How do I reconcile the biochemistry textbook descriptions of protons?

[docnet]

One of the main lessons from general and organic chemistry was excess protons in aqueous solutions exist in the form of hydronium ions.
However, in biochemistry textbooks, protons are individual in descriptions, for example, of the pumps in the electron transport chain, photosynthetic complexes and ATP synthase. This has always seemed contradictory to me. Why are protons being treated like ions such as Na+ or I-? It would make more sense to me if the proteins pumped proteins by the successive protonation and deprotonation of neighboring amino acids, which is surely how it really is in reality?

Separate question:
In a biochemistry textbook, descriptions of the speculated mechanism of photosystems were bafflingly complicated. Is there any literature about the evolutionary development of these photosystems from a simpler molecule? After taking several undergraduate and graduate level molecular biology courses, I'm confused by the lack of literature on how evolution by natural selection gives arise to specific proteins/complexities in cells. I'm in the middle of reading the selfish gene, so maybe my question will be answered soon.

 

[Ygggdrasil]

For proton transfer across membranes in ion channels see:
https://www.chemistryworld.com/news/getting-a-look-at-water-wires/3001794.article

For your second question, I have not studied the evolution of photosystems very much, but here's a review paper I found discussing it:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1693113/

Note that there are simpler systems that pump protons in response to light (e.g. bacteriorhodopsin), so the evolution of the photosystems can be decoupled from the evolution of the rest of the modern photosynthetic apparatus in cyanobacterial and chloroplasts.

 

[docnet]

For proton transfer across membranes in ion channels see:
https://www.chemistryworld.com/news/getting-a-look-at-water-wires/3001794.article

Interesting, this is the first time I read of a water wire, and it transports protons.

For your second question, I have not studied the evolution of photosystems very much, but here's a review paper I found discussing it:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1693113/

Thank you. This satisfied my curiosity and made me learn something about evolution.

Note that there are simpler systems that pump protons in response to light (e.g. bacteriorhodopsin), so the evolution of the photosystems can be decoupled from the evolution of the rest of the modern photosynthetic apparatus in cyanobacterial and chloroplasts.

Another question I always had in biochemistry was "how does absorption of a photon lead to conformational changes of the protein? After reading this page I was reminded of my question. Since then I took classes in inorganic chemistry and physics. The process could be: when an electron absorbs a photon within the right range of wavelengths, the electron gets excited and occupies a higher molecular orbital that has a different geometry than the orbital occupied by the ground state electron. This change in geometry leads to a change in electromagnetic repulsive forces exerted by the electron on the surrounding, and thereby the local conformation of the protein changes slightly. Does this sound crackpotty?

 

[Ygggdrasil]

Another question I always had in biochemistry was "how does absorption of a photon lead to conformational changes of the protein? After reading this page I was reminded of my question. Since then I took classes in inorganic chemistry and physics. The process could be: when an electron absorbs a photon within the right range of wavelengths, the electron gets excited and occupies a higher molecular orbital that has a different geometry than the orbital occupied by the ground state electron. This change in geometry leads to a change in electromagnetic repulsive forces exerted by the electron on the surrounding, and thereby the local conformation of the protein changes slightly. Does this sound crackpotty?

For rhodopsin proteins (such as bacteriorhodopsin or the opsin proteins that underlie our own vision), the proteins contain a molecule called retinal that can undergo a cis-trans isomerization upon the absorption of light. The change in shape of the retinal molecule propagates to the rest of the protein, causing the protein to change its overall shape. So, photoisomerization of a small molecule underlies the conformational change of the entire protein.

 

[docnet]

For rhodopsin proteins (such as bacteriorhodopsin or the opsin proteins that underlie our own vision), the proteins contain a molecule called retinal that can undergo a cis-trans isomerization upon the absorption of light. The change in shape of the retinal molecule propagates to the rest of the protein, causing the protein to change its overall shape. So, photoisomerization of a small molecule underlies the conformational change of the entire protein.

After reading your explanation, I did a quick google search and found this nice description of photoisomerization of a molecule called azobenzene using molecular orbital theory. It's a compelling picture.

https://chemistry.stackexchange.com/questions/31730/photoisomerization-of-azobenzene