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3.1 The chemical structures of DNA and RNA

Table 3.1 Nomenclature of the major bases and nucleosides found in DNA and RNA

5 end ′

– O

P O

O

Base

Deoxyribonucleoside

Ribonucleoside

N

Adenine Guanine Cytosine Thymine

Deoxyadenosine Deoxyguanosine Deoxycytidine

Adenosine Guanosine

O

NH

G

5 ′

CH 2

N N

NH 2

O

Cytidine

1 ′

4 ′

Deoxythymidine or Thymidine

_

Uracil

_

Uridine

3 ′

2 ′

O

– O

The nomenclature of nucleosides is derived from the names of the bases as shown in Table 3.1. Deoxythymidine is often simpli fied to thymidine, since the ribonucleotide equivalent is rarely found in cellular nucleic acids. Nucleotides are in turn named from the nucleoside, for example adenosine monophosphate (AMP), adenosine diphosphate (ADP), and deoxyadenosine triphosphate (dATP). The names are usually abbreviated, but it is worth learning the full versions from the table. PAUSE AND THINK Give the full names of the nucleotides that have the abbreviations dCTP, GDP, and TMP. DNA and RNA are linear polynucleotides in which an ester bond links the phosphate group of one nucleotide to the 3 ′ hydroxyl group of the next. Thus, the 5 ′ carbon of one sugar is linked to the 3 ′ carbon of the next by a phosphate and two ester bonds, a structure termed a phosphodiester bond or phosphodiester linkage. Figure 3.6 shows a short section of DNA consisting of four nucleotides in which the phosphodiester linkage is labelled. It also illustrates the polarity of polynucleotides. At one end of the molecule there is a 5 ′ phosphate that is not linked to another sugar, while at the other end there is a free 3 ′ hydroxyl group. The two ends are thus termed the 5 ′ and 3 ′ ends , respectively. Base pairing is crucial for the function of DNA and RNA Cellular DNA and RNA molecules vary greatly in length but can contain thousands or even, in the case of genomic DNA, millions of nucleotides. It is the order of the bases in DNA and RNA mol ecules that constitutes their information content. The feature of base structure that enables them to carry the information for cod ing proteins and have the capacity to direct their own replication is their capacity for complementary base pairing . Erwin Chargaff, working in the 1940s, established that the four nucleotides are not necessarily present in DNA in equal amounts, but in any DNA sample the ratio of purines to pyrimidines is approximately 1:1. Moreover, he found that the number of adenine molecules is equal to the number of thymine molecules and the number of guanine

P O

NH 2

N

O

N

A

CH 2 O

N

N

O

– O

P O

O

H 3 C

NH

O

T

O

N

CH 2 O

Answer: Deoxycytidine triphosphate, guanosine diphosphate, and thymidine monophosphate.

O

NH 2

– O

P O

N

O

C

N O

CH 2 O

5

1 ′

4 ′

3 ′

2 ′

O

3 end ′

molecules is equal to the number of cytosine molecules. Chargaff’s ‘rules’ provided an important clue to the scientists who determined the three-dimensional structure of DNA. The ratios observed by Chargaff are explained by the observation that pairs of bases have the capacity to hydrogen bond with each other, forming specific purine–pyrimidine pairs: A with T (or with U in RNA) and G with C (see Figure 3.7). These hydrogen-bonded structures are known as Watson–Crick base pairs. Figure 3.6 A short length of a single strand of DNA, showing the 5 ′ and 3 ′ ends. An individual nucleotide, thymine (T), is in enclosed in a box and one phosphodiester bond is highlighted. Source : Alberts et al. Essential Cell Biology , Edn 4. Garland Science, 2014.

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