Editing Ribosome (section)

=== Translation ===
{{Main|Translation (biology)}}

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 to make the protein. Using the mRNA as a template, the ribosome traverses each codon (3&nbsp;[[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]]).<ref name="Savir-2013">{{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 }}</ref> 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;<ref>{{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 }}</ref><ref name="Konevega-2004">{{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&nbsp;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 }}</ref> 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.

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,"<ref>{{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 }}</ref> and it is thought that they might be remnants of the [[RNA world]].<ref>{{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 }}</ref>

[[File:Ribosomer i arbete.png|frame|none|'''Figure 5:''' Translation of mRNA (1) by a ribosome (2)(shown as <span style="color:#0000AA;">small</span> and <span style="color:#AA0000;">large</span> subunits) into a <span style="color:#AA00AA;">polypeptide chain</span> (3). The ribosome begins at the start codon of RNA (<span style="color:#00AA00;">AUG</span>) and ends at the stop codon (<span style="color:#00AA00;">UAG</span>).]]

In Figure&nbsp;5, both ribosomal subunits (<span style="color:#0000AA;">small</span> and <span style="color:#AA0000;">large</span>) 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]]''.

==== Cotranslational folding ====
The ribosome is known to actively participate in the [[protein folding]].<ref>{{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 }}</ref><ref>{{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 }}</ref> 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.<ref>{{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 }}</ref><ref>{{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 }}</ref> 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.<ref>{{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 }}</ref>