MoBio Building Blocks - Nucleotides Chapter 3

A nucleotide is composed of three parts: pentose, base and phosphate group. In DNA or RNA, a pentose is associated with only one phosphate group, but a cellular free nucleotide (such as ATP) may contain more than one phosphate group. If all phosphate groups are removed, a nucleotide becomes a nucleoside.

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Figure 3-A-1. The general structure of nucleotides. Left: computer model. Right: a simplified representation.

Pentose

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Figure 3-A-2. The chemical structure of pentose which contains five carbon atoms, labeled as C1' to C5'. The pentose is called ribose in RNA and deoxyribose in DNA, because the DNA's pentose lacks an oxygen atom at C2'. Recalling that RNA stands for "ribonucleic acid", and DNA for "deoxyribonucleic acid".

Bases

There are five different bases, each is denoted by a single letter as given in the parenthesis:

Adenine (A), Cytosine (C), Guanine (G), Thymine (T), and Uracil (U).

Among them,

A, C, G and T exist in DNA;

A, C, G and U exist in RNA.

Their chemical structures are shown in the following figure. A and G contain a pair of fused rings, classified as purines. C, T, and U contain only one ring, classified as pyrimidines.

Figure 3-A-3. Chemical structures of bases in DNA and RNA. The red dot is connected to the pentose.

We note that the chemical structure of uracil is simpler than thymine. This gives a good reason why RNA uses uracil, instead of thymine. However, why does DNA use thymine? The major requirement in designing DNA bases is that they must be able to form pairs. But adenine can pair with uracil as perfectly as with thymine (see Section B). Then, why DNA chooses a more complex base? This question had been puzzling researchers for many years, until they understood the DNA repairing mechanism (see Chapter 7 Section F).