How do I reconcile the biochemistry textbook descriptions of protons?

In summary, the main lesson from chemistry is that excess protons in aqueous solutions exist in the form of hydronium ions. However, in biochemistry textbooks, protons are described individually, leading to confusion about their treatment as ions. The process of proton transfer across membranes in ion channels is also discussed in relation to photosystems and their evolutionary development from simpler molecules. Additionally, the mechanism of how absorption of a photon leads to conformational changes in proteins is explained through the example of rhodopsin proteins and the photoisomerization of a small molecule.
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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.
 
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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.
 
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Ygggdrasil said:
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.

Ygggdrasil said:
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.

Ygggdrasil said:
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?
Screen Shot 2020-08-16 at 1.55.48 PM.png
 
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docnet said:
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.
 
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Ygggdrasil said:
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
 
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Related to How do I reconcile the biochemistry textbook descriptions of protons?

1. How do protons contribute to the overall structure and function of biological molecules?

Protons play a crucial role in the structure and function of biological molecules. They are responsible for determining the overall charge of a molecule, which affects its interactions with other molecules and its ability to participate in chemical reactions.

2. How do protons interact with other molecules in biological systems?

Protons interact with other molecules through a variety of mechanisms, including hydrogen bonding, electrostatic interactions, and acid-base reactions. These interactions are essential for maintaining the stability and function of biological systems.

3. How is the movement of protons regulated in biological systems?

The movement of protons in biological systems is regulated by specialized proteins called proton pumps. These pumps use energy to actively transport protons across cell membranes, creating concentration gradients that are essential for various cellular processes.

4. How do protons contribute to the production of ATP in cellular respiration?

Protons play a critical role in the production of ATP in cellular respiration. During the electron transport chain, protons are pumped across the inner mitochondrial membrane, creating a gradient. This gradient is then used by ATP synthase to produce ATP from ADP and inorganic phosphate.

5. How do protons affect the pH of biological systems?

Protons are a major contributor to the pH of biological systems. The concentration of protons, or acidity, can greatly affect the structure and function of biological molecules. Maintaining a specific pH is crucial for proper functioning of enzymes and other biological processes.

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