Talk:CH391L/S12/Pigments

• Jeffrey E. Barrick 13:09, 25 March 2012 (EDT):Please add references to your figure captions.
  • Yi Kou 07:43, 26 March 2012 (EDT):Added.

• Jeffrey E. Barrick 13:09, 25 March 2012 (EDT):For the chromobacteria section, many of these pigments seem to have evolved because they are antibacterial agents (like pyocyanin). It doesn't really matter if these are colored or not for their function. Aside from uv protection and harvesting light energy, I guess color is a random side-effect of the molecular structure in many cases. Is there also a connection that colored compounds (such as heme) are often redox-active?
  • Yi Kou 07:43, 26 March 2012 (EDT): I did some research, it is common for a pigment to be redox related if the pigment is generated as antibiotic for competing other organisms (and often these are related to either disturbing or maintaining the inside reducing power), famous example is pyocyanin from phenazines[1],other examples can be seen[2][3].

• Jeffrey E. Barrick 13:09, 25 March 2012 (EDT):We've also talked about how sometimes symbiotic bacteria lend their properties to multicellular animals, like the example of luciferase and squid. I wonder if any colors in higher animals are derived from bacterial symbionts in specialized organelles or horizontal transfer of bacterial genes, rather than from eukaryotic .
  • Yi Kou 09:01, 26 March 2012 (EDT): I did some research, but not so satisfying: using symbionts to show the color are mainly the marine animals. Besides squid, angler fish is another one. There other two I can find is one carotenoid pigment and one heme proteins. I do not think they are involved in gene transfer.

• Jeffrey E. Barrick 13:09, 25 March 2012 (EDT):Wow, those radiotrophic fungi are crazy.
  • Yi Kou 07:54, 26 March 2012 (EDT):Yes, I think they are the "toughest" organisms. A link for this: Radiotrophic fungi.

• Ben Slater 16:37, 25 March 2012 (EDT): You mentioned in your presentation that you weren't sure why β-carotene is missing the typical isoprenoid structure in the center. This occurs because the isoprenoid condensation joining the two 20-carbon precursors is a head-to-head condensation instead of head-to-tail as in the previous steps. A good way to spot this is the release of two pyrophosphates instead of one. Another good way indicator is the existence of the characteristic "forked tongues" on both ends instead of just one end.
  • Yi Kou 08:43, 26 March 2012 (EDT):I find this needs a little bit more explanation. β-carotene is not missing the typical isoprenoid structure, I was wondering at the time of counting the right 8 isoprene units by counting the double bond (which is usually the method for terpenoid, as is often seen in the steroid synthesis, esp lanosterol). Actually, head to tail or head to head does not have relation to how many double bonds/typical isoprene there are in the structure. Head to tail can also result in right number, and also with release of the two PPis (esp. lanosterol or other steroids I remember). β-carotene has nine double bonds out of 8 isoprene building block because of an cyclopropane containing prephytoene intermediate formed during the synthesis (catalyzed by phytoene synthase using GGPP to make phytoene). Chemically, I think this kind of formation is not favored (though releasing high energy PPis), but may be under phytoene synthase, the cyclization is favored with delta G compensated biochemically or structurally (since head to tail connection easily result in future multi-ring structure).

beta carotene bio-synthesis, http://upload.wikimedia.org/wikipedia/commons/8/89/Carotenoid_synthetic_pathway.svg

Ref

<biblio>

1. pyocyanin pmid=17526704
2. Mutactimycin pmid=15323124
3. unknown pmid=20502566