The primary structure of DNA consists of a string of nucleotides joined together by phosphodiester linkages.

NUCLEOTIDES DNA is typically a very long molecule and is therefore termed a macromolecule. For example, within each human chromosome is a single DNA molecule that, if stretched out straight, would be several centimeters in length, thousands of times longer than the cell itself. In spite of its large size, DNA has quite a simple structure: it is a polymer—that is, a chain made up of many repeating units linked together. The repeating units of DNA are nucleotides, each comprised of three parts: (1) a sugar, (2) a phosphate group, and (3) a nitrogen-containing base.

The sugars of nucleic acids—called pentose sugars—have five carbon atoms, numbered 1′, 2′, 3′, and so forth (Figure 8.7). The sugars of DNA and RNA are slightly different in structure. RNA’s sugar, called ribose, has a hydroxyl group (—OH) attached to the 2′-carbon atom, whereas DNA’s sugar, or deoxyribose, has a hydrogen atom (—H) at this position and therefore contains one oxygen atom fewer overall. This difference gives rise to the names ribonucleic acid (RNA) and deoxyribonucleic acid (DNA). This minor chemical difference is recognized by most of the cellular enzymes that interact with DNA or RNA, thus providing specific functions for each nucleic acid. Furthermore, the additional oxygen atom in the RNA nucleotide makes it more reactive and less chemically stable than DNA. For this reason, DNA is better suited to serve as the long-term carrier of genetic information.

The second component of a nucleotide is its nitrogenous base, which may be either of two types: a purine or a pyrimidine (Figure 8.8). Each purine consists of a six-­member ring attached to a five-member ring, whereas each pyrimidine consists of a six-member ring only. Both DNA and RNA contain two purines, adenine and guanine (A and G), which differ in the positions of their double bonds and in the groups attached to the six-member ring. Three pyrimidines are common in nucleic acids: cytosine (C), thymine (T), and uracil (U). Cytosine is present in both DNA and RNA; however, thymine is restricted to DNA, and uracil is found only in RNA. The three pyrimidines differ in the groups or atoms attached to the carbon atoms of the ring and in the number of double bonds in the ring. In a nucleotide, the nitrogenous base always forms a covalent bond with the 1′-carbon atom of the sugar (see Figure 8.7). A deoxyribose or a ribose sugar and a base together are referred to as a nucleoside.

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The third component of a nucleotide is the phosphate group, which consists of a phosphorus atom bonded to four oxygen atoms (Figure 8.9). Phosphate groups are found in every nucleotide and frequently carry a negative charge, which makes DNA acidic. The phosphate group is always bonded to the 5′-carbon atom of the sugar (see Figure 8.7) in a nucleotide.

The DNA nucleotides are properly known as deoxyribonucleotides, or deoxyribonucleoside 5′-monophosphates. Because there are four types of bases, there are four different kinds of DNA nucleotides (Figure 8.10). The equivalent RNA nucleotides are termed ribonucleotides, or ribonucleoside 5′-monophosphates. RNA molecules sometimes contain additional rare bases, which are modified forms of the four common bases. These modified bases will be discussed in more detail when we examine the function of RNA molecules in Chapter 10. The names for DNA bases, nucleotides, and nucleosides are shown in Table 8.2. TRY PROBLEM 21

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POLYNUCLEOTIDE STRANDS DNA is made up of many nucleotides, which are connected by covalent bonds that link the 5′-phosphate group of one nucleotide to the 3′-hydroxyl group of the next nucleotide (Figure 8.11; it should be noted that the structures shown in this illustration are flattened into two dimensions, while the molecule itself is three-dimensional, as shown in Figure 8.12a). These bonds, called phosphodiester linkages, are strong covalent bonds; a series of nucleotides linked in this way constitutes a polynucleotide strand. The backbone of the polynucleotide strand is composed of alternating sugars and phosphates; the bases project away from the long axis of the strand. The negative charges of the phosphate groups are frequently neutralized by their association with positively charged proteins, metals, or other molecules.

An important characteristic of the polynucleotide strand is its direction, or polarity. At one end of the strand, a free phosphate group (meaning that it’s unattached on one side) is attached to the 5′-carbon atom of the sugar in the nucleotide. This end of the strand is therefore referred to as the 5′ end. The other end of the strand, referred to as the 3′ end, has a free OH group attached to the 3′-carbon atom of the sugar. RNA nucleotides are also connected by phosphodiester linkages to form similar polynucleotide strands (see Figure 8.11).