Talk:RuBisCO

Rubisco was a science collaboration of the week.
View the changes made during that week.

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Since when has this enzyme been called rubisCO instead of rubisco? It was rubisco (or usually, its long name) when I was in grad school working on photosynthesis, and the website linked to from the article calls it rubisco. Can we change it back so that rubisco has the article and rubisCO is the redirect? -- Marj 18:28, 6 Oct 2004 (UTC)

I have moved the article to the short from of the name since that's what people call it in practice and since there is some technical issues with / in titles.--nixie 05:32, 11 August 2005 (UTC)

Calvin Cycle diagram

Hey I just made/added an overview of the calvin cycle for this page and the calvin cycle page, I was wondering what everybody thinks. I'm worried it's to complicated/busy, I am wondering if i should dumb it down (ie get rid of the molecule diagrams). Anything else to change, I really want it to be great. Adenosine | Talk 08:34, September 2, 2005 (UTC)

I think it is good to include such a diagram on this page. Please check the structure of 3-phosphoglycerate; I think you have a carbon with 5 bonds and an extra hydrogen. Is it reasonable to show the carboxyl group as protonated at physiological pH? I like the idea of science articles that start simple and then have the details towards the end. Maybe there could be a simplified figure right at the start of the article. --JWSchmidt 13:35, 2 September 2005 (UTC)

Questions about Figure 2:

File:TwoRuBisCOquestions.png --JWSchmidt 20:41, 2 September 2005 (UTC)

You'd start to think I don't study this stuff every day in school... fixed. Adenosine | Talk 20:52, September 3, 2005 (UTC)

I tried making a new version (Image:Calvin-cycle3.png) that emphasizes the labels for RuBisCO and "Phase 1". It allows my old eyes to better see "RuBisCO" in the thumbnail view. If you think the modified version is okay, it probably could be compressed to a smaller file size. --JWSchmidt 09:12, 5 September 2005 (UTC)

I like that edit very much Adenosine | Talk 09:19, September 5, 2005 (UTC)

Many changes

I'm trying to learn the editing procedures/protocols (so patience please) and I have started to make many changes to this entry to hopefully improve it, based on the latest literature and consensus views on this enzyme. More to come, including references to better document the changes I have made. Need to create a User name - ARP for now 130.126.53.185 23:49, 29 November 2005 (UTC)

Thanks for all of your work on this article. --JWSchmidt 01:28, 30 November 2005 (UTC)

Added figure.

Added a figure showing the complete enzyme. I think this image should replace or at least accompany figure 1, but I'm just learning this whole system.

Made some minor changes in the text - links. Will add refs soon. ARP 17:16, 30 November 2005 (UTC)

Feel free to change the image for Figure 1. Figure 1 resides withing a "protein information box". The information box is generated by a "template": Template:Protbox_start. You can edit the "Photo" and "Caption" parameters for the template where it is used right at the start of the RuBisCO edit window:

{{Protbox start|Name=[[RuBisCO]]|Photo=RuBisCO.jpg|Caption='''Figure 1'''. Charged domains [<span style="color:#ff0000;">red</span>(<big>-</big>), <span style="color:#0000ff;">blue</span>(+)] on [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?form=6&db=t&Dopt=s&uid=30476 RuBisCO] allow it to assemble into tightly packed multi-meric complexes, maximizing the number of copies of this inefficient enzyme inside plant cells.....

Just replace "RuBisCO.jpg" with the name of a better image and add a descriptive caption for the new image. --JWSchmidt 19:47, 30 November 2005 (UTC)

Added references and some text changes

I'll have to mess around with replacing/switching Figs 1&4.ARP 21:59, 30 November 2005 (UTC)

Switched figures

OK, I've switched figs 1 and 4. Added one more ref to 'genetic engineering' section and made some small text changes. Also note that in Fig 2, Ribulose 1-phosphate (& its structure) should be replaced by Ribulose 5-phosphate - I've emailed the original author and hopefully he will change it.ARP 16:22, 1 December 2005 (UTC)

Switched figures

OK, I've switched figs 1 and 4. Added one more ref to 'genetic engineering' section and made some small text changes. Also note that in Fig 2, Ribulose 1-phosphate (& its structure) should be replaced by Ribulose 5-phosphate - I've emailed the original author and hopefully he will change it.ARP 16:22, 1 December 2005 (UTC)

rubiscos structure

Rubisco consists of eight large L chains (56 kd) and eight small S chains (14 kd) giving an L8S8 octo-dimer. NOT four L chains and eight S chains!

Metabolic control

The article states that "RuBisCO is the primary rate-limiting enzyme of the Calvin cycle." - NO NO NO! Under normal physiological conditions, according to Quick et al (1991), Rubisco has a control coefficient of 0.05-0.15 (the sum total of the control coefficients of every enzyme in a given pathway being 1). Only when growth has taken place in low light, and light intensity is suddenly increased (or CO2 is suddenly decreased), does rubisco's control coefficient increase to coefficient ranges where this statement might be accurate (>0.5).

Under the "normal" high light intensities typical of outdoors on sunny days, the rubisco control coefficient is 0.8 - see the paper following Quick (Stitt et al., 1991). Studies in the Quick paper were conducted using growth chamber conditions - low light!!!. Thus the statement is correct. ARP 19:22, 20 December 2006 (UTC)

RuBisCo engineered to have all the essential amino acids

has anyone engineered rubisco to have a wider variety of amino acids as structural aspects That is making the essential amino acids part of rubisco while maintaining rubisco function If rubisco was full of things like methionine phenylalanine, valine, threonine, tryptophan, isoleucine, leucine, and lysine Cysteine, tyrosine, histidine and arginine then eating plants with this Rubiscos presence would provide all the essential amino acids Considering that RuBisCo makes up a majority of the protein on Earth I think that it should be upgraded to deliver all the amino acids necessary to live People could get all of their protein from engineered rubisco leaves n grass —Preceding unsigned comment added by 169.237.215.179 (talk) 21:26, 15 June 2009 (UTC) People can already get all the protein they need, and other things, from spinach leaves. --Agesworth 05:52, 17 June 2009 (UTC) —Preceding unsigned comment added by Agesworth (talk • contribs)

Importance

Considering that RuBisCo makes up a majority of the protein on Earth I think that it should be upgraded to high/top level importance. Anyone else agree? —The preceding unsigned comment was added by R-Bowen J (talk • contribs) 08:11, 19 December 2006 (UTC).

Even if it is the most common protein, that does not mean it "makes up a majority of the protein on Earth". --JWSchmidt 02:58, 1 February 2007 (UTC)

I agree with the 1st guy - high or even top importance! Aaadddaaammm (talk) 15:02, 3 November 2008 (UTC)

I've changed the importance to high as it is the single most abundant protein on Earth. Smartse (talk) 00:48, 23 May 2009 (UTC)

Beautifully referenced

I came across today an article referring to RuBisCo in the journal Nature (Vol 447; 14 June 2007; pp. 781-782), and looked RuBisCo up on Wikipedia. This Wiki on RuBisCo reads quite well, and the referencing, detailed as it is, is impressive. Keep up the good job, contributors. AppleJuggler 03:34, 26 June 2007 (UTC)

Removed last section, "RuBisCO and carbon sequestration"

I removed the last section, because I think the connection between carbon sequestration RuBisCO specifically (as opposed to other proteins in photoautotrophs) is a red herring. The idea that addition of nutrients to ecosystems increases carbon sequestration is old and important. But there's nothing special about RuBisCO to this phenomenon: photoautotrophs require lots of proteins to successfully convert CO₂ into organic matter in a form that will not rapidly be converted back to CO₂ by heterotrophic organisms. Furthermore, I know of no evidence that in nitrogen-limited plants, added nitrogen is preferentially assimilated into RuBisCO as opposed to other biomolecules. So I don't think this section is really on-topic.

I have retained the reference to the carbon cycle under "Further reading", although I guess using my logic above it could be removed.

Otherwise, I think this is a first-rate article! Asteen (talk) 14:59, 20 April 2008 (UTC)

RuBisCO vs Rubisco

I propose that all RuBisCOs should be changed to Rubisco - got a problem with that? Aaadddaaammm (talk) 15:00, 3 November 2008 (UTC)

I'd !vote for keeping it as is - it's more descriptive. -- MarcoTolo (talk) 17:00, 3 November 2008 (UTC)

It may be more descriptive, but it just looks so ugly to me. 141.14.217.217 (talk) 08:49, 5 November 2008 (UTC)

I agree it looks really bad in articles. I have certainly never written RuBisCO by hand and can't imagine many other people doing so. Smartse (talk) 23:49, 22 May 2009 (UTC)

reference check

I just took this out of the article:

In the initial reaction of RuBisCO in the light, the RuBP that was separated from RuBisCO binds with the carbamylated enzyme and after proton abstraction produces Enediol that can react with carbon dioxide. A limitation of either RuBisCO or RuBP at any stage will make the reaction insensitive to any other factor including carbon dioxide. For this reason, the leading C3 model that is based on a limitation of RuBisCO at low carbon dioxide levels such as compensation point is incorrect, since it cannot support life on the planet<ref>http://www.farazdaghi.com/</ref>. (added by Hfarazdaghi)

Can an expert verify the content and provide a citation to a specific published article rather than to this website? User Hfarazdaghi seems to run the cited website. --JWSchmidt (talk) 03:27, 14 June 2009 (UTC)

I suspect that edits from 99.231.80.189 such as this one are also from User:Hfarazdaghi. I think we need to remove all links to www.farazdaghi.com from the article. We need citations to peer-reviewed publications. --JWSchmidt (talk) 04:10, 14 June 2009 (UTC)

1) To satisfy yourself, Please check the latest volume of Advances in Photosynthesis and Respiration. Photosynthesis in Silico, A. Laisk, L. Nedbal and Govindjee (eds.), Photosynthesis in silico: Understanding Complexity from Molecules to Ecosystems, pp. 275–294.

c 2009 Springer Science+Business Media B.V.

Chapter 12: Modeling the Kinetics of Activation and Reaction of Rubisco from Gas Exchange Hadi Farazdaghi

2) Rubisco has been the origin of oxygenic life and is the main controller of CO2/O2 ratio on the planet. It is the only natural substance that can sequester CO2 and store it in vegetation.

3) Interested parties are welcome to comment directly on the site of www.farazdaghi.com —Preceding unsigned comment added by 99.231.80.189 (talk) 19:48, 12 July 2009 (UTC) The site also refers to other published articles. —Preceding unsigned comment added by 99.231.80.189 (talk) 20:46, 12 July 2009 (UTC)

Hi there, do you have any references to PubMed-listed journals that deal with this topic? This would deal with the problem easily, since we have no way of verifying if "www.farazdaghi.com" is run by an expert on Rubisco or accurately summarises the references that it cites. Tim Vickers (talk) 17:11, 20 July 2009 (UTC)

Mechanism

Hi. A question came up on the reference desk Wikipedia:Reference_desk/Science#the organic chemistry of carbon dioxide fixation (i.e. mechanism of RuBisCO) about the mechanism of co2 capture, I found these [1] which is more detailed than the article about the active site in the enzyme - could this be incorporated into the article, or linked to? . maybe as further reading - thanks? I'm not a biochemist so I will leave it to whoever has got the article into it's present state - more expert than me.83.100.250.79 (talk) 15:13, 12 September 2009 (UTC)