I wound up on the Wikipedia pages about opsins because I was wondering about the word as used in the context of a story I was reading.
What a fascinating investigation it was – however, although the wiki pages make every effort to be clear, there were several things that were mentioned by, or possibly implied by, what I was reading that I would like to understand further. Please forgive me if any part of my curiosity is misguided or misinformed.
“Microbial rhodopsins are found in all three domains of life: Archaea, Bacteria, and Eukaryota, as well as in viruses.”
Wow. I always thought of viruses as just strings of RNA or DNA with nanite-like capabilities. I never thought of them having, er, guts. Do they use their rhodopsins for light-triggered mechanical things (like gates), or do they use them as light sensors? When people are talking about rhodopsins and they say “light sensor,” is the human eye kind of light-sensing (“There’s the sun.”) exactly the same thing/process as when light-sensing is used within a cell to, say, open a channel? Is “light sensing” as used for human vision just a more elaborate version of whatever viruses use rhodopsin for?
“Bacteriorhodopsins pump protons out of the cell.”
Are we talking about the protons of atoms? Is it possible to very briefly tell me what the purpose of this is?
Anabaena sensory rhodopsin: “The ratio of its cis and trans chromophore forms depends on the wavelength of illumination, thus providing a mechanism for a single protein to signal the color of light, for example, to regulate color-sensitive processes such as chromatic adaptation in photosynthesis.”
Sometimes just the very words of a certain phrase will get me excited because of their seeming implications. Like, someone will say, “transdermal phosphorescence”***** and I’ll be, like, “Does that mean what I think it means?” This is sort of like that. Can you tell me in a general way what “chromatic adaptation in photosynthesis” means?
*as far as I know, this is not a real thing. Oh wait, maybe it is. They have glow-in-the-dark tattoos.
Yes, a proton pump in a membrane moves single protons, as in a H[sup]+[/sup] ion. This generates a concentration gradient across the membrane. Such a gradient is used in mitochondria to make ATP which powers many cellular functions.
Specifically in Bacteriorhodopsins the proton gradient created is also converted to chemical energy.
In the stomach a similar pump action is used to acidify the stomach contents.
Wow … so we take apart atoms to get energy. I guess I knew that, after all it’s what metabolism is. But I never thought about it that way.
So…is that fission? When our cells take apart protons for energy, does that result in leptons and quarks and things? Do we harvest the particles, or just the energy?
This sounded weird to me, but I looked it up and it’s true, some odd viruses have rhodopsin genes. It looks like these genes don’t come from ancestral viruses but were instead “stolen” from some more complex organism. The viruses aren’t using them directly, but are instead causing the infected cell to make these proteins. What the virus gets out of this is not clear at this point…
Yup, as long as you dump the virus part. When light hits your eye it activates channels in your light-detecting (rod and cone) cells, causing ions to move around, which causes the cells to fire off an electrical signal that your brain interprets as “light”.
What Iggy said.
In some opsins from some organisms, the protein complex that makes up the channels can reorganize a bit (usually by swapping out components or adding extra components, but in some cases just by changing the folding of the proteins) to deal with different intensities of light or different colors of light so as to more efficiently convert the light to chemical energy.
Different compounds have different affinities for electrons, so for certain molecules you can pull a hydrogen atom off while leaving its electron behind, producing a proton (a hydrogen atom without its electron). In standard oxygen-burning metabolism, basically, you pull protons off of carbon-containing molecules like sugars, move the protons around, and dump both them and the carbon-with-extra-electrons atom onto oxygen, producing water and carbon dioxide (i.e., CH2 and O2 turn into H2O and CO2). Under the right circumstances, “the moving the protons” around step gives you energy. It’s called the Krebs cycle, and it’s a pretty complicated pile of machinery.
Oh, duh, of course not. Fission is splitting a nucleus, not “splitting an atom.” My bad.
About the Krebs cycle …* read read read read read* … you are **not ** kidding!
I think it will be really interesting to find out what a virus is doing with that rhodopsin gene. Or, I hope it will.
Thank you all for your succinct explanations. It is so cool to have this resource. And you wouldn’t believe how much achieving some measure of understanding in one area can inform your investigation of another area. For instance, I have a friend who’s an old radio enthusiast/ repairman. He is teaching me about electronics from that angle, and that knowledge gave me a much better grip on understanding the electron transport chain.
In addition to various rhodopsins (in the broad sense), there are other proteins with chromophores found in a wide variety of life forms: cryptochromes and phytochrome. These are involved in circadian rhythms and, in the case of cryptochrome, magnetoreception. Magnetoreception is present not just in many flying animals (bats, birds, insects) but in earthworms, sea slugs, and even some bacteria! (The human eye contains cryptochrome; some researchers think humans have some undiscovered magnetic sense!)
By any chance, Brujaja, was the story you read from Clarkesworld magazine? This month’s issue http://clarkesworldmagazine.com/ has a story called Pathways by Nancy Kress that has a doctor using opsins as part of a genetically engineered “algae” that is used in a patient’s brain to hopefully study her genetic disease and generally learn more about how our brains work.