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In waterthis losesan H+ion tobecome-COO-.estersEstersare formed by a condensationreactionbetweenacid and an alcohol.'.Or,O_[_r/+Ho_l___Lr/I'acid\|oHalcoholacid\o"+ H"N-J- IamtneNitrogenalsooccursin severalring compounds,includingimportant constituentsof nucleicacids:purinesand pyrimidines.)n'^4rtnI|\l+H20o-c-esterIo/"C(a pyrimidine)ll cytosinetN-C-HHgroupthe sulfhydrylgroup.In the aminoacidcysteineiscalleda sulfhydrylform,-t-Snmayexistin the reducedSULFHYDRYLGROUPlrlform, -C-S-S-Cor more rarelyin an oxidized,cross-bridgingPHOSPHATESInorganicphosphateis a stableion formed fromphosphoricacid,H3PO4.lt is often written as Pi.Phosphateesterscan form between a phosphateand a free hydroxyl group.Phosphategroups are often attached to proteins in this way.carboxylgroup, or two or more phosphategroups,givesan acid anhydride.Hzol*THzoalso written ashigh-energyacyl phosphatebond (carboxylic-phosphoricacidanhydride)found insome metabolites-t_o^,o-PHzoLTHzophosphoanhydride-ahighenergybond found inmoleculessuchas ATP-oalsowritten asWATERWATERSTRUCTURETwo atoms, connected by a covalent bond, may exert different attractionsforthe electronsof the bond.
In suchcasesthe bond is polar,with one endslightlynegativelycharged(6-) and the other slightlypositivelycharged(6+).Moleculesof water join together transientlyin a hydrogen-bondedlattice.Evenat 37oC,15o/ooI the water moleculesare joined tofour othersin a short-livedassemblvknownas a "flickeringcluster.".:tt:'il,::,:electronegativeregronAlthough a water moleculehasan overallneutralcharge(havingthe samenumberof electronsand protons),the electronsare asymmetricallydistributeo,which makesthe moleculepolar.The oxygennucleusdrawselectronsawayfrom the hydrogennuclei,leavingthesenucleiwith a smallnet positivecharge.The excessof electron density on the oxygen atom createsweakly negativeregionsat the other two cornersof an imaginarytetrahedron.H Y D R O G EBNO N D SBecausethey are polarized,twoadjacentH2Omoleculescan forma linkageknown as a hydrogenbond. Hydrogenbondshaveonly about 1/20the strengthof a covalentbond.Hydrogenbondsare strongestwhenthe three atoms lie in a straightline.6-H""!,,,l,uHThe cohesivenature of water isresponsiblefor many of its unusualproperties,suchas high surfacetension,specificheat, and heat of vaporization.bond lengthshydrogenbond0 .
2 7n mQ rrrrrrrrrrrrrrrrrrrH -Oo-.tor'tthydrogen bondcovalentbondH Y D R O P H I LMI CO L E C U L E SH Y D R O P H O BMI CO L E C U L E SSubstancesthat dissolvereadilyin water are termed hydrophilic.Theyarecomposedof ionsor polar moleculesthat attractwater moleculesthroughelectricalchargeeffects.Water moleculessurroundeachion or polar moleculeon the surfaceof a solidsubstanceand carrvit into solution.Moleculesthat containa preponderanceof nonpolarbondsare usuallyinsolubleinwater and are termed hydrophobic.Thisistrue, especially,of hydrocarbons,whichcontainmany C-H bonds.Water moleculesare not attractedto suchmoleculesand sohave little tendencyto surroundthem andcarrythem into solution.HHH\/C.\\H-Clonicsubstancessuchas sodiumchloridedissolvebecausewater moleculesareattracted to the positive (Na+)or negative(Cl) chargeof eachion.H/Polarsubstancessuchas ureadissolvebecausetheir moleculesform hydrogenbondswith thesurroundingwater molecules.HIHHo\ .
HC,/\WATERAS A SOLVENTMany substances,suchas householdsugar,dissolvein water. That is,theirmoleculesseparatefrom eachother, eachbecomingsurroundedby water molecules.in aWhen a substancedissolvesliquid,the mixture is termed a solution.The dissolvedsubstance(in this casesugar)isthe solute,and the liquid thatdoesthe dissolving(in this casewater)is the solvent.Water is an excellentsolvent for many substancesbecauseof its polar bonds.sugarcrystals u g a rm o l e c u l eACIDSION EXCHANGEHYDROGENSubstancesthat releasehydrogenionsinto solutiona r e c a l l e da c i d s .Positivelychargedhydrogenions(H+)can spontaneouslymove from one water moleculeto another,therebycreatingtwo ionic species.HHHCI-+Cfhydrochloricacid(strongacid)hydrogenionionchlorideoilililrH-oMany of the acidsimportant in the cellare only partiallydissociated,and they are thereforeweak acids-for example,the carboxylgroup (-COOH),which dissociatesto give ahydrogenion in solutionn..P, +oo/,/-Hhydroxyl ionhydronium ion(water acting as (water acting asa weak acid)a weak base)oftenwrittenas: Hro iH*+-c/\H* + oHhydroxylnrl:Xn"nNote that this is a reversible reaction.hydrogenionsareisrapidlyreversible,Sincethe processPurewatershuttlingbetweenwatermolecules.continuallyof hydrogenionsandconcentrationa steady-statecontainshydroxylions(both10-'M).pHBASES( w e a ka c i d )pHThe acidityof asolutionis definedby the concentrationof H+ ions it possesses.Forconvenienceweusethe pH scale,where1 021 03pH = log,o[H+]10112A1o-s510-661o-71 08789For pure water1 o1 010[H+] = 10-7moles/liter1o-111 01 21110131014NH:+H*-NHo*ionammonia hydrogenionammonium51o-41 0ethat reducethe number of hydrogenions inSubstancessolutionare calledbases.Somebases,suchas ammonia,combinedirectlywith hydrogenions.12IIOther bases,suchas sodiumhydroxide,reducethe number ofH* ionsindirectly,by making OH- ionsthat then combinedirectlywith H' ionsto make H2O.NaOHs o d i u mh y d r o x i d e(strong base)NasodiumionMany basesfound in cellsare partiallydissociatedand are termedweak bases.Thisis true of compoundsthat containan aminogroup (-NH2),which has a weak tendency to reversiblyacceptan H' ion from water, increasingthe quantity of free OH- ions.14-NHz+H*--NH:*WEAKCHEMICALBONDSVAN DERWAALSATTRACTIONSOrganicmoleculescan interactwith other moleculesthrough threetypes of short-rangeattractive forces known as noncovalentbonds:van der Waals attractions,electrostaticattractions,and hydrogenbonds.The repulsionof hydrophobicgroupsfrom water is alsoimportantfor ordering biologicalmacromolecules.lf two atoms are too closetogether they repel each othervery strongly.
For this reason,an atom can often betreated as a soherewith a fixed radius.The characteristic"size" lor eachatom is specifiedby a uniquevan derWaals radius.The contact distancebetween any twononcovalentlybondedatoms isthe sum of their van derWaalsradii.&0 . 1 5n mradiusWeak chemicalbondshave lessthan 1/20the strengthof a strongcovalentbond. Theyare strong enough to providetight bindingonly when many of them are formed simultaneously.H Y D R O G EBNO N D SAs already describedfor water (seePanel2-2),hydrogenbondsform when a hydrogenatom is"sandwiched" betweentwo electron-attractingatoms(usuallyoxygenor nitrogen).Hydrogenbondsare strongestwhen the three atomsarei n a s t r a i g h tl i n e :to-"nnnro\N-HIIltR-C-HR-C-HIc : o l l l l l l l lHl t- Nllli l i l i l i l i lH - NFFC-RIITwo bases,G and C, hydrogen-bondedin DNA or RNA.FigH.N-Hililill\'C-C\\\.H-. L.: ///.NilililililtH\/N-C.,/\\'bllllllltn-N',,/tHtl0 . 1 5n msingle-bondedcaroonSHYDROGENBONDSIN WATERAmino acidsin polypeptidechainshydrogen-bondedtogether.c:oAt very short distancesany two atoms show a weakbonding interactiondue to their fluctuatingelectricalcharges.The two atomswill be attractedto eachotherin this way until the distancebetweentheir nucleiisapproximatelyequalto the sum of their van der Waalsradii.Although they are individuallyvery weak, van derWaalsattractionscan becomeimoortant when twomacromolecularsurfacesfit very closetogether,becausemany atomsare involved.Note that when two atomsform a covalentbond, thecentersof the two atoms (the two atomic nuclei)aremuch closertogether than the sum of the two van derW a a l sr a d i i .T h u s .|||||/Examplesin macromolecules:I0 .
1 4n mradiusAny moleculesthat can form hydrogenbondsto eachothercan alternativelyform hydrogenbondsto water molecules.Becauseof this competitionwith water molecules,thehydrogenbondsformed betweentwo moleculesdissolvedin water are relativelyweak.HYDROPHOBICFORCESWater forces hydrophobic groups together,becausedoing so minimizestheir disruptiveeffects on the hydrogen-bondedwaternetwork. Hydrophobicgroupsheldtogether in this way are sometimessaidto be held together by "hydrophobicbonds,"eventhough the apparentattractionis actuallycausedby a repulsionfrom thewater.INATTRACTIONSELECTROSTATICA Q U E O UsSO L U T I O N SChargedgroupsare shieldedby theirinteractionswith water molecules.Electrostaticattractions are thereforequite weak in water.Attractive forces occur both between fully chargedgroups(ionicbond) and betweenthe partiallychargedgroupson polar molecules.Similarly,ions in solutioncan clusteraroundchargedgroupsand further weakenthese attractions.CIoo,.O-C//I\],rr.t,rNa@NaclNa+1mmHH -.-N CI\[/In the absenceof water, electrostaticforces are very strong.They are responsiblefor the strengthof suchmineralsasmarbleand agate,and for crystalformation in commontable salt.NaCl.a crystalofsalt,NaClCl,^Na\The force of attraction between the two charges,6+and 5-, falls off rapidlyasthe distancebetweenthechargesincreases..HH.N6+'.,o.H-SELECTROSTATICATTRACTIONSIHCIal\Despitebeing weakenedby water and salt,electrostaticattractions are very important inbiologicalsystems.For example,an enzymethatbindsa positivelychargedsubstratewill oftenhave a negativelychargedamino acidsidechainat the appropriateplace.MONOSACCHARIDESMonosaccharidesusuallyhavethe generalformula (CH2O)',where n can be 3, 4, 5, 6,7, or 8, and havetwo or more hydroxylgroups.Theyeither containan aldehydegroup ( -c(l ) and are calledaldosesor a ketone group ( ).:o ) and are calledketoses.3-carbon(TRIOSES)S-carbon(PENTOSES)6-carbon(HEXOSES)H,O\^//LH,Ota/II-OHIH-C -OHIH-C -OHIH-C -OHIg l y c er a1d e h y d enboseH-CUo/roH-Cc'I-OHH-CI-OH"tHH-C{-OHIHO-C-HIH-C -OHH-CH-CHI-OHI-OHIHg Iu c o s eHHIIIH-C -OHIH-C -OHIH-C -OHIIIc:oH-C -OHH-C -OHUuYHIH-C -OHIc*-oI-OHH-CIHHribulosed i hydroxyacetoneIHO-C-HIH-C -OHIH-C -OHH-CI -OHIHfructoseRINGFORMATIONISOMERSIn aqueoussolution,the aldehydeor ketone group of a sugarmoleculetendsto reactwith a hydroxylgroup of the samemolecule,therebyclosingthe moleculeinto a ring.Many monosaccharidesdiffer only in the spatialarrangementof atoms-that is,they are isomers.For example,glucose,galactose,and mannosehavethe sameformula (C6H,'2Ojbutdiffer in the arrangementof groupsaround one or two carbonatoms.H'.
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