I’m looking for a thoughtful discussion post on the given topic/question and a thoughtful response to my classmate’s post.

There are 20 primary amino acids that make up all proteins. But why those 20? Why Leucine? Arginine? Glutamine? Tryptophan? Why not a side chain with just two carbons, or three or four in a straight chain? Why not one with two hydroxyl groups? Or other shapes? Or containing other elements? What factors do you think might be involved?

You must POST ONE ANSWER to this question (70%), AND you must COMMENT ON ONE OTHER ANSWER (30%).

DON’T FORGET TO REFERENCE THE INFORMATION IN YOUR POST; textbook and peer-reviewed sources only. 

Lecture Slides I: https://docs.google.com/presentation/d/1rCC5CStyU5…

Lecture Slides II: https://docs.google.com/presentation/d/1dKioWhejJR…

Lecture Slides III: https://docs.google.com/presentation/d/1hPYC3FzZfw…

Textbook: Biochemistry: A Short Course, 4th Edition, by Tymoczko, Berg, Gatto, Stryer, ISBN 9781319114633

Classmate’s Post: 

The study of the origin of the 20 amino acids we have today has been an ongoing debate in the scientific world. It is believed that protein synthesis was the result of the RNA World, which dates back 4 billion years ago. At this point in time, cofactors were essential in performing redox reactions and electron transfer (Doig 2017), therefore proteins were not required. Instead, amino acids were utilized to aid in folding. The 20 amino acids that were chosen to perform this function were favorable because of their key properties including but not limited to charge, size and hydrophobicity (Doig 2017). Additionally, it is hypothesized that the first organisms on earth utilized organic material that was readily available, which would favor the highly abundant amino acids in this primitive environment (Weber 1981).

Weber and Miller studied this same question in 1981 when they suggested that protein synthesis did not occur as a result from the RNA world because life was already biochemically stable and proteins were not needed. Weber and Miller detail the positive properties of each amino acid and its contributions to protein function (Weber 1981). One of the overarching hallmarks that give these 20 amino acids an advantage is the predominance of carbon, hydrogen, nitrogen, oxygen and sulfur. These atoms are naturally occurring in the earth and thus their abundance proves more useful for protein synthesis than other atoms such as metals and halogens which are rarer and pose other issues for proteins such as excess water solubility and nucleophilic attack, respectively (Weber 1981). Additionally, the functional groups on the 20 amino acids are known to be more stable and possess the ability to form hydrogen bonds and electrostatic interactions. This is more favorable in comparison to other functional groups such as esters, ketones and nitriles. Lastly, the biosynthetic cost of forming these amino acids is low compared to their counterparts (Doig 2018).

This question is especially interesting to me because I work with proline and leucine in my current lab, and I frankly have never thought about how they came to form this larger group of our core 20 amino acids. I believe that this question remains somewhat unanswered, though significant progress has been made. The main takeaway that I gained from my research is that the 20 amino acids that we have today possessed atoms that were readily available in the primitive environment and favorable with low biosynthetic cost.

Sources:

Doig AJ. Frozen, but no accident – why the 20 standard amino acids were selected. FEBS J. 2017 May;284(9):1296-1305. doi: 10.1111/febs.13982. Epub 2017 Jan 13. PMID: 27926995.

Weber, A. L., & Miller, S. L. (1981). Reasons for the occurrence of the twenty coded protein amino acids. Journal of Molecular Evolution, 17(5), 273–284. doi:10.1007/bf01795749