(54)--医学细胞生物学Chapter2FromWatertoDNATheChemist.pdf

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1、P1:GIGWY001-02WY001-Bolsover-v2.clsAugust 21,200318:222FROM WATER TO DNA:THECHEMISTRY OF LIFEOrganisms are made up of a lot of different chemicals.These vary in size,from smallmolecules like water to large molecules like DNA,and interact and associate in manydifferent ways to generate the processes

2、of life.In this chapter we will introduce some basicconcepts of how these chemicals are made and interact.We will then describe the mostimportant of these chemicals:water,carbohydrates,nucleotides,amino acids,and lipids.THE CHEMICAL BOND:SHARING ELECTRONSWater is the most abundant substance in organ

3、isms.Cells are rich in water.Cytoplasmconsistsoforganellesfloatinginawaterymediumcalledcytosolthatalsocontainsproteins.The situation is not so different outside our cells.Although we are land animals living inair,most of our cells are bathed in a watery fluid called extracellular medium.We willthere

4、fore start by considering water itself.Figure 2.1a shows a molecule of water,consisting of one atom of oxygen and twohydrogen atoms,joined to form an open V shape.The lines represent covalent bondsformed when atoms share electrons,each seeking the most stable structure.Oxygen has agreater affinity f

5、or electrons than does hydrogen so the electrons are not distributed equally.The oxygen grabs a greater share of the available negative charge than do the hydrogenatoms.The molecule of water is polarized,with partial negative charge on the oxygen andpartial positive charges on the two hydrogens.We w

6、rite the charge on each hydrogen as+Cell Biology:A Short Course,Second Edition,by Stephen R.Bolsover,Jeremy S.Hyams,Elizabeth A.Shephard,Hugh A.White,Claudia G.WiedemannISBN 0-471-26393-1 CopyrightC?2004 by John Wiley&Sons,Inc.19P1:GIGWY001-02WY001-Bolsover-v2.clsAugust 21,200318:2220FROM WATER TO D

7、NA:THE CHEMISTRY OF LIFE(a)(b)+2HClClHO+Figure 2.1.Water is a polar molecule while the chlorine molecule is nonpolar.to indicate that it is smaller than the charge on a single hydrogen nucleus.The oxygen atomhas the small net negative charge 2.Molecules that,like water,have positive regionssticking

8、out one side and negative regions sticking out the other are called polar.Figure2.1b showsamoleculeofchlorinegas.Itconsistsoftwochlorineatoms,eachofwhich consists of a positively charged nucleus surrounded by negatively charged electrons.Like oxygen,chlorine atoms tend to accept electrons when they

9、become available,but thebattle is equal in the chlorine molecule:The two atoms share their electrons equally and themolecule is nonpolar.+ClCleClClNaNa+e(a)(b)Na+NaFigure 2.2.Formation of sodium chloride,an ionic compound.P1:GIGWY001-02WY001-Bolsover-v2.clsAugust 21,200318:22INTERACTIONS WITH WATER:

10、SOLUTIONS21Figure 2.2a shows what happens when a chlorine molecule is allowed to react withthe metal sodium.Each atom of chlorine takes over one electron from a sodium atom.Thisleavesthesodiumatomswithasinglepositivechargebecausethereisnowonemorepositivecharge on the sodium nucleus than negatively c

11、harged surrounding electrons.Similarly,each chlorine atom now has a single negative charge because it now has one more electronthan there are positive charges in its nucleus.Chemical species that have either gained orlost electrons,and that therefore bear an overall charge,are called ions.The reacti

12、on ofchlorine and sodium has produced sodium ions and chloride ions.Positively charged ionslikesodiumarecalledcationswhilenegativelychargedoneslikechloridearecalledanions.The positively charged sodium ions and the negatively charged chloride ions now attracteach other strongly.If there are no other

13、chemicals around,the ions will arrange themselvesto minimize the distance between sodium and chloride,and the resulting well-packed arrayof ions is a crystal of sodium chloride,shown in Figure 2.2b.INTERACTIONS WITH WATER:SOLUTIONSIonic Compounds Will Dissolve Only in Polar SolventsFigure 2.3a shows

14、 one molecule of octane,the main constituent of gasoline.Octane is anexample of a nonpolar solvent.Electrons are shared equally between carbon and hydrogen,and the component atoms do not bear a net charge.Figure 2.3b shows a small crystal of sodium chloride immersed in octane.At the edgeof the cryst

15、al,positively charged sodium ions are being pulled in toward the center ofthe crystal by the negative charge on chloride ions,and negatively charged chloride ionsare being pulled in toward the center of the crystal by the positive charge on sodium ions.The sodium and chloride ions will not leave the

16、 crystal.Sodium chloride is insoluble inoctane.However,sodium chloride will dissolve in water,and Figure 2.4a shows why.Thechlorideionatthetopleftisbeingpulledintothecrystalbythepositivechargeonitssodiumionneighbors,butatthesametimeitisbeingpulledoutofthecrystalbythepositivechargeon the hydrogen ato

17、ms of nearby water molecules.Similarly,the sodium ion at the bottomleft is being pulled into the crystal by the negative charge on its chloride ion neighbors,butat the same time it is being pulled out of the crystal by the negative charge on the oxygenatoms of nearby water molecules.The ions are not

18、 held in the crystal so tightly and canleave.Once the ions have left the crystal,they become surrounded by a hydration shell ofwater molecules,all oriented in the appropriate direction(Fig.2.4b)oxygen inward fora positive ion like sodium,hydrogen inward for a negative ion like chloride.A chemicalspe

19、cies in solution,whether in water or in any other solvent,is called a solute.Liquidswhose main constituent is water are called aqueous.Acids Are Molecules That Give H+to WaterWhen we exercise,our muscle cells can become acid,and this is what creates the painof cramping muscles and the heart pain of

20、angina.Acidity is important in all areas ofbiology,from the acidity gradient that drives our mitochondria(page 261)to the ecologicalconsequences of acid rain.Acid solutions contain a high concentration of hydrogen ions.The hydrogen atom isunusual in that it only has one electron while,in its most co

21、mmon isotope,its nucleusP1:GIGWY001-02WY001-Bolsover-v2.clsAugust 21,200318:2222FROM WATER TO DNA:THE CHEMISTRY OF LIFECCHHHCCHHHHCCHHHHCCCHHHHHHH(a)+octanesodium chloride(b)Figure 2.3.(a)Structure of the nonpolar compound octane.(b)Ionic compounds are insoluble innonpolar prises a single proton.In

22、gasses at very low pressure it is possible for bare protonsto exist alone and be manipulated,for example,in linear accelerators.However,in waterprotons never exist alone but always associate with another molecule,for example,withwater to create the H3O+ion.Acid solutions are those with an H3O+concen

23、tration higherthan 100 nmol liter1.Sour cream contains lactic acid.Pure lactic acid has the structure shown at the left ofFigure 2.5a.The COOH part in the box is called a carboxyl group.Both oxygens have atendency to pull electrons away from the hydrogen and,in aqueous solution,the hydrogenis donate

24、d with a full positive charge to a molecule of water.The electron is left behind onthe now negatively charged lactate ion.CH3CH(OH)COOH+H2O CH3CH(OH)COO+H3O+P1:GIGWY001-02WY001-Bolsover-v2.clsAugust 21,200318:22INTERACTIONS WITH WATER:SOLUTIONS23+water+2(a)(b)NaClHHOHHOHHOHHOHHOHHOHHOHHOClHHOHHOHHOH

25、HOHHOHHOHHOHHOHHOHHONaHHOHHOHHOHHOHHOHHOHHOHHOHHOHHOHHOHHOHHOHHOHHOHHOHHOHHOHHOHHOHHOHHOHHOHHOHHOHHOHHOHHOHHOHHOHHOHHOHHOHHOHHOHHOHHOHHOHHOHHOHHOHHOHHOHHOHHOHHOHHOHHOHHOHHOsodium chlorideFigure 2.4.Ionic compounds dissolve readily in water.P1:GIGWY001-02WY001-Bolsover-v2.clsAugust 21,200318:2224FROM

26、 WATER TO DNA:THE CHEMISTRY OF LIFEH3O+H2OCOCHOHHHlactic acidlactate ionHCOHCOCHOHHHHCOCH3NCH3trimethylamineCH3CH3HCH3protonatedtrimethylamine ionCH3H3O+H2O(a)(b)NFigure 2.5.Acids and bases,respectively,give up and accept H+when dissolved in water.For convenience we often write this asCH3CH(OH)COOH

27、CH3CH(OH)COO+H+Here we are using H+as a convenient symbol to denote H3O+.We do not mean that thereare real H+ions,that is,bare hydrogen nuclei,in aqueous solutions.The equilibrium constant,Kafor the dissociation of lactic acid,is defined asKa=CH3CH(OH)COOeH+eCH3CH(OH)COOHewhere the square brackets r

28、efer,by convention,to concentrations and the subscripts,e,denote that these are the concentrations of each species at equilibrium.Dissolving lots of lactic acid in water produces an acid solution,that is,one with a highconcentration of H+(really H3O+)ions.For historical reasons,the acidity of a solu

29、tion isgiven as the pH,defined thus:pH=log10(H+)where H+is measured in moles per literPure water has a pH of 7,corresponding to H+=100 nmol liter1this is said to beneutral as regards pH.If the pH is lower than this,then there is more H+about and thesolution is acid.Cytosol has a pH that lies very sl

30、ightly on the alkaline side of neutrality,atabout 7.2.The pH of a solution determines the ratio of lactate to undissociated lactic acid.Asthe H+concentration rises and pH falls,the equilibrium is pushed over from lactate towardlacticacid.AtpH3.9,theconcentrationsoflactateandlacticacidbecomeequal.Loo

31、kingatP1:GIGWY001-02WY001-Bolsover-v2.clsAugust 21,200318:22INTERACTIONS WITH WATER:SOLUTIONS25the equation above,we can therefore see that when this happens Ka=H+.Just as acidityisgivenonthelogarithmicpHscalesoisthescaleofstrengthsofdifferentacids,pKabeingdefined as log10Ka.The pKais the pH at whic

32、h the concentration of the dissociated acidis equal to the concentration of the undissociated acid.For an acid that is weaker than lacticacid,the pKais higher than 3.9,meaning that the acid is less readily dissociated and needsa lower concentration of protons before it will give up its H+.For an aci

33、d that is strongerthan lactic acid,the pKais less than 3.9:Such an acid is more readily dissociated and needsa higher H+concentration before it will accept H+and form undissociated acid.Bases Are Molecules That Take H+from WaterTrimethylamineisthecompoundthatgivesrottingfishitsunpleasantsmell.Puretr

34、imethy-lamine has the structure shown at the left of Figure 2.5b.When trimethylamine is dissolvedinwater,itacceptsanH+tobecomethepositivelychargedtrimethylamineionshownontheright of the figure.We refer to molecules that have accepted H+ions as protonated,using“proton”as a short way of saying“hydroge

35、n nucleus.”Dissolving lots of trimethylaminein water produces an alkaline solution,that is,one with a low concentration of H+ions andhence a pH greater than 7.The solution never runs out of H+completely because new H+are formed from water:H2O OH+H+Thus if we keep adding trimethylamine to water and u

36、sing up H+,we end up with a lowconcentration of H+,but lots of OH.The pH of a solution determines the position of equilibrium between protonated anddeprotonated trimethylamine,and as before we define the pKaas the pH at which theconcentrationofprotonatedanddeprotonatedbasearethesame.ThepKaoftrimethy

37、lamineis9.74,meaningthattheconcentrationofH+mustfalltothelowlevelof109.74molliter1,that is,0.2 nmol liter1,before half of the trimethylamines will give up their H+s.Isoelectric PointThe large molecules called proteins(page 183)have many acidic and basic sites that willgive up or accept an H+as the p

38、H changes.In alkaline solutions proteins will tend to havean overall negative charge because the acidic sites have lost an H+and bear a negativecharge.As the pH falls,the acidic sites accept an H+and become uncharged,and basicsites also accept an H+to gain a positive charge.Thus as the pH falls from

39、 an initial highvalue,the overall charge on the protein becomes less and less negative and then more andmore positive.The pH at which the protein has no overall charge is called the isoelectricpoint.The isoelectric points of different proteins are different,and this property is usefulin separating t

40、hem during analysis(page 178).The majority of intracellular proteins havean isoelectric point that is less than 7.2,so that at normal intracellular pH they bear a netnegative charge.A Hydrogen Bond Forms When a Hydrogen Atom Is SharedWe have seen how oxygen tends to grab electrons from hydrogen,form

41、ing a polar bond.Nitrogen and sulfur are similarly electron-grabbing.If a hydrogen attached to an oxygen,P1:GIGWY001-02WY001-Bolsover-v2.clsAugust 21,200318:2226FROM WATER TO DNA:THE CHEMISTRY OF LIFEHHNCCNCNCHNCNdeoxyriboseHHHCCCCHCdeoxyriboseOONHHHNHthymine(T)adenine(A)a hydrogen bond cannot form

42、here because the N H N atoms are not in a straight lineOOHHHHO(a)(b)hydrogen bondFigure 2.6.The hydrogen bond.nitrogenorsulfurbyacovalentbondgetsclosetoasecondelectron-grabbingatom;thenthatsecond atom also grabs a small share of the electrons to form what is known as a hydrogenbond.The atom to which

43、 the hydrogen is covalently bonded is called the donor because itis losing some of its share of electrons;the other electron-grabbing atom is the acceptor.For a hydrogen bond to form,the donor and acceptor must be within a fixed distance of oneanother(typically 0.3 nm)with the hydrogen on a straight

44、 line between them.P1:GIGWY001-02WY001-Bolsover-v2.clsAugust 21,200318:22CARBOHYDRATES:CANDY AND CANES27Liquid water is so stable because the individual molecules can hydrogen bond,asillustrated in Figure 2.6a.Hydrogen bonding also plays a critical role in allowing DNA tostore and replicate genetic

45、information.Figure 2.6b shows how the base pairs(page 69)of DNA form hydrogen bonds in which hydrogen atoms are shared between nitrogen andoxygen and between nitrogen and nitrogen.BIOLOGICAL MACROMOLECULESVery large molecules,or macromolecules,are central to the working of cells.Large bi-ological mo

46、lecules are polymers:they are assembled by joining together small,simplermolecules,which are therefore called monomers.Chemical technology has mimickednature by producing many important polymerspolyethylene is a polymer of ethylenemonomers.Cells make a number of macromolecules that we will introduce

47、,together withtheir monomer building blocks,in this chapter.CARBOHYDRATES:CANDY AND CANESCarbohydratessugars and the macromolecules built from themhave many differentroles in cells and organisms.An Assortment of SweetsAll carbohydrates are formed from the simple sugars called monosaccharides.Figure

48、2.7shows the monosaccharide called glucose.The form shown at the top has five carbonsjoined each to the other with an oxygen atom completing the ring.As well as the oxygenin the ring,glucose has five other oxygens,each in an OH(hydroxyl)group.Glucoseeasily switches between the three forms,or isomers

49、,illustrated in Figure 2.7.The tworing structures are stereo isomers:although they comprise the same atoms connected bythe same bonds,they represent two different ways of arranging the atoms in space.Thetwo stereo isomers,named and,continually interconvert in solution via the open-chainform.Figure 2

50、.8 shows five other monosaccharides that we will meet again in this book.Like glucose,each of these monosaccharides can adopt an open-chain form and a numberof ring structures.In Figure 2.8 we show each sugar in a form that it adopts quite often.Thesesugarssharewithglucosethetwocharacteristicsofmono