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A ribosome () is a ribonucleoprotein particle found in all cells, both prokaryotic and eukaryotic, responsible for the synthesis of proteins. A ribosome functions as a molecular machine in the translation of strands of messenger RNA (mRNA) and production of a protein. A ribosome links amino acids together in the order specified by the of mRNA molecules to form polypeptide chains. A ribosome is made up of a large and a small subunit, each consisting of one or more ribosomal RNA molecules and many ribosomal proteins. The ribosomes and associated molecules are also known as the translational apparatus.
Ribosome biogenesis is the process of making ribosomes. This is an energy-consuming, dynamic process, requiring the synthesis of around 200 proteins in the processing of ribosomal RNAs and assembling them with ribosomal proteins to make the ribosomes subunits.
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 is one of 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 because the Catalysis peptidyl transferase activity that links amino acids together is performed by the ribosomal RNA.
Ribosomes from bacteria, archaea, and (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 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.
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.
A ribosome is largely made up of specialized non-coding RNA 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 as one to translate the mRNA into a polypeptide chain during protein synthesis.
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 70Svedberg 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 .
| + Ribosome of E. coli (a bacterium) |
| 31 |
| 5S (120 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.
| + Ribosome of Pyrococcus furiosus (an archaeon) |
| 42 |
| 5S (120 nt) |
| 26 |
| + eukaryotic cytosolic ribosomes ( R. norvegicus) (2026). 9780495114642, Cengage Learning Services. ISBN 9780495114642
|
| 49 |
| 5.8S (160 nt) |
| 5S (120 nt) |
| 33 |
During 1977, Czernilofsky published research that used 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.
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.
The first papers giving the structure of the ribosome at atomic resolution were published almost simultaneously in late 2000. The 50S (large prokaryotic) subunit was determined from the Archaea Haloarcula marismortui and the Bacteria Deinococcus radiodurans, and the structure of the 30S subunit was determined from the bacterium Thermus thermophilus. These structural studies were awarded the Nobel Prize in Chemistry in 2009. In May 2001 these coordinates were used to reconstruct the entire T. thermophilus 70S particle at 5.5 Å resolution.
Two papers were published in November 2005 with structures of the Escherichia coli 70S ribosome. The structures of a vacant ribosome were determined at 3.5 Å resolution using X-ray crystallography. Then, two weeks later, a structure based on cryo-electron microscopy was published, which depicts the ribosome at 11–15 Å resolution in the act of passing a newly synthesized protein strand into the protein-conducting channel.
The first atomic structures of the ribosome complexed with tRNA and mRNA molecules were solved by using X-ray crystallography by two groups independently, at 2.8 Å and at 3.7 Å. These structures allow one to see the details of interactions of the Thermus thermophilus ribosome with mRNA and with bound at classical ribosomal sites. Interactions of the ribosome with long mRNAs containing Shine-Dalgarno sequences were visualized soon after that at 4.5–5.5 Å resolution. In 2023, a cryo-electron microscopy study reported a 1.55 Å structure of the Escherichia coli 70S ribosome in the translating state, providing near-atomic detail of rRNA modifications, tRNA-mRNA interactions, and ion coordination. The high-resolution map enabled identification of ribosomal polymorphism sites and visualization of transient chimeric hybrid states associated with tRNA translocation at approximately 2 Å resolution. These findings improved structural understanding of the ribosome's functional regions and offered valuable insights for antibiotic design.
In 2011, the first complete atomic structure of the eukaryotic 80S ribosome from the yeast Saccharomyces cerevisiae was obtained by crystallography. The model reveals the architecture of eukaryote-specific elements and their interaction with the universally conserved core. At the same time, the complete model of a eukaryotic 40S ribosomal structure in Tetrahymena thermophila was published and described the structure of the 40S subunit, as well as much about the 40S subunit's interaction with eIF1 during translation initiation. Similarly, the eukaryotic 60S subunit structure was also determined from Tetrahymena thermophila in complex with eIF6. In addition, high-resolution cryo-EM structures of a thermophilic eukaryotic 80S ribosome captured in two rotational states at ~2.9 Å and ~3.0 Å resolution revealed atomistic details of the eukaryotic translocation mechanism and conformational dynamics of eEF2 during GTP hydrolysis.
Ribosomes act as catalysts in two extremely important biological processes called peptidyl transfer and peptidyl hydrolysis.
In summary, ribosomes have two main functions: Decoding the message, and the formation of peptide bonds. These two functions reside in the ribosomal subunits. Each subunit is made of one or more rRNAs and many r-proteins. The small subunit (30S in bacteria and archaea, 40S in eukaryotes) has the decoding function, whereas the large subunit (50S in bacteria and archaea, 60S in eukaryotes) catalyzes the formation of peptide bonds, referred to as the peptidyl-transferase activity. The bacterial (and archaeal) small subunit contains the 16S rRNA and 21 r-proteins ( Escherichia coli), whereas the eukaryotic small subunit contains the 18S rRNA and 32 r-proteins (Saccharomyces cerevisiae, although the numbers vary between species). The bacterial large subunit contains the 5S and 23S rRNAs and 34 r-proteins ( E. coli), with the eukaryotic large subunit containing the 5S, 5.8S, and 25S/28S rRNAs and 46 r-proteins ( S. cerevisiae; again, the exact numbers vary between species).
Although catalysis of the peptide bond involves the C2 hydroxyl of RNA's P-site adenosine in a proton shuttle mechanism, other steps in protein synthesis (such as translocation) are caused by changes in protein conformations. Since their Active site is made of RNA, ribosomes are classified as "," and it is thought that they might be remnants of the RNA world.
In Figure 5, both ribosomal subunits (small and large) assemble at the start codon (towards the 5' end of the Messenger RNA). The ribosome uses Transfer RNA that matches the current codon (triplet) on the mRNA to append an amino acid to the polypeptide chain. This is done for each triplet on the mRNA, while the ribosome moves towards the 3' end of the mRNA. Usually in bacterial cells, several ribosomes are working parallel on a single mRNA, forming what is called a polyribosome or polysome.
Ribosomes are sometimes referred to as , but the use of the term organelle is often restricted to describing sub-cellular components that include a phospholipid membrane, which ribosomes, being entirely particulate, do not. For this reason, ribosomes may sometimes be described as "non-membranous organelles".
As amino acids gradually appeared in the RNA world under prebiotic conditions, their interactions with catalytic RNA would increase both the range and efficiency of function of catalytic RNA molecules. Thus, the driving force for the evolution of the ribosome from an ancient self-replicating machine into its current form as a translational machine may have been the selective pressure to incorporate proteins into the ribosome's self-replicating mechanisms, so as to increase its capacity for self-replication. (2026). 9783319394688, Springer, Cham. ISBN 9783319394688
Heterogeneity in ribosome composition was first proposed to be involved in translational control of protein synthesis by Vince Mauro and Gerald Edelman. They proposed the ribosome filter hypothesis to explain the regulatory functions of ribosomes. Evidence has suggested that specialized ribosomes specific to different cell populations may affect how genes are translated. Some ribosomal proteins exchange from the assembled complex with copies suggesting that the structure of the in vivo ribosome can be modified without synthesizing an entire new ribosome.
Certain ribosomal proteins are absolutely critical for cellular life while others are not. In budding yeast, 14/78 ribosomal proteins are non-essential for growth, while in humans this depends on the cell of study. Other forms of heterogeneity include post-translational modifications to ribosomal proteins such as acetylation, methylation, and phosphorylation. Arabidopsis, Viral internal ribosome entry sites (IRESs) may mediate translations by compositionally distinct ribosomes. For example, 40S ribosomal units without eS25 in yeast and mammalian cells are unable to recruit the CrPV IGR IRES.
Heterogeneity of ribosomal RNA modifications plays a significant role in structural maintenance and/or function and most mRNA modifications are found in highly conserved regions. The most common rRNA modifications are Pseudouridine and 2'-O-methylation of ribose.
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