Editing Transfer RNA (section)

== Structure ==
[[File:TRNA-Phe yeast en.svg|thumb|Secondary cloverleaf structure of a tRNA encoding for phenylalanine.]]
[[File:TRNA-Phe yeast 1ehz.png|thumb|Tertiary structure of tRNA. <span style="color:#E4D00A;">''CCA tail''</span> in yellow, <span style="color:purple;">''acceptor stem''</span> in purple, <span style="color:orange;">''variable loop''</span> in orange, <span style="color:red;">''D arm''</span> in red, <span style="color:blue;">''anticodon arm''</span> in blue with ''anticodon'' in black, <span style="color:green;">''T arm''</span> in green.]] [[File:Trna.gif|thumb|3D animated GIF showing the structure of phenylalanine-tRNA from yeast (PDB ID 1ehz). White lines indicate base pairing by hydrogen bonds. In the orientation shown, the acceptor stem is on top and the anticodon on the bottom.<ref name="tRNA proteopedia">{{cite web |url=https://proteopedia.org/wiki/index.php/Transfer_RNA_%28tRNA%29| title=Transfer RNA (tRNA) | author=<!--Not stated--> | website=Proteopedia.org | access-date= 7 November 2018}}</ref>]]
The structure of tRNA can be decomposed into its [[primary structure]], its [[Nucleic acid secondary structure|secondary structure]] (usually visualized as the ''cloverleaf structure''), and its [[tertiary structure]]<ref name="itoh">{{cite journal | vauthors = Itoh Y, Sekine S, Suetsugu S, Yokoyama S | title = Tertiary structure of bacterial serenocysteine tRNA | journal = Nucleic Acids Research | volume = 41 | issue = 13 | pages = 6729–6738 | date = July 2013 | pmid = 23649835 | pmc = 3711452 | doi = 10.1093/nar/gkt321 }}</ref> (all tRNAs have a similar L-shaped 3D structure that allows them to fit into the [[P-site|P]] and [[A-site|A]] sites of the [[ribosome]]). The cloverleaf structure becomes the 3D L-shaped structure through coaxial stacking of the helices, which is a common [[nucleic acid tertiary structure|RNA tertiary structure]] motif. The lengths of each arm, as well as the loop 'diameter', in a tRNA molecule vary from species to species.<ref name="itoh" /><ref name="goodenbour2006">{{cite journal | vauthors = Goodenbour JM, Pan T | title = Diversity of tRNA genes in eukaryotes | journal = Nucleic Acids Research | volume = 34 | issue = 21 | pages = 6137–6146 | date = 29 October 2006 | pmid = 17088292 | pmc = 1693877 | doi = 10.1093/nar/gkl725 | url = }}</ref>
The tRNA structure consists of the following:
* The '''acceptor stem''' is a 7- to 9-base pair (bp) stem made by the base pairing of the 5′-terminal nucleotide with the 3′-terminal nucleotide (which contains the CCA tail used to attach the amino acid). The acceptor stem may contain non-Watson-Crick base pairs.<ref name="itoh" /><ref>{{cite journal | vauthors = Jahn M, Rogers MJ, Söll D | title = Anticodon and acceptor stem nucleotides in tRNA(Gln) are major recognition elements for E. coli glutaminyl-tRNA synthetase | journal = Nature | volume = 352 | issue = 6332 | pages = 258–260 | date = July 1991 | pmid = 1857423 | doi = 10.1038/352258a0 | bibcode = 1991Natur.352..258J | s2cid = 4263705 }}</ref>
* The '''CCA tail''' is a [[cytosine]]-cytosine-[[adenine]] sequence at the 3′ end of the tRNA molecule. The amino acid loaded onto the tRNA by [[aminoacyl tRNA synthetase]]s, to form [[aminoacyl-tRNA]], is covalently bonded to the 3′-hydroxyl group on the CCA tail.<ref name="ibba">{{cite journal | vauthors = Ibba M, Soll D | title = Aminoacyl-tRNA synthesis | journal = Annual Review of Biochemistry | volume = 69 | issue = 1 | pages = 617–650 | date = June 2000 | pmid = 10966471 | doi = 10.1146/annurev.biochem.69.1.617 }}</ref> This sequence is important for the recognition of tRNA by enzymes and critical in translation.<ref name="pmid392600">{{cite journal | vauthors = Sprinzl M, Cramer F | title = The -C-C-A end of tRNA and its role in protein biosynthesis | journal = Progress in Nucleic Acid Research and Molecular Biology | volume = 22 | pages = 1–69 | date = 1979 | pmid = 392600 | doi = 10.1016/s0079-6603(08)60798-9| isbn = 978-0-12-540022-0 }}</ref><ref name="pmid9242921">{{cite journal | vauthors = Green R, Noller HF | title = Ribosomes and translation | journal = Annual Review of Biochemistry | volume = 66 | pages = 679–716 | date = 1997 | pmid = 9242921 | doi = 10.1146/annurev.biochem.66.1.679 }}</ref> In prokaryotes, the CCA sequence is transcribed in some tRNA sequences. In most prokaryotic tRNAs and eukaryotic tRNAs, the CCA sequence is added during processing and therefore does not appear in the tRNA gene.<ref>{{cite journal | vauthors = Aebi M, Kirchner G, Chen JY, Vijayraghavan U, Jacobson A, Martin NC, Abelson J | title = Isolation of a temperature-sensitive mutant with an altered tRNA nucleotidyltransferase and cloning of the gene encoding tRNA nucleotidyltransferase in the yeast Saccharomyces cerevisiae | journal = The Journal of Biological Chemistry | volume = 265 | issue = 27 | pages = 16216–16220 | date = September 1990 | doi = 10.1016/S0021-9258(17)46210-7 | pmid = 2204621 | display-authors = etal | doi-access = free }}</ref>
* The [[D arm|'''D loop''']] is a 4- to 6-bp stem ending in a loop that often contains [[dihydrouridine]].<ref name="itoh" />
* The '''anticodon loop''' is a 5-bp stem whose loop contains the [[#Anticodon|anticodon]].<ref name="itoh" />
* The [[T arm|'''TΨC loop''']] is named so because of the characteristic presence of the unusual base Ψ in the loop, where Ψ is [[pseudouridine]], a modified [[uridine]]. The modified base is often found within the sequence 5'-TΨCGA-3', with the T ([[ribothymidine]], m5U) and A forming a base pair.<ref>{{cite journal |last1=Chan |first1=CW |last2=Chetnani |first2=B |last3=Mondragón |first3=A |title=Structure and function of the T-loop structural motif in noncoding RNAs. |journal=Wiley Interdisciplinary Reviews. RNA |date=September 2013 |volume=4 |issue=5 |pages=507–22 |doi=10.1002/wrna.1175 |pmid=23754657|pmc=3748142}}</ref>
* The '''variable loop''' or ''V loop'' sits between the anticodon loop and the ΨU loop and, as its name implies, varies in size from 3 to 21 bases. In some tRNAs, the "loop" is long enough to form a rigid stem, the ''variable arm''.<ref name="pmid35882385">{{cite journal | vauthors = Prabhakar A, Krahn N, Zhang J, Vargas-Rodriguez O, Krupkin M, Fu Z, Acosta-Reyes FJ, Ge X, Choi J, Crnković A, Ehrenberg M, Puglisi EV, Söll D, Puglisi J  | title = Uncovering translation roadblocks during the development of a synthetic tRNA | journal = Nucleic Acids Res | volume= 50| date = Jul 2022 | issue = 18 | pages = 10201–10211 | pmid = 35882385 | doi = 10.1093/nar/gkac576 | pmc = 9561287 }}</ref> tRNAs with a V loop more than 10 bases long is classified as "class II" and the rest is called "class I".<ref>{{cite journal |last1=Brennan |first1=T. |last2=Sundaralingam |first2=M. |title=Structure, of transfer RNA molecules containing the long variable loop |journal=Nucleic Acids Research |date=1 November 1976 |volume=3 |issue=11 |pages=3235–3252 |doi=10.1093/nar/3.11.3235|doi-access=free|pmid=794835 |pmc=343166 }}</ref>

===Anticodon===
An '''anticodon'''<ref>{{cite journal | vauthors = Felsenfeld G, Cantoni GL | title = Use of thermal denaturation studies to investigate the base sequence of yeast serine sRNA | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 51 | issue = 5 | pages = 818–826 | date = May 1964 | pmid = 14172997 | pmc = 300168 | doi = 10.1073/pnas.51.5.818 | bibcode = 1964PNAS...51..818F | doi-access = free }}</ref> is a unit of three [[nucleotides]] corresponding to the three bases of an [[mRNA]] [[genetic code|codon]]. Each tRNA has a distinct anticodon triplet sequence that can form 3 [[Complementarity (molecular biology)|complementary]] [[base pair]]s to one or more codons for an amino acid. Some anticodons pair with more than one codon due to [[wobble base pair]]ing. Frequently, the first nucleotide of the anticodon is one not found on mRNA: [[inosine]], which can [[hydrogen bond]] to more than one base in the corresponding codon position.<ref name="Stryer2002" />{{rp|29.3.9}} In [[genetic code]], it is common for a single amino acid to be specified by all four third-position possibilities, or at least by both [[pyrimidine]]s and [[purine]]s; for example, the amino acid [[glycine]] is coded for by the codon sequences GGU, GGC, GGA, and GGG. Other modified nucleotides may also appear at the first anticodon position—sometimes known as the "wobble position"—resulting in subtle changes to the genetic code, as for example in [[mitochondria]].<ref>{{cite journal | vauthors = Suzuki T, Suzuki T | title = A complete landscape of post-transcriptional modifications in mammalian mitochondrial tRNAs | journal = Nucleic Acids Research | volume = 42 | issue = 11 | pages = 7346–7357 | date = June 2014 | pmid = 24831542 | pmc = 4066797 | doi = 10.1093/nar/gku390 }}</ref> The possibility of wobble bases reduces the number of tRNA types required: instead of 61 types with one for each sense codon of the standard genetic code), only 31 tRNAs are required to translate, unambiguously, all 61 sense codons.<ref name="crick" /><ref>Lodish H, Berk A, Matsudaira P, Kaiser CA, Krieger M, Scott MP, Zipursky SL, Darnell J. (2004). ''Molecular Cell Biology''. WH Freeman: New York. 5th ed.{{ISBN|978-0716743668}}{{page needed|date=April 2019}}</ref>