Ribosome 25766 226094653 2008-07-16T20:16:25Z TimVickers 1635280 Reverted edits by [[Special:Contributions/132.239.107.224|132.239.107.224]] ([[User talk:132.239.107.224|talk]]) to last version by MattieTK [[Image:Biological cell.svg|thumb|350px|Diagram of a typical [[eukaryotic]] cell, showing subcellular components including '''ribosomes''' (3).<br/> [[Organelle]]s:<br/> (1) [[nucleolus]]<br/> (2) [[cell nucleus|nucleus]]<br/> (3) ribosomes (little dots)<br/> (4) [[vesicle (biology)|vesicle]]<br/> (5) rough [[endoplasmic reticulum]] (ER)<br/> (6) [[Golgi apparatus]]<br/> (7) [[Cytoskeleton]]<br/> (8) smooth ER<br/> (9) [[mitochondrion|mitochondria]]<br/> (10) [[vacuole]]<br/> (11) [[cytoplasm]]<br/> (12) [[lysosome]]<br/> (13) [[centriole]]s within [[centrosome]]]] '''Ribosomes''' (''from '''ribo'''nucleic acid and "Greek: '''soma''' (''meaning'' body)"'') are complexes of [[RNA]] and [[protein]] that are found in all [[cell (biology)|cell]]s. Ribosomes from [[bacteria]] and [[archaea]] are smaller than the ribosomes from [[eukaryote]]s, although all three domains of life have significantly different ribosomes. Interestingly, the ribosomes in the [[mitochondrion]] of eukaryotic cells resemble those in bacteria, reflecting the evolutionary origin of this [[organelle]].<ref>{{cite journal |author=Benne R, Sloof P |title=Evolution of the mitochondrial protein synthetic machinery |journal=BioSystems |volume=21 |issue=1 |pages=51–68 |year=1987 |pmid=2446672 |doi=10.1016/0303-2647(87)90006-2}}</ref> The ribosome functions in the expression of the genetic code from nucleic acid into [[protein]], in a process called ''[[translation (biology)|translation]]''. Ribosomes do this by catalyzing the assembly of individual [[amino acid]]s into [[polypeptide]] chains; this involves binding a [[messenger RNA]] and then using this as a template to join together the correct sequence of amino acids. This reaction uses adapters called [[transfer RNA]] molecules, which read the sequence of the messenger RNA and are attached to the amino acids. ==Description== '''Ribosomes''' are about 20[[Nanometre|nm]] (200 [[Ångström]]) in diameter and are composed of 65% [[ribosomal RNA]] and 35% [[ribosomal protein]]s (known as a [[Ribonucleoprotein]] or RNP). They [[translation (genetics)|translate]] [[mRNA|messenger RNA (mRNA)]] to build [[polypeptide]] chains (e.g., [[protein]]s) using amino acids delivered by [[tRNA|transfer RNA (tRNA)]]. Their active sites are made of RNA, so ribosomes are now classified as "[[ribozyme]]s."<ref>{{cite journal |author=Rodnina MV, Beringer M, Wintermeyer W |title=How ribosomes make peptide bonds |journal=Trends Biochem. Sci. |volume=32 |issue=1 |pages=20–6 |year=2007 |pmid=17157507 |doi=10.1016/j.tibs.2006.11.007}}</ref> Ribosomes build proteins from the genetic instructions held within [[messenger RNA]]. Free ribosomes are suspended in the [[cytosol]] (the semi-fluid portion of the [[cytoplasm]]); others are bound to the [[rough endoplasmic reticulum]], giving it the appearance of roughness and thus its name, or to the [[nuclear envelope]]. As ribozymes are partly constituted from RNA, it is thought that they might be remnants of the [[RNA world]].<ref>{{cite journal |author=Cech T |title=Structural biology. The ribosome is a ribozyme |journal=Science |volume=289 |issue=5481 |pages=878–9 |year=2000 |pmid=10960319 | doi = 10.1126/science.289.5481.878 <!--Retrieved from CrossRef by DOI bot-->}}</ref> Catalysis of the [[peptide bond]] involves the C2 hydroxyl of RNA's P-site adenosine in a protein shuttle mechanism. The full function (i.e. translocation) of the ribosome is reliant on changes in protein conformations. Ribosomes are sometimes referred to as [[organelle]]s, but the use of the term ''organelle'' is often used only in reference to sub-cellular components that include a phosholipid membrane, which ribosomes, being entirely particulate, do not. For this reason, ribosomes may sometimes be described as "non-membranous organelles". Ribosomes are an extremely important structure in the cell. Ribosomes were first observed in the mid-1950s by [[Romania]]n cell biologist [[George Palade]] using an [[electron microscope]] as dense particles or granules<ref>G.E. Palade. (1955) "A small particulate component of the cytoplasm." ''J Biophys Biochem Cytol.'' Jan;1(1): pages 59-68. PMID 14381428</ref> for which he would win the [[Nobel Prize]]. The term "ribosome" was proposed by scientist Richard B. Roberts in 1958: {{Quotation|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; this seems a very satisfactory name, and it has a pleasant sound. The present confusion would be eliminated if “ribosome” were adopted to designate ribonucleoprotein particles in sizes ranging from 35 to 100S.|Roberts, R. B.|Microsomal Particles and Protein Synthesis<ref>Roberts, R. B., editor. (1958) "Introduction" in ''Microsomal Particles and Protein Synthesis.'' New York: Pergamon Press, Inc.</ref>}} The structure and function of the ribosomes and associated molecules, known as the ''translational apparatus'', has been of research interest since the mid-twentieth century and is a very active field of study today. [[Image:ribosome structure fixed.png|frame|'''Figure 2 :''' Large (1) and small (2) subunit fit together]] Ribosomes consist of two subunits (Figure 1) that fit together (Figure 2) and work as one to translate the [[mRNA]] into a polypeptide chain during protein synthesis (Figure 3). [[Bacterial]] subunits consist of one or two and [[eukaryotic]] of one or three very large [[RNA]] molecules (known as ribosomal RNA or [[rRNA]]) and multiple smaller protein molecules. [[Crystallography|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 act as a scaffold that may enhance the ability of rRNA to synthesize protein rather than directly participating in catalysis (See: [[Ribozyme]]). ==Biogenesis== {{main|Ribosome biogenesis}} In bacterial cells, ribosomes synthesize with cytoplasm to enable the [[Transcription (genetics)|transcription]] of multiple ribosome gene [[operon]]s. In eukaryotes and some bacterial cells, the process takes place both in the cell cytoplasm and in the nucleolus of eukaryotic cells. It 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. ==Ribosome locations== Ribosomes are classified as being either "free" or "membrane-bound." ===Free ribosomes=== Free ribosomes are free to move about anywhere in the [[cytoplasm]] (within the [[cell membrane]]). Proteins that are formed from free ribosomes are used within the cell. Proteins containing [[disulfide bonds]] using [[cysteine]] [[amino acids]] cannot be produced outside of the [[lumen (anatomy)|lumen]] of the endoplasmic reticulum. ===Membrane-bound ribosomes=== When certain proteins are synthesized by a ribosome they can become "membrane-bound". The newly produced polypeptide chains are inserted directly into the [[endoplasmic reticulum]] by the ribosome and are then transported to their destinations. Bound ribosomes usually produce proteins that are used within the cell membrane or are expelled from the cell via ''[[exocytosis]]''. Free and membrane-bound ribosomes differ only in their spatial distribution; they are identical in structure and function. Whether the ribosome exists in a free or membrane-bound state depends on the presence of a [[signal peptide|ER-targeting signal sequence]] on the protein being synthesized. ==Structure== [[Image:10 small subunit.gif|thumb|350px|right|Atomic structure of the 30S Subunit from ''[[Thermus thermophilus]]''. Proteins are shown in blue and the single RNA strand in orange.<ref name=Schluenzen>{{cite journal |author=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 |year=2000 |pmid=11007480 | doi = 10.1016/S0092-8674(00)00084-2 <!--Retrieved from CrossRef by DOI bot-->}}</ref>]] The ribosomal subunits of [[bacteria]]s and [[eukaryote]]s are quite similar.<ref name = alberts> The Molecular Biology of the Cell, fourth eddition. Brusce Alberts, et al. Garland Science (2002) pg. 342 ISBN 0-8153-3218-1</ref> Bacteria have 70[[Svedberg|S]] ribosomes, each consisting of a small ([[30S]]) and a large ([[50S]]) subunit. Their large subunit is composed of a [[5S ribosomal RNA|5S]] [[RNA]] subunit (consisting of 120 nucleotides), a 23S RNA subunit (2900 nucleotides) and 34 [[protein]]s. The 30S subunit has a 1540 nucleotide RNA subunit ([[16S ribosomal RNA|16S]]) bound to 21 proteins.<ref name = alberts/> Eukaryotes have 80S ribosomes, each consisting of a small ([[40S]]) and large ([[60S]]) subunit. Their large subunit is composed of a 5S RNA (120 nucleotides), a 28S RNA (4700 nucleotides), a 5.8S subunit (160 nucleotides) and ~49 proteins. The 40S subunit has a 1900 nucleotide (18S) RNA and ~33 proteins.<ref name = alberts/> The ribosomes found in [[chloroplast]]s and [[mitochondria]] of eukaryotes also consist of large and small subunits bound together with [[protein]]s into one 70S particle.<ref name = alberts/> These [[organelles]] are believed to be descendants of [[bacteria]] (see [[Endosymbiotic theory]]) and as such their ribosomes are similar to those of bacteria.<ref> The Molecular Biology of the Cell, fourth edition. Bruce Alberts, et al. Garland Science (2002) pg. 808 ISBN 0-8153-3218-1</ref> The various ribosomes share a core structure which is quite similar despite the large differences in size. 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.<ref name = alberts/> 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.<ref name = alberts/> 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.<ref name=Recht>{{cite journal |author=Recht MI, Douthwaite S, Puglisi JD |title=Basis for bacterial specificity of action of aminoglycoside antibiotics |journal=EMBO J |volume=18 |issue=11 |pages=3133–8 |year=1999 |pmid=10357824 | doi = 10.1093/emboj/18.11.3133 <!--Retrieved from CrossRef by DOI bot-->}}</ref> 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]].<ref> O'Brien, T.W., The General Occurrence of 55S Ribosomes in Mammalian Liver Mitochondria. J. Biol. Chem., 245:3409 (1971).</ref> ===Atomic structure=== [[Image:10 large subunit.gif|thumb|350px|right|Atomic structure of the 50S Subunit from ''[[Haloarcula marismortui]]''. Proteins are shown in blue and the two RNA strands in orange and yellow.<ref name=Ban>{{cite journal |author=Ban N, Nissen P, Hansen J, Moore P, Steitz T |title=The complete atomic structure of the large ribosomal subunit at 2.4 [[Ångström|A]] resolution |journal=Science |volume=289 |issue=5481 |pages=905–20 |year=2000 |pmid=10937989 | doi = 10.1126/science.289.5481.905 <!--Retrieved from CrossRef by DOI bot-->}}</ref> The small patch of green in the center of the subunit is the active site.]] 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, in the order of a few [[Ångström]]s. The first papers giving the structure of the ribosome at atomic resolution, were published in rapid succession in late 2000. First, the 50S (large bacteria) subunit from the [[archea]], ''Haloarcula marismortui'' was published.<ref name=Ban/> Soon after the structure of the 30S subunit from ''[[Thermus thermophilus]]'' was published.<ref name=Schluenzen/> Shortly thereafter a more detailed structure was published.<ref>Wimberly BT, Brodersen DE, Clemons WM Jr, Morgan-Warren RJ, Carter AP, Vonrhein C, Hartsch T, Ramakrishnan V. Structure of the 30S ribosomal subunit. ''Nature.'' 2000 Sep 21;407(6802):327-39. PMID 11014182</ref> Early the next year (May 2001) these coordinates were used to reconstruct the entire ''[[Thermus thermophilus|T. thermophilus]]'' 70S particle at 5.5 Ångström resolution.<ref>Yusupov MM, Yusupova GZ, Baucom A, Lieberman K, Earnest TN, Cate JH, Noller HF. Crystal structure of the ribosome at 5.5 [[Ångström|Å]] resolution. ''Science.'' 2001 May 4;292(5518):883-96. Epub 2001 Mar 29. PMID 11283358</ref> Two papers were published in November 2005 with structures of the ''[[Escherichia coli]]'' 70S ribosome. The structures of vacant ribosome were determined at 3.5 Ångström resolution using [[x-ray crystallography]].<ref>Schuwirth BS, Borovinskaya MA, Hau CW, Zhang W, Vila-Sanjurjo A, Holton JM, Cate JH. Structures of the bacterial ribosome at 3.5 Ångström resolution. ''Science.'' 2005 Nov 4;310(5749):827-34. PMID 16272117</ref> Then, two weeks later, a structure based on cryo-[[electron microscope|electron microsopy]] was published,<ref>Mitra K, Schaffitzel C, Shaikh T, Tama F, Jenni S, Brooks CL 3rd, Ban N, Frank J. Structure of the ''E. coli'' protein-conducting channel bound to a translating ribosome. ''Nature.'' 2005 Nov 17;438(7066):318-24. PMID 16292303</ref> which depicts the ribosome at 11-15 Ångström resolution in the act of passing a newly synthesized protein strand into the protein-conducting channel. 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<ref>Selmer, M., Dunham, C.M., Murphy, F.V IV, Weixlbaumer, A., Petry S., Kelley, A.C., Weir, J.R. and Ramakrishnan, V. (2006). Structure of the 70S ribosome complexed with mRNA and tRNA. Science , 313, 1935-1942. PMID 16959973 </ref> and at 3.7 Ångström.<ref> Korostelev A, Trakhanov S, Laurberg M, Noller HF. Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangements. Cell. 2006 Sep 22;126(6):1065-77</ref> 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 sequences were visualized soon after that at 4.5 to 5.5 Ångström resolution.<ref>Yusupova G, Jenner L, Rees B, Moras D, Yusupov M. Structural basis for messenger RNA movement on the ribosome. Nature. 2006 Nov 16;444(7117):391-4</ref> ==Function== {{main|Translation (biology)}} Ribosomes are the workhorses of [[protein biosynthesis]], the process of translating RNA into [[protein]]. The mRNA comprises a series of [[codon]]s that dictate to the ribosome the sequence of the [[amino acid]]s needed to make the protein. Using the mRNA as a template, the ribosome traverses each codon of the mRNA, pairing it with the appropriate amino acid. This is done using molecules of [[transfer RNA]] (tRNA) containing a complementary [[anticodon]] on one end and the appropriate amino acid on the other. Protein synthesis begins at a [[start codon]] near the 5' end of the RNA. The small ribosomal subunit, typically bound to a tRNA containing the amino acid [[methionine]], binds to an AUG codon on the mRNA and recruits the large ribosomal subunit. The large ribosomal subunit contains three tRNA binding sites, designated A, P, and E. The A site binds an aminoacyl-tRNA (a tRNA bound to an amino acid); the P site binds a peptidyl-tRNA (a tRNA bound to the peptide being synthesized); and the E site binds a free tRNA before it exits the ribosome. [[Image:ribosome.png|frame|none|'''Figure 3 :''' Translation of mRNA (1) by a ribosome (2) into a <font color=#AA00AA>polypeptide chain</font> (3). The mRNA begins with a start [[codon]] (<font color="#00AA00">AUG</font>) and ends with a stop codon (<font color="#00AA00">UAG</font>).]] In Figure 3, both ribosomal subunits (<font color="#0000AA">small</font> and <font color="#AA0000">large</font>) assemble at the start codon (towards the 5' end of the mRNA). The ribosome uses [[tRNA]] which 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 we call a ''polyribosome'' or ''[[polysome]]''. ==References== {{reflist|2}} ==See also== <div style="-moz-column-count:3; column-count:3;"> *[[Translation (genetics)|Translation]] *[[bacterial translation]] *[[Eukaryotic translation]] *[[Nucleolus]] *[[Wobble base pair]] *[[rRNA]] *[[Endoplasmic reticulum]] *[[Post-translational modification]] *[[Aminoglycoside]]s </div> ==External links== * [http://www.bio.cmu.edu/Courses/BiochemMols/ribosome/70S.htm 70S Ribosome Architecture Animation of a working ribosome]. Requires the Chime browser plugin from [http://www.mdl.com/products/framework/chime/ this site] (where registration is required). * [http://news.com.com/Lab+computer+simulates+ribosome+in+motion/2100-11395_3-5907401.html Lab computer simulates ribosome in motion] * [http://www.cytochemistry.net/Cell-biology/ribosome.htm Role of the Ribosome], Gwen V. Childs, copied [http://cellbio.utmb.edu/cellbio/ribosome.htm here] * [http://www.pdb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] [http://home.rcsb.org/ © RCSB Protein Data Bank]: ** [http://www.pdb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb10_1.html Ribosome] ** [http://www.pdb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb81_1.html Elongation Factors] {{organelles}} {{Ribosome subunits}} {{NCBI-scienceprimer}} [[Category:Ribozymes]] [[Category:Protein biosynthesis]] [[Category:Organelles]] [[ar:ريبوسوم]] [[bs:Ribozomi]] [[bg:Рибозома]] [[ca:Ribosoma]] [[cs:Ribozom]] [[cy:Ribosom]] [[da:Ribosom]] [[de:Ribosom]] [[el:Ριβόσωμα]] [[es:Ribosoma]] [[eo:Ribosomo]] [[eu:Erribosoma]] [[fa:ریبوزوم]] [[fo:Ribosom]] [[fr:Ribosome]] [[gl:Ribosoma]] [[ko:리보솜]] [[hr:Ribosomi]] [[id:Ribosom]] [[ia:Ribosoma]] [[it:Ribosoma]] [[he:ריבוזום]] [[la:Ribosoma]] [[lb:Ribosom]] [[lt:Ribosoma]] [[mk:Рибозом]] [[ms:Ribosom]] [[nl:Ribosoom]] [[ja:リボソーム]] [[no:Ribosom]] [[oc:Ribosòma]] [[pl:Rybosom]] [[pt:Ribossomo]] [[ro:Ribozom]] [[ru:Рибосома]] [[simple:Ribosome]] [[sk:Ribozóm]] [[sl:Ribosom]] [[sr:Рибозом]] [[sh:Ribozom]] [[fi:Ribosomi]] [[sv:Ribosom]] [[th:ไรโบโซม]] [[vi:Ribosome]] [[tr:Ribozom]] [[uk:Рибосома]] [[zh:核糖体]]