Talk:Transfer RNA

Untitled

The user User:Czernilofsky added two sentences to the page, citing their own work. I don't think either sentence is comprehensible to the audience of the page, and the citations are also not done in Wikipedia style. https://en.wikipedia.org/w/index.php?title=Transfer_RNA&direction=next&oldid=440394507 - I'm a n00b, or I would revert it myself. Someone want to revert it? Rescdsk (talk) 19:37, 17 September 2014 (UTC)

The first sentence has either got a typo or somebody made a joke: the 'genetic-code' (i.e. codons) are afaik three letter sequences not four letter sequences. Or am i just a bit daft? ;) Thunderudder (talk) 09:39, 9 February 2012 (UTC)

what does the primary structure look like? Pelirojopajaro 05:33, 5 January 2007 (UTC)

The article does describe it, specific sequences are not given since there are numerous tRNA sequences. In general (in the article) it is a small RNA chain (73-93 nucleotides), for more details look at the features section. If you check out the link Sprinzl tRNA compilation, you can get a list of 1000s of tRNAs, Hichris 16:51, 5 January 2007 (UTC)

the term "degenerate" is not used correctly. Active contributor 02:00, 22 March 2007 (UTC)

Not sure what you mean, just looking quickly at the history it looked fine. In this context, degenerate means "having more than one codon representing an amino acid; also being such a codon" Hichris 13:37, 22 March 2007 (UTC)

Is it just me or does that merge suggestion seem quite weird? Sakkura 22:51, 3 May 2007 (UTC)

I'm guessing someone saw a stub article and thought that integrating it into the tRNA entry would "fix the stub"....not realizing the enormity of the situation. -- MarcoTolo 11:34, 26 May 2007 (UTC)

Psyched-out Biology Groupie Seeks Help

I am a non-biologist, but have some crude idea of the function of transfer RNA, from reading popular accounts of protein biosynthesis. The subject is correctly marked as of high importance, yet at present I can understand the first sentence of the article and practically nothing else. It's enough to make me turn to Creationism - I can understand that. Could the technicalities please be postponed, and the article given a proper introduction, with suitable links? A suitably expanded version of the 'History' section should probably come soon after the Introduction: at any rate, it should appear before the specialist material.

[User:Rwb001 10:33, 19 July 2007 (UTC)]

What about the following for an introduction? I'll make the change on 19 May 2011, if there are no comments. TRNAtest (talk) 06:13, 17 May 2011 (UTC)tRNAtest

Actually, I think the following is better.

Transfer RNA (tRNA) is an adaptor molecule composed of RNA used in biology to bridge the three-letter genetic code in messenger RNA (mRNA) with the three-letter code of amino acids in proteins. The role of tRNA as an adaptor is best understood by considering its three-dimensional structure. One end of the tRNA carries the genetic code in a three-nucleotide sequence called the anticodon. The anticodon forms three base pairs with a codon in mRNA during protein biosynthesis. The mRNA encodes a protein as a series of contiguous codons, each of which is recognized by a particular tRNA. On the other end of its three-dimensional structure, each tRNA is covalently attached to the amino acid that corresponds to the anticodon sequence. This covalent attachment to the tRNA 3’ end is catalyzed by enzymes called aminoacyl-tRNA synthetases. 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.

During protein synthesis, tRNAs are delivered to the ribosome by proteins called elongation factors (EF-Tu in bacteria, eEF-1 in eukaryotes), which aid in decoding the mRNA codon sequence. Once delivered, a tRNA already bound to the ribosome transfers the growing polypeptide chain from its 3’ end to the amino acid attached to the 3’ end of the newly-delivered tRNA, a reaction catalyzed by the ribosome.

TRNAtest (talk) 01:43, 24 May 2011 (UTC) (who forgot to sign the entry)

References

tRNA-like sequence

What is tRNA-like sequence \ t-element ? Does it deserve a mention in the article? Just stumbled upon this term while reading on Reelin-related articles (TBR1 to be exact)... --CopperKettle 02:48, 26 March 2009 (UTC)

Other functions of tRNA

tRNA does so much more than just generation of proteins. Can someone add some additional functions or make this a stub?

--Pjlmac (talk) 04:10, 14 April 2010 (UTC)

I don't think this article should be made in to a stub, but it's true that there could be an additional section on what else tRNAs do. --Jonatp (talk) 21:49, 15 April 2010 (UTC)

Binding to ribosome

An expansion of this section:

The ribosome has three binding sites for tRNA molecules that span the space between the two ribosomal subunits: the A (aminoacyl), P (peptidyl), and E (exit) sites. In addition, the ribosome has two other sites for tRNA binding that are used during mRNA decoding or during the initiation of protein synthesis. These are the T site (named elongation factor Tu) and I site (Initiation) . By convention, the tRNA binding sites are denoted with the site on the small ribosomal subunit listed first and the site on the large ribosomal subunit listed second. For example, the A site is often written A/A, the P site, P/P, and the E site, E/E.

Once translation initiation is complete, the first aminoacyl tRNA is located in the P/P site, ready for the elongation cycle described below. During translation elongation, tRNA first binds to the ribosome as part of a complex with elongation factor Tu (EF-Tu) or its eukaryotic (eEF-1)or archaeal counterpart. This initial tRNA binding site is called the A/T site. In the A/T site, the A-site half resides in the small ribosomal subunit where the mRNA decoding site is located. The mRNA decoding site is where the mRNA codon is read out during translation. The T-site half resides mainly on the large ribosomal subunit where EF-Tu or eEF-1 interacts with the ribosome. Once mRNA decoding is complete, the aminoacyl-tRNA is bound in the A/A site and is ready for the next peptide bond to be formed to its attached amino acid. The peptidyl-tRNA, which transfers the growing polypeptide to the aminoacyl-tRNA bound in the A/A site, is bound in the P/P site. Once the peptide bond is formed, the tRNA in the P/P site is deacylated, or has a free 3’ end, and the tRNA in the A/A site carries the growing polypeptide chain. To allow for the next elongation cycle, the tRNAs then move through hybrid A/P and P/E binding sites, before completing the cycle and residing in the P/P and E/E sites. Once the A/A and P/P tRNAs have moved to the P/P and E/E sites, the mRNA has also moved over by one codon and the A/T site is vacant, ready for the next round of mRNA decoding. The tRNA bound in the E/E site then leaves the ribosome.

The P/I site is actually the first to bind to aminoacyl tRNA, which is delivered by an initiation factor called IF2 in bacteria. However, the existence of the P/I site in eukaryotic or archaeal ribosomes has not yet been confirmed.

The above was added by TRNAtest (talk) 01:43, 24 May 2011 (UTC) (who forgot to sign).

Animation to add:

The range of conformations adopted by tRNA as it transits the A/T through P/E sites on the ribosome. The Protein Data Bank (PDB) codes for the structural models used as end points of the animation are given. Both tRNAs are modeled as phenylalanine-specific tRNA from Escherichia coli, with the A/T tRNA as a homology model of the deposited coordinates. Color coding as shown for tRNA tertiary structure. Adapted from.

TRNAtest (talk) 05:48, 24 May 2011 (UTC)tRNAtest

How many nitrogenous bases does tRNA have? My A+P textbooks says tRNAs use over 50(!) Is that true? I thought that A, U, C, G were all. Could someone in the know add something to the article about these extra bases? — Preceding unsigned comment added by 174.70.58.119 (talk) 03:24, 1 September 2011 (UTC)

References

Missing aminoacyl tRNA synthetases

The article states that, sometimes, certain organisms can lack one or more of these enzymes. Does that "sometimes" refer to the life of an individual of those organisms, or rather to different moments in time throughout the evolution of life? In other words, can genes for aminoacyl tRNA synthetases be switched off and on during the lifetime of an organism? And if so, why? 62.37.29.52 (talk) 14:47, 4 September 2012 (UTC)

Assessment comment

The comment(s) below were originally left at Talk:Transfer RNA/Comments, and are posted here for posterity. Following several discussions in past years, these subpages are now deprecated. The comments may be irrelevant or outdated; if so, please feel free to remove this section.

Rated "high" as high school/SAT biology content, important to translation (biology). The article needs references/sources. - tameeria 01:13, 19 February 2007 (UTC)

Last edited at 01:13, 19 February 2007 (UTC). Substituted at 09:10, 30 April 2016 (UTC)

syntax

"Highly expressed genes seem to be enriched in codons that are exclusively using codons that will be decoded by these modified tRNAs"

probably some syntax issue here?

How does each tRNA find its specific amino acid?

How does each tRNA find its specific amino acid? And why are the tRNA-amino acid couples so faithful? 86.184.52.111 (talk) 12:40, 16 January 2018 (UTC)

I am sorry, is this a question for a test? Or is it a note about some unclear parts in this Wikipedia article? --Helixitta (t.) 18:46, 17 January 2018 (UTC)

Neither. Has science found an answer for this question yet? There does not seen to be any thermodynamic reasons why one tRNA should pair with its amino acid. So what drives it? 86.186.93.14 (talk) 02:54, 20 December 2018 (UTC)

There are twenty different types of tRNA, with each for the twenty different amino acids. You can recognise the twenty different tRNAs from their respective anticodon loop. For example methionine has genetic code AUG so its anti codon will be UAC. Methionine tRNA will have UAC as the anticodon. Light Green Botanist (talk) 12:23, 21 January 2023 (UTC)

I think the question is about how each tRNA knows to attach to the aminoacyl instead of how translation works, so aminoacyl tRNA synthetase is the article to look at. These synthases actually read the anticodon using an anticodon binding domain. They are very unusually specific in the world of enzymes due to that reading. Artoria2e5 🌉 12:42, 4 October 2023 (UTC)

make page: hypernymous mutation (not merely genetical but structural, or genetical that affects tRNA which is part of the biolanguage) = ontic alteration = superordinate mutation

When the constituents of the DNA or the RNA change, or when some tRNAs change, are added, deleted, replaced, etc (some deletions might have no impact though). — Preceding unsigned comment added by 2a02:587:411d:5ac7:df1:66f5:4880:9629 (talk • contribs)

The request makes no sense unless you look at the edit adding it (Special:Diff/1028462643). The "singularity" page ultimately talks about doi:10.1126/science.abg3029. The authors trimmed away some serine codons and a stop codon, then proceeded to do an expanded genetic code. So in a way we do have a page for that (also the part in genetic code about how it varies from evolution). --Artoria2e5 🌉 10:53, 22 December 2023 (UTC)

Structure of tRNA- anticodon loop

In its current form the paragraph on tRNA anticodon loop structure attempts a sentence of education on double-stranded polarity. Considering these are features of all base pairing and not unique to the anticodon, as well as the incorrect usage of terminology in the explanation, this should be edited. This is not the appropriate location for educating on anti-parallel base pairing. Examples: All base pairing is anti-parallel not "in reverse order". By implying that tRNA use a special reverse order sequence in base pairing would be improper for anyone familiar with base-pairing and might result in an inversion of the sequence.

tRNA have a structure. The terms 5'-3' and 3'5' do not indicate different structure, only different readings or descriptions of the linear structure. By convention, sequence is read and written 5'-3' even when the molecule is double stranded, unless otherwise indicated, mimicking left to right reading, the polarity of genes and translational reading frames (This latter reason, is less pronounced as genome based sequence require that some genes are represented as template rather than coding strands.)

Solution: Describing the single strand mRNA codon, and tRNA anticodon as "complementary" should be sufficient. Perhaps with an example codon: 5'AUG anticodon: 5'CAU and a duplexed version showing the anti-parallel feature of double strand sequence. A link or reference to a description of double stranded (including fold back) anti-parallel nucleic acids could also be used. 2600:8807:1C0A:9600:28A4:8FAF:5C54:7170 (talk) 06:11, 29 January 2023 (UTC)

transfer RNA topic introduction

The introductory paragraph has been muddied by some poorly placed sentences on the relative size of tRNA genes and processing across domains. Without mention of polymerase III gene structure this information is not comprehensible. With editing it could be placed within the article, but it does not belong in the first paragraph. Furthermore those sentences were placed without regard to affect on the paragraph structure and separating two sentences whose meaning requires sequential order. Sentence beginning "The tRNA does this..." "this" is no longer defined. Solution: remove offending sentences. Make following sentence independent of sequence. "The tRNA accomplishes the task of decoding the mRNA by..." 2600:8807:1C0A:9600:28A4:8FAF:5C54:7170 (talk) 06:25, 29 January 2023 (UTC)