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Chapter 8 Nucleotides and Nucleic Acids

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FIGURE 8-1 Structure of nucleotides. (a) General structure showing the numbering convention for the pentose ring. This is a ribonucleotide. In deoxyribonucleotides the —OH group on the 2' carbon (in red) is replaced with —H. (b) The parent compounds of the pyrim-idine and purine bases of nucleotides and nucleic acids, showing the numbering conventions.

FIGURE 8-1 Structure of nucleotides. (a) General structure showing the numbering convention for the pentose ring. This is a ribonucleotide. In deoxyribonucleotides the —OH group on the 2' carbon (in red) is replaced with —H. (b) The parent compounds of the pyrim-idine and purine bases of nucleotides and nucleic acids, showing the numbering conventions.

and nucleosides the carbon numbers are given a prime (') designation to distinguish them from the numbered atoms of the nitrogenous bases.

The base of a nucleotide is joined covalently (at N-1 of pyrimidines and N-9 of purines) in an A^-glycosyl bond to the 1' carbon of the pentose, and the phosphate is esterified to the 5' carbon. The A^-glycosyl bond is formed by removal of the elements of water (a hydroxyl group from the pentose and hydrogen from the base), as in O-glycosidic bond formation (see Fig. 7-31).

Both DNA and RNA contain two major purine bases, adenine (A) and guanine (G), and two major pyrimidines. In both DNA and RNA one of the pyrimidines is cytosine (C), but the second major pyrimidine is not the same in both: it is thymine (T) in DNA and uracil (U) in RNA. Only rarely does thymine occur in RNA or uracil in DNA. The structures of the five major bases are shown in Figure 8-2, and the nomenclature of their corresponding nucleotides and nucleosides is summarized in Table 8-1.

Nucleic acids have two kinds of pentoses. The recurring deoxyribonucleotide units of DNA contain 2'-deoxy-D-ribose, and the ribonucleotide units of RNA contain D-ribose. In nucleotides, both types of pentoses are in their ^-furanose (closed five-membered ring) form. As Figure 8-3 shows, the pentose ring is not planar but occurs in one of a variety of conformations generally described as "puckered."

Figure 8-4 gives the structures and names of the four major deoxyribonucleotides (deoxyribonucleo-side 5'-monophosphates), the structural units of DNAs, and the four major ribonucleotides (ribonucleoside 5'-monophosphates), the structural units of RNAs. Specific

Ribonucleoside

FIGURE 8-2 Major purine and pyrimidine bases of nucleic acids.

Some of the common names of these bases reflect the circumstances of their discovery. Guanine, for example, was first isolated from guano (bird manure), and thymine was first isolated from thymus tissue.

FIGURE 8-2 Major purine and pyrimidine bases of nucleic acids.

Some of the common names of these bases reflect the circumstances of their discovery. Guanine, for example, was first isolated from guano (bird manure), and thymine was first isolated from thymus tissue.

long sequences of A, T, G, and C nucleotides in DNA are the repository of genetic information.

Although nucleotides bearing the major purines and pyrimidines are most common, both DNA and RNA also

Ribose Ring Form And Straight Chain

FIGURE 8-3 Conformations of ribose. (a) In solution, the straight-chain (aldehyde) and ring (^-furanose) forms of free ribose are in equilibrium. RNA contains only the ring form, ^-D-ribofuranose. Deoxy-ribose undergoes a similar interconversion in solution, but in DNA exists solely as ^-2'-deoxy-D-ribofuranose. (b) Ribofuranose rings in nucleotides can exist in four different puckered conformations. In all cases, four of the five atoms are in a single plane. The fifth atom (C-2' or C-3') is on either the same (endo) or the opposite (exo) side of the plane relative to the C-5' atom.

FIGURE 8-3 Conformations of ribose. (a) In solution, the straight-chain (aldehyde) and ring (^-furanose) forms of free ribose are in equilibrium. RNA contains only the ring form, ^-D-ribofuranose. Deoxy-ribose undergoes a similar interconversion in solution, but in DNA exists solely as ^-2'-deoxy-D-ribofuranose. (b) Ribofuranose rings in nucleotides can exist in four different puckered conformations. In all cases, four of the five atoms are in a single plane. The fifth atom (C-2' or C-3') is on either the same (endo) or the opposite (exo) side of the plane relative to the C-5' atom.

8.1 Some Basics

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