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Berg JM, Tymoczko JL, Stryer L. Biochemistry. 5th edition. New York: W H Freeman; 2002.


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The nucleic acids DNA and RNA are well suited to function as the carriers of geneticinformation by virtue of their covalent structures. These macromolecules arelinear polymers built up from similar units connected end toend (Figure 5.1). Each monomer unit withinthe polymer consists of three components: a sugar, a phosphate, and a base. Thesequence of bases uniquely characterizes a nucleic acid and represents a form oflinear information.


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5.1.1. RNA and DNA Differ in the Sugar Component and One of the Bases

The sugar in deoxyribonucleic acid (DNA) isdeoxyribose. The deoxy prefix indicates that the 2′ carbonatom of the sugar lacks the oxygen atom that is linked to the 2′ carbon atom ofribose (the sugar in ribonucleic acid, orRNA), as shown in Figure5.2. The sugars in nucleic acids are linked to one another byphosphodiester bridges. Specifically, the 3′-hydroxyl (3′-OH) group of the sugarmoiety of one nucleotide is esterified to a phosphate group, which is, in turn,joined to the 5′-hydroxyl group of the adjacent sugar. The chain of sugarslinked by phosphodiester bridges is referred to as the backboneof the nucleic acid (Figure 5.3). Whereasthe backbone is constant in DNA and RNA, the bases vary from one monomer to thenext. Two of the bases are 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 shown in Figure 5.4.


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Figure 5.2

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


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Figure 5.3

Backbones of DNA and RNA. The backbones of these nucleic acids are formed by 3′-to-5′phosphodiester linkages. A sugar unit is highlighted in red and aphosphate group in blue.


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Figure 5.4

Purines and Pyrimidines. Atoms within bases are numbered without primes. Uracil instead ofthymine is used 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 stated earlier and as indicated by its name, the sugar units in RNAare riboses rather than deoxyriboses. Ribose contains a 2′-hydroxyl group notpresent in deoxyribose. As a consequence, in addition to the standard 3′→5′linkage, a 2′→5′ linkage is possible for RNA. This later linkage is important inthe removal of introns and the joining of exons for the formation of mature RNA(Section 28.3.4). The otherdifference, as already mentioned, is that one of the four major bases in RNA isuracil (U) instead of thymine (T).

Note that each phosphodiester bridge has a negative charge. This negative chargerepels nucleophilic species such as hydroxide ion; consequently, phosphodiesterlinkages are much less susceptible to hydrolytic attack than are other esterssuch as carboxylic acid esters. This resistance is crucial for maintaining theintegrity of information stored in nucleic acids. The absence of the 2′-hydroxylgroup in DNA further increases its resistance to hydrolysis. The greaterstability of DNA probably accounts for its use rather than RNA as the hereditarymaterial in all modern cells and in many viruses.


Structural Insights, Nucleic Acids

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


A unit consisting of a base bonded to a sugar is referred to as anucleoside. The four nucleosideunits in RNA are called adenosine, guanosine, cytidine, anduridine, whereas those in DNA are calleddeoxyadenosine, deoxyguanosine, deoxycytidine, andthymidine. In each case, N-9 of a purine or N-1 of apyrimidine is attached to C-1′ of the sugar (Figure 5.5). The base lies above the plane of sugar when thestructure is written in the standard orientation; that is, the configuration ofthe N-glycosidic linkage is β. Anucleotide is a nucleosidejoined to one or more phosphate groups by an ester linkage. The most common siteof esterification in naturally occurring nucleotides is the hydroxyl groupattached to C-5′ of the sugar. A compound formed by the attachment of aphosphate group to the C-5′ of a nucleoside sugar is called a nucleoside5′-phosphate or a5′-nucleotide. For example, ATP isadenosine 5′-triphosphate. Anothernucleotide is deoxyguanosine 3′-monophosphate (3′-dGMP; Figure 5.6). This nucleotide differs from ATP in that itcontains guanine rather than adenine, contains deoxyribose rather than ribose(indicated by the prefix “d”), contains one rather than three phosphates, andhas the phosphate esterified to the hydroxyl group in the 3′ rather than the 5′position. Nucleotides are the monomers that are linked to form RNA and DNA. Thefour nucleotide units in DNA are called deoxyadenylate, deoxyguanylate,deoxycytidylate, and deoxythymidylate, andthymidylate. Note that thymidylate contains deoxyribose; byconvention, the prefix deoxy is not added because thymine-containing nucleotidesare only rarely found in RNA.


Figure 5.6

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


The abbreviated notations pApCpG or pACG denote a trinucleotide of DNA consistingof the building blocks deoxyadenylate monophosphate, deoxycytidylatemonophosphate, and deoxyguanylate monophosphate linked by a phosphodiesterbridge, where “p” denotes a phosphate group (Figure 5.7). The 5′ end will often have a phosphate attached to the5′-OH group. Note that, like a polypeptide (see Section 3.2), a DNA chain has polarity. One end ofthe chain has a free 5′-OH group (or a 5′-OH group attached to a phosphate),whereas the other end has a 3′-OH group, neither of which is linked to anothernucleotide. By convention, the base sequence is written in the5′-to-3′ direction. Thus, thesymbol ACG indicates that the unlinked 5′-OH group is on deoxyadenylate, whereasthe unlinked 3′-OH group is on deoxyguanylate. Because of this polarity, ACG andGCA correspond to different compounds.


Figure 5.7

Structure of a DNA Chain. The chain has a 5′ end, which is usually attached to a phosphate, anda 3′ end, which is usually a free hydroxyl group.


A striking characteristic of naturally occurring DNA molecules is their length. ADNA molecule must comprise many nucleotides to carry the genetic informationnecessary for even the simplest organisms. For example, the DNA of a virus suchas polyoma, which can cause cancer in certain organisms, is as long as 5100nucleotides in length. We can quantify the information carrying capacity ofnucleic acids in the following way. Each position can be one of four bases,corresponding to two bits of information (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 single DNA molecule consistingof two chains of 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 molecules from higher organisms can be much larger. The human genomecomprises approximately 3 billion nucleotides, divided among 24 distinct DNAmolecules (22 autosomes, x and y sex chromosomes) of different sizes. One of thelargest known DNA molecules is found in the Indian muntjak, an Asiatic deer; itsgenome is nearly as large as the human genome but is distributed on only 3chromosomes (Figure 5.9). The largest ofthese chromosomes has chains of more than 1 billion nucleotides. If such a DNAmolecule could be fully extended, it would stretch 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. Cells from a female Indian muntjak (right) contain three pairs ofvery large chromosomes (stained orange). The cell shown is a hybridcontaining a pair of human chromosomes (stained green) forcomparison. <(Left) (more...)


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