Array ( [0] => {{Short description|Synthesizes proteins in cells}} [1] => [[File:ribosome shape.png|thumb|Large (red) and small (blue) subunits of a ribosome]] [2] => {{Organelle diagram}} [3] => [4] => '''Ribosomes''' ({{IPAc-en|ˈ|r|aɪ|b|ə|z|oʊ|m|,_|-|s|oʊ|m}}) are [[molecular machine|macromolecular machines]], found within all [[cell (biology)|cells]], that perform [[Translation (biology)|biological protein synthesis]] ([[messenger RNA]] translation). Ribosomes link [[amino acids]] together in the order specified by the [[codon]]s of messenger RNA molecules to form [[polypeptide]] chains. Ribosomes consist of two major components: the small and large ribosomal subunits. Each subunit consists of one or more [[ribosomal RNA]] molecules and many [[ribosomal protein]]s ({{Nowrap|r-proteins}}).{{cite thesis | vauthors = Konikkat S | url = http://repository.cmu.edu/dissertations/608/ | title = Dynamic Remodeling Events Drive the Removal of the ITS2 Spacer Sequence During Assembly of 60S Ribosomal Subunits in S. cerevisiae | archive-url = https://web.archive.org/web/20170803051524/http://repository.cmu.edu/dissertations/608/ | archive-date = 3 August 2017 | publisher = Carnegie Mellon University | date = February 2016 | degree = Ph.D. }}{{cite book |url=https://books.google.com/books?id=TA9rjr034h8C |title=Allgemeine und Molekulare Botanik |vauthors=Weiler EW, Nover L |date=2008 |publisher=Georg Thieme Verlag |isbn=9783131527912 |location=Stuttgart |pages=532 |language=de}}{{cite journal | vauthors = de la Cruz J, Karbstein K, Woolford JL | title = Functions of ribosomal proteins in assembly of eukaryotic ribosomes in vivo | journal = Annual Review of Biochemistry | volume = 84 | pages = 93–129 | date = 2015 | pmid = 25706898 | pmc = 4772166 | doi = 10.1146/annurev-biochem-060614-033917 }} The ribosomes and associated molecules are also known as the ''translational apparatus''. [5] => [6] => ==Overview== [7] => The sequence of [[DNA]] that encodes the sequence of the [[amino acids]] in a protein is transcribed into a [[messenger RNA]] (mRNA) chain. Ribosomes bind to messenger RNAs and use their sequences{{what|date=January 2024}} to determine the correct sequence of amino acids to generate a given 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|anti-codon]] 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 [[protein folding|fold]] to produce a functional three-dimensional structure. [8] => [9] => A ribosome is made from [[biomolecular complex|complexes]] of RNAs and proteins and is therefore a [[Ribonucleoprotein particle|ribonucleoprotein complex]]. Each ribosome is composed of small (30[[Svedberg|S]]) and large (50[[Svedberg|S]]) components, called subunits, which are bound to each other: [10] => [11] => # (30S) has mainly a decoding function and is also bound to the mRNA [12] => # (50S) has mainly a catalytic function and is also bound to the aminoacylated tRNAs. [13] => [14] => The synthesis of proteins from their building blocks takes place in four phases: initiation, elongation, termination, and 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.{{cite web|url=https://nature.com/scitable/definition/translation-rna-translation-173|title=Scitable by nature translation / RNA translation}} When a ribosome finishes reading an mRNA molecule, the two subunits separate and are usually broken up but can be reused. Ribosomes are [[ribozyme]]s because the [[Catalysis|catalytic]] [[peptidyl transferase]] activity that links amino acids together is performed by the ribosomal RNA.{{cite journal | vauthors = Tirumalai MR, Rivas M, Tran Q, Fox GE | title = The Peptidyl Transferase Center: a Window to the Past | journal = Microbiol Mol Biol Rev | volume = 85 | issue = 4 | pages = e0010421 | date = November 2021 | pmid = 34756086 | pmc = 8579967 | doi = 10.1128/MMBR.00104-21}} [15] => [16] => Ribosomes are often associated with the intracellular membranes that make up the [[endoplasmic reticulum#Rough endoplasmic reticulum|rough endoplasmic reticulum]]. [17] => [18] => Ribosomes from [[bacteria]], [[archaea]], and [[eukaryote]]s 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 [[antibiotic]]s to kill bacteria by inhibiting their ribosomes while leaving human ribosomes unaffected. In all species, more than one ribosome may move along a single mRNA chain at one time (as a [[polysome]]), each "reading" a specific sequence and producing a corresponding protein molecule. [19] => [20] => The [[mitochondrial ribosome]]s of eukaryotic cells functionally resemble many features of those in bacteria, reflecting the likely evolutionary origin of mitochondria.{{cite journal | vauthors = Benne R, Sloof P | title = Evolution of the mitochondrial protein synthetic machinery | journal = Bio Systems | volume = 21 | issue = 1 | pages = 51–68 | year = 1987 | pmid = 2446672 | doi = 10.1016/0303-2647(87)90006-2 | bibcode = 1987BiSys..21...51B }}{{cite web|url=http://www.cs.stedwards.edu/chem/Chemistry/CHEM43/CHEM43/Ribosomes/Ribosome.HTML|title=Ribosomes|access-date=2011-04-28|url-status=dead|archive-url=https://web.archive.org/web/20090320163538/http://www.cs.stedwards.edu/chem/Chemistry/CHEM43/CHEM43/Ribosomes/Ribosome.HTML|archive-date=2009-03-20}} [21] => [22] => ==Discovery== [23] => Ribosomes were first observed in the mid-1950s by [[Romanian-American]] cell biologist [[George Emil Palade]], using an [[electron microscope]], as dense particles or granules.{{cite journal | vauthors = Palade GE | title = A small particulate component of the cytoplasm | journal = The Journal of Biophysical and Biochemical Cytology | volume = 1 | issue = 1 | pages = 59–68 | date = January 1955 | pmid = 14381428 | pmc = 2223592 | doi = 10.1083/jcb.1.1.59 }} They were initially called '''Palade granules''' due to their granular structure. The term "ribosome" was proposed in 1958 by Howard M. Dintzis:{{cite web |last1=Rheinberger |first1=Hans-Jörg |title=A Brief History of Protein Biosynthesis and Ribosome Research |url=https://mediatheque.lindau-nobel.org/topics/a-brief-history-of-protein-biosynthesis-and-ribosome-research |website=Lindau Nobel Laureate Meetings |date=September 2022 |access-date=2023-08-16}} [24] => {{Blockquote|During the course of the symposium a semantic difficulty became apparent. To some of the participants, "microsomes" mean the ribonucleoprotein particles of the microsome fraction contaminated by other protein and lipid material; to others, the microsomes consist of protein and lipid contaminated by particles. The phrase "microsomal particles" does not seem adequate, and "ribonucleoprotein particles of the microsome fraction" is much too awkward. During the meeting, the word "ribosome" was suggested, which has a very satisfactory name and a pleasant sound. The present confusion would be eliminated if "ribosome" were adopted to designate ribonucleoprotein particles in sizes ranging from 35 to 100S.|Albert Claude|Microsomal Particles and Protein Synthesis{{cite book | veditors = Roberts RB | date = 1958 | chapter = Introduction | title = Microsomal Particles and Protein Synthesis | url = https://archive.org/details/microsomalpartic00biop | location = New York | publisher = Pergamon Press, Inc. }}}} [25] => [26] => [[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.{{cite web |url=https://www.nobelprize.org/nobel_prizes/medicine/laureates/1974/ |title=The Nobel Prize in Physiology or Medicine 1974 |work=Nobelprize.org |publisher=The Nobel Foundation |access-date=10 December 2012 |url-status=live |archive-url=https://web.archive.org/web/20130126131649/http://www.nobelprize.org/nobel_prizes/medicine/laureates/1974/ |archive-date=26 January 2013 }} 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.{{cite web|url=http://nobelprize.org/nobel_prizes/chemistry/laureates/2009/|title=2009 Nobel Prize in Chemistry|publisher=The Nobel Foundation|access-date=10 December 2012|url-status=live|archive-url=https://web.archive.org/web/20120428061419/http://www.nobelprize.org/nobel_prizes/chemistry/laureates/2009/|archive-date=28 April 2012}} [27] => [28] => == Structure == [29] => [[File:Peptide syn.svg|thumb|upright=1.3|Ribosomes assemble [[polymer]]ic protein molecules, the order of which is controlled by the [[messenger RNA]]'s molecule sequence.]] [30] => [[File:Ribosome Structure.png|thumb|[[Ribosomal RNA]] composition for [[prokaryote]]s and [[eukaryote]]s]] [31] => [32] => The ribosome is a complex cellular machine. It is largely made up of specialized RNA known as [[ribosomal RNA]] (rRNA) as well as dozens of distinct proteins (the exact number varies slightly between species). The ribosomal proteins and rRNAs are arranged into two distinct ribosomal pieces of different sizes, known generally as the large and small subunits of the ribosome. Ribosomes consist of two subunits that fit together and work as one to translate the mRNA into a polypeptide chain during protein synthesis. Because they are formed from two subunits of non-equal size, they are slightly longer on the axis than in diameter. [33] => [34] => === Prokaryotic ribosomes === [35] => Prokaryotic ribosomes are around 20 [[Nanometre|nm]] (200 [[Ångström|Å]]) in diameter and are composed of 65% rRNA and 35% [[ribosomal protein]]s.{{cite journal|author1-link=Charles Kurland| vauthors = Kurland CG |title=Molecular characterization of ribonucleic acid from Escherichia coli ribosomes|journal=Journal of Molecular Biology|volume=2|issue=2|pages=83–91|doi=10.1016/s0022-2836(60)80029-0|year=1960}} Eukaryotic ribosomes are between 25 and 30 [[Nanometre|nm]] (250–300 Å) in diameter with an rRNA-to-protein ratio that is close to 1.{{cite journal | vauthors = Wilson DN, Doudna Cate JH | title = The structure and function of the eukaryotic ribosome | journal = Cold Spring Harbor Perspectives in Biology | volume = 4 | issue = 5 | pages = a011536 | date = May 2012 | pmid = 22550233 | pmc = 3331703 | doi = 10.1101/cshperspect.a011536 }} [[Crystallography|Crystallographic]] work{{cite journal | vauthors = Nissen P, Hansen J, Ban N, Moore PB, Steitz TA | title = The structural basis of ribosome activity in peptide bond synthesis | journal = Science | volume = 289 | issue = 5481 | pages = 920–30 | date = August 2000 | pmid = 10937990 | doi = 10.1126/science.289.5481.920 | bibcode = 2000Sci...289..920N | s2cid = 8370119 | url = http://pdfs.semanticscholar.org/0baa/9ba2a4d098674984113142bbf1ffca35700c.pdf | archive-url = https://web.archive.org/web/20201130102727/http://pdfs.semanticscholar.org/0baa/9ba2a4d098674984113142bbf1ffca35700c.pdf | url-status = dead | archive-date = 2020-11-30 }} 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 (see: [[Ribozyme]]). [36] => [37] => [[Image: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.]] [38] => [39] => The ribosomal subunits of [[prokaryote]]s and [[eukaryote]]s are quite similar.{{cite book | vauthors = Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P | chapter = Membrane-bound Ribosomes Define the Rough ER | chapter-url = https://www.ncbi.nlm.nih.gov/books/NBK26841/#A2204 | title = Molecular Biology of the Cell | edition = 4th | location = New York | publisher = Garland Science | date = 2002 | isbn = 978-0-8153-4072-0 | pages = 342 }} [40] => [41] => 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. [42] => [43] => Prokaryotes have 70[[Svedberg|S]] ribosomes, each consisting of a small ([[30S]]) and a large ([[50S]]) subunit. ''E. coli'', for example, has a [[16S ribosomal RNA|16S]] RNA subunit (consisting of 1540 nucleotides) that is bound to 21 proteins. The large subunit is composed of a [[5S ribosomal RNA|5S]] RNA subunit (120 nucleotides), a 23S RNA subunit (2900 nucleotides) and 31 [[protein]]s. [44] => [45] => :{| class="wikitable float-right" style="text-align:center" [46] => |+ Ribosome of ''E. coli'' (a bacterium){{rp|962}} [47] => |- [48] => ! width="25%"| ribosome [49] => ! width="25%"| subunit [50] => ! width="25%"| rRNAs [51] => ! width="25%"| r-proteins [52] => |- [53] => | rowspan="3" | 70S || rowspan="2" | 50S || 23S (2904 [[Nucleotide|nt]]) || rowspan="2" | 31 [54] => |- [55] => | 5S (120 nt) [56] => |- [57] => | 30S || 16S (1542 nt) || 21 [58] => |} [59] => [60] => 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.{{cite journal | vauthors = Collatz E, Küchler E, Stöffler G, Czernilofsky AP | title = The site of reaction on ribosomal protein L27 with an affinity label derivative of tRNA Met f | journal = FEBS Letters | volume = 63 | issue = 2 | pages = 283–6 | date = April 1976 | pmid = 770196 | doi = 10.1016/0014-5793(76)80112-3 | doi-access = free }}{{cite journal | vauthors = Czernilofsky AP, Collatz EE, Stöffler G, Kuechler E | title = Proteins at the tRNA binding sites of Escherichia coli ribosomes | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 71 | issue = 1 | pages = 230–4 | date = January 1974 | pmid = 4589893 | pmc = 387971 | doi = 10.1073/pnas.71.1.230 | bibcode = 1974PNAS...71..230C | doi-access = free }} 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.{{cite journal | vauthors = Czernilofsky AP, Kurland CG, Stöffler G | title = 30S ribosomal proteins associated with the 3'-terminus of 16S RNA | journal = FEBS Letters | volume = 58 | issue = 1 | pages = 281–4 | date = October 1975 | pmid = 1225593 | doi = 10.1016/0014-5793(75)80279-1 | doi-access = free }} [61] => [62] => ===Archaeal ribosomes=== [63] => Archaeal ribosomes share the same general dimensions of bacteria ones, being a 70S ribosome made up from a 50S large subunit, a 30S small subunit, and containing three rRNA chains. However, on the sequence level, 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.{{cite book | vauthors = Cullen KE |title=Encyclopedia of Life Science |date=2009 |publisher=Facts On File |location=New York |isbn=9780470015902 |chapter=Archaeal Ribosomes|pages=1–5 |doi=10.1002/9780470015902.a0000293.pub3|s2cid=243730576 }}{{cite journal | vauthors = Tirumalai MR, Anane-Bediakoh D, Rajesh R, Fox GE | title = Net Charges of the Ribosomal Proteins of the ''S10'' and ''spc'' Clusters of Halophiles Are Inversely Related to the Degree of Halotolerance | journal = Microbiol. Spectr. | volume = 9 | issue = 3 | pages = e0178221 | date = November 2021 | pmid = 34908470 | pmc = 8672879 | doi = 10.1128/spectrum.01782-21}}{{cite journal | vauthors = Wang J, Dasgupta I, Fox GE | title = Many nonuniversal archaeal ribosomal proteins are found in conserved gene clusters | journal = Archaea | volume = 2 | issue = 4 | pages = 241–51 | date = 28 April 2009 | pmid = 19478915 | pmc =2686390 | doi = 10.1155/2009/971494 | doi-access = free }} [64] => [65] => ===Eukaryotic ribosomes=== [66] => {{main|Eukaryotic ribosome}} [67] => [68] => Eukaryotes have 80S ribosomes located in their cytosol, each consisting of a [[Eukaryotic small ribosomal subunit (40S)|small (40S)]] and [[Eukaryotic large ribosomal subunit (60S)|large (60S) subunit]]. Their 40S subunit has an [[18S ribosomal RNA|18S RNA]] (1900 nucleotides) and 33 proteins.{{cite journal | vauthors = Ben-Shem A, Garreau de Loubresse N, Melnikov S, Jenner L, Yusupova G, Yusupov M | title = The structure of the eukaryotic ribosome at 3.0 Å resolution | journal = Science | volume = 334 | issue = 6062 | pages = 1524–9 | date = December 2011 | pmid = 22096102 | doi = 10.1126/science.1212642 | bibcode = 2011Sci...334.1524B | s2cid = 9099683 | doi-access = free }}{{cite journal | vauthors = Rabl J, Leibundgut M, Ataide SF, Haag A, Ban N | title = Crystal structure of the eukaryotic 40S ribosomal subunit in complex with initiation factor 1 | journal = Science | volume = 331 | issue = 6018 | pages = 730–6 | date = February 2011 | pmid = 21205638 | doi = 10.1126/science.1198308 | hdl = 20.500.11850/153130 | bibcode = 2011Sci...331..730R | s2cid = 24771575 | url = https://www.research-collection.ethz.ch/bitstream/20.500.11850/153130/1/eth-5105-01.pdf | hdl-access = free }} The large subunit is composed of a [[5S ribosomal RNA|5S RNA]] (120 nucleotides), [[28S ribosomal RNA|28S RNA]] (4700 nucleotides), a [[5.8S ribosomal RNA|5.8S RNA]] (160 nucleotides) subunits and 49 proteins.{{cite journal | vauthors = Klinge S, Voigts-Hoffmann F, Leibundgut M, Arpagaus S, Ban N | title = Crystal structure of the eukaryotic 60S ribosomal subunit in complex with initiation factor 6 | journal = Science | volume = 334 | issue = 6058 | pages = 941–8 | date = November 2011 | pmid = 22052974 | doi = 10.1126/science.1211204 | bibcode = 2011Sci...334..941K | s2cid = 206536444 }} [69] => [70] => :{| class="wikitable float-right" style="text-align:center" [71] => |+ eukaryotic cytosolic ribosomes (''R. norvegicus''){{cite book | vauthors = Garrett R, Grisham CM | title = Biochemistry | edition = 4th | publisher = Cengage Learning Services | date = 2009 | isbn = 978-0-495-11464-2 }}{{rp|65}} [72] => |- [73] => ! width="25%"| ribosome [74] => ! width="25%"| subunit [75] => ! width="25%"| rRNAs [76] => ! width="25%"| r-proteins [77] => |- [78] => | rowspan="4" | 80S || rowspan="3" | 60S || 28S (4718 nt) || rowspan="3" | 49 [79] => |- [80] => | 5.8S (160 nt) [81] => |- [82] => | 5S (120 nt) [83] => |- [84] => | 40S || 18S (1874 nt) || 33 [85] => |} [86] => [87] => During 1977, Czernilofsky published research that used [[affinity label]]ing 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.{{cite journal | vauthors = Fabijanski S, Pellegrini M | title = Identification of proteins at the peptidyl-tRNA binding site of rat liver ribosomes | journal = Molecular & General Genetics | volume = 184 | issue = 3 | pages = 551–6 | year = 1977 | pmid = 6950200 | doi = 10.1007/BF00431588 | s2cid = 9751945 }} [88] => [89] => === Plastoribosomes and mitoribosomes === [90] => {{main|Mitochondrial ribosome|Chloroplast#Chloroplast ribosomes}} [91] => In eukaryotes, ribosomes are present in [[mitochondria]] (sometimes called [[mitochondrial ribosome|mitoribosomes]]) and in [[plastid]]s such as [[chloroplast]]s (also called plastoribosomes). They also consist of large and small subunits bound together with [[protein]]s 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 ribosomal RNA#Presence in organelle ribosomes|5S rRNA]], replaced by other structures in animals and fungi.{{cite journal | vauthors = Agrawal RK, Sharma MR | title = Structural aspects of mitochondrial translational apparatus | journal = Current Opinion in Structural Biology | volume = 22 | issue = 6 | pages = 797–803 | date = December 2012 | pmid = 22959417 | pmc = 3513651 | doi = 10.1016/j.sbi.2012.08.003 }} In particular, ''[[Leishmania]] tarentolae'' has a minimalized set of mitochondrial rRNA.{{cite journal | vauthors = Sharma MR, Booth TM, Simpson L, Maslov DA, Agrawal RK | title = Structure of a mitochondrial ribosome with minimal RNA | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 106 | issue = 24 | pages = 9637–42 | date = June 2009 | pmid = 19497863 | pmc = 2700991 | doi = 10.1073/pnas.0901631106 | bibcode = 2009PNAS..106.9637S | doi-access = free }} In contrast, plant mitoribosomes have both extended rRNA and additional proteins as compared to bacteria, in particular, many pentatricopetide repeat proteins.{{cite journal | vauthors = Waltz F, Nguyen TT, Arrivé M, Bochler A, Chicher J, Hammann P, Kuhn L, Quadrado M, Mireau H, Hashem Y, Giegé P | title = Small is big in Arabidopsis mitochondrial ribosome | journal = Nature Plants | volume = 5 | pages = 106–117 | date = January 2019 | issue = 1 | doi = 10.1038/s41477-018-0339-y | pmid = 30626926 | s2cid = 58004990 }} [92] => [93] => The [[cryptomonad]] and [[chlorarachniophyte]] algae may contain a [[nucleomorph]] that resembles a vestigial eukaryotic nucleus.{{cite journal | vauthors = Archibald JM, Lane CE | title = Going, going, not quite gone: nucleomorphs as a case study in nuclear genome reduction | journal = The Journal of Heredity | volume = 100 | issue = 5 | pages = 582–90 | year = 2009 | pmid = 19617523 | doi = 10.1093/jhered/esp055 | doi-access = free }} Eukaryotic 80S ribosomes may be present in the compartment containing the nucleomorph.{{Cite web|title=Specialized Internal Structures of Prokaryotes {{!}} Boundless Microbiology|url=https://courses.lumenlearning.com/boundless-microbiology/chapter/specialized-internal-structures-of-prokaryotes/|access-date=2021-09-24|website=courses.lumenlearning.com}} [94] => [95] => ===Making use of the differences=== [96] => The differences between the bacterial and eukaryotic ribosomes are exploited by [[medicinal chemistry|pharmaceutical chemists]] to create [[antibiotic]]s 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.{{cite journal | vauthors = Recht MI, Douthwaite S, Puglisi JD | title = Basis for prokaryotic specificity of action of aminoglycoside antibiotics | journal = The EMBO Journal | volume = 18 | issue = 11 | pages = 3133–8 | date = June 1999 | pmid = 10357824 | pmc = 1171394 | doi = 10.1093/emboj/18.11.3133 }} 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]].{{cite journal | vauthors = O'Brien TW | title = The general occurrence of 55 S ribosomes in mammalian liver mitochondria | journal = The Journal of Biological Chemistry | volume = 246 | issue = 10 | pages = 3409–17 | date = May 1971 | doi = 10.1016/S0021-9258(18)62239-2 | pmid = 4930061 | doi-access = free }} A noteworthy counterexample is the antineoplastic antibiotic [[chloramphenicol]], which inhibits bacterial 50S and eukaryotic mitochondrial 50S ribosomes.{{Cite journal|date=1970-08-17|title=Chloramphenicol-lnduced Bone Marrow Suppression|url=https://jamanetwork.com/journals/jama/fullarticle/356164|journal=JAMA|language=en|volume=213|issue=7|pages=1183–1184|doi=10.1001/jama.1970.03170330063011|pmid=5468266|issn=0098-7484}} 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.{{cite journal | vauthors = Newman SM, Boynton JE, Gillham NW, Randolph-Anderson BL, Johnson AM, Harris EH | title = Transformation of chloroplast ribosomal RNA genes in Chlamydomonas: molecular and genetic characterization of integration events | journal = Genetics | volume = 126 | issue = 4 | pages = 875–88 | date = December 1990 | doi = 10.1093/genetics/126.4.875 | pmid = 1981764 | pmc = 1204285 }} [97] => [98] => ===Common properties=== [99] => 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 [[RNA Tertiary Structure|tertiary structural motifs]], for example [[pseudoknot]]s that exhibit [[Nucleic acid tertiary structure#Coaxial stacking|coaxial stacking]]. The extra [[RNA]] in the larger ribosomes is in several long continuous insertions,{{cite journal | vauthors = Penev PI, Fakhretaha-Aval S, Patel VJ, Cannone JJ, Gutell RR, Petrov AS, Williams LD, Glass JB| title = Supersized ribosomal RNA expansion segments in Asgard archaea | journal = Genome Biology and Evolution | date = August 2020 | volume = 12 | issue = 10 | pages = 1694–1710 | pmid = 32785681 | doi = 10.1093/gbe/evaa170 | pmc = 7594248 | doi-access = free }} 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 [[ribozyme|RNA]]; the proteins reside on the surface and seem to stabilize the structure. [100] => [101] => ===High-resolution structure=== [102] => [[Image:10 large subunit.gif|thumb|200px|right| '''Figure 4:''' Atomic structure of the 50S subunit from ''[[Haloarcula|Haloarcula marismortui]]''. Proteins are shown in blue and the two RNA chains in brown and yellow.{{cite journal | vauthors = Ban N, Nissen P, Hansen J, Moore PB, Steitz TA | title = The complete atomic structure of the large ribosomal subunit at 2.4 A resolution | journal = Science | volume = 289 | issue = 5481 | pages = 905–20 | date = August 2000 | pmid = 10937989 | doi = 10.1126/science.289.5481.905 | citeseerx = 10.1.1.58.2271 | bibcode = 2000Sci...289..905B }} The small patch of green in the center of the subunit is the active site.]] [103] => [104] => 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 [[ångström]]s. [105] => [106] => 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|archaeon]] ''Haloarcula marismortui'' and the bacterium ''[[Deinococcus radiodurans]]'',{{cite journal | vauthors = Schluenzen F, Tocilj A, Zarivach R, Harms J, Gluehmann M, Janell D, Bashan A, Bartels H, Agmon I, Franceschi F, Yonath A | title = Structure of functionally activated small ribosomal subunit at 3.3 angstroms resolution | journal = Cell | volume = 102 | issue = 5 | pages = 615–23 | date = September 2000 | pmid = 11007480 | doi = 10.1016/S0092-8674(00)00084-2 | s2cid = 1024446 | doi-access = free }} and the structure of the 30S subunit was determined from ''[[Thermus thermophilus]]''.{{cite journal | vauthors = Wimberly BT, Brodersen DE, Clemons WM, Morgan-Warren RJ, Carter AP, Vonrhein C, Hartsch T, Ramakrishnan V | title = Structure of the 30S ribosomal subunit | journal = Nature | volume = 407 | issue = 6802 | pages = 327–39 | date = September 2000 | pmid = 11014182 | doi = 10.1038/35030006 | bibcode = 2000Natur.407..327W | s2cid = 4419944 }} These structural studies were awarded the Nobel Prize in Chemistry in 2009. In May 2001 these coordinates were used to reconstruct the entire ''[[Thermus thermophilus|T. thermophilus]]'' 70S particle at 5.5 [[Ångström|Å]] resolution.{{cite journal | vauthors = Yusupov MM, Yusupova GZ, Baucom A, Lieberman K, Earnest TN, Cate JH, Noller HF | title = Crystal structure of the ribosome at 5.5 A resolution | journal = Science | volume = 292 | issue = 5518 | pages = 883–96 | date = May 2001 | pmid = 11283358 | doi = 10.1126/science.1060089 | bibcode = 2001Sci...292..883Y | s2cid = 39505192 | doi-access = free }} [107] => [108] => 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 [[Ångström|Å]] resolution using [[X-ray crystallography]].{{cite journal | vauthors = Schuwirth BS, Borovinskaya MA, Hau CW, Zhang W, Vila-Sanjurjo A, Holton JM, Cate JH | title = Structures of the bacterial ribosome at 3.5 A resolution | journal = Science | volume = 310 | issue = 5749 | pages = 827–34 | date = November 2005 | pmid = 16272117 | doi = 10.1126/science.1117230 | bibcode = 2005Sci...310..827S | s2cid = 37382005 }} Then, two weeks later, a structure based on [[Cryogenic electron microscopy|cryo-electron microscopy]] was published,{{cite journal | vauthors = Mitra K, Schaffitzel C, Shaikh T, Tama F, Jenni S, Brooks CL, Ban N, Frank J | title = Structure of the E. coli protein-conducting channel bound to a translating ribosome | journal = Nature | volume = 438 | issue = 7066 | pages = 318–24 | date = November 2005 | pmid = 16292303 | pmc = 1351281 | doi = 10.1038/nature04133 | bibcode = 2005Natur.438..318M }} which depicts the ribosome at 11–15 [[Ångström|Å]] resolution in the act of passing a newly synthesized protein strand into the protein-conducting channel. [109] => [110] => 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 [[Ångström|Å]]{{cite journal | vauthors = Selmer M, Dunham CM, Murphy FV, Weixlbaumer A, Petry S, Kelley AC, Weir JR, Ramakrishnan V | title = Structure of the 70S ribosome complexed with mRNA and tRNA | journal = Science | volume = 313 | issue = 5795 | pages = 1935–42 | date = September 2006 | pmid = 16959973 | doi = 10.1126/science.1131127 | bibcode = 2006Sci...313.1935S | s2cid = 9737925 }} and at 3.7 [[Ångström|Å]].{{cite journal | vauthors = Korostelev A, Trakhanov S, Laurberg M, Noller HF | title = Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangements | journal = Cell | volume = 126 | issue = 6 | pages = 1065–77 | date = September 2006 | pmid = 16962654 | doi = 10.1016/j.cell.2006.08.032 | s2cid = 13452915 | doi-access = free }} These structures allow one to see the details of interactions of the ''[[Thermus thermophilus]]'' ribosome with [[mRNA]] and with [[tRNA]]s bound at classical ribosomal sites. Interactions of the ribosome with long mRNAs containing [[Shine-Dalgarno sequence]]s were visualized soon after that at 4.5–5.5 [[Ångström|Å]] resolution.{{cite journal | vauthors = Yusupova G, Jenner L, Rees B, Moras D, Yusupov M | title = Structural basis for messenger RNA movement on the ribosome | journal = Nature | volume = 444 | issue = 7117 | pages = 391–4 | date = November 2006 | pmid = 17051149 | doi = 10.1038/nature05281 | bibcode = 2006Natur.444..391Y | s2cid = 4419198 }} [111] => [112] => 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|40S subunit]], as well as much about the 40S subunit's interaction with [[eIF1]] during [[Translation (biology)|translation initiation]]. Similarly, the eukaryotic [[60S|60S subunit]] structure was also determined from ''[[Tetrahymena thermophila]]'' in complex with [[eIF6]]. [113] => [114] => == Function == [115] => Ribosomes are minute particles consisting of RNA and associated proteins that function to synthesize proteins. Proteins are needed for many cellular functions, such as repairing damage or directing chemical processes. Ribosomes can be found floating within the cytoplasm or attached to the [[endoplasmic reticulum]]. Their main function is to convert genetic code into an amino acid sequence and to build protein polymers from amino acid monomers. [116] => [117] => Ribosomes act as catalysts in two extremely important biological processes called peptidyl transfer and peptidyl hydrolysis.{{cite web |title=Specialized Internal Structures of Prokaryotes |series=Boundless Microbiology |website=courses.lumenlearning.com |url=https://courses.lumenlearning.com/boundless-microbiology/chapter/specialized-internal-structures-of-prokaryotes/ |access-date=2018-09-27}} The "PT center is responsible for producing protein bonds during protein elongation". [118] => [119] => 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).{{cite journal |author1=Lafontaine, D. |author2=Tollervey, D. |year=2001 |title=The function and synthesis of ribosomes |journal=Nat Rev Mol Cell Biol |volume=2 |issue=7 |pages=514–520 |doi=10.1038/35080045|pmid=11433365 |hdl=1842/729 |s2cid=2637106 |hdl-access=free }} [120] => [121] => === Translation === [122] => {{Main|Translation (biology)}} [123] => [124] => Ribosomes are the workplaces of [[protein biosynthesis]], the process of translating [[mRNA]] into [[protein]]. The mRNA comprises a series of [[codon]]s which are decoded by the ribosome so as to make the protein. Using the mRNA as a template, the ribosome traverses each codon (3 [[nucleotide]]s) of the mRNA, pairing it with the appropriate amino acid provided by an [[aminoacyl-tRNA]]. Aminoacyl-tRNA contains a complementary [[anticodon]] on one end and the appropriate amino acid on the other. For fast and accurate recognition of the appropriate tRNA, the ribosome utilizes large conformational changes ([[conformational proofreading]]).{{cite journal | vauthors = Savir Y, Tlusty T | date = April 2013 | title = The ribosome as an optimal decoder: A lesson in molecular recognition | journal = Cell | volume = 153 | issue = 2 | pages = 471–479 | pmid = 23582332 | doi = 10.1016/j.cell.2013.03.032 | doi-access = free | bibcode = 2013APS..MARY46006T }} The small ribosomal subunit, typically bound to an aminoacyl-tRNA containing the first amino acid [[methionine]], binds to an AUG codon on the mRNA and recruits the large ribosomal subunit. The ribosome contains three RNA binding sites, designated A, P, and E. The [[A-site]] binds an aminoacyl-tRNA or termination release factors;{{cite journal | vauthors = Korkmaz G, Sanyal S | date = September 2017 | title = ''Escherichia coli'' | journal = The Journal of Biological Chemistry | volume = 292 | issue = 36 | pages = 15134–15142 | pmid = 28743745 | pmc = 5592688 | doi = 10.1074/jbc.M117.785238 | doi-access = free }}{{cite journal | vauthors = Konevega AL, Soboleva NG, Makhno VI, Semenkov YP, Wintermeyer W, Rodnina MV, Katunin VI | date = January 2004 | title = Purine bases at position 37 of tRNA stabilize codon-anticodon interaction in the ribosomal A site by stacking and {{nobr|Mg{{sup|2+}}-dependent}} interactions | journal = RNA | volume = 10 | issue = 1 | pages = 90–101 | pmid = 14681588 | pmc = 1370521 | doi = 10.1261/rna.5142404 }} the [[P-site]] binds a peptidyl-tRNA (a tRNA bound to the poly-peptide chain); and the [[E-site]] (exit) binds a free tRNA. Protein synthesis begins at a [[start codon]] AUG near the 5' end of the mRNA. mRNA binds to the P site of the ribosome first. The ribosome recognizes the start codon by using the [[Shine-Dalgarno sequence]] of the mRNA in prokaryotes and [[Kozak consensus sequence|Kozak box]] in eukaryotes. [125] => [126] => 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|catalytic core]] is made of RNA, ribosomes are classified as "[[ribozyme]]s,"{{cite journal | vauthors = Rodnina MV, Beringer M, Wintermeyer W | date = January 2007 | title = How ribosomes make peptide bonds | journal = Trends in Biochemical Sciences | volume = 32 | issue = 1 | pages = 20–26 | pmid = 17157507 | doi = 10.1016/j.tibs.2006.11.007 }} and it is thought that they might be remnants of the [[RNA world]].{{cite journal | author = Cech, T.R. | date = August 2000 | title = Structural biology. The ribosome is a ribozyme | journal = Science | volume = 289 | issue = 5481 | pages = 878–879 | pmid = 10960319 | doi = 10.1126/science.289.5481.878 | s2cid = 24172338 }} [127] => [128] => [[File:Ribosomer i arbete.png|frame|none|'''Figure 5:''' Translation of mRNA (1) by a ribosome (2)(shown as small and large subunits) into a polypeptide chain (3). The ribosome begins at the start codon of RNA (AUG) and ends at the stop codon (UAG).]] [129] => [130] => In Figure 5, both ribosomal subunits (small and large) assemble at the start codon (towards the 5' end of the [[Messenger RNA|mRNA]]). The ribosome uses [[Transfer RNA|tRNA]] 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]]''. [131] => [132] => ==== Cotranslational folding ==== [133] => The ribosome is known to actively participate in the [[protein folding]].{{cite journal | vauthors = Banerjee D, Sanyal S | date = October 2014 | title = Protein folding activity of the ribosome (PFAR) – a target for antiprion compounds | journal = Viruses | volume = 6 | issue = 10 | pages = 3907–3924 | pmid = 25341659 | pmc = 4213570 | doi = 10.3390/v6103907 | doi-access = free }}{{cite journal | vauthors = Fedorov AN, Baldwin TO | date = December 1997 | title = Cotranslational protein folding | journal = The Journal of Biological Chemistry | volume = 272 | issue = 52 | pages = 32715–32718 | pmid = 9407040 | doi = 10.1074/jbc.272.52.32715 | doi-access = free }} The structures obtained in this way are usually identical to the ones obtained during protein chemical refolding; however, the pathways leading to the final product may be different.{{cite journal | vauthors = Baldwin RL | date = June 1975 | title = Intermediates in protein folding reactions and the mechanism of protein folding | journal = Annual Review of Biochemistry | volume = 44 | issue = 1 | pages = 453–475 | pmid = 1094916 | doi = 10.1146/annurev.bi.44.070175.002321 }}{{cite journal | vauthors = Das D, Das A, Samanta D, Ghosh J, Dasgupta S, Bhattacharya A, Basu A, Sanyal S, Das Gupta C | date = August 2008 | title = Role of the ribosome in protein folding | journal = Biotechnology Journal | volume = 3 | issue = 8 | pages = 999–1009 | pmid = 18702035 | doi = 10.1002/biot.200800098 | url = http://repository.ias.ac.in/8881/1/313.pdf }} In some cases, the ribosome is crucial in obtaining the functional protein form. For example, one of the possible mechanisms of folding of the deeply [[knotted protein]]s relies on the ribosome pushing the chain through the attached loop.{{cite journal | vauthors = Dabrowski-Tumanski P, Piejko M, Niewieczerzal S, Stasiak A, Sulkowska JI | date = December 2018 | title = Protein knotting by active threading of nascent polypeptide chain exiting from the ribosome exit channel | journal = The Journal of Physical Chemistry B | volume = 122 | issue = 49 | pages = 11616–11625 | pmid = 30198720 | doi = 10.1021/acs.jpcb.8b07634 | s2cid = 52176392 }} [134] => [135] => === Addition of translation-independent amino acids === [136] => Presence of a ribosome quality control protein Rqc2 is associated with mRNA-independent protein elongation.{{cite journal | vauthors = Brandman O, Stewart-Ornstein J, Wong D, Larson A, Williams CC, Li GW, Zhou S, King D, Shen PS, Weibezahn J, Dunn JG, Rouskin S, Inada T, Frost A, Weissman JS | date = November 2012 | title = A ribosome-bound quality control complex triggers degradation of nascent peptides and signals translation stress | journal = Cell | volume = 151 | issue = 5 | pages = 1042–1054 | pmid = 23178123 | pmc = 3534965 | doi = 10.1016/j.cell.2012.10.044 }}{{cite journal | vauthors = Defenouillère Q, Yao Y, Mouaikel J, Namane A, Galopier A, Decourty L, Doyen A, Malabat C, Saveanu C, Jacquier A, Fromont-Racine M | date = March 2013 | title = Cdc48-associated complex bound to 60S particles is required for the clearance of aberrant translation products | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 110 | issue = 13 | pages = 5046–5051 | pmid = 23479637 | pmc = 3612664 | doi = 10.1073/pnas.1221724110 | doi-access = free | bibcode = 2013PNAS..110.5046D }} This elongation is a result of ribosomal addition (via tRNAs brought by Rqc2) of '''''CAT''' tails'': ribosomes extend the [[C-terminus|'''''C'''''-terminus]] of a stalled protein with random, translation-independent sequences of [[alanine|'''''a'''''lanines]] and [[threonine|'''''t'''''hreonines]].{{cite journal | vauthors = Shen PS, Park J, Qin Y, Li X, Parsawar K, Larson MH, Cox J, Cheng Y, Lambowitz AM, Weissman JS, Brandman O, Frost A | date = January 2015 | title = Protein synthesis. Rqc2p and 60S ribosomal subunits mediate mRNA-independent elongation of nascent chains | journal = Science | volume = 347 | issue = 6217 | pages = 75–78 | pmid = 25554787 | pmc = 4451101 | doi = 10.1126/science.1259724 | bibcode = 2015Sci...347...75S }}{{cite press release |author1=Keeley, J. |author2=Gutnikoff, R. |date=2015-01-02 |df=dmy-all |title=Ribosome studies turn up new mechanism of protein synthesis |publisher=[[Howard Hughes Medical Institute]] |url=http://www.hhmi.org/news/ribosome-studies-turn-new-mechanism-protein-synthesis |access-date=2015-01-16 |url-status=live |archive-url=https://web.archive.org/web/20150112034722/http://www.hhmi.org/news/ribosome-studies-turn-new-mechanism-protein-synthesis |archive-date=2015-01-12 }} [137] => [138] => ==Ribosome locations== [139] => Ribosomes are classified as being either "free" or "membrane-bound". [140] => [141] => [[Image:Protein translation.gif|thumb|200px|'''Figure 6:''' A ribosome translating a protein that is secreted into the [[endoplasmic reticulum]].]] [142] => [143] => Free and membrane-bound ribosomes differ only in their spatial distribution; they are identical in structure. Whether the ribosome exists in a free or membrane-bound state depends on the presence of an [[signal peptide|ER-targeting signal sequence]] on the protein being synthesized, so an individual ribosome might be membrane-bound when it is making one protein, but free in the cytosol when it makes another protein. [144] => [145] => Ribosomes are sometimes referred to as [[organelle]]s, 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". [146] => [147] => ===Free ribosomes=== [148] => Free ribosomes can move about anywhere in the [[cytosol]], but are excluded from the [[cell nucleus]] and other organelles. Proteins that are formed from free ribosomes are released into the cytosol and used within the cell. Since the cytosol contains high concentrations of [[glutathione]] and is, therefore, a [[redox|reducing environment]], proteins containing [[disulfide bonds]], which are formed from oxidized cysteine residues, cannot be produced within it. [149] => [150] => ===Membrane-bound ribosomes=== [151] => When a ribosome begins to synthesize proteins that are needed in some organelles, the ribosome making this protein can become "membrane-bound". In eukaryotic cells this happens in a region of the endoplasmic reticulum (ER) called the "rough ER". The newly produced polypeptide chains are inserted directly into the ER by the ribosome undertaking [[vectorial synthesis]] and are then transported to their destinations, through the [[secretory pathway]]. Bound ribosomes usually produce proteins that are used within the plasma membrane or are expelled from the cell via ''[[exocytosis]]''.{{cite book | vauthors = Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P | chapter = Membrane-bound Ribosomes Define the Rough ER | chapter-url = https://www.ncbi.nlm.nih.gov/books/NBK26841/#A2204 | title = Molecular Biology of the Cell | edition = 4th | location = New York | publisher = Garland Science | date = 2002 | isbn = 978-0-8153-4072-0 }} [152] => [153] => ==Biogenesis== [154] => {{Main|Ribosome biogenesis}} [155] => [156] => In bacterial cells, ribosomes are synthesized in the cytoplasm through the [[Transcription (genetics)|transcription]] of multiple ribosome gene [[operon]]s. In eukaryotes, the process takes place both in the cell cytoplasm and in the [[nucleolus]], which is a region within the [[cell nucleus]]. The assembly process involves the coordinated function of over 200 proteins in the synthesis and processing of the four rRNAs, as well as assembly of those rRNAs with the ribosomal proteins.{{cite journal |last1=Kressler |first1=Dieter |last2=Hurt |first2=Ed |last3=Babler |first3=Jochen |date=2009 |title=Driving ribosome assembly |url=http://doc.rero.ch/record/17283/files/kressler_dra.pdf |journal=Biochimica et Biophysica Acta (BBA) - Molecular Cell Research |volume=1803 |issue=6 |pages=673–683 |doi=10.1016/j.bbamcr.2009.10.009 |pmid=19879902}} [157] => [158] => == Origin == [159] => The ribosome may have first originated as a protoribosome,{{cite journal |last=Dance |first=Amber |title=How did life begin? One key ingredient is coming into view - A Nobel-prizewinning scientist's team has taken a big step forward in its quest to reconstruct an early-Earth RNA capable of building proteins. |date=28 February 2023 |journal=[[Nature (journal)|Nature]] |volume=615 |issue=7950 |pages=22–25 |doi=10.1038/d41586-023-00574-4 |pmid=36854922 |doi-access=free }} possibly containing a peptidyl transferase centre (PTC), in an [[RNA world]], appearing as a self-replicating complex that only later evolved the ability to synthesize proteins when [[amino acid]]s began to appear.{{cite journal | vauthors = Noller HF | title = Evolution of protein synthesis from an RNA world | journal = Cold Spring Harbor Perspectives in Biology | volume = 4 | issue = 4 | pages = a003681 | date = April 2012 | pmid = 20610545 | pmc = 3312679 | doi = 10.1101/cshperspect.a003681 }} Studies suggest that ancient ribosomes constructed solely of [[Ribosomal RNA|rRNA]] could have developed the ability to synthesize [[peptide bond]]s.{{cite book | vauthors = Dabbs ER | date = 1986 | title = Mutant studies on the prokaryotic ribosome. | publisher = Springer-Verlag | location = New York }}{{cite journal | vauthors = Noller HF, Hoffarth V, Zimniak L | title = Unusual resistance of peptidyl transferase to protein extraction procedures | journal = Science | volume = 256 | issue = 5062 | pages = 1416–9 | date = June 1992 | pmid = 1604315 | doi = 10.1126/science.1604315 | bibcode = 1992Sci...256.1416N }}{{cite journal | vauthors = Nomura M, Mizushima S, Ozaki M, Traub P, Lowry CV | title = Structure and function of ribosomes and their molecular components | journal = Cold Spring Harbor Symposia on Quantitative Biology | volume = 34 | pages = 49–61 | year = 1969 | pmid = 4909519 | doi = 10.1101/sqb.1969.034.01.009 }}{{cite journal | vauthors = Krupkin M, Matzov D, Tang H, Metz M, Kalaora R, Belousoff MJ, Zimmerman E, Bashan A, Yonath A | title = A vestige of a prebiotic bonding machine is functioning within the contemporary ribosome | journal = Phil. Trans. R. Soc. B | volume = 366 | issue = 1580 | pages = 2972–8 | date = Oct 2011 | pmid = 21930590 | doi = 10.1098/rstb.2011.0146 | pmc = 3158926 }}{{cite journal | vauthors = Bose T, Fridkin G, Davidovich C, Krupkin M, Dinger N, Falkovich AH, Peleg Y, Agmon I, Bashan A, Yonat A | title = Origin of life: protoribosome forms peptide bonds and links RNA and protein dominated worlds | journal = Nucleic Acids Res | volume = 50 | issue = 4 | pages = 1815–1828 | date = Feb 2022 | pmid = 35137169 | doi = 10.1093/nar/gkac052 | pmc = 8886871 }} In addition, evidence strongly points to ancient ribosomes as self-replicating complexes, where the rRNA in the ribosomes had informational, structural, and catalytic purposes because it could have coded for [[Transfer RNA|tRNAs]] and proteins needed for ribosomal self-replication.{{cite journal | vauthors = Root-Bernstein M, Root-Bernstein R | title = The ribosome as a missing link in the evolution of life | journal = Journal of Theoretical Biology | volume = 367 | pages = 130–158 | date = February 2015 | pmid = 25500179 | doi = 10.1016/j.jtbi.2014.11.025 | doi-access = free }} Hypothetical cellular organisms with self-replicating RNA but without DNA are called [[ribocyte]]s (or ribocells).{{cite journal | vauthors = Yarus M | title = Primordial genetics: phenotype of the ribocyte | journal = Annual Review of Genetics | volume = 36 | pages = 125–51 | year = 2002 | pmid = 12429689 | doi = 10.1146/annurev.genet.36.031902.105056 }}{{cite book | doi=10.1007/978-94-007-4899-6_3|chapter = The Origin of Virions and Virocells: The Escape Hypothesis Revisited|title = Viruses: Essential Agents of Life| pages=43–60|year = 2012| vauthors = Forterre P, Krupovic M | isbn=978-94-007-4898-9}} [160] => [161] => As amino acids gradually appeared in the RNA world under prebiotic conditions,{{cite journal | vauthors = Caetano-Anollés G, Seufferheld MJ | title = The coevolutionary roots of biochemistry and cellular organization challenge the RNA world paradigm | journal = Journal of Molecular Microbiology and Biotechnology | volume = 23 | issue = 1–2 | pages = 152–77 | year = 2013 | pmid = 23615203 | doi = 10.1159/000346551 | s2cid = 41725226 }}{{cite journal | vauthors = Saladino R, Botta G, Pino S, Costanzo G, Di Mauro E | title = Genetics first or metabolism first? The formamide clue | journal = Chemical Society Reviews | volume = 41 | issue = 16 | pages = 5526–65 | date = August 2012 | pmid = 22684046 | doi = 10.1039/c2cs35066a | hdl = 11573/494138 }} 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.{{cite journal | vauthors = Fox GE| title = Origin and Evolution of the Ribosome| journal = Cold Spring Harb Perspect Biol | volume = 2 | issue = 9 | date = September 2010 | pages = a003483| pmid = 20534711 | doi = 10.1101/cshperspect.a003483| pmc = 2926754| doi-access = free }}{{cite book | vauthors = Fox GE | veditors = Hernández G, Jagus R| year = 2016| title = Evolution of the Protein Synthesis Machinery and Its Regulation| chapter= Origins and early evolution of the ribosome | url = https://doi.org/10.1007/978-3-319-39468-8 |pages=31–60|location = Switzerland | publisher = Springer, Cham| doi = 10.1007/978-3-319-39468-8| isbn=978-3-319-39468-8 | s2cid = 27493054}} [162] => [163] => == Heterogeneous ribosomes == [164] => Ribosomes are compositionally heterogeneous between species and even within the same cell, as evidenced by the existence of cytoplasmic and mitochondria ribosomes within the same eukaryotic cells. Certain researchers have suggested that heterogeneity in the composition of ribosomal proteins in mammals is important for gene regulation, ''i.e.'', the specialized ribosome hypothesis.{{cite journal | vauthors = Shi Z, Fujii K, Kovary KM, Genuth NR, Röst HL, Teruel MN, Barna M | title = Heterogeneous Ribosomes Preferentially Translate Distinct Subpools of mRNAs Genome-wide | journal = Molecular Cell | volume = 67 | issue = 1 | pages = 71–83.e7 | date = July 2017 | pmid = 28625553 | pmc = 5548184 | doi = 10.1016/j.molcel.2017.05.021 | publisher = Elsevier BV | doi-access = free }}{{cite journal | vauthors = Xue S, Barna M | title = Specialized ribosomes: a new frontier in gene regulation and organismal biology | journal = Nature Reviews. Molecular Cell Biology | volume = 13 | issue = 6 | pages = 355–369 | date = May 2012 | pmid = 22617470 | pmc = 4039366 | doi = 10.1038/nrm3359 | publisher = Springer Science and Business Media LLC }} However, this hypothesis is controversial and the topic of ongoing research.{{cite journal | vauthors = Ferretti MB, Karbstein K | title = Does functional specialization of ribosomes really exist? | journal = RNA | volume = 25 | issue = 5 | pages = 521–538 | date = May 2019 | pmid = 30733326 | pmc = 6467006 | doi = 10.1261/rna.069823.118 | publisher = Cold Spring Harbor Laboratory | doi-access = free }}{{cite journal | vauthors = Farley-Barnes KI, Ogawa LM, [[Susan J. Baserga|Baserga SJ]] | title = Ribosomopathies: Old Concepts, New Controversies | journal = Trends in Genetics | volume = 35 | issue = 10 | pages = 754–767 | date = October 2019 | pmid = 31376929 | pmc = 6852887 | doi = 10.1016/j.tig.2019.07.004 | publisher = Elsevier BV }} [165] => [166] => Heterogeneity in ribosome composition was first proposed to be involved in translational control of protein synthesis by Vince Mauro and [[Gerald Edelman]].{{cite journal | vauthors = Mauro VP, Edelman GM | title = The ribosome filter hypothesis | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 99 | issue = 19 | pages = 12031–6 | date = September 2002 | pmid = 12221294 | pmc = 129393 | doi = 10.1073/pnas.192442499 | bibcode = 2002PNAS...9912031M | doi-access = free }} 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.{{cite journal | vauthors = Xue S, Barna M | title = Specialized ribosomes: a new frontier in gene regulation and organismal biology | journal = Nature Reviews. Molecular Cell Biology | volume = 13 | issue = 6 | pages = 355–69 | date = May 2012 | pmid = 22617470 | pmc = 4039366 | doi = 10.1038/nrm3359 }} Some ribosomal proteins exchange from the assembled complex with [[cytosol]]ic copies{{cite journal | vauthors = Mathis AD, Naylor BC, Carson RH, Evans E, Harwell J, Knecht J, Hexem E, Peelor FF, Miller BF, Hamilton KL, Transtrum MK, Bikman BT, Price JC | title = Mechanisms of In Vivo Ribosome Maintenance Change in Response to Nutrient Signals | journal = Molecular & Cellular Proteomics | volume = 16 | issue = 2 | pages = 243–254 | date = February 2017 | pmid = 27932527 | pmc = 5294211 | doi = 10.1074/mcp.M116.063255 |doi-access=free }} suggesting that the structure of the ''in vivo'' ribosome can be modified without synthesizing an entire new ribosome. [167] => [168] => Certain ribosomal proteins are absolutely critical for cellular life while others are not. In [[Saccharomyces cerevisiae|budding yeast]], 14/78 ribosomal proteins are non-essential for growth, while in humans this depends on the cell of study.{{cite journal | vauthors = Steffen KK, McCormick MA, Pham KM, MacKay VL, Delaney JR, Murakami CJ, Kaeberlein M, Kennedy BK | display-authors = 6 | title = Ribosome deficiency protects against ER stress in Saccharomyces cerevisiae | journal = Genetics | volume = 191 | issue = 1 | pages = 107–118 | date = May 2012 | pmid = 22377630 | pmc = 3338253 | doi = 10.1534/genetics.111.136549 | publisher = Genetics Society of America }} Other forms of heterogeneity include post-translational modifications to ribosomal proteins such as acetylation, methylation, and phosphorylation.{{cite journal | vauthors = Lee SW, Berger SJ, Martinović S, Pasa-Tolić L, Anderson GA, Shen Y, Zhao R, Smith RD | display-authors = 6 | title = Direct mass spectrometric analysis of intact proteins of the yeast large ribosomal subunit using capillary LC/FTICR | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 99 | issue = 9 | pages = 5942–5947 | date = April 2002 | pmid = 11983894 | pmc = 122881 | doi = 10.1073/pnas.082119899 | doi-access = free | bibcode = 2002PNAS...99.5942L }} ''Arabidopsis'',{{cite journal | vauthors = Carroll AJ, Heazlewood JL, Ito J, Millar AH | title = Analysis of the Arabidopsis cytosolic ribosome proteome provides detailed insights into its components and their post-translational modification | journal = Molecular & Cellular Proteomics | volume = 7 | issue = 2 | pages = 347–369 | date = February 2008 | pmid = 17934214 | doi = 10.1074/mcp.m700052-mcp200 | doi-access = free }}{{cite journal | vauthors = Odintsova TI, Müller EC, Ivanov AV, Egorov TA, Bienert R, Vladimirov SN, Kostka S, Otto A, Wittmann-Liebold B, Karpova GG | display-authors = 6 | title = Characterization and analysis of posttranslational modifications of the human large cytoplasmic ribosomal subunit proteins by mass spectrometry and Edman sequencing | journal = Journal of Protein Chemistry | volume = 22 | issue = 3 | pages = 249–258 | date = April 2003 | pmid = 12962325 | doi = 10.1023/a:1025068419698 | s2cid = 10710245 }}{{cite journal | vauthors = Yu Y, Ji H, Doudna JA, Leary JA | title = Mass spectrometric analysis of the human 40S ribosomal subunit: native and HCV IRES-bound complexes | journal = Protein Science | volume = 14 | issue = 6 | pages = 1438–1446 | date = June 2005 | pmid = 15883184 | pmc = 2253395 | doi = 10.1110/ps.041293005 }}{{cite journal | vauthors = Zeidan Q, Wang Z, De Maio A, Hart GW | title = O-GlcNAc cycling enzymes associate with the translational machinery and modify core ribosomal proteins | journal = Molecular Biology of the Cell | volume = 21 | issue = 12 | pages = 1922–1936 | date = June 2010 | pmid = 20410138 | pmc = 2883937 | doi = 10.1091/mbc.e09-11-0941 }} Viral [[internal ribosome entry site|internal ribosome entry sites (IRESs)]] may mediate translations by compositionally distinct ribosomes. For example, 40S ribosomal units without [[RPS25|eS25]] in yeast and mammalian cells are unable to recruit the [[Cripavirus internal ribosome entry site|CrPV IGR IRES]].{{cite journal | vauthors = Landry DM, Hertz MI, Thompson SR | title = RPS25 is essential for translation initiation by the Dicistroviridae and hepatitis C viral IRESs | journal = Genes & Development | volume = 23 | issue = 23 | pages = 2753–2764 | date = December 2009 | pmid = 19952110 | pmc = 2788332 | doi = 10.1101/gad.1832209 }} [169] => [170] => 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.{{cite journal | vauthors = Decatur WA, Fournier MJ | title = rRNA modifications and ribosome function | journal = Trends in Biochemical Sciences | volume = 27 | issue = 7 | pages = 344–51 | date = July 2002 | pmid = 12114023 | doi = 10.1016/s0968-0004(02)02109-6 }}{{cite journal | vauthors = Natchiar SK, Myasnikov AG, Kratzat H, Hazemann I, Klaholz BP | title = Visualization of chemical modifications in the human 80S ribosome structure | journal = Nature | volume = 551 | issue = 7681 | pages = 472–477 | date = November 2017 | pmid = 29143818 | doi = 10.1038/nature24482 | bibcode = 2017Natur.551..472N | s2cid = 4465175 }} The most common rRNA modifications are [[Pseudouridine|pseudouridylation]] and [[2'-O-methylation]] of ribose.{{cite journal | vauthors = Guo H | title = Specialized ribosomes and the control of translation | journal = Biochemical Society Transactions | volume = 46 | issue = 4 | pages = 855–869 | date = August 2018 | pmid = 29986937 | doi = 10.1042/BST20160426 | s2cid = 51609077 }} [171] => [172] => == See also == [173] => {{Div col|colwidth=18em}} [174] => * [[Aminoglycoside]]s [175] => * [[Molecular machine#Biological|Biological machines]] [176] => * [[Posttranslational modification]] [177] => * [[Protein dynamics]] [178] => * [[RNA tertiary structure]] [179] => * [[Translation (genetics)]] [180] => * [[Wobble base pair]] [181] => * [[Ada Yonath]]—Israeli crystallographer known for her pioneering work on the structure of the ribosome, for which she won the [[Nobel Prize]]. [182] => {{Div col end}} [183] => [184] => == References == [185] => {{reflist|25em}} [186] => [187] => == External links == [188] => {{commons category|Ribosomes}} [189] => * [http://news.cnet.com/Lab+computer+simulates+ribosome+in+motion/2100-11395_3-5907401.html Lab computer simulates ribosome in motion] [190] => * [https://web.archive.org/web/20061027104335/http://www.cytochemistry.net/Cell-biology/ribosome.htm Role of the Ribosome], Gwen V. Childs, copied [https://web.archive.org/web/20071024162617/http://cellbio.utmb.edu/cellbio/ribosome.htm here] [191] => * [http://www.proteopedia.org/wiki/index.php/Ribosome Ribosome] in [http://www.proteopedia.org ''Proteopedia'']—The free, collaborative 3D encyclopedia of proteins & other molecules [192] => * [http://www.expasy.org/cgi-bin/lists?ribosomp.txt Ribosomal proteins families in ExPASy] {{Webarchive|url=https://web.archive.org/web/20110430181946/http://expasy.org/cgi-bin/lists?ribosomp.txt |date=2011-04-30 }} [193] => * [http://www.pdb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] {{Webarchive|url=https://web.archive.org/web/20091027143923/http://www.pdb.org/pdb/static.do?p=education_discussion%2Fmolecule_of_the_month%2Findex.html |date=2009-10-27 }} [https://web.archive.org/web/20070205000027/http://home.rcsb.org/ © RCSB Protein Data Bank]: [194] => ** [http://www.pdb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb10_1.html Ribosome] {{Webarchive|url=https://web.archive.org/web/20101114002238/http://www.pdb.org/pdb/static.do?p=education_discussion%2Fmolecule_of_the_month%2Fpdb10_1.html |date=2010-11-14 }} [195] => ** [http://www.pdb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb81_1.html Elongation Factors] {{Webarchive|url=https://web.archive.org/web/20110316083658/http://www.pdb.org/pdb/static.do?p=education_discussion%2Fmolecule_of_the_month%2Fpdb81_1.html |date=2011-03-16 }} [196] => ** [http://www.faqs.org/health/bios/79/George-Palade.html Palade] [197] => * [http://www.pdbe.org/emsearch/ribosome 3D electron microscopy structures of ribosomes at the EM Data Bank (EMDB)] [198] => * {{NCBI-scienceprimer}} [199] => [200] => {{organelles}} [201] => {{GeneticTranslation}} [202] => {{Ribosome subunits}} [203] => {{Authority control}} [204] => [205] => [[Category:Ribosome| ]] [206] => [[Category:Ribozymes]] [207] => [[Category:Protein biosynthesis]] [] => )
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Ribosome

The Wikipedia page on Ribosome provides an in-depth description of this essential cellular component responsible for protein synthesis. A ribosome is a large molecular complex composed of ribosomal RNA (rRNA) and proteins.

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A ribosome is a large molecular complex composed of ribosomal RNA (rRNA) and proteins. It is primarily found in the cytoplasm of cells but can also be found in the mitochondria and chloroplasts. The page outlines the structure of ribosomes, which consist of two subunits: a small subunit and a large subunit. These subunits come together during protein synthesis to form a functional ribosome. The composition and arrangement of rRNA and proteins within these subunits are described in detail, including their roles in catalyzing various steps of translation. The page discusses the various types of ribosomes found in different organisms, such as prokaryotes and eukaryotes. It highlights the structural and functional differences between these ribosomes and the significance of their divergence in evolutionary terms. Additionally, the page explains the process of protein synthesis and the crucial role of ribosomes in translating the genetic information stored in mRNA into functional proteins. It covers the initiation, elongation, and termination steps of translation and the involvement of ribosomal subunits and tRNA molecules in these processes. The regulation and control of ribosome activity are also discussed, highlighting the importance of ribosome biogenesis, modification, and turnover for maintaining cellular homeostasis. The page mentions the influence of various factors, such as environmental conditions and cellular demands, on ribosome production and function. Furthermore, the page explores the significance of ribosomes in cell biology and human health. It delves into ribosome-related diseases, such as Diamond-Blackfan anemia, and the role of antibiotics that target ribosomes in treating bacterial infections. Overall, the Wikipedia page on Ribosome provides a comprehensive overview of this vital cellular structure, covering its structure, function, regulation, and importance in various biological processes.

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