Talk:Ribosome/Archive 1

Ribosome creation

It would be useful to describe theories how ribosomes were created in evolution.

Yes, it would. But it might also be premature to commit such a discussion to an encyclopedia, as work testing a leading hypothesis has really just started to be published. The Noller lab, in gradually stripping proteins from native ribosomes without totally destroying activity, helped advance the idea that the RNA, rather than the proteins, participate in crucial ribosome function. More recently, the Strobel lab has been trying to identify more exactly (large subunit RNA is still a huge molecule!) what part of the RNA is responsible for peptidyl transfer:

  G. W. Muth, L. Ortoleva-Donnelly and S. A. Strobel, A single adenosine
  with a neutral pK[a] in the ribosomal peptidyl transferase center,
  Science 289, 947-950 (2000).

It might be useful to have a good idea of how it all works before going very far in trying to describe inferences as to how it came to work that way.

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It is true that theories about the evolution of ribosomes, although extremely intriguing, are quite speculative at this time. However, it may be useful to mention the auto-catalytic capabilities of RNA molecules in general (the 'RNA world' hypothesis) as a possible starting point for the modern translational machinery. Wikipedia link: RNA_world

WK

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It would be much more appropriate for Wikipedia if the RNA World POV were lost from the article. There is no proof at this time that an "RNA World" existed, and using the provocative name is more prejudicial than probable. ManVhv 08:07, 15 July 2007 (UTC)

Also, please sign your talk page comments with four tilde characters (~~~~) in the future. To add a comment, indent your reply, rather than inserting horizontal lines. Thanks! ManVhv 08:08, 15 July 2007 (UTC)

More Structure

I am writing my thesis about the ribosome, so I plan to expand the structural aspects of this page. Maybe some of the chemistry involved. Feel free to change anything I add. I like how the page starts, very general, so I will add to the bottom.

I just uploaded an original picture of the 50S subunit; the 30S and 70S subunits are forthcoming.

--vossman 14:04, September 1, 2005 (UTC)

Hi.

In my opinion, and from reading the ribozyme page, Ribosomes are not ribozymes (see comment in opening para of article). For the ribosome to work it requires the protein scaffold, it is not an RNA only enzyme. So at best ribosomes might be called ribo-proteozymes. Just a thought. Reveldrummond 00:44, 16 December 2005 (UTC)

I guess you could argue that a ribozyme might have protein subunits. This recent article says, "the ribosome is a ribozyme".

The ribosome is a ribozyme, because all the chemistry is performed by the RNA. Efforts are ongoing by the Green lab at Hopkins and Strobel and Steitz labs at Yale to produce a protein free peptidyl transferase RNA, but so far have been unsucessful. --vossman 03:25, 16 December 2005 (UTC)

FIGURE WRONG!! I am soory, I don't know the proper way of writing here, but I just wanna mention that The figure shows WRONG unit of lenght, the ribosome is not that big. it is aproximately 200 A not nm or 20 nm.

Amount of rRNAs in subunits

The mammalian 40S subunit contains 18S rRNA. The 60S subunit contains 5S, 5.8S and 28S RNA. This is not consistent with the text that says that each subunit contains one or two rRNAs. Prokaryotic ribosomes have indeed 1 or two rRNAs: the 30S subunit contains 16S rRNA, the 50S subunit contains 5S and 23S rRNA.--User:AAM | Talk 20:05, 11 May 2006 (UTC)

Size of Ribosome [nm]

"FIGURE WRONG!! I am soory, I don't know the proper way of writing here, but I just wanna mention that The figure shows WRONG unit of lenght, the ribosome is not that big. it is aproximately 200 A not nm or 20 nm."

I just wanted to emphasize that the size of ribosome in this article (the size of ribosome in nm is desplayed below the ribosome in figure 2) is about 10 times bigger than in reality, and there is some difference in size (nm) between the eukaryotic and prokaryotic ribosome. See http://en.wikibooks.org/wiki/Cell_biology:Size_of_cells or http://nai.arc.nasa.gov/news_stories/news_detail.cfm?ID=137 for quite exact size in nm.

See link TimVickers 20:56, 31 March 2007 (UTC)

Erm, 200 Angstroms == 20 nm by definition. That is in the correct range for ribosomes, it's ~3000 nucleotides packed with a few dozens proteins. Even the links you provided confirm that. -Lp 70.81.26.125 19:56, 1 September 2007 (UTC)

Where are they produced

Can we include information as to what organelle produces Ribosomes, or did I just miss it? AdamBiswanger1 23:44, 25 October 2006 (UTC)

In prok's ribosomes form in the cytosol (no organelle), but in euk's ribosomes are produced in the nucleolus and exported. This page is very prok focused, so I don't think it fits in. --vossman 01:12, 26 October 2006 (UTC)

Definition of Ribosomes/Organelles

Organelles are generally defined as having lipid or phospholipid membranes. Ribosomes have no such membranes (they consist only of rRNA and proteins), so they shouldn't be technically classified as organelles, yet the article classifies them as such anyway. Have I missed something here? 68.221.210.250 01:20, 4 January 2007 (UTC)JackMerridew

As discussed at Organelle, different people use the term "organelle" in different ways. Some people count ribosomes as a type of organelle. --JWSchmidt 01:39, 4 January 2007 (UTC)

I agree with JWSchmidt, organelle isnt a well defined term and is used in many ways. - Zephyris _Talk 10:06, 4 January 2007 (UTC)

Okay, I can accept that. It would be nice if there were more definitive criteria for defining an organelle, though. I admit to some confusion. —The preceding unsigned comment was added by 68.221.216.6 (talk) 22:18, 5 January 2007 (UTC).

I can't accept that. Organelles are membrane bounded compartments or at least discrete membrane associated assemblies. Some people try to stretch

the definition to the cytoskeleton, but even this distorts the meaning of organelle. I'm a professor at a medical school, and I find that this definition has confused many students. The Ribosome is properly termed a macromolecular assembly or macromolecule, not an organelle. Sludtke42 20:57, 8 May 2007 (UTC)

Figuring that silence doesn't help, rather than removing any remark, I added a sentence that states that "organelle" is contested. I also put a matching remark in the organelle article. Tom Lougheed 21:13, 18 August 2007 (UTC)

Personally, I would never describe a ribosome, spliceosome, exosome, proteasome or degradosome as organelles. These are all just large enzymes. Tim Vickers 21:36, 18 August 2007 (UTC)

It seems over the past several years the -omes have taken on their own sort of category and are clearly distinct from organelles. Pdcook (talk) 16:41, 8 October 2009 (UTC)

Yes the ribosome is very clearly not an organelle. The ribosome is a protein with RNA components. Seeing as there seems to be a consensus on this above me I'll put it in. --Bmdubs (talk) 04:41, 30 September 2011 (UTC)

Looks like it's write protected. Someone who has privileges needs to edit that. It's a big mistake for Wikipedia.--Bmdubs (talk) 04:50, 30 September 2011 (UTC)

I replaced organelle with ribonucleoprotein. I do take issue with the above statement "the ribosome is a protein with RNA components". Are you sure about that? --Paul (talk) 09:39, 30 September 2011 (UTC)

Yes I'm pretty sure. I'll try to find an article describing it so you can cite it to prevent it from being put to an organelle again. I would not call the ribosome a ribonucleoprotein because they are not found in the nucleus. As far as I know they are always found in the cytoplasm but I can find an article to make that clear later.--Bmdubs (talk) 13:39, 30 September 2011 (UTC)

Yeah I don't know why it's called a "ribonucleoprotein" but it appears it is. I think it's probably comes from having protein and nucleotide components of the protein structure, not from the nucleus. Can you cite this paper for the phrase on the ribosome being a ribonucleoprotein.--Bmdubs (talk) 05:22, 1 October 2011 (UTC)

Ribonucleoprotein (RNP) indicates a complex that contains both RNA and protein. If you look at the structure of the ribosome it is predominantly RNA, proteins are tacked onto the outside. Furthermore, the RNA molecules are clearly conserved across all life whereas the proteins are not. Carl Woese's articles are probably the best to cite for much of this, however there are also plenty of textbooks that should cover it too. --Paul (talk) 05:05, 4 October 2011 (UTC)

Please revise

In the section structure it is said that prokrayotes have 70S ribosomes (30S sub nit and 50S sub unit) Doesn't that make 80S :S

Not needed. Logically you would think so, but S refers to Svedburg units which are bases on density/sedimentation so the units are NOT additive they are determined experimentally. Hichris 15:44, 14 February 2007 (UTC)

denis kostic

Subunit function

The article currently states that the large subunit contains the A, P, and E sites for tRNA binding. I believe that these three sites are, in prokaryotes at least, located on the 16S rRNA and, therefore, on the small 30S subunit, not the large 50S subunit. Am I wrong? Is this true for eukaryotes as well? Nllewellyn 14:27, 3 September 2007 (UTC)

Hm, I wonder if you can really pinpoint the sites to one location (being the 16S rRNA or whatever). In enzymes catalytic or allosteric sites aren't always part of one subunit but can be spread over both, so therefore I'd say that the A, P and E sites are formed by both the 30S and 50S subunit.. In any case the larger part of any of the 'gaps' is situated in the 50S part. Then again, the interaction between tRNA, mRNA and rRNA does occur in the 30S subunit... But correct tRNA loading is regulated by more than that. Jack the Stripper 18:08, 9 September 2007 (UTC)

Thanks for the thoughtful response, Jack. You've expressed better what I was thinking myself: that the binding pockets are formed by both units, with the 50S contributing more of the pocket, while the tRNA-mRNA-rRNA association occurs locally on the 16S rRNA in the 30S subunit. Thanks for taking the time to help clear that up for me. Nllewellyn 10:15, 10 September 2007 (UTC)

You're welcome :) Jack the Stripper 12:12, 10 September 2007 (UTC)

I will look up the appropriate references when I have more time, but I believe the E-site is exclusively on the large subunit while the P and A sites are formed by both the large and small subunits. The small subunit portion of the A and P-site is the interface between the tRNA and the mRNA--in the A-site this is the decoding center. The large subunit portion of the P and A site is the peptidyl transferase center.

There is an extra parenthesis in the first line of function.

"Ribosomes are the workhorses of protein biosynthesis, the process of translating RNA) into protein."

Ribosomes are found in cells containing nuclei

I just noticed that the sentence "Ribosomes (from ribonucleic acid and "greek: soma (meaning body)") are complexes of RNA and protein that are found in all cells that contain nuclei. " is a bit misleading, because "nucleus" is a membrane bound organelle which exists in all eukaryotic organisms, whereas ribosomes also exist in prokaryotes which by definition do not have nucleus, but a nucleoid which doesn't have membrane. Am I right? If I'm not, then this shouldn't be corrected in this article Kazkaskazkasako 18:52, 11 November 2007 (UTC)

Prokaryotes have ribosomes as well. Jack the Stripper 17:39, 14 November 2007 (UTC)

I'm alarmed that this sentence is still in the article. Am I misreading it? Clearly prokaryotes have ribosomes and don't have nuclei. I'm going to change the sentence. Pdcook (talk) 16:58, 8 October 2009 (UTC)

I simply removed the "with nuclei" from the sentence. It now reads "...are complexes of RNA and protein that are found in all cells." Anyone have a better idea? Pdcook (talk) 17:08, 8 October 2009 (UTC)

16s?

The 16S rRNA seems to have disappeared from the structure of the bacterial small subunit (was it ever there??) —Preceding unsigned comment added by 130.126.91.51 (talk) 22:06, 30 January 2008 (UTC)

Sv "solubility"

Sv refers to sedimentation, not solubility. Cupton (talk) 17:44, 4 November 2008 (UTC)

Thank you, corrected. Tim Vickers (talk) 17:51, 4 November 2008 (UTC)

Ångströms verses picometres

I had converted the units in the article to SI (i.e. from ångströms to picometres). Tim Vickers has reverted me noting (on my talk page) that ångströms are still used in structural biology. This is a very common dilemma: should WP tend more toward consistancy with the field (using whatever weird, wacky, outdated, ambiguous, etc. units, abbreviations, symbols, etc. happen to be used out there) or should it tend more toward consistancy with itself (generally prefering SI). I tend toward the latter and so stick by my edit: if structural biologists want to live in the past clinging to the ångström, let it be their problem; why should we follow their misguided lead? ... maybe because it's their field ... yeah, maybe. I still say that there is little place for such units here but I'm not about to get into an edit war about it: Tim has a decent point. JIMp _talk·cont 17:34, 24 June 2009 (UTC)

I'm going to side with Tim Vickers here. Most (all?) scholarly publications (Biochemistry, the Journal of Biological Chemistry, Nature, Science, etc) allow (and in some cases insist on) the use of Angstrom. This is particularly the case in structural biology. True, it is not an SI unit (neither is Svedberg for that matter), but it is conventional and convenient (on the scale of an atomic radius or bond). Pdcook (talk) 16:46, 8 October 2009 (UTC)

what it does mostly

ribosome are some times called workers in the assembly line .the function is factories to produce proteins. —Preceding unsigned comment added by 76.237.8.191 (talk) 06:37, 2 October 2009 (UTC)

What is your point? Pdcook (talk) 16:47, 8 October 2009 (UTC)

Good Article

Why was this article delisted? I see no reasons given here Talk:Ribosome/GAR. Graham Colm ^Talk 10:17, 8 November 2009 (UTC)

Reducing environment preventing the formation of disulphide bonds

Hi, you may like to extend the sentence regarding disulphide bonds not being able to be formed due to the reducing environment of the cytosol to include the fact that it is the ratio of glutathione (GSH - reduced)to GSSH (oxidised) of 50:1 in the cytosol that creates the reduced environment and this drives the system towards creating Cys-SH bonds and away from Cys-S-S-Cys (disulphide bonds). Just a thought as this sentence feels tacked on at the moment. Thanks —Preceding unsigned comment added by C2012875 (talk • contribs) 11:43, 17 November 2009 (UTC)

Seems reasonable to me. I'm always happy to mention my favorite tripeptide! :) Tim Vickers (talk) 16:53, 17 November 2009 (UTC)

protein translating animation

In the animation, which part is the ribosome? Is it the yellow molecule, the green one, or both? Vyroglyph (talk) 02:45, 15 March 2010 (UTC)

Animations take too long to load

Is it possible to reduce the size of the animated images, make them faster to load, or include them as linked media? I am working on an old but not ancient Mac, but my internet connection is very fast. Still, my browser freezes up for well over a minute when I try to scroll past the animated images.

Bakerccm (talk) 00:41, 24 August 2010 (UTC)Chris

Seconded - I get near 100% cpu utilization on a fairly new Mac - 173.67.2.22 (talk) 20:47, 12 January 2011 (UTC)

More than a year since the last comment on this topic, I'm going to add my agreement. The ribosome page seems to make my browser consistently freeze while using a reasonably-new computer. I'd love to "be bold" on this matter and fix it myself but it's really outside the scope of my ability to help out. Please, someone, address this issue! Ehb (talk) 05:13, 19 January 2012 (UTC)

My work PC, which slows to a crawl when doing absolutely anything does not have a problem with this page. I'm using windows XP with Chrome Mike _talk 05:22, 19 January 2012 (UTC)

I have no problems loading this page. Graham Colm (talk) 07:39, 19 January 2012 (UTC)

Peptide syn.png image

The image at the top of the page -- Peptide syn.png -- is outdated. I think that it was made before the E-site was added. Kalaracey (talk) 00:37, 3 December 2010 (UTC)

more resources

hello I recently wrote a paper on the structure and function of the ribosome. I've uploaded it here: http://dl.dropbox.com/u/17286416/BioPaperNoPics.docx Sorry if this isn't appropriate here... everything is cited. just want to help improve the article because it seems to be lacking. Kalaracey (talk) 12:40, 27 April 2011 (UTC)

Wrong use of RNP

I removed "(known as a ribonucleoprotein or RNP)" from the sentence saying "... 65% ribosomal RNA and 35% ribosomal proteins." A ribosomal protein is not an RNP - rather is the ribosome.

--Felix Tritschler (talk) 11:49, 5 October 2011 (UTC)

Edit request on 11 February 2012

Membrane-bound ribosomes: http://www.ncbi.nlm.nih.gov/books/NBK26841/#A2204

There are no sources for this section of the wiki page. Conveniently the information is also lacking in substance. Please add this source to this section so that people viewing the page may link to better and more accurate information on the subject, "Membrane-bound Ribosomes".

Andrewalsterda (talk) 01:06, 11 February 2012 (UTC)

 Done andy4789 ★ · (talk? contribs?) 16:45, 11 February 2012 (UTC)

Edit request on 17 June 2012

The sentence "ribosomes are partly constituted from RNA" does not sound right to me. I would replace it with "ribosomes consist partly of RNA"

Giacomo Consalez (talk) 19:41, 17 June 2012 (UTC)

Done. --Captaincollect1970 (talk) 20:34, 17 June 2012 (UTC)