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asaroj27

tRNA controversy

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tRNA doesn't have Thymine, its the DNA group that has thymine. For the RNA group it has Uracil in its place.

 

As for the function of these, they are just different bits of the genetic code.

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Thymine is in DNA. DNA has four bases: Adenine (A), Thymine (T), Guanine (G) and Cytosine ©. DNA has two strands with these four bases bonded to each other and able to make long sequences millions of bases long in and arranged in a number of chromosomes. Sites on the DNA which are more 'open' for the start of making messenger RNA (called transcription) tend to have runs of Adenine and Thymine because there are only two hydrogen bonds between A and T. G and C on opposite strands have three hydrogen bonds. RNA is found in three forms - tRNA, rRNA and mRNA. The Adenines are bonded to Uracil (U) a different base from thymine. IMHO the uracil can be recognised by enzymes that bind to RNA. Is that what you meant?

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Actually the main reason is not to recognize RNA.

Or rather it is the other way round. Thymine is formed by methylation of uracil. So in other words, it is additionally modified in the DNA (for stability and fidelity).

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There are modified nucleotides in tRNA's that are specific and are not found in other RNA's or DNA. However IIRC they are post transcriptional modifications. It might also be worth adding that cytosine is only a methyl and an amino group away from thymine, therefore also very close to uracil. So it also has it's use in strand directed mismatch repair post DNA replication.

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lecture2_2.htmlStructure of tRNA

 

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 P and A sites of the ribosome).

 

The 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 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).

 

hello,

The cloverleaf model of tRNA shows that tRNA contains three non-base-paired loops: D, anticodon, and TpsiC loop

my question is that in TpsiC loop why T is presnt.BEfore giving any answer please know the stucture of tRNA

 

hello,

i am sorry to say that you have to check the three dimensional structure of tRNA and then tell me .

The cloverleaf model of tRNA shows that tRNA contains three non-base-paired loops: D, anticodon, and TpsiC loop

my question is that in TpsiC loop why T is presnt.BEfore giving any answer please know the stucture of tRNA

 

hello

YOU have to know that tRNA is the only RNA which contains Thymine.

The T arm is a 5 bp stem containing the sequence TΨC where Ψ is a pseudouridine and T is Thymine. ok and my question is on this T.

 

hello

you should know sir that tRNA is the only RNA which contains Thymine.

The cloverleaf model clearly shows that tRNA contains three non-base-paired loops: D, anticodon, and TpsiC loop. The T arm is a 5 bp stem containing the sequence TΨC where Ψ is a pseudouridine & T is a Thymine.

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Is English not your primary language? I only ask because your post is practically incoherent. I'm not trying to insult you, just saying that it is difficult to decipher what you are saying/asking.

 

Yes, the T arm of tRNA has thymine. Are you asking why this is the case?

 

It seems, from your first post in the thread, that you already have some wild speculation about "controversy". What controversy?

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Is English not your primary language?

I think that's a fair assessment, but there's no reason they cannot still come here and ask questions. A difficult time expressing ideas in English is no reason to avoid asking questions.

 

 

It seems, from your first post in the thread, that you already have some wild speculation about "controversy". What controversy?

 

What are you talkiing about? What controversy? Serously... I'm not seeing it.

Is English not your first language? :D

 

;)

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Actually the main reason is not to recognize RNA.

Or rather it is the other way round. Thymine is formed by methylation of uracil. So in other words, it is additionally modified in the DNA (for stability and fidelity).

 

Thanks for the correction. I should have sussed this out. However, the controversy of the OP is about the presence of T in tRNA hence he/she regards this as controversial. So far, he/she has not recived an answer.

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Thanks for the correction. I should have sussed this out. However, the controversy of the OP is about the presence of T in tRNA hence he/she regards this as controversial. So far, he/she has not recived an answer.

 

I think that maybe the point is that several ribonucleotides in tRNA undergo post transcriptional modification that results in different nucleotides appearing. One is pseudouridine (psi greek symbol) and another is a single thymine ribonucleotide. As CharonY already pointed out thymine is merely a methylated form of uracil, so deduction follows that the presence of thymine is actually a result of a post-transcriptional modification, or else a deliberate incorporation, either way the result is the same. I still fail to see any controvesy whatsoever in this.

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I also fail to see any controversies, and was therefore not able to address the question. The follow-up post makes it clearer what is meant, but as already mentioned, the tRNA is post-transcriptionally modified in several areas, especially the uridine. Again, that is basic textbook, no controversies here. These modifications influence the structural integrity of the tRNA. For instance, the composition of modified bases is markedly different in thermophilic as compared to psychrophilic organisms in order to ensure a functional tRNA despite extreme high/low temperatures.

 

It could be that the misunderstanding was just the result of maybe slightly awkward wording in the OP. In any case, a number of enzymes

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I think that's a fair assessment, but there's no reason they cannot still come here and ask questions. A difficult time expressing ideas in English is no reason to avoid asking questions.

 

 

 

 

What are you talkiing about? What controversy? Serously... I'm not seeing it.

Is English not your first language? :D

 

;)

 

I'm sorry that you seem to have comprehension problems. Perhaps you could go back and read the title of this thread once more, before you emberrass yourself further.

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I see the title. I still don't see the controversy.

 

I concede, I missed that part in the title when I last replied to you, but my primary point remains. There's no need to be a jerk to people, especially if they are not native english speakers. It's hard enough already for them, and takes courage to come to a place like this and ask when they can barely find the words. They really don't need responses from ignorant fools who are trying to make themselves feel better by putting others down making it harder for them.

 

 

</soapbox>

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It was not my intent to be insulting. Clearly there is no controversy over the structure/sequence of tRNA. I find the assertion made in the op/title a little odd though, even for a non native English speaker.

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That's fair. Thank you for clarifying your position.

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I also fail to see any controversies, and was therefore not able to address the question. The follow-up post makes it clearer what is meant, but as already mentioned, the tRNA is post-transcriptionally modified in several areas, especially the uridine. Again, that is basic textbook, no controversies here. These modifications influence the structural integrity of the tRNA. For instance, the composition of modified bases is markedly different in thermophilic as compared to psychrophilic organisms in order to ensure a functional tRNA despite extreme high/low temperatures.

 

It could be that the misunderstanding was just the result of maybe slightly awkward wording in the OP. In any case, a number of enzymes

 

Charon Y could you please give me some references to papers etc.. online. I want to read up further on this because it seems odd that one or two bases affect the integrity of a crosslinked 3-D structure.

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You may have misunderstood my point. It was talking not about the modification of one or two bases, but those throughout the whole tRNA.

 

You may want read up on Dalluge et al. 1997 (one of the few papers I remmeber on this subject). Journal of Bacteriology (so it should be long free by now). IIRC it dealt with the high abundance of pseudouridine in psychrophiles.

 

However, giving that structural RNAs are single stranded molecules, it is not that much surprising that even single nucleotide modifcations can have profound effects on their local structure. For more info on this you should read up on models for RNA folding (papers from Michael Zuker's group might be a good starting point).

 

More specifically, the modifications in the T-arm contribute to stabilizing the (L-shaped) tertiary structure of the tRNA.

 

However, as always, things are a bit more complicated. As tRNA are the structural element of the genetic code modification not only are involved in maintaining a certain tertiary structure, but are also involved in the actual translation process, most notably in wobble pariring.

Edited by CharonY

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Got it now. The Dalluge et al paper explains it very clearly and should ameliorate the apparent 'controversy':

 

With regard to modification patterns, however, we find that

tRNA from psychrophilic and psychrotrophic bacteria is in

general significantly hypomodified compared to that of organisms

which grow optimally at higher temperatures. The psychrophiles

and psychrotroph studied here contain, on average, 10

to 15 modified nucleosides (Fig. 1), compared with approximately

29 for mesophilic bacteria such as Salmonella typhimurium

(5) and E. coli (18) or as many as 31 for the archaeal

hyperthermophile Pyrobaculum islandicum, which grows optimally

at 1008C (15, 34). All of the posttranscriptionally modified

nucleosides identified in the presently studied bacteria are

known to be involved in the maintenance of basic structural

characteristics of tRNA molecules.

 

http://jb.asm.org/cgi/reprint/179/6/1918?ck=nck

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Thymine and Uracil differ by the extra methyl group on thymine. The affect of this extra methyl group is to create extra surface tension in the water. It helps to form the DNA double helix. Without this methyl group RNA, is able to form both single and double helixes. The methyl group is like a little drop of oil and is better shield in the double helix. RNA would be under extra tension in the water if it contained the methyl group and tried to be a single helix. It would be messed up and would not function properly.

 

The DNA double helix also have a double helix of structured water within the major and minor groves of the double helix. This surface tension is still felt by the water within the water double helix. This is transferred to the hydrogen bonding between the bases allowing the double helix to bind slightly stronger for stability. The surface tension within the water increases the hydrogen bonding potential of the water-DNA composite. I am a little ahead of the curve so this may take another tens years to figure out.

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I am a little ahead of the curve so this may take another tens years to figure out.

Asoraj,

 

I'd caution you to take what Pioneer says with a grain of salt. He often has some really good ideas, but unfortunately many (if not most) of them completely fail due to starting from false premises. Just FYI.

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Just to add, the reason tRNA got its name isnt because it has Thymine. Its because it stands for 'transfer RNA', which is very important in protein synthesis.

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hello sir

Before Newton every one knows that apple fall on earth But he was the only guy who observe it keenly & gave the concept of GRAVITY. I am very keenly observing this thread & i noticed that people thought that this thread is useless. but i am great beliver of science. i think that science world is the only place where you can findout the answer's of what, why & how?

and i came to know the answer of this thread by the help of CharonY & other members of this forum. and i am very thankful to these peoples.

think that if the uracil is replaced by thymine in the RNA artificially what will be the impact on RNA.

Thanks for your sugession

tRNA is transfer RNA not because it is important in protein synthesis. it is transfer RNA because it transfer the amino acid in translation. Like that everything which is going on, has some reasons. I want only healthy disscusion.

i am apologise if i hurt you or anyother person.I will always try to make sure that no one will hurted by me.My intention is only to know the reasons by the help of science. and one thing more that i am not good in english.and i think that english is not require to know the science.

once again thankyou very much.

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think that if the uracil is replaced by thymine in the RNA artificially what will be the impact on RNA.

 

It would be less efficiently paired to tRNAduring translation, unless perhaps if it was on the third codon.

 

Uricil is methylated thymine, and can make the same Watson-Crick base pairs, so I don't think translation would stop all together.

 

I'm not sure if RNA polemerase has the ability to build an mRNA with TTP, however.

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Thanks for your sugession

tRNA is transfer RNA not because it is important in protein synthesis. it is transfer RNA because it transfer the amino acid in translation. Like that everything which is going on, has some reasons. I want only healthy disscusion.

...lol, I was trying to keep it simple for you since I didnt realise you knew of translation. Translation is a part of protein synthesis so my point remains the same and I stand by my original comment:

 

Just to add, the reason tRNA got its name isnt because it has Thymine. Its because it stands for 'transfer RNA', which is very important in protein synthesis.

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