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Deoxyribonucleic acid is an extremely long polymer made from monomeric units called deoxyribonucleotides (dNTPs), which are often simply called nucleotides. Nucleotides are made up of three components: a base, a sugar, and a phosphate group. Figure 3.1 shows a deoxyribonucleotide, deoxyadenosine triphosphate, on the left. On the right is the corresponding ribonucleotide, adenosine triphosphate or ATP. As mentioned in Chapter 2, ATP is the cell's primary energy currency. As we will see in Chapter 5, ATP also plays a critical role as one of the four nucleotides in RNA, taking the place of the deoxyadenosine triphosphate in DNA. Note that deoxyribose, unlike ribose, has no hydroxyl (OH) group on its 2′ carbon.

Four bases are found in DNA; they are the two purines guanine (G) and adenine (A) and the two pyrimidines thymine (T) and cytosine (C) (Figure 3.2). The lines represent covalent bonds formed when atoms share electrons, each seeking the most stable structure.

The combined base and sugar is known as a nucleoside to distinguish it from the phosphorylated form, which is called a nucleotide. Four different nucleotides are used to make DNA. They are 2′‐deoxyguanosine‐5′‐triphosphate (dGTP), 2′‐deoxyadenosine‐5′‐triphosphate (dATP), 2′‐deoxythymidine‐5′‐triphosphate (dTTP), and 2′‐deoxycytidine‐5′‐triphosphate (dCTP).

DNA molecules are very large. The single chromosome of the bacterium Escherichia coli is made up of two strands of DNA that are hydrogen‐bonded together to form a single circular molecule comprising 9 million nucleotides. DNA molecules in eukaryotes are even larger: the DNA molecules in humans comprise on average 260 million nucleotides, and a cell has 46 of these massive molecules, each forming one chromosome. We inherit 23 chromosomes from each parent. Each set of 23 chromosomes encodes a complete copy of our genome and is made up of 6 × 10⁹ nucleotides (or 3 × 10⁹base pairs – see below).

Figure 3.3 illustrates the structure of the DNA chain. As nucleotides are added to the chain by the enzyme DNA polymerase (Chapter 4), they lose two phosphate groups. The last (the α phosphate) remains and forms a phosphodiester bond between successive deoxyribose residues. This bond is formed between the hydroxyl group on the 3′ carbon of the deoxyribose of the last nucleotide in the DNA chain and the α‐phosphate group attached to the 5′ carbon of the nucleotide that the polymerase will add to the chain. The linkage gives rise to the sugar‐phosphate backbone of a DNA molecule. A DNA chain has polarity because its two ends are different. In the first nucleotide in the chain, the 5′ carbon of the deoxyribose is phosphorylated but otherwise free. This is called the 5′ end of the DNA chain. At the other end is a deoxyribose with a free hydroxyl group on its 3′ carbon. This is the 3′ end.