Structure of mRNA

2.5.1. Primary Structure

In contrast to DNA, messenger RNA, as well as other cellular RNA species, is a single-stranded polynucleotide. It consists of four kinds of linearly arranged ribonucleoside residues - adenosine (A), guanosine (G), cytidine (C), and uridine (U) -sequentially connected by phosphodiester bonds between the 3'-position of the ribose of one nucleoside and the 5'-position of the adjacent one (Fig. 2.3). The terminal nucleoside, the 5'-position of which does not participate in forming the internucleotide bond, is referred to as the 5'-end of RNA. The terminal nucleoside with free 3'-hydroxyl is referred to as the 3'-end. It is accepted practice to read and write RNA nucleotide sequences from the 5'- to the 3'-end, i.e. in the direction of the internucleotide phosphodiester bond from the 3'-position to the 5'-position of the neighbor (3'-P-5' bond direction). This direction corresponds to the polarity of mRNA readout by the ribosome.

The terminal 5'-position in natural mRNAs is always substituted. In prokaryotic organisms this end is either simply phosphorylated (Fig. 2.3) or carries the triphosphate group. Eukaryotic mRNAs generally have a special group, the so-called cap, at the terminal 5'-position (Furuichi & Miura, 1975; Furuichi et al., 1975). The cap is the N'-methylated residue of guanosine 5'-triphosphate linked with the 5'-terminal nucleoside by the 5'-5' pyrophosphate bond (Fig. 2.4). Eukaryotic cells possess a special system including guanylyl transferase and methyl transferase, enzymes that are responsible for mRNA capping. In addition, the capping is usually accompanied by methylation of the 2'-hydroxyl group of ribose and the base in the 5'-terminal nucleoside adjacent to the cap. Often the 5'-terminal residue in mRNA is a purine nucleoside, either G or A.

The 3'-terminal hydroxyl of natural mRNA remains unsubstituted. Thus, this end possesses two hydroxyl groups in cis-position (cis-glycol group) (see Fig. 2.3).

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