Ribosome
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 and production of a protein. A ribosome links amino acids together in the order specified by the codons 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.
Overview
The sequence of DNA that encodes the sequence of the amino acids in a protein is transcribed into a messenger RNA 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 molecules, which enter the ribosome and bind to the messenger RNA chain via an anticodon stem loop. For each coding triplet 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 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 ribozymes because the catalytic peptidyl transferase activity that links amino acids together is performed by the ribosomal RNA.
Ribosomes from bacteria, archaea, and eukaryotes 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 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. 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 as well as dozens of distinct ribosomal proteins. 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.
Prokaryotic
Bacteria
l ribosomes are around 20 nm in diameter and are composed of 65% rRNA and 35% ribosomal proteins. Eukaryotic ribosomes are between 25 and 30 nm 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 proteinImage:010 small subunit-1FKA.gif|thumb|Molecular structure of the 30S subunit from Thermus thermophilus. Proteins are shown in blue and the single RNA chain in brown.
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 and a large subunit. E. coli, for example, has a 16S RNA subunit that is bound to 21 proteins. The large subunit is composed of a 5S RNA subunit, a 23S RNA subunit and 31 proteins.
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
l 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 recent sources have truly measured their sedimentation coefficients. However, on the sequence and structual 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.Eukaryote
s have 80S ribosomes located in their cytosol, each consisting of a small and large subunit. Their 40S subunit has an 18S RNA and 33 proteins. The large subunit is composed of a 5S RNA, 28S RNA, a 5.8S RNA subunits and 49 proteins.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 and in plastids such as chloroplasts. 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.