Talk:Transcription (genetics)

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[edit] 2008 Major upgrade?

New Article Hi i´m Lukas Müller and i´m coming from Köln in Germany. i´m Studying biology at the Heidelberg-University, one of the best universities in germany and i want to ask, if we can make the site "Transcription" new so we can get a perfect article.

Please see the page section called #Major Edits - Procedure?, below, for discussion of major changes. --JWSchmidt (talk) 21:18, 3 January 2008 (UTC)

[edit] Harvard Papers?

"By the late 1960s several papers that came out of the Harvard University Biological Laboratories established the basic mechanics of gene expression in bacteria."

This information is not related to this article in context and will be deleted. If you're going to include this you might as well include all the articles on pub med because the "basic mechanics of gene expression in bacteria" is a communitative effort not just exclusivly by faculty in Harvard. Although I presume they had made their contributions as well. It's just not correct to include one place that contributed to gene expression, so I assume the person who included this is maybe from the school itself.

[edit] Reverse transcriptase

According to the current article, transcription refers solely to DNA>RNA transcription, and even goes to far as to link to Crick's central dogma (DNA is transcribed to RNA which is translated to polypeptides, never the other way around). Someone should make it clear from the start that transcription, while usually used to refer to DNA>RNA transcription, might also refer to RNA>DNA transcription. -- Ec5618 23:39, 4 December 2005 (UTC)

I added a beginning of informations plus a little scheme I made earlier ... I think it should be in another page, but I don't know how to do ;-P. Hope someone will ! -- Totophe64

[edit] Eukaryotic Transcription

Edit 4/2/06 explanation Most eukaryotes have 4 RNA polymerases, plants have 5. Although RNAP is a commonly used abbreviation for bacterial and bacteriophage RNA polymerases, it is almost never used for eukaryotic RNA polymerases. I have substituted Pol I, II and III. (This will also need to be done in the subsections.) I have also included Pol A, B, and C not only in recognition of the work of Pierre Chambon and Andre Sentenac (vs. the nomenclature of William Rutter and Robert Roeder), but at some point the gene names (eg., RPA1, RPB1, RPC1) will come up as this section expands, and this edit will help clarify this nomenclature. -opus118

Organization and additional items needed "Perhaps one way of organizing this section is to group the different RNA polymerases: Archaea, bacteria, chloroplast, and eukaryotic nuclear RNA polymerases form one related group. Bacteriophage T7-like and mitochondrial RNA polymerases form a second, DNA polymerase I-derived group (does reverse transcriptase fall into this category?), and then a diverse mixture of bacteriophage and viral RNA polymerases that do not fall within the above two categories. There should be some emphasis on common mechanisms and related subunits. For example: 1) the β'βα2ω subunits of bacteral RNA polymerase have sequence-related homologs in chloroplast RNA polymerase, archaeal RNA polymerase and Pol I, II and III. 2) The 12 (?) subunits of archaeal RNA polymerase have homologs in Pol I, II and III (with Pol III containing 5 additional unique subunits); 3) TBP is a transcription factor for archaeal, Pol I, Pol II, and Pol III transcription. 4) A TFIIB-related factor is common for archaeal, Pol II and pol III transcription. 5)TFIIH functions for Pol I and II transcription. 6) Promoter opening occurs with an upstream to downstream polarity with all polymerases. 7) Stem-loop structures at sites of termination are common (with the possible exception of Pol III). 8) The mechanism of catalysis for RNA chain elongation is identical (the active site region is highly conserved). 9) bacterial GreA/GreB, TFIIS and Rpc11 all stimulate a 3' to 5' ribonucleolytic activity at the RNA polymerase active site by inserting a finger-like structure in the nucleotide substrate feeding pore of RNA polymerase to place a pair of acidic residues near the catalytic site that chelates an additional Mg2+ ion for hydrolysis. It is the polymerase-unique properties that might be best dealt with in subsections. -opus18

[edit] Termination

  • Garbeled section needs Editing. Something missing or duplicated etc in the "sentence(s)":
  • in the DNA template. or where a GC-rich inverted
  • 4 A residues. the inverted repeat forms
  • dissociate from the DNA template. where the -35 region
  • See the following surround section.

*Rho-dependent termination uses a termination factor called ρ factor(rho factor) to stop RNA synthesis at specific sites. This protein binds and runs along the mRNA towards the RNAP. When ρ-factor reaches the RNAP, it causes RNAP to dissociate from the DNA, terminating transcription. Other termination mechanisms include where RNAP comes across a region with repetitious thymidine residues in the DNA template. or where a GC-rich inverted repeat followed by 4 A residues. the inverted repeat forms a stable stem loop structure in the Rna, which causes the RNA to dissociate from the DNA template. where the -35 region and the -10 ("Pribnow box") region comprise the basic prokaryotic promoter, and |T| stands for the terminator. The DNA on the template strand between the +1 site and the terminator is transcribed into RNA, which is then translated into protein.

DLH 17:37, 10 September 2006 (UTC)

[edit] category

Surely this article should be under Molecular Biology? answer: WHY? Where else should it be?

[edit] order?

Is there any reason why it shows "see also" and "external links" then more of the article, then another "external links" section? If I dont' get any replies within a week or so, I'll go ahead and move the rest of the article up, and combine the two "external links" sections. jf 22:20, 23 May 2006 (UTC)

[edit] Other

"For instance, in eukaryotes the genetic material (DNA), and therefore transcription, is primarily localized to the nucleus, where it is separated from the cytoplasm (where translation occurs) by the nuclear membrane." This sentence has a very unclear structure*.

[edit] I miss the pictures!!!

YES! I do!!!!!!! Somebody, add some, please, it would be VERY IMPORTANT!!! Myrmeleon formicarius 12:42, 12 March 2007 (UTC)

[edit] Contradictions in Direction

In transcription, DNA is read 3'-->5' and RNA is produced 5'-->3'.

So, in an image of DNA being read by RNA polymerase, short strands would be expected at the 3' end, and long strands at the 5' end. The first diagram has this backwards.

I can't see what I'm missing, and since this is marked as a high priority for improvement, I thought this could use clarification, but since I suspect some actual biologists edit this page, I won't do it myself.

(Didn't log on the first time I posted this.)

Triacylglyceride 17:46, 13 May 2007 (UTC)triacylglyceride

I believe the image is marked incorrectly. Where transcription started the transcripts will be longest; the picture indicates the opposite. BTW your username is kinda funny, since it's usually either triacylglycerol or triglyceride :P -Sakkura 19:27, 9 September 2007 (UTC)
I think Triacylglyceride is right. Short RNA strands will be found near the start of transcription (3' end on the template strand) and the longest RNA strands near the end. Forluvoft 00:02, 10 September 2007 (UTC)
Aye, that was a brain fart by me. It certainly looks correct now, although maybe you shouldn't take my word for it :P Sakkura 00:54, 14 September 2007 (UTC)

[edit] Scientists Discover the Dynamics of Transcription

One surprising finding was how inefficient the transcription process really is, particularly during its first two stages,� says Dr. Singer. �It turns out that only one percent of polymerases that bind to the gene actually remain on to help in synthesizing an RNA molecule. Transcription is probably inefficient for a reason. [1] Brian Pearson 02:10, 7 August 2007 (UTC)

[edit] 5', 3', direction of transcription, etc....

We're making this much more complicated than it has to be. We're too fixated on the directionality from the point of view of the template strand (because it's the actual physical template for RNA). But in reality, when molecular biologists talk about gene regulation, they talk about directionality from the point of view of the coding (non-template) strand. Maybe this is because the coding strand has the sequence of the resulting protein in the correct orientation. Thus, to molecular biologists, the 5' end of a gene is always near the promoter.


Hopefully this will make things clearer (if I don't screw it up):

RNA is synthesized using the template strand of DNA. RNA is synthesized from the 5' end to the 3' end. On the DNA template strand, this is 3' to 5'.

On the coding strand, however, transcription proceeds from 5' to 3'. Although RNA might not even touch the coding strand, the RNA will be an exact replica of the coding strand. Since RNA translation into protein occurs from 5' to 3', the DNA coding strand also shows what the protein sequence will look like, in the correct orientation (no reverse complementation necessary). So scientists usually like to work with the coding strand. Forluvoft 01:31, 27 September 2007 (UTC)

[edit] Reverse transcription

I added reverse transcription to the "See also" list. Does it really need its own section in this article? Forluvoft 03:53, 27 September 2007 (UTC)

It's called reverse transcription for a reason, so yes, it should have its own section here since it is a form of transcription (albeit unusual) Sakkura 00:00, 7 October 2007 (UTC)
Ok. Forluvoft 00:48, 7 October 2007 (UTC)

[edit] Transcription cartoons

I made and added some transcription cartoons. Let me know if something needs to be tweaked. The cartoons are really simplistic and I would envision them instead on an "Introduction to Molecular Genetics" page instead of this one. If this page ever gets to FA status, it will need much more detailed and accurate diagrams. Forluvoft 18:03, 12 October 2007 (UTC)

Yeah, they are quite simplistic, but it's far better than nothing. Especially for laymen. The protein complex at the promoter does look more like a eukaryotic preinitiation complex than what typically goes on in prokaryotes, but at least enhancers and whatnot are excluded, so I think they can be used as a general illustration for both eukaryotes and prokaryotes. Sakkura 10:53, 17 October 2007 (UTC)

[edit] Major Edits - Procedure?

Hi, new here. I'm currently doing a great deal of study of the transcription / translation area as an undergraduate at Cambridge - not saying that my opinion is any more valid than the next undergraduate and it certainly isn't compared to a PHD student, but I noticed quite a few holes here. I wondered what the procedure would be if I wanted to perform some major edits, probably adding a great deal more about Eukaryotic transcription (basal transcription factors, pol I-III etc) and doing some major rearrangements. I don't want to step on anyone's toes, but I'd like to do something useful. Martyn Axon (talk) 16:27, 27 December 2007 (UTC)

It would be great if we could improve the Wikipedia transcription article to featured article quality. If you want to start from scratch, create a page called Martyn Axon/Transcription. Alternatively, we could just start making major changes to the current article. Examples of featured biology articles. --JWSchmidt (talk) 21:26, 3 January 2008 (UTC)