FIGURE 6-4 Purines and pyrimidines.
The dotted lines indicate the sites of attachment ot the bases to the sugars. For simplicity, hydiogens are Omitted from the sugars and bases in subsequent figures, except where pertinent to the illustration.
through a 3'-hydroxyl and a second sugar esterified to it through a S'-hydroxyl. Phosphodiester linkages create the repeating, sugar-phosphate backbone of the polynucleotide chain, which is a regtdar feature of DNA. In contrast, the order of the bases along the polynucleotide chain is irregular. This irregularity as well as the long length is, as we shall see, the basis for the enormous information content of DNA.
The phosphodiester linkages impart an inherent polarity to the DNA chain. This polarity is defined by the asymmetry of the nucleotides and the way they are joined. DNA chains have a free 5'-phosphate or 5'-hydroxyl at one end and a free 3'-phosphate or 3'-hydroxyl at the other end. The convention is to write DNA sequences from the 5' end (on the left) to the 3' end, generally with a 5'-phosphate and a 3'-hydroxy!.
The bases in DNA fall into two classes, purines and pyrimidines. The purines are adenine and guanine, and the pyrimidines are cytosine and thymine. The purines are derived from the double-ringed structure shown in Figure 6-4. Adenine and guanine share this essential structure but with different groups attached. Likewise, cytosine and thymine are variations on the single-ringed structure shown in Figure 6-4. The figure also shows the numbering of the positions in the purine and pyrrolidine rings. The bases are attached to the deoxyribose by glycosidic. linkages at N1 of the pyrimidines or at N9 of the purines.
Each of the bases exists in two alternative tautomeric states, which are in equilibrium with each other. The equilibrium lies far to the side of the conventional structures shown in Figure 6-4, which are the predominant states and the ones important for base pairing. The nitrogen atoms attached to the purine and pyrtmidine rings are in the amino form in the predominant slate and only rarely assume the imino configuration. Likewise, the oxygen atoms attached to the guanine and thymine normally have the keto form and only rarely take on the enol configuration. As examples, Figure 6-5 shows tautomerization of cytosine into the imino form (a) and guanine into the enol form (b). As we shall see, the capacity to form an alternative tautomer is a frequent source of errors during DNA synthesis.
The Two Strands of the Double Helix Are Held Together by-Base Pairing in an Antiparalle! Orientation
The double helix is composed of two polynucleotide chains that are held together by weak, noncovalent bonds between pairs of bases, as shown in Figure 6-3. Adenine on one chain is always paired with thymine on the other chain and, likewise, guanine is always paired with cytosine. The two strands have the same helical geometry but base pairing holds them together with the opposite polarity. That is. the base at the 5' end of one strand is paired with the base at the 3' end of the other strand. The strands are said to have an antiparallel orientation. This antiparallel orientation is a stereochemical consequence of the way that adenine and thymine, and guanine and cytosine, pair with each together.
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