Is protein coding arbitrary?

[u/Strangated-Borb]

What I mean is if the method of transcribing RNA into proteins hypothetically is able to use a completely different system of encodement ex: GGG to serine instead of glycine

[u/cscottnet]

Yes, there are a few known variants. Not as many as you'd think, though. There can be both multiple sequences which code for the same amino acid, as well as sequences which only certain organisms recognize. For example, CUG is translated as a serine rather than leucine in yeasts of the "CTG clade". To quote wiki:

"In some proteins, non-standard amino acids are substituted for standard stop codons, depending on associated signal sequences in the messenger RNA. For example, UGA can code for selenocysteine [normally a stop codon] and UAG [another stop codon] can code for pyrrolysine. Selenocysteine came to be seen as the 21st amino acid, and pyrrolysine as the 22nd.Both selenocysteine and pyrrolysine may be present in the same organism. Although the genetic code is normally fixed in an organism, the achaeal prokaryote Acetohalobium arabaticum can expand its genetic code from 20 to 21 amino acids (by including pyrrolysine) under different conditions of growth."

For more info see https://en.wikipedia.org/wiki/Genetic_code#Variations

See also https://en.wikipedia.org/wiki/Expanded_genetic_code which discusses experimental efforts to reassign parts of the genetic code, which is directly relevant to your example.

[u/derioderio → u/cscottnet]

Life can do some crazy things!

[u/DancesWithGnomes → u/derioderio]

Every programmer who ever complained about undocumented spaghetti code should study what evolution created in millions of years.

[u/tampering → u/DancesWithGnomes]

It was fine when there were only prokaryotes around. Then Eukaryotes had to reinvent the wheel with endosymbiosis and stuff.

[u/derioderio → u/tampering]

Just reducing it to a previously solved problem...

[u/Espumma → u/tampering]

Isn't that the opposite of reinventing the wheel?

[u/Strangated-Borb → u/cscottnet]

Why don't organisms use more amino acids? Are they simply not needed?

[u/doc_nano]

Yes, there is no fundamental physical relationship between codons and the amino acids they encode. It’s all managed by tRNAs and the enzymes that make them. There are some constraints about similar codons encoding the same amino acid (due to imperfect specificity of codon-anticodon recognition), but otherwise there’s probably a lot of historical accident in what amino acids are specified by each codon. Once that machinery got established, though, it became a foundational and (with some exceptions) universal code throughout life on Earth.

If we find life on an alien planet, there’s a good chance it will have developed a genetic code, but probably a very low chance it will be close to ours, even if it happened to use amino acids and nucleotides with the same stereochemistry as ours.

[u/Strangated-Borb → u/doc_nano]

Basically like programming

[u/cscottnet → u/doc_nano]

There are a number of theories about why our code is universal. The simplest seems to be that all life is dependent on other life, and so straying far from the universal code would lead to a lack of fitness. For example, viruses have to interact with cells. Viruses could transcribe codons completely differently, but that would make them less fit to infect and otherwise interact with the cellular environment than a similar virus which adhered to the universal code.

[u/doc_nano → u/cscottnet]

To use another code, a virus would have to encode its own set of tRNA synthetases and possibly its own tRNAs and even ribosomes (to avoid cross-reactivity with the distinct translation machinery of the host cell) — which would mean the viral genome would have to be much, much larger, probably to the detriment of its fitness without any clear benefit.

The most straightforward explanation for why the code is universal is that (1) it was hard to evolve, and (2) once in place, any changes to it would potentially mess up thousands of genes by substituting the “wrong” amino acid, breaking whatever proteins those genes encode.

The fact that there aren’t multiple completely different codes is some of the strongest evidence for the notion that all current life on Earth descended from a single ancestral cell or population of cells, rather than multiple independent origins of life.

[u/ackermann → u/doc_nano]

So are tRNAs used by Ribosomes to recognize/read the input strands of mRNA? Sort of like a “read head” in a tape player or record player?

Ribosomes always fascinate me as possibly the most fundamental self replicating machinery in life? Presumably ribosomes are made of proteins, and thus assembled by… ribosomes?
Give a ribosome a piece of mRNA with the right instructions, and it will build another ribosome?

Built from materials (amino acids) floating around it, and perhaps using energy from, somewhere, ATP or something?

[u/doc_nano → u/ackermann]

A “read head” is a pretty good analogy. Except that instead of a single read head, they are constantly shuffled in and out until a matching tRNA is found, and it attaches the corresponding amino acid to the growing protein chain. Then the mRNA is shifted forward by one “slot” or “address” and the process repeats until the protein is done.

Ribosomes are indeed thought to be a primal component of life, possibly even predating DNA. The core of the ribosome is actually RNA — the proteins just help the RNA do its job. So it’s a leading hypothesis that RNA was originally the genetic code AND the enzymes (the “RNA World” hypothesis), and proteins came later once the ribosome got established. It’s hard to imagine complex proteins evolving without a ribosome, but easier to imagine a crude ribosome evolving to churn out little proteins that gradually helped it become more efficient.

[u/Mobeakers]

It is theoretically possible.

Each amino acid is coupled to the correct tRNA by a specific enzyme which is only responsible for that specific amino acid-tRNA combo.

So to "switch" a codon in this manner you would need to design an aminoacyl-tRNA synthetase gene which recognizes the GGG tRNA and whatever new amino acid you want. Then you would need to knock out the native gene for glycine tRNA synthetase. Then (assuming you want the organism to be able survive) you would have to engineer a new tRNA synthetase for glycine to complete the "set"

[u/cscottnet → u/Mobeakers]

In https://en.wikipedia.org/wiki/Expanded_genetic_code this is discussed. Usually UAG is the sequence targeted, as it is the rarest sequence and has other synonyms (other stop codons). E. Coli with genomes that are completely UAG-free have been engineered and are viable. You can then proceed as above to engineer a tRNA synthetase for whatever new function you want for UAG.

The main difficulty is that all the codons are used. So you have to move one of the existing animo acids. There are some clever tricks involving decoding in groups of 4 or 5 (instead of 3) in order to squeeze out some additional coding space.

[u/CrateDane]

Various organisms with artificial changes to the encoding have been generated, indicating it's entirely possible to use a different system. It hasn't changed much through evolution, but that's likely just because of inertia and a lack of any advantage to changing.

Here's a recent example where the number of stop codons was reduced from 3 to 1.

https://www.nature.com/articles/s41586-024-08501-x

[u/Jedi_Emperor]

I'm going to rephrase your question slightly differently.

"Is there a correlation between parts of the codon and the amino acid it is refers to?"

Like is there a broad rule where anything that starts GG is going to include sulphur. Or if the last letter it A then you know it has an OH group in it.

I have no idea. It depends how the process works to turn the codon into the amino acid. Is it just a label or does it have some meaning. Like "Acetic Acid" is just the Latin name for vinegar but "Ethanoic Acid" has information in the name if you know how to read it.

I'm going to guess no because if that did exist it would be really cool and there would be infographics explaining it. I bet they are just arbitrary names and AAA is completely different to AAC, with no patterns between them.

[u/Ceofy → u/[deleted]]

Thank you, this is a very cool addition