Transfer RNA
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2008-07-07T11:48:39Z
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[[Image:Schema ARNt 448 658.png|thumb|Transfer RNA From {{PDB|6tna}} {{Proteopedia|6tna}}]]
'''Transfer RNA''' (abbreviated '''tRNA''') is a small [[RNA]] (usually about 74-95 nucleotides) that transfers a specific [[amino acid]] to a growing polypeptide chain at the ribosomal site of protein synthesis during [[translation (biology)|translation]]. It has a [[Directionality (molecular biology)|3' terminal]] site for amino acid attachment. This covalent linkage is catalyzed by an [[aminoacyl tRNA synthetase]]. It also contains a three [[nucleotide|base]] region called the [[anticodon]] that can base pair to the corresponding three base [[codon]] region on [[mRNA]]. Each type of tRNA molecule can be attached to only one type of amino acid, but because the [[genetic code]] contains multiple codons that specify the same amino acid, tRNA molecules bearing different anticodons may also carry the same amino acid.
==Structure==
[[Image:3d tRNA.png|thumb|right|Structure of tRNA. ''CCA tail'' in orange, ''Acceptor stem'' in purple, ''D arm'' in red, ''Anticodon arm'' in blue with ''Anticodon'' in black, ''T arm'' in green.]]
tRNA has [[primary structure]], [[secondary structure]] (usually visualized as the ''cloverleaf structure''), and [[tertiary structure]] (all tRNAs have a similar L-shaped 3D structure that allows them to fit into the [[translation (biology)|P and A sites]] of the [[ribosome]]).
#The [[5' end|5'-terminal]] [[phosphate]] group.
#The acceptor stem is a 7-bp stem made by the base pairing of the 5'-terminal nucleotide with the 3'-terminal nucleotide (which contains the CCA 3'-terminal group used to attach the amino acid). The acceptor stem may contain non-Watson-Crick base pairs.
#The CCA tail is a CCA sequence at the 3' end of the tRNA molecule. This sequence is important for the recognition of tRNA by enzymes critical in translation. In prokaryotes, the CCA sequence is transcribed. In eukaryotes, the CCA sequence is added during processing and therefore does not appear in the tRNA gene.
#The [[D arm]] is a 4 bp stem ending in a loop that often contains [[dihydrouridine]].
#The anticodon arm is a 5-bp stem whose loop contains the [[Transfer RNA#Anticodon|anticodon]].
#The [[T arm]] is a 5 bp stem containing the sequence TΨC where Ψ is a [[pseudouridine]].
#Bases that have been modified, especially by [[methylation]], occur in several positions outside the anticodon. The first anticodon base is sometimes modified to [[inosine]] (derived from adenine) or [[pseudouridine]] (derived from uracil).
==Anticodon==
An '''anticodon'''<ref>{{cite journal |author=Felsenfeld G, Cantoni G |title=Use of thermal denaturation studies to investigate the base sequence of yeast serine sRNA |journal=Proc Natl Acad Sci U S A |volume=51 |issue= |pages=818–26 |year= 1964|pmid=14172997 |doi=10.1073/pnas.51.5.818}}</ref> is a unit made up of three [[nucleotides]] that correspond to the three bases of the codon on the mRNA. Each tRNA contains a specific anticodon triplet sequence that can base-pair to one or more codons for an amino acid. For example, one codon for [[lysine]] is AAA; the anticodon of a lysine tRNA might be UUU. Some anticodons can pair with more than one codon due to a phenomenon known as [[wobble base pair]]ing. Frequently, the first nucleotide of the anticodon is one of two not found on mRNA: [[inosine]] and [[pseudouridine]], which can [[hydrogen bond]] to more than one base in the corresponding codon position. In the [[genetic code]], it is common for a single amino acid to be specified by all four third-position possibilities; for example, the amino acid [[glycine]] is coded for by the codon sequences GGU, GGC, GGA, and GGG.
To provide a one-to-one correspondence between tRNA molecules and codons that specify amino acids, 61 tRNA molecules would be required per cell. However, many cells contain fewer than 61 types of tRNAs because the wobble base is capable of binding to several, though not necessarily all, of the codons that specify a particular amino acid.<ref>Lodish H, Berk A, Matsudaira P, Kaiser CA, Krieger M, Scott MP, Zipursky SL, Darnell J. (2004). Molecular Biology of the Cell. WH Freeman: New York, NY. 5th ed.</ref>
==Aminoacylation==
[[Aminoacylation]] is the process of adding an aminoacyl group to a compound. It produces tRNA molecules with their CCA 3' ends covalently linked to an [[amino acid]].
Each tRNA is [[aminoacylation|aminoacylated]] (or ''charged'') with a specific amino acid by an [[aminoacyl tRNA synthetase]]. There is normally a single aminoacyl tRNA synthetase for each amino acid, despite the fact that there can be more than one tRNA, and more than one anticodon, for an amino acid. Recognition of the appropriate tRNA by the synthetases is not mediated solely by the anticodon, and the acceptor stem often plays a prominent role.
Reaction:
#amino acid + ATP → aminoacyl-AMP + PPi
#aminoacyl-AMP + tRNA → aminoacyl-tRNA + AMP
==Binding to Ribosome==
The ribosome has three binding sites for tRNA molecules: the A, P and E sites. During translation the A site binds an incoming aminoacyl-tRNA as directed by the codon currently occupying this site. This codon specifies the next amino acid to be added to the growing peptide chain. The A site only works after the first aminoacyl-tRNA has attached to the P site. The P-site codon is occupied by peptdyl-tRNA that is a tRNA with multiple amino acids attached as a long chain. The P site is actually the first to bind to aminoacyl tRNA. This tRNA in the P site carries the chain of amino acids that has already been synthesized. The E site is occupied by the empty tRNA as it is about to exit the ribosome.
==tRNA genes==
Organisms vary in the number of tRNA [[genes]] in their [[genome]]. The [[nematode]] worm ''[[Caenorhabditis elegans|C. elegans]]'', a commonly used model organism in [[genetics]] studies, has 29,647 <ref>WormBase web site, http://www.wormbase.org, release WS187, date 25-Jan-2008.</ref> genes in its [[cell nucleus|nuclear]] genome, of which 620 code for tRNA.<ref>Spieth, J. and Lawson, D. Overview of gene structure (January 18, 2006), WormBook, ed. The C. elegans Research Community, WormBook, doi/10.1895/wormbook.1.65.1, http://www.wormbook.org</ref><ref>Hartwell LH, Hood L, Goldberg ML, Reynolds AE, Silver LM, Veres RC. (2004). ''Genetics: From Genes to Genomes'' 2nd ed. McGraw-Hill: New York, NY. p 264.</ref> The budding yeast ''[[Saccharomyces cerevisiae]]'' has 275 tRNA genes in its genome. In the human genome, which according to current estimates has about 27,161 genes <ref>Ensembl release 48 - Dec 2007 http://www.ensembl.org</ref> in total, there are about 4,421 [[non-coding RNA]] genes, which include tRNA genes. There are 22 [[mitochondria]]l tRNA genes;<ref>''Ibid.'' p 529.</ref> 497 nuclear genes encoding cytoplasmic tRNA molecules and there are 324 tRNA-derived putative [[pseudogenes]].<ref name=Lander>{{cite journal |author=Lander E. et al. |title=Initial sequencing and analysis of the human genome |journal=Nature |volume=409 |issue=6822 |pages=860–921 |year=2001 |pmid=11237011 |doi=10.1038/35057062}}</ref>
Cytoplasmic tRNA genes can be grouped into 49 families according to their anticodon features. These genes are found on all [[chromosomes]], except 22 and Y chromosome. High clustering on 6p is observed (140 tRNA genes), as well on 1 chromosome.<ref name=Lander />
tRNA molecules are transcribed (in [[eukaryotic]] cells) by [[RNA polymerase III]],<ref>{{cite journal | author=White RJ| title=Regulation of RNA polymerases I and III by the retinoblastoma protein: a mechanism for growth control? | journal=Trends in Biochemical Sciences | year=1997| volume=22| issue=3| pages=77–80 | doi=10.1016/S0968-0004(96)10067-0}}</ref> unlike [[messenger RNA]] which is transcribed by [[RNA polymerase II]]. pre-tRNAs contain introns; in bacteria these self-[[Splicing (genetics)|splice]], whereas in eukaryotes and [[archaea]] they are removed by tRNA splicing [[endonuclease]].<ref>{{cite journal | author=Abelson J, Trotta CR, Li H| title=tRNA Splicing| journal=J Biol Chem| year=1998| volume=273| issue=21| pages=12685–12688| doi= 10.1074/jbc.273.21.12685| pmid=9582290}}</ref>
==History==
The existence of tRNA was first hypothesized by [[Francis Crick]], based on the assumption that there must exist an adapter molecule capable of mediating the translation of the RNA alphabet into the protein alphabet. Significant research on structure was conducted in the early 1960s by [[Alex Rich]] and [[Don Caspar]], two researchers in Boston, the [[Jacques Fresco]] group in [[Princeton University]] and a [[United Kingdom]] group at [[King's College London]].<ref>{{cite journal |author=Brian F.C. Clark |title=The crystal structure of tRNA |journal=J. Biosci. |volume=31 |issue=4 |pages=453–7 |year=2006 |month=October |url=http://www.ias.ac.in/jbiosci/oct2006/453.pdf |pmid=17206065 |doi=10.1007/BF02705184 }}</ref> A later publication reported the primary structure in 1965 by [[Robert W. Holley]]. The secondary and tertiary structures were derived from [[X-ray crystallography]] studies reported independently in 1974 by [[Kim Sung-Hou|American]] and British research groups headed, respectively, by Alexander Rich and [[Aaron Klug]].
==References==
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==See also==
* [[mRNA]]
* [[tmRNA]]
* [[non-coding RNA]] and [[intron]]s
* [[translation (genetics)|translation]]
* [[Kim Sung-Hou]]
* [[wobble hypothesis]]
==External links==
* [http://news.bbc.co.uk/2/hi/health/3762664.stm tRNA could be the cause of heart attack]
* [http://www.staff.uni-bayreuth.de/~btc914/search/index.html Sprinzl tRNA compilation]
* [http://lowelab.ucsc.edu/GtRNAdb/ Collection of tRNAs identified from complete genomes]
* [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/pdb15_1.html Transfer RNA]
** [http://www.pdb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb16_1.html Aminoacyl-tRNA Synthetases]
** [http://www.pdb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb81_1.html Elongation Factors]{{Nucleic acids}}
[[Category:RNA]]
[[Category:Protein biosynthesis]]
[[Category:Non-coding RNA]]
[[bg:Транспортна РНК]]
[[ca:ARN de transferència]]
[[cs:TRNA]]
[[da:TRNA]]
[[de:TRNA]]
[[et:Transpordi-RNA]]
[[es:ARN de transferencia]]
[[fr:Acide ribonucléique de transfert]]
[[it:RNA transfer]]
[[he:TRNA]]
[[la:TRNA]]
[[lt:TRNR]]
[[hu:Transzfer RNS]]
[[nl:Transfer RNA]]
[[ja:転移RNA]]
[[oc:Acid ribonucleïc de transferiment]]
[[pl:TRNA]]
[[pt:ARN transportador]]
[[ru:ТРНК]]
[[sk:Transferová ribonukleová kyselina]]
[[sr:Антикодон]]
[[sv:Transport-RNA]]
[[tr:Taşıyıcı RNA]]
[[zh:TRNA]]