Talk:Rhodopsin

Page expansion

Hi, This is a good start on the rhodopsin page. Someone needs to expand it a bit (i.e. add 11-cis in front of the first retinaldehyde and add all-trans in front of the second. More important, rhodopsin absorbs green light (500 nm) not purple. Purple is not even a color of light. It results from the eye simultaneously registering red and blue light, which is what you get when you remove the green light from the mixture of colored light we call white. Rhodopsin looks purple because it absorbs green. It would also be good to add that there are lots of invertebrate rhodopsins besides the vertebrate ones. Otherwise, my 25 years of research experience with rhodopsin says you have done an excellent job. Best regards, James W. Lewis

I don't know why Emperorbma believed that rhodopsin absorbed the most at purple. If I understand the descriptions right, rhodopsin is really crimson (purplish-red), which makes sense since its peak absorbance is at a hue I call algæ (green-cyan), at 498 nm. Why can't I find a photograph of rhodopsin? lysdexia 01:55, 23 Nov 2004 (UTC)

All-trans retinal or a11-trans retinal

"light = 11-cis-retinal -> a11-trans-retinal -> conformational change in rhodopsin -> activate transducin (G protein) -> activate cGMP-phosphodiesterase -> cGMP hydrolyzes -> levels reduced in outer segment -> cGMP-sensitive Na+/Ca2+ channels in PM close -> PM hyperpolarized -> glutamate release inhibited = ø rod cell neurotransmitter released -> detected by bipolar cells -> stimulate ganglion cells -> transmit signal to brain"

Links

Online vitamins guide [1] was moved to vitamins article. Biophys 03:32, 14 November 2006 (UTC)

Merging?

This article should be merged with opsin. Any thoughts? Biophys 19:42, 5 September 2007 (UTC)

I'd recommend against the merge. The relationships among the opsins are complex, and can be better explained with separate articles. --Arcadian 22:29, 5 September 2007 (UTC)

I agree as long as Rhodopsin and photopsins (for example) are separate articles, as it is right now. If we had an article about rhodopsins as a family that includes photopsins, then a merging could be considered, since both articles would represent the same proteins, but only with and without retinal... Right now the system of articles about these proteins seems to be rather complicated, but I do not have a clear idea how to improve this. Biophys 00:40, 10 September 2007 (UTC)

Having an article on opsin and another one on superfamily rhodopsin makes as much sense as having an article on wineglasses, and another one on wineglasses with wine in them. When the term "rhodopsin" occurs by itself, it rarely refers to the superfamily. This is an arcane use of the term that comes up mainly in the context of the two major clades of opsins, type 1 opsin (also known as bacterial rhodopsin) and type 2 opsin (also known as metazoan or eukaryote rhodopsin).

By itself, the word "rhodopsin" usually refers either to human rhodopsin, or more broadly, to the rh1 family of vertebrate visual opsins (generally rod opsins used for low-light vision). I think making rh1 opsins the topic of this article would be more encyclopedic than focusing only on the human variant.

Then there's rh2, "a rhodopsin-like opsin," also known as "one of the rhodopsins" or "a rhodopsin." I have never seen it referred to simply as "rhodopsin" without some sort of qualification. Rh2 is a cone opsin (except in the special case of frogs). Rh1 evolved from rh2 by gene duplication.

The there are rhA and rhB, found in lampreys. These two are equally distantly related to rh2 and rh1. While rh2 was present in the nearest common ancestor of vertebrates, rh1 was not, but was present in the nearest common ancestor of jawed fishes (or jawed vertebrates). Lampreys are vertebrates but not jawed fishes. Their rhodopsin-like molecules are considered important to understanding the evolution of rhodopsin. Zyxwv99 (talk) 22:01, 20 August 2015 (UTC)

I guess the idea was to keep this page for one specific human protein, while other pages above are about groups of proteins. My very best wishes (talk) 03:13, 16 March 2019 (UTC)

Overcompentence?

I think metazoan might not be "good style". Most readers will need to follow the link in "is expressed in metazoan photoreceptor cell" to learn that it is animal. So please don't be so sharp that others bleed. 91.152.95.139 (talk) 08:54, 8 May 2008 (UTC)

I agree though I wouldn't call the practice of using unnecessary jargon at all competent. 'Metazoa' is best reserved for when a distinction has to be made with Protozoa. When the comparison is with bacteria, 'animals' will do. --Bendž|Ť 11:03, 8 May 2008 (UTC)

Intro sentence

Rhodopsin [...] is responsible for [...] the formation of the photoreceptor cells

Really? I would have guessed that the photoreceptor cells are responsible for the formation of rhodopsin. How does rhodopsin cause the photoreceptors to spring into existence? AxelBoldt (talk) 03:30, 10 March 2009 (UTC)

You are correct. Intro sentence has been edited accordingly.Biolprof (talk) 01:59, 20 May 2012 (UTC)

Picture on the right of the page

Hi everybody! Why is there picture of SRII, which is of course retinal-bound seven-helical transmembrane protein, but it is bacterial and not GPCR? --VGmonster (talk) 13:51, 16 June 2009 (UTC)

Removing the "Bleaching" section due to numerous errors and paucity of relevant information

The current version of the "Bleaching" section contains no relevant information and consists almost exclusively of factual errors. Just a few examples:

1. The section refers to "the threshold". What threshold? Rhodopsin is activated by a single photon of light. Photon absorption is a quantum event lacking a threshold. If the section refers to psychophysical experiments, then they have nothing to say about the photobleaching of rhodopsin.
2. The rest of the section describes an unrelated and unreferenced psychophysical experiment. The properties of photoreceptors and rhodopsin are measured more directly with single-cell recordings, patch clamp recordings, and other electrophysiological techniques.
3. What is "the vibrational energy derived from light"?
4. The section states that photoreceptors convert energy of light into electricity and pass it to bipolar cells. This description is inaccurate in several ways. First, photoreceptors form chemical synapses, not electrical synapses, with bipolar cells. Glutamate is used as neurotransmitter. Photoreceptor cells do form electrical synapses between each other, but not with bipolar cells. Second, photoreceptors do not "convert" the energy of light into electricity. The energy of the phototransduction chain comes from metabolic processes. In fact, photoreceptor cells are hyperpolarized by light, which means that their membrane current decreases with light exposure (in vertebrates).
5. What does the electroretinogram tell us about the photobleaching of rhodopsin? The retina has multiple populations of cells with varying responses to light and no direct relationship to changes in the properties of rhodopsin can be elucidated from the ERG.

I am removing the entire section.

Yatsenko DV (talk) 01:03, 27 July 2009 (UTC)

Light pollution, blue light, and visual purple (Rhodopsin)

Hi. Can we add this as information or link to Rhodopsin or a related article? There are also references that state lack of exposure to blue light during the day suppresses melatonin generation at night, potentially leading to sleep deprivation. Please ensure that this information is found on Wikipedia somewhere. Thanks. ~AH1 ^(discuss!) 20:04, 20 July 2012 (UTC)

photobleaches to what ?

First paragraph> 'Exposed to light, the pigment immediately photobleaches, and it....' okay so it 'photobleaches', but to what ? (i skimmed the photobleaching wikipage) i could guess, does it increase or reduce light transmission/reflection, or something else?? i guess it's not simple but an approximate outline would help understanding before drowning further into the article — Preceding unsigned comment added by 78.149.14.120 (talk) 16:56, 24 May 2013 (UTC)

Bravo

Can't begin to tell you how pleased I was to read the first paragraph and almost understand what was being said. I knew going in that it was going to be over my head, but normally that doesn't deter me. Wikipedia has the deserved reputation of starting out with the egghead explanation and never giving a layman's version. I may have been partially responsible for spreading that reputation. You guys usually do suck a this.

However, today you surprised me. Yeah, I still have to struggle, but I won't have to leave wikipedia to do that. Thanks for the help! ...and well done!deepsack (talk) 01:12, 16 May 2014 (UTC)

Conflating definitions of rhodopsin

This article is conflating two different senses of the word rhodopsin.

1. any opsin + the chromophore retinal

2. a rod opsin found in jawed vertebrates (gnathostomes), used for scotopic (dark adapted) vision - the gene is known as Rh1 - the opsin is called either Rh1 or the Rh1 opsin

Definition #2 has several variants:

a) any rod opsin (coded for by the gene Rh1, used for dark-adapted vision, found only in gnathostomes, although lampreys have a close relative, RhA)

b) human rod opsin (OPN2)

Either of these two variant definitions can be with or without the chromophore (retinal), or at all stages of the visual cycle.

With the chromophore it's also calld visual purple.

There is also a family of rod-opsin-like opsins found in vertebrates. It includes the rod opsin Rh1, the blue-green cone opsin Rh2 (extinct in mammals), as well as RhA and RhB (found in lampreys) - usually indicated by "rhodopsins" (plural)

Ideally these should be two separate articles. In the meanwhile, we should at leaest clarify the difference within this article.

Zyxwv99 (talk) 00:46, 15 September 2015 (UTC)

UPDATE:

Here are some references on this:

• Medical Neurobiology (book)

"Rhodopsin is the only term for the specific photopigment contained in rods. Rhodopsin is also a generic term for any retinal-containing opsin, including that in cones."

• Fish Physiology: Sensory Systems Neuroscience

"In the literature, some terminological confusion occurs because the term "rhodopsin" is sometimes exclusively applied to rod rhodopsin or even to rod opsin. Throughout this chapter, we use the term "rhodopsin" as defined earlier, that is, designating the class of photopigments that contain the chromophore 11-cis-retinal."

• Photoreceptor for Curling Behavior in Peranema trichophorum and Evolution of Eukaryotic Rhodopsins

"We are using the traditional (premolecular biology) operational definition of rhodopsin, namely, a protein that forms a chromophore with a retinal molecule and that has a light-sensing function."

Zyxwv99 (talk) 00:07, 22 September 2015 (UTC)

another UPDATE:

It looks like this article was originally about rhodopsin in sense #2. You can see the very first edit if you go to the history page, click on 250 items per page, then scroll to the bottom. It reads:

Rhodopsin, also known as visual purple, is a retinal pigment that is mostly concentrated in the rod cells. It is a derivative of Vitamin A that is synthesized in the retina and used to detect light. It is most sensitive to purple light, which is why it is "visual purple,"...

On 18 May 2015 User:171.66.219.128 changed the hatnote to it's current state:

"This article is about the rhodopsin superfamily of retinal-binding seven-transmembrane proteins, including animal and bacterial representatives, with emphasis on function. For additional information on the protein structure, see retinylidene protein."

Before that it read:

"This article is about the visual rhodopsin of vertebrates. For other types of rhodopsin, see retinylidene protein."

The older hatnote was there since 21 March 2006, when it was added by User:Tameeria.

Zyxwv99 (talk) 02:17, 22 September 2015 (UTC)

Anatomy and physiology of farm animals

Give two examples integral membrane proteins that form channels across the membrane animal cell 102.144.251.95 (talk) 16:06, 26 June 2022 (UTC)

Wiki Education assignment: CHEM 378 - Biochemistry Lab - spring 2023

This article was the subject of a Wiki Education Foundation-supported course assignment, between 30 January 2023 and 20 May 2023. Further details are available on the course page. Student editor(s): Midnightrain0528 (article contribs). Peer reviewers: Nmneuro.

— Assignment last updated by Nmneuro (talk) 00:08, 16 May 2023 (UTC)