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3.1 The chemical structures of DNA and RNA

Nucleotides are the building blocks of DNA and RNA Nucleic acids are polymers of nucleotides , which each consist of a pentose sugar, a nitrogenous base, and one or more phosphates, as shown in Figure 3.2. A nucleoside is a sugar plus base, while the addition of phosphate makes it a nucleotide. Figure 3.3 shows the structures of the pentose sugars found in DNA and RNA in more detail. The carbons are numbered 1 ′ , 2 ′ , 3 ′ , etc. using the ′ or ‘prime’ symbol to distinguish them from carbons in the nitrogenous bases, which are numbered simply 1, 2, 3, etc. The pentose sugar is 2 ′ -deoxyribose in deoxyribonucleotides or ribose in ribonucleotides. The difference is that 2 ′ -deoxyribose (often simply termed deoxyribose) lacks a hydroxyl group on the 2 ′ carbon. We can envisage each of the bonds that link the phosphate and the base to the pentose sugar as being formed through the loss of a molecule of water, as shown in Figure 3.4. The actual biochemi cal reactions by which nucleotides are synthesized in the cell are a lot more complex than this, but the simplification is helpful to understand the structure of the nucleotide and the nomencla tures used for the bonds. Phosphates are salts of phosphoric acid. Therefore, the bond that links the phosphate to the sugar in nucle ic acids forms between an acid (phosphoric acid) and an alco hol (the hydroxyl group attached to the 5 ′ carbon of the pentose ring), making it an ester or phosphoester bond (Figure 3.4). Note that the bonds between linked phosphates are termed phospho anhydride bonds (Figure 3.2). The bond between the sugar and the base is a bond between a carbohydrate (the sugar) and another molecule, making it a glycosidic bond.

5’

HOCH 2 O OH C H H

HOCH 2 O OH C 1’ C 2’ 3’ C 3 OH OH H H 4’ C H H

H C

H

C C OH H

2-Deoxyribose

Ribose

Figure 3.3 The structures of 2 ′ -deoxyribose and ribose, the pentose sugars found in DNA and RNA, respectively. The carbons are numbered 1 ′ , 2 ′ , 3 ′ , etc. Note that the structures are identical except that 2 ′ -deoxyribose (often simply termed deoxyribose) lacks a hydroxyl group on the 2 ′ carbon.

As also shown in Figure 3.4, at cellular pH the phosphates are negatively charged through the loss of protons from their unbond ed hydroxyl groups. This ability to donate protons explains the acidic nature of DNA and RNA. Nitrogenous bases are ringed structures, which are classified as purines if based on a double-ringed structure, and pyrimidines if they are single-ringed. Each nucleotide of DNA contains one of four bases, as shown in Figure 3.5. RNA also contains three of these four bases, but it contains uracil as a fourth base instead of thymine. Additional unusual and modified bases with specific functions do occur in cellular DNA and RNA, but adenine (A), guanine (G), cytosine (C), thymine (T), and uracil (U) are the fun damental five.

(a)

(b)

Deoxyribonucleotide

Ribonucleotide

O–

O–

–

O

O–

P

P

O

O

O–

O

–

O

O–

P

P

NH 2

NH 2

O

C C C N N

H

O

N

H

O–

O

–

O

C

O–

C

C

P

P

CH 2

O

CH 2

O

N

O

N

C

N

O

C

O

O

C

C

H H

C

C

H H

C

N

C

N

H

H

H

H

H

H

OH OH

OH H

triphosphate

ribose

adenine

triphosphate deoxyribose

adenine

adenosine

adenosine

Figure 3.2 The structural formula of a nucleotide. (a) A deoxyribonucleotide (component of DNA). (b) A ribonucleotide (component of RNA). Each nucleotide contains a pentose (five carbon) sugar (blue), a nitrogenous base (green), and one to three phosphates (yellow). In these examples the base is adenine and there are three phosphates, making these nucleotides deoxyadenosine triphosphate (dATP) and adenosine triphosphate (ATP) respectively. The difference between the deoxyribonucleotide and the ribonucleotide is in the structure of the sugar, highlighted in red. Further details of the structures and nomenclature of nucleotides are explained in the text. Source : Alberts et al. Essential Cell Biology , Edn. 4. Garland Science.

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