The ribosome is the large macromolecular machine responsible for translation of the genetic code from nucleic acid into protein. It ranges in mass from 2.5 million daltons in bacteria to more than 4 million daltons in eukaryotic cells. In both cases approximately two-thirds of this mass is RNA and about one-third is protein. The RNA component is important not only in its relative contribution to the mass of the ribosome: it also plays the central part in its function. The ribosome is thus one of a growing number of macromolecular machines known to have essential RNA components widely thought to reflect the early evolution of life in an RNA world. Not surprisingly, given their fundamental role in the decoding of genetic information, ribosomes are highly conserved both in structure and in function.

The outline structure and the components of the ribosome are illustrated schematically in Figure 11-3.1. Ribosomes were first identified as large macromolecular complexes before their function was established, and were termed the 70S particle (in the case of bacterial ribosomes) and the 80S particle (in the case of eukaryotic ribosomes) at a time when all that was known about them was the speed at which they sedimented in the ultracentrifuge: S stands for Svedberg, a unit of sedimentation velocity. This terminology is still used for the different components of the ribosome and sometimes for the ribosome itself and its subunits (Figure 11-3.1).

All ribosomes are composed of two subunits (Figure 11-3.1): a small subunit that mediates the decoding interaction between the mRNA codon and the tRNA anticodon, and a large subunit that catalyzes peptide bond formation. These distinct events are integrated at the subunit interface of the ribosome where the tRNA substrates bind (Figure 11-3.2). To sequentially add amino acids to a growing polypeptide chain, the ribosome undergoes gross movements that shift the position of the tRNA-mRNA complex. These movements, termed translocation, occur at the subunit interface and must be coordinated by the RNA-RNA, RNA-protein and protein-protein bridges between the large and small subunits.

The mechanism by which these interactions between the large and the small subunit contribute to the decoding of the mRNA is described in the next sections, where we shall see that the crucial part played by the rRNAs is reflected in their remarkably conserved secondary and tertiary structure. Certain nucleotide stretches in the rRNAs are conserved across all species: for example 16 of 17 contiguous nucleotides in 16S rRNA are more than 95% conserved across the three kingdoms of life. Some ribosomal proteins also are highly conserved, and these probably are those most critical to ribosome function; other ribosomal proteins are not present in all species.

Atomic structures of both the small and the large subunits of the ribosome have been obtained by X-ray crystallography and help us to understand how the different components contribute to its central functions. The interface between the small and large subunits of the ribosome is rich in ribosomal RNA (rRNA) elements and relatively poor in ribosomal proteins (Figure 11-3.2). On the exterior (solvent) side of the particle, ribosomal proteins are more evenly distributed. A number of the ribosomal proteins have unusual structures, consisting of globular domains embedded in the exterior face of the particle with long extended arms that snake their way into the core of the rRNA structure. These arms are generally enriched in basic amino acids and are thought to act as mortar in packing the negatively charged rRNA phosphate backbone into a compact tertiary structure.

Biochemical and genetic evidence long pointed to a critical role for rRNA in translation. The crystal structures of both ribosomal subunits confirm that rRNA is the primary component in the functional centers at the interface of the ribosomal subunits where the tRNA substrates bind and interact (Figure 11-3.2). Binding of model tRNA substrates (that represent the CCA-ends of the aminoacylated tRNAs) to the large ribosomal subunit crystals identified the active site for peptide bond formation. There are no protein elements within 18 Å of the region where peptide bond formation must occur. Thus, the ribosome is a ribozyme providing critical evidence for the existence of an RNA world early in evolution.

The large rRNAs from the two ribosomal subunits can be subdivided into distinct regions, or domains, based on their secondary structures. The 16S (or 18S in eukaryotes) rRNA is divided into three major and one minor domain whereas the 23S (or 28S) rRNA is divided into 6 different domains. The organization of the rRNA domains in the two subunits is strikingly different. In the small subunit, each rRNA domain is largely limited to one area of the subunit: the body, the platform, the head, or the penultimate stem. In contrast, the rRNA elements in the large subunit are intricately interwoven (Figure 11-3.3). It has been suggested that this organization reflects the functional differences of the subunits: interdomain flexibility is suited to the large scale movements of translocation performed by the small subunit whereas stability provided by the interwoven RNA domains is suited to protection of the active site by the large subunit.

ribosomal protein: the protein component of the ribosome.

ribosomal RNA (rRNA): the RNA component of the ribosome.

ribosomal RNA domain: the secondary structural representation of the large ribosomal RNAs can easily be divided into smaller regions that are referred to as domains although this is a misnomer: these domains do not refer to an independent structural unit.

translocation: the defined three-nucleotide movement of the mRNA-tRNA complex through the interface region between the ribosomal subunits responsible for directional translation of a gene.