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Berg JM, Tymoczko JL, Stryer L. Biochemistry. Fifth edition. Brand-new York: W H Freeman; 2002.

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The nucleic acids DNA and also RNA space well suited to function as the carrier of geneticinformation through virtue of your covalent structures. This macromolecules arelinear polymers collected from similar units linked end toend (Figure 5.1). Each monomer unit withinthe polymer consists of 3 components: a sugar, a phosphate, and also a base. Thesequence of bases unique characterizes a main point acid and represents a form oflinear information.


5.1.1. RNA and also DNA differ in the sugar Component and One that the Bases

The street in deoxyribonucleic acid (DNA) isdeoxyribose. The deoxy prefix shows that the 2′ carbonatom that the sugar lacks the oxygen atom that is attached to the 2′ carbon atom ofribose (the street in ribonucleic acid, orRNA), as shown in Figure5.2. The sugars in nucleic acids are attached to one another byphosphodiester bridges. Specifics the 3′-hydroxyl (3′-OH) group of the sugarmoiety that one nucleotide is esterified come a phosphate group, which is, in turn,joined come the 5′-hydroxyl group of the nearby sugar. The chain the sugarslinked by phosphodiester bridges is referred to as the backboneof the nucleic acid (Figure 5.3). Whereasthe backbone is continuous in DNA and RNA, the bases differ from one monomer to thenext. Two of the bases room derivatives of purine—adenine (A)and guanine (G)—and two of pyrimidine—cytosine (C) and thymine(T, DNA only) or uracil (U, RNA only), as presented in figure 5.4.


Figure 5.2

Ribose and Deoxyribose. Atoms are numbered with primes to differentiate them from atoms inbases (see number 5.4).


Figure 5.3

Backbones that DNA and also RNA. The backbones of these main point acids are developed by 3′-to-5′phosphodiester linkages. A street unit is highlighted in red and aphosphate team in blue.


Figure 5.4

Purines and Pyrimidines. Atoms within bases are numbered without primes. Uracil rather ofthymine is provided in RNA.

RNA, like DNA, is a long unbranched polymer consisting of nucleotides joined by3′→5′ phosphodiester bonds (see Figure5.3). The covalent structure of RNA differs from that of DNA in tworespects. As declared earlier and also as indicated by that is name, the sugar devices in RNAare riboses quite than deoxyriboses. Ribose consists of a 2′-hydroxyl team notpresent in deoxyribose. Together a consequence, in enhancement to the traditional 3′→5′linkage, a 2′→5′ link is feasible for RNA. This later linkage is vital inthe removed of introns and also the joining of exons because that the development of tires RNA(Section 28.3.4). The otherdifference, as already mentioned, is that one of the four significant bases in RNA isuracil (U) instead of thymine (T).

Note the each phosphodiester bridge has actually a negative charge. This an unfavorable chargerepels nucleophilic types such as hydroxide ion; consequently, phosphodiesterlinkages space much less susceptible come hydrolytic attack than are other esterssuch as carboxylic acid esters. This resistance is crucial for keeping theintegrity of details stored in nucleic acids. The lack of the 2′-hydroxylgroup in DNA further increases its resistance to hydrolysis. The greaterstability the DNA probably accounts because that its use rather than RNA as the hereditarymaterial in all modern cells and also in numerous viruses.

Structural Insights, nucleic Acids

offers a three-dimensional perspective on nucleotide structure, basepairing, and other facets of DNA and also RNA structure.

A unit consisting of a base bonded to a street is referred to as anucleoside. The four nucleosideunits in RNA are referred to as adenosine, guanosine, cytidine, anduridine, vice versa, those in DNA are calleddeoxyadenosine, deoxyguanosine, deoxycytidine, andthymidine. In each case, N-9 that a purine or N-1 of apyrimidine is attached to C-1′ of the sugar (Figure 5.5). The basic lies above the plane of sugar as soon as thestructure is written in the traditional orientation; that is, the construction ofthe N-glycosidic linkage is β. Anucleotide is a nucleosidejoined come one or much more phosphate groups by an ester linkage. The most typical siteof esterification in naturally developing nucleotides is the hydroxyl groupattached come C-5′ the the sugar. A compound formed by the attachments of aphosphate group to the C-5′ the a nucleoside sugar is called a nucleoside5′-phosphate or a5′-nucleotide. Because that example, ATP isadenosine 5′-triphosphate. Anothernucleotide is deoxyguanosine 3′-monophosphate (3′-dGMP; number 5.6). This nucleotide different from ATP in the itcontains guanine rather than adenine, includes deoxyribose quite than ribose(indicated by the prefix “d”), includes one rather than three phosphates, andhas the phosphate esterified come the hydroxyl team in the 3′ fairly than the 5′position. Nucleotides space the monomers the are attached to type RNA and also DNA. Thefour nucleotide devices in DNA are dubbed deoxyadenylate, deoxyguanylate,deoxycytidylate, and also deoxythymidylate, andthymidylate. Note that thymidylate includes deoxyribose; byconvention, the prefix deoxy is not added because thymine-containing nucleotidesare just rarely uncovered in RNA.

Figure 5.6

Nucleotides adenosine 5′ -triphosphate (5′-ATP) anddeoxyguanosine 3′-monophosphate (3′-dGMP).

The abbreviated symbol pApCpG or pACG represent a trinucleotide that DNA consistingof the building blocks deoxyadenylate monophosphate, deoxycytidylatemonophosphate, and deoxyguanylate monophosphate connected by a phosphodiesterbridge, whereby “p” denotes a phosphate team (Figure 5.7). The 5′ end will frequently have a phosphate attached to the5′-OH group. Keep in mind that, favor a polypeptide (see ar 3.2), a DNA chain has polarity. One finish ofthe chain has a cost-free 5′-OH group (or a 5′-OH team attached come a phosphate),whereas the other finish has a 3′-OH group, neither of i m sorry is attached to anothernucleotide. By convention, the basic sequence is written in the5′-to-3′ direction. Thus, thesymbol ACG suggests that the unlinked 5′-OH team is on deoxyadenylate, whereasthe unlinked 3′-OH team is ~ above deoxyguanylate. Therefore polarity, ACG andGCA exchange mail to various compounds.

Figure 5.7

Structure the a DNA Chain. The chain has actually a 5′ end, i beg your pardon is generally attached come a phosphate, anda 3′ end, i beg your pardon is commonly a cost-free hydroxyl group.

A striking properties of naturally occurring DNA molecules is your length. ADNA molecule must consist of many nucleotides to lug the hereditary informationnecessary for even the easiest organisms. Because that example, the DNA of a virus suchas polyoma, i beg your pardon can cause cancer in certain organisms, is as lengthy as 5100nucleotides in length. We can quantify the information carrying capacity ofnucleic acids in the adhering to way. Each position have the right to be one of 4 bases,corresponding to two bits of info (22 = 4). Thus, a chain of5100 nucleotides corresponds to 2 × 5100 = 10,200 bits, or 1275 bytes (1 byte =8 bits). The E. Coli genome is a solitary DNA molecule consistingof two chains the 4.6 million nucleotides, corresponding to 9.2 million bits, or1.15 megabytes, of information (Figure5.8).

Figure 5.8

Electron Micrograph of part of the E. Coligenome.

DNA molecule from higher organisms have the right to be much larger. The human genomecomprises about 3 exchange rate nucleotides, divided amongst 24 unique DNAmolecules (22 autosomes, x and also y sex chromosomes) of different sizes. Among thelargest recognized DNA molecules is discovered in the Indian muntjak, one Asiatic deer; itsgenome is virtually as big as the human genome but is distributed on only 3chromosomes (Figure 5.9). The biggest ofthese chromosomes has chains of an ext than 1 billion nucleotides. If such a DNAmolecule might be totally extended, it would certainly stretch much more than 1 foot in length.Some plants contain even larger DNA molecules.

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Figure 5.9

The Indian Muntjak and Its Chromosomes. Cell from a female Indian muntjak (right) contain 3 pairs ofvery huge chromosomes (stained orange). The cell presented is a hybridcontaining a pair of human being chromosomes (stained green) forcomparison. <(Left) (more...)

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