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

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Biochemistry. 5th edition.

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Section 5.1A Nucleic Acid Consists of Four Kinds of Bases Linked to a Sugar-Phosphate Backbone

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

Figure 5.1. Polymeric Structure of Nucleic Acids.

Figure 5.1

Polymeric Structure of Nucleic Acids.

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

The sugar in deoxyribonucleic acid (DNA) is deoxyribose. The deoxy prefix indicates that the 2′ carbon atom of the sugar lacks the oxygen atom that is linked to the 2′ carbon atom of ribose (the sugar in ribonucleic acid, or RNA), as shown in Figure 5.2. The sugars in nucleic acids are linked to one another by phosphodiester bridges. Specifically, the 3′-hydroxyl (3′-OH) group of the sugar moiety 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 sugars linked by phosphodiester bridges is referred to as the backbone of the nucleic acid (Figure 5.3). Whereas the backbone is constant in DNA and RNA, the bases vary from one monomer to the next. 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.

Figure 5.2. Ribose and Deoxyribose.

Figure 5.2

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

Figure 5.3. Backbones of DNA and RNA.

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 a phosphate group in blue.

Figure 5.4. Purines and Pyrimidines.

Figure 5.4

Purines and Pyrimidines. Atoms within bases are numbered without primes. Uracil instead of thymine is used in RNA.

RNA, like DNA, is a long unbranched polymer consisting of nucleotides joined by 3′→5′ phosphodiester bonds (see Figure 5.3). The covalent structure of RNA differs from that of DNA in two respects. As stated earlier and as indicated by its name, the sugar units in RNA are riboses rather than deoxyriboses. Ribose contains a 2′-hydroxyl group not present 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 in the removal of introns and the joining of exons for the formation of mature RNA (Section 28.3.4). The other difference, as already mentioned, is that one of the four major bases in RNA is uracil (U) instead of thymine (T).

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

5.1.2. Nucleotides Are the Monomeric Units of Nucleic Acids

Structural Insights, Nucleic Acids

Image mouse.jpg offers a three-dimensional perspective on nucleotide structure, base pairing, and other aspects of DNA and RNA structure.

A unit consisting of a base bonded to a sugar is referred to as a nucleoside. The four nucleoside units in RNA are called adenosine, guanosine, cytidine, and uridine, whereas those in DNA are called deoxyadenosine, deoxyguanosine, deoxycytidine, and thymidine. In each case, N-9 of a purine or N-1 of a pyrimidine is attached to C-1′ of the sugar (Figure 5.5). The base lies above the plane of sugar when the structure is written in the standard orientation; that is, the configuration of the N-glycosidic linkage is β. A nucleotide is a nucleoside joined to one or more phosphate groups by an ester linkage. The most common site of esterification in naturally occurring nucleotides is the hydroxyl group attached to C-5′ of the sugar. A compound formed by the attachment of a phosphate group to the C-5′ of a nucleoside sugar is called a nucleoside 5-phosphate or a 5-nucleotide. For example, ATP is adenosine 5-triphosphate. Another nucleotide is deoxyguanosine 3′-monophosphate (3′-dGMP; Figure 5.6). This nucleotide differs from ATP in that it contains guanine rather than adenine, contains deoxyribose rather than ribose (indicated by the prefix “d”), contains one rather than three phosphates, and has 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. The four nucleotide units in DNA are called deoxyadenylate, deoxyguanylate, deoxycytidylate, and deoxythymidylate, and thymidylate. Note that thymidylate contains deoxyribose; by convention, the prefix deoxy is not added because thymine-containing nucleotides are only rarely found in RNA.

Figure 5.6. Nucleotides Adenosine 5′ -triphosphate (5′-ATP) and deoxyguanosine 3′-monophosphate (3′-dGMP).

Figure 5.6

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

The abbreviated notations pApCpG or pACG denote a trinucleotide of DNA consisting of the building blocks deoxyadenylate monophosphate, deoxycytidylate monophosphate, and deoxyguanylate monophosphate linked by a phosphodiester bridge, where “p” denotes a phosphate group (Figure 5.7). The 5′ end will often have a phosphate attached to the 5′-OH group. Note that, like a polypeptide (see Section 3.2), a DNA chain has polarity. One end of the 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 another nucleotide. By convention, the base sequence is written in the 5-to-3direction. Thus, the symbol ACG indicates that the unlinked 5′-OH group is on deoxyadenylate, whereas the unlinked 3′-OH group is on deoxyguanylate. Because of this polarity, ACG and GCA correspond to different compounds.

Figure 5.7. Structure of a DNA Chain.

Figure 5.7

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

A striking characteristic of naturally occurring DNA molecules is their length. A DNA molecule must comprise many nucleotides to carry the genetic information necessary for even the simplest organisms. For example, the DNA of a virus such as polyoma, which can cause cancer in certain organisms, is as long as 5100 nucleotides in length. We can quantify the information carrying capacity of nucleic acids in the following way. Each position can be one of four bases, corresponding to two bits of information (22 = 4). Thus, a chain of 5100 nucleotides corresponds to 2 × 5100 = 10,200 bits, or 1275 bytes (1 byte = 8 bits). The E. coli genome is a single DNA molecule consisting of two chains of 4.6 million nucleotides, corresponding to 9.2 million bits, or 1.15 megabytes, of information (Figure 5.8).

Figure 5.8. Electron Micrograph of Part of the E. coli genome.

Figure 5.8

Electron Micrograph of Part of the E. coli genome. [Dr. Gopal Murti/Science Photo Library/Photo Researchers.]

DNA molecules from higher organisms can be much larger. The human genome comprises approximately 3 billion nucleotides, divided among 24 distinct DNA molecules (22 autosomes, x and y sex chromosomes) of different sizes. One of the largest known DNA molecules is found in the Indian muntjak, an Asiatic deer; its genome is nearly as large as the human genome but is distributed on only 3 chromosomes (Figure 5.9). The largest of these chromosomes has chains of more than 1 billion nucleotides. If such a DNA molecule could be fully extended, it would stretch more than 1 foot in length. Some plants contain even larger DNA molecules.

Figure 5.9. The Indian Muntjak and Its Chromosomes.

Figure 5.9

The Indian Muntjak and Its Chromosomes. Cells from a female Indian muntjak (right) contain three pairs of very large chromosomes (stained orange). The cell shown is a hybrid containing a pair of human chromosomes (stained green) for comparison. [(Left) (more...)

By agreement with the publisher, this book is accessible by the search feature, but cannot be browsed.

Copyright © 2002, W. H. Freeman and Company.
Bookshelf ID: NBK22490

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