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\Mhenrequired to provide energy, the fatty acid chains are released from triacylglycerolsand broken dor,rminto two-carbon units. These Wvo-carbonunits are identical tothose derived from the breakdor,rrnof glucose and they enter the same energyyielding reaction pathways, as will be described later in this chapter.Triglyceridesserve as a concentrated food reserve in cells, because they can be broken downto produce about six times as much usable energy,weight for weight, as glucose.Fatty acids and their derivatives such as triacylglycerols are examples oflipids.
Lipids comprise a loosely defined collection of biological molecules thatare insoluble in water, while being soluble in fat and organic solvents such asbenzene. They typically contain either long hydrocarbon chains, as in the fattyacids and isoprenes,or multiple linked rings, as inthe steroids.The most important function of fatty acids in cells is in the construction ofcell membranes. These thin sheets enclose all cells and surround their internalorganelles. They are composed largely of phospholipids, which are smallmolecules that, like triacylglycerols, are constructed mainly from fatty acids andglycerol. In phospholipids the glycerol is joined to two fatty acid chains, however,rather than to three as in triacylglycerols. The "third" site on the glycerol is linkedto a hydrophilic phosphate group, which is in turn attached to a smallhydrophilic compound such as choline (see Panel 2-5).
Each phospholipidh y d r o p h i l i cc a r b o x y l i ca c i d h e a do\h y d r o p h o b i ch y d r o c a r b o nt a i l(A)(B)(c)Figure2-21 A fatty acid.A fatty acid iscomposedof a hydrophobichydrocarbonchainto which is attacheda hydrophiliccarboxylicacidgroup.Palmiticacidisshown here.Differentfatty acidshavedifferenthydrocarbontails.(A)Structuralformula.Thecarboxylicacidgroupisshownin its ionizedform.(B)Ball-andstickmodel.(C)Space-fillingmodel.THECHEMICALCOMPONENTSOFA CELLrwohydrophobicfatty acidtails59Figure2-22 Phospholipidstructure andthe orientationof phospholipidsinmembranes.In an aqueousenvironment,the hydrophobictailsof phospholipidspacktogetherto excludewater.Herethey haveformed a bilayerwith thehydrophilicheadof eachphospholipidfacingthe water.Lipidbilayersaretheasdiscussedinbasisfor cellmembranes,detailin Chapter10.oa00ltff00f000ofoop h o s p h o l i p i dm o t e c u t emolecule, therefore, has a hydrophobic tail composed of the two fatty acidchains and a hydrophilic head, where the phosphate is located.
This gives themdifferent physical and chemical properties from triacylglycerols,which are predominantly hydrophobic. Molecules such as phospholipids, with both hydrophobic and hydrophilic regions, are termed amphiphilic.The membrane-forming property of phospholipids results from theiramphiphilic nature. Phospholipids will spread over the surface of water toform a monolayer of phospholipid molecules, with the hydrophobic tails facing the air and the hydrophilic heads in contact with the water. TWo suchmolecular layers can readily combine tail-to-tail in water to make a phospholipid sandwich, or lipid bilayer.
This bilayer is the structural basis of all cellmembranes (Figure 2-22).AminoAcidsArethe Subunitsof ProteinsAmino acids are a varied class of molecules with one defining property: they allpossessa carboxylic acid group and an amino group, both linked to a single carbon atom called the cr-carbon (Figure 2-23). Their chemical variety comes fromthe side chain that is also attached to the cx-carbon.The importance of aminoacids to the cell comes from their role in making proteins, which are polymersof amino acids joined head-to-tail in a long chain that is then folded into a threedimensional structure unique to each type of protein. The covalent linkagebetween two adjacent amino acids in a protein chain forms an amide (seePanel2-l), and it is called a peptide bond; the chain of amino acids is also known as apolypeptide (Figure 2-24).
Regardlessof the specific amino acids from which itis made, the pollpeptide has an amino (NH2) group at one end (its N-terminus)and a carboxyl (COOH) group at its other end (its C-terminus).This givesit a definite directionality-a structural (as opposed to an electrical) polarity.Each of the 20 amino acids found commonly in proteins has a different sidechain attached to the o-carbon atom (seePanel 3-1, pp.
128-129).All organisms,amtnogroupc ar D o x yIgroups i d ec h a i n( R )n o n i o n i z e df o r m(A)i o n i z e df o r m(B)(c)Figure2-23 The amino acid alanine.(A)In the cell,wherethe pH is closeto 7,the freeaminoacidexistsin its ionizedinto aform;but when it is incorporatedpolypeptidechain,the chargeson theaminoand carboxylgroupsdisappear.(B)A ball-and-stickmodeland (C)amodelof alanine(H,white;space-fillingC, black;O, red;N,blue).60Chapter2:CellChemistryand BiosynthesisFigure 2-24 A small part of a protein molecule.The four amino acidsshown are linkedtogether by three peptide bonds,one of which ishighlightedin yellow.One of the amino acidsis shadedin gray.The aminoacid sidechainsare shown in red.The two ends of a polypeptidechainarechemicallydistinct.Oneend,the N-terminus,terminatesin an aminogroup,and the other,the C-terminus,in a carboxylgroup.The sequenceisalwaysreadfrom the N-terminalend; hencethis sequenceisPhe-Ser-Glu-Lys.N-terminalend o{p o l y p e p t i d ec h a i nIN_HIH-C -CH?IO=CIN-HH-C -CHr-oHt-whether bacteria,archea,plants, or animals,haveproteins made of the same20amino acids.How this preciseset of 20 cameto be chosenis one of the mysteries of the evolution of life; there is no obviouschemicalreasonwhy other aminoacidscould not haveservedjust aswell.
But once the choicewas established,itcould not be changed;too much dependedon it.Like sugars,all amino acids,exceptglycine,existasoptical isomersin D- andL-forms(seePanel3-l). But only L-forms€ueeverfound in proteins(althoughDamino acids occur as part of bacterial cell walls and in some antibiotics). Theorigin of this exclusiveuse of l-amino acids to make proteins is another evolutionarymystery.The chemicalversatility of the 20 amino acidsis essentialto the function ofproteins.Five of the 20 amino acidshave side chainsthat can form ions in neutral aqueoussolution and thereby can carry a charge(Figure2-25). The othersare uncharged;some are polar and hydrophilic, and some are nonpolar andhydrophobic.As we discussin Chapter3, the propertiesof the amino acid sidechainsunderlie the diverseand sophisticatedfunctions of proteins.O=CGluLysN-H,,HH - C - C H , --C H ? - C H r - C H ) --N - H l|\HO=CC-terminalend ofp o l y p e p t i d ec h a i n11pHasparticacidpK-4.7glutamicacidpK-4.7histidinelysineargrnrnepK-6.5pK-10.2pK-12Figure2-25 The charge on amino acidside chainsdepends on the pH.
The fivedifferentsidechainsthat can carryachargeare shown.CarboxylicacidscanreadilyloseH+in aqueoussolutiontoform a negativelychargedion, which isdenoted by the suffix"-atei'asinaspartdteor glutamote.A comparablesituationexistsfor amines.which inaqueoussolutioncan take up H+to forma positivelychargedion (whichdoes nothavea specialname).Thesereactionsarerapidlyreversible,and the amountsof thetwo forms,chargedand uncharged,dependon the pH of the solution.At ahigh pH, carboxylicacidstend to bechargedand aminesuncharged.At a lowpH,the oppositeis true-the carboxylicacidsare unchargedand aminesarecharged.The pH at which exactlyhalf ofthe carboxylicacidor amineresiduesarechargedis known as the pK of that aminoacid sidechain (indicatedbyyellowstripe).In the cellthe pH is closeto 7, andalmostall carboxylicacidsand aminesarein theirfullychargedform.THECHEMICALCOMPONENTSOFA CELL61o()Pl"oFigure2-26Chemicalstructureofadenosinetriphosphate(ATP).(A)Structuralformula.(B)Space-fillingmodel.In (8)the colorsof the atomsareC, black;N, b/ue;H, white;O, red; andP,yellow.H.a-N-ra-NH,\-"oo'inllI"\oto'\o"'xozclt oX^,t-a.)HnllnOH OH"rlJt'(A)(B)NucleotidesArethe Subunitsof DNAand RNAA nucleotide is a molecule made up of a nitrogen-containing ring compoundlinked to a five-carbon sugar, which in turn carries one or more phosphategroups (Panel2-6, pp.116-117).
The five-carbon sugar can be either ribose ordeoxyribose. Nucleotides containing ribose are known as ribonucleotides, andthose containing deoxyribose as deoxyribonucleotides.The nitrogen-containingrings are generally referred to as basesfor historical reasons:under acidic conditions they can each bind an H+ (proton) and thereby increase the concentrationof OH- ions in aqueous solution.
There is a strong family resemblance betweenthe different bases. Cyfosine (C), thymine (T), and uracil (U) are called pyrimidines becausethey all derive from a six-membered pyrimidine ring; guanine (G)and adenine (A) are purinecompounds, and theyhave a second, five-memberedring fused to the six-membered ring. Each nucleotide is named for the base itcontains (seePanel 2-6).Nucleotides can act as short-term carriers of chemical energy.Above all others, the ribonucleotide adenosine triphosphate, or ATP (Figure 2-26), transfersenergy in hundreds of different cell reactions. ATP is formed through reactionsthat are driven by the energy released by the oxidative breakdown of foodstuffs.Its three phosphates are linked in seriesby two phosphoanhydride bonds,whoserupture releaseslarge amounts of useful energy.The terminal phosphate group inparticular is frequently split off by hydrolysis, often transferring a phosphate toother molecules and releasing energy that drives energy-requiring biosyntheticreactions (Figure 2-27).
Other nucleotide derivatives are carriers for the transferof other chemical groups, as will be described later.The most fundamental role of nucleotides in the cell, however, is in the storage and retrieval of biological information. Nucleotides serve as building blocksfor the construction of nucleic aclds-long pol].rynersin which nucleotide subunitsare covalently linked by the formation of a phosphodiester bond between thep h o s p h o a n h y d r i dbeo n d sTITIoo-ortlP -O-P-O-PP-O_o Pi l it l t lol oo oenergy froms u n l i g h ot rfrom foodHzoo-H*+Io-P-oH+iloInorganrcp h o s p h a t e( P i )e n e r g ya v a i l a b l ef o r c e l l u l a rw o r kand {or chemicalsynthesisFigure2-27 The ATPmoleculeservesasan energycarrierin cells.Theenergyrequiringformationof ATPfrom ADPandinorganicphosphateis coupledto theoxidationof foodstuffsenergy-yielding(in animalcells,fungi,and somebacteria)or to the captureof light energy(in plantThe hydrolysiscellsand somebacteria).of this ATPbackto ADPand inorganicphosphatein turn providesthe energytodrivemanvcell reactions.62Chapter2: CellChemistryand BiosynthesisFigure2-28A smallpartof onechainof a deoxyribonucleicacid(DNA)molecule.Fournucleotidesareshown.Oneof thephosphodiesterbondsthatlinksadjacentnucleotideresiduesishighlightedinyellow,andoneofthenucleotidesisshadedin gray.Nucleotidesarelinkedtogetherbyaphosphodiesterlinkagebetweenspecificcarbonatomsof theribose,knownasthe5'and3'atoms.Forthisreason,oneendof a polynucleotidegroupandtheother,thechain,the5' end,willhavea freephosphategroup.3' end,a freehydroxylThelinearsequenceof nucleotidesin apolynucleotidechainiscommonlyabbreviatedby a one-lettercode,andthesequenceisalwaysreadfromthe5'end.IntheexampleillustratedthesequenceisG-A-T-C.phosphate group attached to the sugar of one nucleotide and a hydroxyl group onthe sugar of the next nucleotide (Figure 2-28).
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