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As we saw inChapter 2 (Panel 2-6, pp. 116-117), nucleotides are composed of a five-carbonsugar to which are attached one or more phosphate groups and a nitrogen-containing base. In the case of the nucleotides in DNA, the sugar is deoxyriboseattached to a single phosphate group (hence the name deoxyribonucleic acid),and the base maybe either adenine (A),cytosine(C),guanine (G),or thymine (T).The nucleotides are covalently linked together in a chain through the sugarsandphosphates, which thus form a "backbone" of alternating sugar-phosphatesugar-phosphate. Becauseonly the base differs in each of the four types of subunits, each polynucleotide chain in DNA is analogous to a necklace (the backbone) strung with four rypes of beads (the four basesA, C, G, and T).
These samesymbols (A, C, G, and T) are also commonly used to denote the four differentnucleotides-that is, the baseswith their attached sugar and phosphate groups.The way in which the nucleotide subunits are linked together gives a DNAstrand a chemical polarity. If we think of each sugar as a block with a protrudingknob (the 5'phosphate) on one side and a hole (the 3'hydroxyl) on the other (seeFigure 4-3), each completed chain, formed by interlocking knobs with holes, willhave all of its subunits lined up in the same orientation.
Moreover, the two endsof the chain will be easily distinguishable, as one has a hole (the 3'hydroxyl) andthe other a knob (the 5'phosphate) at its terminus. This polarity in a DNA chainis indicated by referring to one end as tl:'e ! end and the other as the ! end.The three-dimensional structure of DNA-the double helix-arises fromthe chemical and structural features of its two polynucleotide chains. Becausethese two chains are held together by hydrogen bonding between the bases onthe different strands, all the bases are on the inside of the double helix, and thesugar-phosphatebackbones are on the outside (seeFigure 4-3).
In each case,a bulkier two-ring base (a purine; see Panel 2-6, pp. 116-l 17) is paired with asingle-ring base (a pyrimidine); A always pairs with T and G with C (Figure197198Chapter4: DNA, Chromosomes,and Genomes$$iiiffiliiiii:ii:iiillilii:i:ilitffib u i l d i n gb l o c k so f D N Aphosphatesuqar\';+K-sugaroasephosphatenedouble-strandedDNA3',5'D N A d o u b l eh e l i xs',Figure4-3 DNA and its building blocks.<CAGA>DNA is made of four types ofnucleotides,which are linkedcovalentlyinto a polynucleotidechain(a DNAstrand)with a sugar-phosphatebackbonefrom which the bases(A,C,G,andT) extend.A DNAmoleculeiscomposedof two DNA strandsheldtogether by hydrogenbonds betweenthe pairedbases.Thearrowheadsattheendsofthe DNAstrandsindicatethepolaritiesof the two strands,which runantiparallelto eachother in the DNAmolecule.In the diagramat the bottomleft of the figure,the DNA moleculeisshown straightenedout; in reality,it istwistedinto a doublehelix,as shownonthe right.Fordetails,seeFigure4-5.Y3'hydrogen-bondedb a s ep a i r s4-4).
This complementary base-pairlng enables the base pairs to be packed inthe energetically most favorable arrangement in the interior of the double helix.In this arrangement, each base pair is of similar width, thus holding the sugarphosphate backbones an equal distance apart along the DNA molecule. To maximize the efficiency of base-pair packing, the two sugar-phosphate backbonesHo\\N - _CC'\C -N\/-L\lIH-N\\C \\Nsugar-phosphatebackboneHC -CC_,-n, , ,o'ladenine[n,,thymineHN -HilililililO.llguanrnell/hydrogenDOnOHcytosineFigure4-4 Complementarybasepairs inthe DNAdouble helix.The shapesandchemicalstructureof the basesallowhydrogenbondsto form efficientlyonlybetweenA and T and betweenG and C.where atomsthat are able to form hydrogenbonds(seePanel2-3, pp. 110-111)can bebrought closetogetherwithout distortingthe doublehelix.As indicated,twohydrogenbonds form betweenA and T,while three form betweenG and C.Thebasescan pairin thisway only if the twopolynucleotidechainsthat containthemareantiparallelto eachother.THESTRUCTUREAND FUNCTIONOF DNA1995'end\ .o-d":,mtnorgroove3'endL=o-l\doI0 .
3 4n mo'o={-o5'end(A)/'..3'endFigure4-5 The DNAdouble helix.(A)A space-fillingmodelof 1.5turnsof theDNAdoublehelix.Eachturn of DNAismadeup of 10.4nucleotidepairs,and thecenter-to-centerdistancebetweenadjacentnucleotidepairsis 3.4nm.Thecoilingof the two strandsaroundeachother createstwo groovesin the doublehelix:the widergrooveis calledthe majorgroove,and the smallerthe minorgroove.(B)A shortsectionof the doublehelixviewedfrom its side,showingfour basepairs.The nucleotidesare linkedtogetherbondsthatcovalentlyby phosphodiesterjoin the 3rhydroxyl(-OH)groupofonesugarto the 5rhydroxylgroup of the nextstrandsugar.Thus,eachpolynucleotidehasa chemicalpolarity;that is,itstwoThe5' end ofdifferent.endsarechemicallythe DNApolymeris by conventionoftenillustratedcarryinga phosphategroup,whilethe 3rend is shownwith a hydroxyl.(B)wind around each other to form a double helix, with one complete turn everyten base pairs (Figure 4-5).The members of each base pair can fit together within the double helix onlyif the two strands of the helix are antiparallel-thatis, only if the polarity of onestrand is oriented opposite to that ofthe other strand (seeFigures 4-3 and 4-4).A consequence of these base-pairing requirements is that each strand of a DNAmolecule contains a sequence of nucleotides that is exactly complementary tothe nucleotide sequence of its partner strand.TheStructureof DNAProvidesa Mechanismfor HeredityGenescarry biological information that must be copied accurately for transmission to the next generation each time a cell divides to form two daughter cells.TWo central biological questions arise from these requirements: how can theinformation for specifying an organism be carried in chemical form, and how isit accurately copied?The discovery of the structure of the DNA double helix wasa landmark in twentieth-century biology because it immediately suggestedanswers to both questions, thereby providing a molecular explanation for theproblem of heredity.
We discuss these answers briefly in this section, and weshall examine them in much more detail in subsequent chapters.DNA encodes information through the order, or sequence, of thenucleotides along each strand. Each base-A, C, T or G-can be considered as aIetter in a four-letter alphabet that spells out biological messagesin the chemical structure of the DNA. As we saw in Chapter 1, organisms differ from oneanother because their respective DNA molecules have different nucleotidesequencesand, consequently,carry different biological messages.But how is thenucleotide alphabet used to make messages,and what do they spell out?As discussed above, it was known well before the structure of DNA wasdetermined that genes contain the instructions for producing proteins.
TheDNA messagesmust therefore somehow encode proteins (Figure 4-6). This relationship immediately makes the problem easier to understand. As discussed inChapter 3, the properties of a protein, which are responsible for its biologicalfunction, are determined by its three-dimensional structure. This structure isdetermined in turn by the linear sequenceof the amino acids of which it is composed. The linear sequence of nucleotides in a gene must therefore somehowspell out the linear sequence of amino acids in a protein. The exact correspondence between the four-letter nucleotide alphabet of DNA and the twenty-letteramino acid alphabet of proteins-the genetic code-is not obvious from theDNA structure, and it took over a decade after the discoverv of the double helix|||loruetI|Irrllllttig e n eCg e n eBT--tg e n eA|gene expresslonprotein Ahi€protein Bdoublet'"txlffiprotein cFigure4-6 The relationshipbetweengeneticinformationcarriedin DNAandproteins(discussedin Chapter1).200Chapter4: DNA,Chromosomes,and Genomesbefore it was worked out.
In Chapter 6 we will describe this code in detail in thecourse of elaborating the process,knoltm as geneexpresslon,through which a cellconverts the nucleotide sequence of a gene first into the nucleotide sequenceofan RNA molecule, and then into the amino acid sequenceof a protein.The complete set of information in an organism'sDNA is called its genorne,and it carries the information for all the proteins and RNA molecules that theorganism will ever synthesize. (The term genome is also used to describe theDNA that carries this information.) The amount of information contained ingenomes is staggering: for example, a typical human diploid cell contains 2meters of DNA double helix.
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