Structure of ribosomes

Ribosomes are cellular particles having an average diameter of 23 nm (1 nm = 10 Å). In E. coli, these are made up of 66% ribosomal RNA (rRNA) and of several kinds of proteins (34%). Since these particles are rich in RNA content, these were called 'ribosomes'. These ribosomes form only a part of what was earlier called microsome fraction by A. Claude in 1943. Since ribosomes'were observed on ER (endoplasmic reticulum) surface in eukaryotes, it was believed for sometime that ribosomes are an integral part of endoplasmic reticulum. However, ribosomes can also be found free in cytoplasm. The attached and free forms of ribosomes are actually interchangeable and correspond to rough and smooth endoplasmic reticula.

Ribosomes are also-often observed in clusters and under these conditions are known as 'polyribosomes', or 'polysomes' rarely also known as ergosomes. The polyribosomes consist of those ribosomes which are actively engaged in protein synthesis and are held together by a string known as mRNA (Fig. 31.8). The dissociation of ribosomes in their subunits and their association to form ribosomes again, are related to their function in protein synthesis. Molecular organization of ribosomes and their function has been studied more intensively in prokaryotes than in eukaryotes, so that their structure and function will be discussed in this section in prokaryotes and important differences found in eukaryotes will be outlined.

Ultrastructure. (a) Ribosomal subunits.A ribosome consists of two subunits, a smaller subunit and a bigger subunit (Fig. 31.9). Association and dissociation of these subunits depend on Mg⁺⁺ ion concentration. If the Mg⁺⁺ ion concentration is lowered, subunits fall apart, while addition of Mg⁺⁺ ion will promote association of subunits into complete ribosomes. If Mg⁺⁺ ion concentration is increased ten fold, two ribosomes combine to form a dimer having a molecular weight twice that of an individual ribosome (Fig. 31.10).

In bacterial cells as well as in chloroplasts of higher plants, sedimentation coefficient of complete ribosomes is 70S, that of smaller subunit is 30S and that of bigger subunit is 50S. In higher organisms, sedimentation coefficient of ribosomes is 80S and those of subunits are 40S and 60S (Table 31.3). The ribosomes in mitochondria of higher organisms vary in size. In plant mitochondria, they are only little smaller than the ribosomes in surrounding cytoplasm (in maize mitochondria, 78S). In mitochondria of lower eukaryotes (e.g. fungi), these are slightly larger than in E. coli (73S in yeast), and in mammalian mitochondria they are much smaller (60S in Xenopus and human mitochondria).


Fine structure of the ribosome is very complex. RNA and proteins are intertwined and arranged in a complex manner in two subunits. Negative staining of isolated ribosomes and their subunits has led to a better understanding of fine structure of this organelle. Different models for the three dimensional structure of ribosome have been proposed in the past. However, the latest and most acceptable model based on electron microscopy was given by J.A. Lake (Scientific American, February, 1981). According to this model, small subunit consists of a head, a base and a platform. Larger subunit, similarly, included a central protuberance, which is flanked on one side by a ridge, and on the other side by a stalk. The association of two subunits and details of their structures according to this model in two different orientations are shown in Figures 31.11 and 31.12. During the years 1982-84, it was shown that atleast four different three-dimensional structures of ribosomes are known one each in eubacteria, archaebacteria, sulphur dependent archaebacteria and in eukaryotes. These structures are only variants of the sarne basic plan shown in Figure 31.11.

(b) Chemical composition. The major components of ribosomes are RNA and proteins. In an entire ribosome, rRNA makes 66% part in prokaryotes and 60% in eukaryotes. In subunits, the proportion of rRNA is larger in larger subunit (70% in prokaryotes and 65% in eukaryotes) than in the smaller subunit (60% in prokaryotes and 50% in eukaryotes). There is no lipid content in ribosomes. The positive charges are not enough to neutralize the negative charges of RNA, so that the ribosomes are strongly negative, binding cations and basic dyes.

The 30S and 50S subunits in prokaryotes may be dissociated to give rise to inactive core particles having sedimentation coefficients of 23S and 40S respectively. These particles (23S and 40S) contain RNA (16S and 23S respectively) and some core proteins. These RNAs in eukaryotes form 28S and 18S particles instead of 23S and 16S as observed in prokaryotes (Table 31.3; Fig. 31.13). Besides these core proteins, there are other proteins called split proteins (SP) in both subunits, which can be further fractionated into acidic and basic proteins. In all, 21 proteins were isolated in smaller subunit (30S) of E. coli ribosome. These are designated as SI to S21. Similarly, in larger subunit (50S) of E. coli ribosome, 31 different proteins are designated as LI to L34 (due to early misassignment, these are not designated LI to L31). In eukaryotes, however, there are 33 proteins in the smaller subunit (40S) and 45 proteins in larger subunit (60S). The sequences of bases in rRNAs and those of amino acids in most ribosomal proteins have also been determined. The organization of these proteins in ribosomes and their relative roles were studied in great detail during 1980s.

When RNA of ribosome was analysed in detail, it could be demonstrated that 60 per cent of RNA is helical (double stranded) and contains paired bases due to intrastrand complementary base pairing (Fig. 31.14). In Escherichia coli, the sequences of 23S and 16S RNAs have been analysed and were found to be specific showing no homology. The larger subunit contains an additional RNA (5S both in prokaryotes and eukaryotes and 5.8S in eukaryotes only). Complete sequence of 5S RNA is now known in E. coli and many eukaryotes and it was shown that 5S RNA is needed for correct assembly of larger subunit.

Dissociation and re constitution. In recent years, it has been possible to dissociate the ribosomal proteins completely, which could be followed by reconstitution of their structure and function. While dissociation is achieved by gradient centrifugation, reconstitution is brought about by adding.rRNAs to corresponding proteins. The steps involved in reconstitution are shown in Figure 31.15.

Reconstitution experiment showed that while some ribosomal proteins play structural role, others play specific functional roles. Location of important proteins and rRNA of ribosomes are shown in Figure 31.16 and several active centres are shown in Figure 31.17. For rRNA, it has been shown that there are common sequences in mRNAs, which pair with a sequence of rRNA, thus helping in mRNA-ribosome binding. It has also been shown that ribosomes are able to distinguish between the entry of correct and incorrect amino acyl-tRNA-EF-Tu-GTP complexes. The three proteins, which help in this function are S-4, S-5 and S-12, as shown with the help of mutations, which make the ribosomes resistant to streptomycin. It has been shown that in susceptible ribosomes, misreading occurs in the presence of streptomycin, but this misreading is reduced in the resistant ribosomes, which have alterations in either protein S-4 or S-5 or S-12.

Biogenesis. The complex organization of ribosome as described earlier, involves specific rRNA (ribosomal RNA) and 50 or more proteins, suggesting that atleast more than 50 genes may be involved in their formation. In bacteria, the genes for 5S, 23S and 16S rRNAs are clustered in one region to form a single operon (for operon model, consult Regulation of Gene Expression 1.  Operon Circuits in Bacteria and other Prokaryotes) working as a functional unit. In eukaryotes, however, the biogenesis of ribosomes is more complex involving several regions of the cell. The 18S and 28S rRNA molecules are synthesized as much bigger molecules in the nucleolar organizer which has multiple copies of DNA responsible for rRNA. The DNA responsible for 5S rRNA is also repetitive (with many copies) but is synthesized outside the nucleolus. Formation of rRNA is coupled with formation of different ribosomal proteins which are synthesized in the cytoplasm. However, most of the subunits of ribosomes are processed in the nucleolus and delivered to the cytoplasm, suggesting a key role of nucleolus in the biogenesis of ribosomes. The detailed structure of nucleolus and its role in rRNA synthesis and assembly of ribosomes is discussed earlier in Physical Basis of Heredity 1.  The Nucleus and the Chromosome.

For the synthesis of rRNA, a transcription initiation factor TIFI is needed, which brings RNA polymerase I to the promoter region (for more details consult Expression of Gene : Protein Synthesis 2.  Transcription in Prokaryotes and Eukaryotes). RNA polymerase I synthesizes precursor rRNA. Ribosomal proteins (rps), about 50 in number, then associate to rRNA gene transcripts. 43S and 48S small nuclear RNAs (SnRNAs), 5S RNA and several acidic proteins are also required for the maintenance of nucleolar structure as well as for assembly and transport of proribosomes. Coregulation of gene transcription maintains regular supply of these components according to demand.

The synthesis of ribosomal RNA on nucleolar genes is shown in the electron microscopic photograph in Figure 31.18. Initially rRNA is synthesized as a 45S molecule, which appears within 2.2 minutes and later gives rise to 41S and 20S rRNAs due to enzymatic action (enzyme endonuclease is utilized). While 41S molecule forms 28S rRNA due to exonuclease action, 20S molecule gives rise to 18S molecule (Fig. 31.19).