A ribosome () is a ribonucleoprotein particle found in all cells that synthesizes proteins by translating genetic information encoded in messenger RNA (mRNA). During translation, the ribosome decodes successive codons in an mRNA molecule and, with the aid of transfer RNA (tRNA), links amino acids into a polypeptide chain. Each ribosome comprises a small and a large subunit, each composed of one or more ribosomal RNA (rRNA) molecules and many ribosomal proteins.
Ribosomes differ in size, composition and organization among bacteria, archaea and eukaryotes, but they share a core structure that reflects a common evolutionary origin. Distinct ribosomes are also found in eukaryotic mitochondria and, in plants and algae, chloroplasts. Ribosomes are assembled through ribosome biogenesis, which involves rRNA synthesis and processing together with the assembly of ribosomal proteins into functional subunits.
First observed by George Emil Palade in 1955, ribosomes have been the subject of extensive structural and functional research. Their discovery was recognized by the Nobel Prize in Physiology or Medicine in 1974, while determination of their atomic structure and mechanism through X-ray crystallography and cryo-electron microscopy was recognized by the Nobel Prize in Chemistry in 2009.
Overview The sequence of RNA that encodes the sequence of the amino acids in a protein is transcribed into a messenger RNA (mRNA) chain. Ribosomes bind to the messenger RNA molecules and use the RNA's sequence of nucleotides to determine the sequence of amino acids needed to generate a protein. Amino acids are selected and carried to the ribosome by transfer RNA (tRNA) molecules, which enter the ribosome and bind to the messenger RNA chain via an anticodon stem loop. For each coding triplet (codon) in the messenger RNA, there is a unique transfer RNA that must have the exact anti-codon match, and carries the correct amino acid for incorporating into a growing polypeptide chain. Once the protein is produced, it can then fold to produce a functional three-dimensional structure.
During translation the synthesis of proteins from their building blocks takes place in four stages: initiation, elongation, termination, and ribosome recycling. The start codon in all mRNA molecules has the sequence AUG. The stop codon may either be UAA, UAG, or UGA; since there are no tRNA molecules that recognize these codons, the ribosome recognizes that translation is complete. When a ribosome finishes reading an mRNA molecule, the two subunits separate and are usually broken up but can be reused. Ribosomes are a kind of enzyme, called ribozymes because the catalytic peptidyl transferase activity that links amino acids together is performed by the ribosomal RNA.
Ribosomes from bacteria, archaea, and eukaryotes (in the three-domain system) resemble each other to a remarkable degree, evidence of a common origin. They differ in their size, sequence, structure, and the ratio of protein to RNA. The differences in structure allow some antibiotics to kill bacteria by inhibiting their ribosomes while leaving human ribosomes unaffected. In all domains, a polysome of two or more ribosomes may move along a single mRNA chain at one time, each reading a specific sequence and producing a corresponding protein molecule.
The mitochondrial ribosomes (mitoribosomes) of eukaryotic cells are distinct from the other ribosomes. They functionally resemble those in bacteria, reflecting the evolutionary origin of mitochondria as endosymbiotic bacteria.
Discovery Ribosomes were first observed in the mid-1950s as dense particles or granules by Romanian-American cell biologist George Emil Palade, using an electron microscope. They were initially called Palade granules due to their granular structure. They were initially called Palade granules due to their granular structure. The term "ribosome" was proposed in 1958 by Howard M. Dintzis:
Albert Claude, Christian de Duve, and George Emil Palade were jointly awarded the Nobel Prize in Physiology or Medicine, in 1974, for the discovery of the ribosome. The Nobel Prize in Chemistry 2009 was awarded to Venkatraman Ramakrishnan, Thomas A. Steitz, and Ada E. Yonath for determining the detailed structure and mechanism of the ribosome.
Structure
A ribosome is a ribonucleoprotein particle made from complexes of ribosomal RNAs and proteins, arranged into two ribosomal subunits, one large and the other small. Ribosomes are complex molecular machines present in all cells both prokaryotic, and eukaryotic. The ribosomal subunits of prokaryotes and eukaryotes are quite similar.
A ribosome is largely made up of specialized non-coding ribosomal RNA (rRNA) as well as dozens of distinct ribosomal proteins (the number varies slightly between species). The ribosomal proteins and rRNAs are arranged into two distinct ribosomal subunits one large and one small. The subunits fit together locking around a strand of mRNA, and work together to translate the mRNA into a polypeptide chain during protein synthesis.
Prokaryotic Bacteria Bacterial ribosomes are around 20 nm (200 Å) in diameter and are composed of 65% rRNA and 35% ribosomal proteins. Eukaryotic ribosomes are between 25 and 30 nm (250–300 Å) in diameter with an rRNA-to-protein ratio that is close to 1. Crystallographic work has shown that there are no ribosomal proteins close to the reaction site for polypeptide synthesis. This suggests that the protein components of ribosomes do not directly participate in peptide bond formation catalysis, but rather that these proteins act as a scaffold that may enhance the ability of rRNA to synthesize protein
The unit of measurement used to describe the ribosomal subunits and the rRNA fragments is the Svedberg unit, a measure of the rate of sedimentation in centrifugation rather than size. This accounts for why fragment names do not add up: for example, bacterial 70S ribosomes are made of 50S and 30S subunits.
Prokaryotes have 70S ribosomes, each consisting of a small (30S) and a large (50S) subunit. E. coli, for example, has a 16S RNA subunit (consisting of 1540 nucleotides) that is bound to 21 proteins. The large subunit is composed of a 5S RNA subunit (120 nucleotides), a 23S RNA subunit (2900 nucleotides) and 31 proteins.
{| class="wikitable float-right" style="text-align:center" |+ Ribosome of E. coli (a bacterium) |- ! width="25%"| ribosome ! width="25%"| subunit ! width="25%"| rRNAs ! width="25%"| r-proteins |- | rowspan="3" | 70S || rowspan="2" | 50S || 23S (2904 nt) || rowspan="2" | 31 |- | 5S (120 nt) |- | 30S || 16S (1542 nt) || 21
Affinity label for the tRNA binding sites on the E. coli ribosome allowed the identification of A and P site proteins most likely associated with the peptidyltransferase activity; labelled proteins are L27, L14, L15, L16, L2; at least L27 is located at the donor site, as shown by E. Collatz and A.P. Czernilofsky. Additional research has demonstrated that the S1 and S21 proteins, in association with the 3′-end of 16S ribosomal RNA, are involved in the initiation of translation.
Archaea Archaeal ribosomes are conventionally quoted as having similar sizes as the bacterial ribosome, being a 70S ribosome made up from a 50S large subunit and a 30S small subunit. The rRNA chains are similarly commonly called 16S, 23S, and 5S, though again few (if any) recent sources have truly measured their sedimentation coefficients. However, on the sequence and structural levels, they are much closer to eukaryotic ones than to bacterial ones. Every extra ribosomal protein archaea have compared to bacteria has a eukaryotic counterpart, while no such relation applies between archaea and bacteria.
{| class="wikitable float-right" style="text-align:center" |+ Ribosome of Pyrococcus furiosus (an archaeon) |- ! width="25%"| ribosome ! width="25%"| subunit ! width="25%"| rRNAs ! width="25%"| r-proteins |- | rowspan="3" | 70S || rowspan="2" | 50S || 23S (3049 nt) || rowspan="2" | 42 |- | 5S (120 nt) |- | 30S || 16S (1495 nt) || 26
Eukaryote
Eukaryotic cells have 80S ribosomes located in their cytosol, each consisting of a small (40S) and large (60S) subunit. Their 40S subunit has an 18S RNA (1900 nucleotides) and 33 proteins. The large subunit is composed of a 5S RNA (120 nucleotides), 28S RNA (4700 nucleotides), a 5.8S RNA (160 nucleotides) subunits and 49 proteins.
{| class="wikitable float-right" style="text-align:center" |+ eukaryotic cytosolic ribosomes (R. norvegicus) |- ! width="25%"| ribosome ! width="25%"| subunit ! width="25%"| rRNAs ! width="25%"| r-proteins |- | rowspan="4" | 80S || rowspan="3" | 60S || 28S (4718 nt) || rowspan="3" | 49 |- | 5.8S (160 nt) |- | 5S (120 nt) |- | 40S || 18S (1874 nt) || 33
During 1977, Czernilofsky published research that used affinity labeling to identify tRNA-binding sites on rat liver ribosomes. Several proteins, including L32/33, L36, L21, L23, L28/29 and L13 were implicated as being at or near the peptidyl transferase center.
Plastoribosomes and mitoribosomes
In eukaryotes, ribosomes are present in mitochondria (sometimes called mitoribosomes) and in plastids such as chloroplasts (also called plastoribosomes). They also consist of large and small subunits bound together with proteins into one 70S particle. These ribosomes are similar to those of bacteria and these organelles are thought to have originated as symbiotic bacteria. Of the two, chloroplastic ribosomes are closer to bacterial ones than mitochondrial ones are. Many pieces of ribosomal RNA in the mitochondria are shortened, and in the case of 5S rRNA, replaced by other structures in animals and fungi. In particular, Leishmania tarentolae has a minimalized set of mitochondrial rRNA. In contrast, plant mitoribosomes have both extended rRNA and additional proteins as compared to bacteria, in particular, many pentatricopetide repeat proteins.
The cryptomonad and chlorarachniophyte algae may contain a nucleomorph that resembles a vestigial eukaryotic nucleus. Eukaryotic 80S ribosomes may be present in the compartment containing the nucleomorph.
Making use of the differences The differences between the bacterial and eukaryotic ribosomes are exploited by pharmaceutical chemists to create antibiotics that can destroy a bacterial infection without harming the cells of the infected person. Due to the differences in their structures, the bacterial 70S ribosomes are vulnerable to these antibiotics while the eukaryotic 80S ribosomes are not. Even though mitochondria possess ribosomes similar to the bacterial ones, mitochondria are not affected by these antibiotics because they are surrounded by a double membrane that does not easily admit these antibiotics into the organelle. A noteworthy counterexample is the antineoplastic antibiotic chloramphenicol, which inhibits bacterial 50S and eukaryotic mitochondrial 50S ribosomes. Ribosomes in chloroplasts, however, are different: Antibiotic resistance in chloroplast ribosomal proteins is a trait that has to be introduced as a marker, with genetic engineering.
Common properties The various ribosomes share a core structure, which is quite similar despite the large differences in size. Much of the RNA is highly organized into various tertiary structural motifs, for example pseudoknots that exhibit coaxial stacking. The extra RNA in the larger ribosomes is in several long continuous insertions, such that they form loops out of the core structure without disrupting or changing it. All of the catalytic activity of the ribosome is carried out by the RNA; the proteins reside on the surface and seem to stabilize the structure.
High-resolution structure
The general molecular structure of the ribosome has been known since the early 1970s. In the early 2000s, the structure has been achieved at high resolutions, of the order of a few ångströms.