving）;enhancesolubilityin&interactionswithwater

1.IfHbondedtoelectronegativeatom（OorN）,sharedelectronpairdisplacedtowardelectronegativeatomsoHispartiallypositive;Hsharedbetweentwoelectronegativeatoms

2.BarepositivelychargednucleusofHcanapproachunsharedpairofouterelectronsofsecondelectronegativeatom-anattractive（weakelectrostatic）interaction（anHbond）

3.Occurbetweenmostpolarmolecules;importantindeterminingstructure&propertiesofwater,alsobetweenpolargroups&largebiologicalmolecules（likeDNA）

4.Strongcollectively;weakindividually（2-5kcal/moleinaqueoussolutions）;aresultofpolarcovalentbonding

C.Hydrophobic（water-fearing）interactions-mostbelievenottruebondssincenotusuallythoughtofasattractionbetweenhydrophobicmolecules

1.Moleculeswithnonpolarcovalentbondslackchargedregionthatcaninteractwithpolesofwatermolecules&arethusinsolubleinwater

2.Hydrophobicmoleculesformintoaggregatesminimizingexposuretopolarsurroundings（fatonchickenorbeefsoup;hydrophobicRgroupscongregateinproteininteriorawayfromH2O）

3.SomebelievetheyaredrivenbyincreasedentropysincenonpolarmoleculesinH2OformH2Ointoorderedcage;whenhydrophobicgroupscluster,H2Obecomesmoredisordered

4.Othersbelievetheremayactuallybeweakbonds

D.vanderWaalsinteractions（forces）-hydrophobicgroupscanformweakbondswithoneanotherbasedonelectrostaticinteractions;duetoslightperturbationsofelectrondistributions

1.Electrondistributionsinnonpolarcovalentbondsarenotalwayssymmetric&varymomenttomoment

2.Electrondensitymaybelargerononesideofatomorother;transientchargeasymmetriesresultinmomentarychargeseparations（dipoles）

3.Iftwosuchmoleculesareveryclosetogether&appropriatelyoriented,twoelectricallyneutralmoleculeswillexperienceweakattractiveforcebondingthemtogether

4.Suchinteractionscaninducesimilarseparationinadjacentmolecules&leadtoadditionalattractiveforcesamongnonpolarmolecules

5.SinglevanderWaalsveryweak（0.1-0.3kcal/mole）&verysensitivetodistance;moleculesmustbeclosetogether&complementaryshapesofinteractingportionsallowcloseapproach

6.Importantbiologicallyaswithinteractionsbetweenantibodiesandviralantigens

TheLife-SupportingPropertiesofWater

I.LifeonEarthtotallydependentonwater（maybeanywhereinUniverse）

II.Uniquewaterstructureresponsibleforproperties:

highlyasymmetric（Oatoneend,2H'satotherend）,highlypolarizedcovalentbonds,formsHbonds

A.EachwaterHbondswithupto4others;formshighlyinterconnectedmolecularnetwork

B.PartiallynegativeOatoneendofmoleculealignswithpartiallypositiveHofanother

C.WatermoleculeshaveunusuallystrongtendencytoadheretoeachotherduetoHbonds

III.HowtheseplentifulHbondsleadtowaterproperties

A.H2Ohashighheatcapacity-heatenergydisruptsHbondsinsteadofcausingmolecularmotion

1.Elevatedmolecularmotionmeasuredastemperatureincreasesotemperaturedoesnotrisefast

B.H2Ohasahighheatofvaporization-Hbondsmustbebrokentoallowevaporation;explainshighenergyneededtoevaporateH2O

1.Whenmammalssweat,heatfrombodyused;explainscoolingeffect

C.Agoodsolvent-dissolvesmanythings（morethananyothersolvent）butisinertitself

1.Solubilizesions&organicmolecules-formsshellaroundionsseparatingthem;Hbondswithorganicmoleculesviapolargroups（e.g.aminoacids&sugars）

2.Determinesstructureofbiologicalmolecules&typesofinteractionsinwhichtheyengage

3.Fluidmatrixaroundwhichinsolublecellfabricconstructed

4.Itisalsothemediumthroughwhichmaterialsmovefromcompartmenttocompartment

5.Itisareactantorproductinmanycellularreactions

6.Italsoprotectscellfromexcessiveheat,cold,damagingradiation

D.HighsurfacetensionduetoHbondingandcapillaryaction

E.Iceislessdensethanliquidwater,soicefloats;veryimportanttoaquaticecosystems

Acids,BasesandBuffers

I.Acids&basesexistinpairs（couples）

A.Acid-amoleculeabletorelease（ordonate）ahydrogeniontomedium;protondissociates&isreleasedintomediumwheneverahydrogenatomlosesanelectron

1.Oncedissociated,protoncancombinewithothermoleculesformingH3O+,H2O,NH3+,etc.

2.Whenacidlosesproton,itbecomesconjugatebaseoftheacid

B.Base-anymoleculecapableofacceptingahydrogenion（proton）

1.Whenbasepicksupproton,itbecomesconjugateacid

2.Acidalwayscontainsonemorepositivechargetha