In the sixty years since the publication of Watson and Crick’s paper, we have all become familiar with the iconic double helix of DNA. The elegant shape of the twisting strands relies on the structure of DNA’s subunits, called nucleotides. As we saw in Chapter 2, nucleotides consist of three components: a 5-carbon sugar, a base, and one or more phosphate groups (Fig. 3.4). Each component plays an important role in DNA structure. The 5-carbon sugars and phosphate groups form the backbone of the molecule, with each sugar linked to the phosphate group of the neighboring nucleotide. The bases sticking out from the sugar give each nucleotide its chemical identity. Each strand of DNA consists of an enormous number of nucleotides linked one to the next.

DNA had been discovered 85 years before its three-dimensional structure was determined, and in the meantime a great deal had been learned about its chemistry, specifically the chemistry of nucleotides. Fig. 3.4 illustrates a nucleotide. In the figure, the 5-carbon sugar is indicated by the pentagon, in which four of the five vertices represent the position of a carbon atom. By convention the carbon atoms of the sugar ring are numbered clockwise with primes (1′, 2′, and so forth, read as “one prime,” “two prime,” and so forth). Technically, the sugar in DNA is 2′-deoxyribose because the chemical group projecting downward from the 2′ carbon is a hydrogen atom (–H) rather than a hydroxyl group (–OH), but for our purposes the term deoxyribose will suffice.

Note in Fig. 3.4 that the phosphate group attached to the 5′ carbon has negative charges on two of its oxygen atoms. These charges are present because at cellular pH (around 7), the free hydroxyl groups attached to the phosphorus atom are ionized by the loss of a proton, and hence are negatively charged. It is these negative charges that make DNA a mild acid, which you will recall from Chapter 2 is a molecule that tends to lose protons to the aqueous environment.

Each base is attached to the 1′ carbon of the sugar and projects above the sugar ring. A nucleotide normally contains one of four kinds of bases, denoted A, G, T, and C (Fig. 3.5). Two of the bases are double-ring structures known as purines; these are the bases adenine (A) and guanine (G), shown across the top of the figure. The other two bases are single-ring structures known as pyrimidines; these are the bases thymine (T) and cytosine (C), shown across the bottom.

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The combination of sugar and base is known as a nucleoside, which is shown in simplified form in Fig. 3.6. A nucleoside with one or more phosphate groups constitutes a nucleotide. More specifically, a nucleotide with one, two, or three phosphate groups is called a nucleoside monophosphate, diphosphate, or triphosphate, respectively (Fig. 3.6). The nucleoside triphosphates are particularly important because, as we will see later in this chapter, they are the molecules that are used to form nucleotide polymers: DNA and RNA. In addition, nucleoside triphosphates have other functions in the cell, notably as carriers of chemical energy in the form of ATP and GTP.