Talk:Photosynthetic reaction centre

Clarifying
Regarding this sentence: "The water molecules that are oxidized in the manganese center are the source of the electrons that reduce the two molecules of Q to QH2"

Would this adding make it more clear?: "The water molecules that are oxidized in the manganese center are the source of the electrons that, through the p680 and the phaeophytin, reduce the two molecules of Q to QH2"

Mistake in graphic
The image in the side of the explanaton of the photosystem 2, spells phaeophytin wrong. https://upload.wikimedia.org/wikipedia/en/thumb/4/44/PSII_new_design.svg/200px-PSII_new_design.svg.png

I don't have the time to change it though, sorry.

Important word change
Old wording was (bolding is mine): When an electron rises to a higher energy level, there is a corresponding increase in the reduction potential of the molecule in which the electron resides occurs. Changed increase to  decrease. The reduction potentials decrease  (become more negative in value) instead of increase. For example, upon excitation the midpoint potential of P680 decreases from +1.1 V to -0.7 V.. MBprof (talk) 20:45, 14 February 2016 (UTC)

removed
Removed from article:

==Bacteria and plants==

Reaction centres are present in all green plants and in many bacteria and algae. Green plants have two reaction centres known as photosystem I and photosystem II. A well understood bacterial reaction centre is that from the Rhodopseudomonus bacteria. Its photosynthetic reaction centre is much simpler than that of green plants and only consists of one protein complex.

Photosystem I typically includes 13 polypeptide chains, more than 60 chlorophyll molecules, a quinone and three 4Fe-4S iron-sulphur clusters. The total molecular mass is in excess of 800kd. Photosystem II contains at least 10 polypeptide chains, more than 30 chlorophyll molecules, a non-heme iron ion and four manganese ions.

Sequence analysis and structural comparisons between bacterial reaction centres and those from green plants reveal a reaction core which is remarkably similar, despite the increased complexity of the reaction centres found in green plants.


 * I removed this because it is rather redundant with the rest of the article, and doesn't compare the bacteria and plants, as the chief purpose of the section was to do, probably. AndyZ 01:02, 1 March 2006 (UTC)


 * I've reinserted a simpler version of the section above. It doesn't describe the structures of each reaction centre, it just serves as an introduction to the three reaction centre types.--Miller 13:32, 1 March 2006 (UTC)

NADPH
Small thing, in the article it says that "The electron chain that follows creates a highly reduced species such as quinone or NADPH, which is used in the Calvin cycle (the dark reactions) and in the Krebs cycle (the citric acid cycle)." I think that NAD+ is used in the Krebs cycle, not NADPH. AndyZ 01:13, 2 March 2006 (UTC)
 * Correct. NAD+ is usedin the TCA cycle. David D. (Talk) 22:31, 4 March 2006 (UTC)

Chlorophyll a vs chlorophyll α
From what I have seen in text books the most common nomenclature used is chlorphyll a, not chlorophyll α. We should figure out a consensus for the standard nomenclature. Originally I had been using chorophyll a in wikipedia but I now notice that someone has gone through and reverted those edits to chorophyll α. A quick google gives over 6 million hits for chorophyll a, as opposed to 150,000 for chlorophyll α. I would side with using chorophyll a as standard nomenclature throughout the photosynthesis articles in wikipedia. David D. (Talk) 22:39, 6 March 2006 (UTC)


 * I reverted the edit; actually though I use chlorophyll a, but the Chlorophyll article used chlorophyll α. I personally use "a" usually, but when I found chlorophyll α on the Chlorophyll article I though it was some general conformity to use α. Perhaps this should be brought up on the Talk:Chlorophyll. AndyZ 01:32, 7 March 2006 (UTC)
 * Yes i think we should bring this up. i think one user swept through and converted them all within the last few months.  i didn't notice the edits at the time otherwise i would have reverted back. David D. (Talk) 03:29, 7 March 2006 (UTC)
 * I looked back and it appears to be User:Twilight Realm who made the a to α edits on the 5th Jan 2006. i have reverted the Chlorophyll page. David D. (Talk) 03:35, 7 March 2006 (UTC)

modified diagram
I have modified the diagram from the article that represent the bacterial RC. i have tried to incorporate in the Q cycle, the cyclic return of electrons via cyt c2 9not finished), proton pumping (not finished), the correct colour of the light (Far Red), the cytoplasmic and periplasmic locations. This is not a final product but I would appreciate some feed back. i don't want to waste my time perfecting this diagram if other users here do not like it. David D. (Talk) 01:22, 8 March 2006 (UTC)
 * Above text refers to an older version of First_satge_sbep.png. David D. (Talk) 21:09, 8 March 2006 (UTC)
 * Eh, thats a huge improvement as far as I'm concerned..... I wish I'd seen it before I *just* did the SVG version of the old. On the light color... that sorta bugged me too... but we can't accurately show 960nm light. In the other diagram (with 680nm light) that would be an approiate color, but it feels wrong claim 960nm as red.. Perhaps we make it black and label it as 960nm IR? Lets work out all the details and I can turn yours into a SVG (or you can do it, see Inkscape) :)--Gmaxwell 02:52, 8 March 2006 (UTC)
 * Good point with regard to the light, its not far red at all. I'm getting mixed up there. I was more worried about the line not being green since one of the misconceptions with regard to photosynthesis is that green light is absorbed by chlorophyll since leaves are green (I know this is bacteria but i still think green has to be avoided). I have adobe illustrator so I normally use that for vector diagrams.  The diagram to the right is more a representation that i canabilised from the original to save some time.


 * May be before we start we should discuss what this figure is trying to show. From my perspective, obviously i have turned it into a more general summary diagram.  is this what we want?  Also we need a key for the colour codes.  I assume dark red is reduced, is blue oxidised?  What is the green P960 meant to represent an bacteriochlorophyll with an energised electron? I am not sure of the nomenclature with regard to the Quinine.  Should the oxidised for be Q? QB should probably only be used when it is associated with the reaction centre. There are other issues too, specifically where to have the protons and electron  that are asociated with the bc1 complex. Sorry to throw so much detail out there but I want you to get an idea of how I was thinking when I added to the diagram. David D. (Talk) 03:41, 8 March 2006 (UTC)

I just had another attempt at the figure but this time I used your SVG version as a starting point. Now you too can play with it using inkscape. I may have saved it in the wrong format since the fonts are not showing up despite them being present in the uploaded version. I don't have time to figure it out at the moment. David D. (Talk) 08:55, 8 March 2006 (UTC)
 * I'll give it a kick later... The fonts may not be showing because the SVG rasterizer in Mediawiki doesn't currently support flowed text (i.e. text on a path). Illustrator might be generating that sort of text by default. I like your improvements. --Gmaxwell 15:40, 8 March 2006 (UTC)
 * i just made my finally changes and the PNG above should show the text that is not showing uo in my SVG version fine. I look forward to seeing your own aditions and suggestions. David D. (Talk) 21:09, 8 March 2006 (UTC)
 * I made some other minor tweaks and fixed the SVG. I think it looks great now. (Illustrator put a LOT of crap into the SVG that bloated up the size, which I also pulled out). --Gmaxwell 00:04, 9 March 2006 (UTC)
 * In retrospect i think that the P960 in the 4th panel should be in the reduced form (dark red). Should the text be a bit bigger? I see what you mean about the bloated size. i think that could well be becuase i saved in the wrong format.  Illustrator gave me about five options for saving the fonts.  I had no idea which one to go with since I usually save the final version as a jpg.  Now, though, i do see the advantages of keeping the vectorial coordinates.  the figures look much better in SVG compared to jpg. David D. (Talk) 01:11, 9 March 2006 (UTC)
 * P960 reduced in the forth seems to make sense to me, but this isn't my area of expertise.. Easy enough to change (you could even change it with a text editor, when we're done I'll clean up the SVG enough to make that easy). I'm wondering if perhaps we should make it vertically oriented, it's generally more acceptable to have tall graphics rather than wide graphics (because small screened client are already scrolling vertically). What do you think? --Gmaxwell 02:37, 9 March 2006 (UTC)
 * The problem with a vertical orientation is that you lose the context with respect to the cytoplasm and membrane. Also, I wonder whether the light wavelength should be specified? While the P960 does have an absorbton maximum at 960 nm it does absorb at other wavelengths too. Specifying the wavelength gives the impression that only that wavelength is absorbed. David D. (Talk) 02:52, 9 March 2006 (UTC)
 * I was under the impression that the response was fairly steep, (obviously anything which happens in finite time is not infinitely steep). but I see how it could be misleading. It would be informative to provide a absorption graph... but a quick google doesn't show anything. We have one on the P680 article but nothing covering this. --Gmaxwell 03:07, 9 March 2006 (UTC)
 * I also looked for an absorbtion spectrum for P960 including primary literature but came up with nothing. I see you made a few more changes to the figure. I think the diagram looks pretty good and is a good representation of the text. I think this figure will help readers understand this more easily.  David D. (Talk) 15:44, 9 March 2006 (UTC)

May I suggest that a high quality and less cluttered version of his crude diagram be used in the green plant section to illustrate the whole electron chain.--Miller 03:24, 9 March 2006 (UTC)
 * I have been thinking about this a bit trying to consider the scope of this article. Photosynthesis and light-dependent reaction already cover the Z-scheme in great deatil. This article is primarily about the reaction centre. With respect to the bacterial RC it makes a bit of sense to include the cyclic electron flow and the associated ETC since it is not covered else where in wikipedia but even that is a stretch with regard to an article on reaction centres. What are your thoughts with regard to the breadth of this article? David D. (Talk) 15:39, 9 March 2006 (UTC)

Are you suggesting that the article be merged with another to make it more general with respect to the light reactions?--Miller 21:09, 9 March 2006 (UTC)
 * I'm suggesting the opposite. This article should focus on the reaction centre not on the Z-scheme or the production of ATP and reducing agents. David D. (Talk) 22:57, 9 March 2006 (UTC)
 * What do you think about the new diagram? If a cleaned up version of that were to be inserted into the article then the Z-scheme wouldn't need to be explained in such detail.--Miller 22:45, 10 March 2006 (UTC)
 * Yes, no, maybe?--Miller 12:50, 11 March 2006 (UTC)

Miller’s nomination for Version 0.5
I started this article some time ago before submitting it for a peer review and a request that it become a featured article. Although it never reached featured article status, maybe owing to its length and obscurity of subject matter, with the help of the users AndyZ, Smurrayinchester, Durova, amongst others, it was brought up to good article status. I also earned my first (and thus far only) barnstar for my contributions to this article so I’m mildly confident that maybe it might be suitable for the test release of the fixed version of Wikipedia.Miller 20:59, 1 August 2006 (UTC)

Proton pumping in plants
Plants have an equivalent to the Q cycle in bacteria, I think


 * Can you clarify this statement? Thanks. LostLucidity (talk) 17:49, 3 April 2008 (UTC)

Centre or Center?
The article is entitled centre, but the lede says center, and most of the article uses center (46 of 48 appearances!). Should the article be retitled? Or should the lede be improved? Should all uses in the article be made consistent? Or should the text explicitly suggest that both spellings are equally valid? Yes, it's a nit, but it's the title of the article! Gnuish (talk) 23:25, 3 September 2021 (UTC)