Polynucleotide chains have nitrogenous bases linked to a sugar-phosphate backbone

KEY TERMS:

• A nucleoside consists of a purine or pyrimidine base linked to position 1 of a pentose sugar.
• Positions on the ribose ring are described with a prime () to distinguish them.
• The difference between DNA and RNA is in the group at the 2 position of the sugar. DNA has a deoxyribose sugar (2–H); RNA has a ribose sugar (2–OH).
• A nucleotide consists of a nucleoside linked to a phosphate group on either the 5 or 3 position of the (deoxy)ribose.
• Successive (deoxy)ribose residues of a polynucleotide chain are joined by a phosphate group between the 3 position of one sugar and the 5 position of the next sugar.
• One end of the chain (conventionally the left) has a free 5 end and the other end has a free 3 end.
• DNA contains the four bases adenine, guanine, cytosine, and thymine; RNA has uracil instead of thymine. 

The basic building block of nucleic acids is the nucleotide. This has three components:

• a nitrogenous base;
• a sugar;
• and a phosphate.

The nitrogenous base is a purine or pyrimidine ring. The base is linked to position 1 on a pentose sugar by a glycosidic bond from N₁ of pyrimidines or N₉ of purines. To avoid ambiguity between the numbering systems of the heterocyclic rings and the sugar, positions on the pentose are given a prime ().

Nucleic acids are named for the type of sugar; DNA has 2–deoxyribose, whereas RNA has ribose. The difference is that the sugar in RNA has an OH group at the 2 position of the pentose ring. The sugar can be linked by its 5 or 3 position to a phosphate group.

A nucleic acid consists of a long chain of nucleotides. Figure 1.7 shows that the backbone of the polynucleotide chain consists of an alternating series of pentose (sugar) and phosphate residues. This is constructed by linking the 5 position of one pentose ring to the 3 position of the next pentose ring via a phosphate group. So the sugar-phosphate backbone is said to consist of 5–3 phosphodiester linkages. The nitrogenous bases "stick out" from the backbone.

Each nucleic acid contains 4 types of base. The same two purines, adenine and guanine, are present in both DNA and RNA. The two pyrimidines in DNA are cytosine and thymine; in RNA uracil is found instead of thymine. The only difference between uracil and thymine is the presence of a methyl substituent at position C₅. The bases are usually referred to by their initial letters. DNA contains A, G, C, T, while RNA contains A, G, C, U.

The terminal nucleotide at one end of the chain has a free 5 group; the terminal nucleotide at the other end has a free 3 group. It is conventional to write nucleic acid sequences in the 5→3 direction—that is, from the 5 terminus at the left to the 3 terminus at the right.