Ribosomal RNA

Particles containing approximately 65% RNA and 35% protein have been isolated from the cells of all organisms including bacteria and these particles are called ribosomes. The ribosome behaves like a small migrating factory that travels along the mRNA template engaging in a rapid cycle of peptide bond synthesis. Ribosomes are major cellular components; in an actively growing bacterium there are roughly 20,000 ribosomes containing 10 % of the total bacterial protein. In eukaryote cells, their proportion is less, but their absolute number is greater. The number of ribosomes is directly related to the protein synthesising activity of the cell. The ribosomes of higher eukaryotic cytoplasm are larger than the bacterial ribosomes. The total content of both RNA and protein is greater; the major RNA molecules are longer and there are more proteins. Eukaryotic cell ribosomes are associated with the endoplasmic reticulum during protein synthesis.

Ribosomes are traditionally described in terms of their (approximate) rate of sedimentation in Svedberg units (S) which is 70S for prokaryotes and 80S for eukaryotes. These ribosomes can be separated by Mg+2 concentration into two smaller molecular weight components (Prokaryotes 30S and 50S or eukaryotes 40S and 60S). These two subunits work together as part of the complete ribosome but each undertakes distinct reactions in protein synthesis. Each containing a major ribosomal RNA (rRNA) molecules and a number of proteins. The small ribosomal subunit contains a single type of rRNA and about 20 proteins in prokaryotes or 30 protein in eukaryotes. The large subunit contains two (prokaryotes) or three (eukaryotes) rRNA and about 30 (prokaryotes) to 40 (eukaryotes) ribosomal proteins. Increasing Mg+2 concentration brings these two molecules together. Only the complete particle functions in polypeptide synthesis.

Each subunit contains a single major rRNA, 16S and 23S for prokaryotes, 18S and 28S in eukaryotic cytosol. There are also minor rRNAs most notably 5S in the large subunit and the eukaryotes have two minor rRNA 5S -5.8S. Both major rRNAs have extensive base pairing, mostly in the form of short, imperfectly paired duplex stems with single stranded loops. Conserved features in the rRNA can be identified by comparing sequences and secondary structures that can be drawn up for a variety of organisms.

In eukaryotes, two internal transcribed spacer (ITS1 and ITS2) separate the 18S, 5.8S and 28S loci (or their homologeus) and an external transcribed spacer (ETS) is located upstream of the 18S gene. The transcribed spacers contains signals for processing the rRNA transcript. Adjacent copies of the rDNA repeat unit are seperated by a nontranscribed spacer (NTS or intergenic spacer).

The evolutionary consequences of mutation differ in each of the segments of rDNA. The length of the rDNA unit varies between different eukaryotic species, ranging from 6.8 kb to 44 kb. Much of the variability in length can be accounted for by the differences in the ETS. The number of rDNA copies also varies between eukaryotic species from a single chromosomal copy to thousands.