Alternatives to amino acids

Question

Amino acids, the building blocks of proteins and, therefore, one of the key components of life as we know it.

There are many amino acids in nature, but they all stem from the same basic structure.

They can polymerize into proteins, complex with metals, and bind to other important compounds.

However, they are have downsides, a limited temperature range, sensitive to strong acids, bases, and oxidizers.

My question is, what known polymers could aliens use in place of amino acids and what conditions would favor the use of those polymers?

Answer 1

My question is, what known polymers could aliens use in place of amino acids and what conditions would favor the use of those polymers?

There are currently zero known polymers that have the ability to do what amino acids could do. Theoretical? Sure - at least, to some extent. All amino acids are really just building blocks. When you get down to it, really no different than the periodic table of elements. Or LEGOs, for that matter. There are twenty amino acids, and they each have pretty unique properties, but it's not the individual amino acids that make it interesting, it's the combinations that make it interesting.

And part of what makes amino acids so incredibly versatile are the restrictions you mention. They're sensitive to strong bases and acids because they contain a base and an acid themselves, not to mention that some R chains also have acidic properties, alongside polar ones, and that's what makes them capable of forming complex structures. Not to mention that, given how unbelievably complicated protein folding is, there's no reason for any practical field of science to try and create a system that can replicate proteins from scratch, especially when it probably won't react well with biology as it stands.

Not to mention that, at least as far as we understand it, the current system is a really good system - evolution, if nothing else, can sharpen knives really well. If you're looking for a system that can do everything amino acids can do, then you're better off using amino acids. Uprooting the entire system and replacing it isn't going to function well.

Unless, of course, you're asking about how you keep the system of the amino acids but play around with the molecule so that it's suitably foreign / alien. In that case, you might want to swap some of those elements around. Trade the acid / base groups on either end for something a bit more exotic - maybe the amino group is now a thiol, and therefore is sulfur-based, not nitrogen based. Maybe the carboxyl group is now an alkyl halide. Maybe you've swapped all the carbon for silicon - why? Well, because of element availability, of course. Your planet has undergone organic chemistry based on these groups as opposed to other because of their relative abundance.

Now, I will point out that, in actuality, it's a lot more complex than to simply be able to say 'They're like us, but their amino acids have thiols instead of amines', but unless you're working hard sci-fi, something like that would be fine. Also, it'd be called 'thiolo acids' instead, because you've replaced the amine group with a thiol.

Answer 2

RNA.

RNA is a fine polymer. The amino acid equivalents are cytosine, guanine, adenine and uracil. RNA still comes in handy for life today. The RNA polymer can (and does!) do many of the activities proteins can do including enzymatic activities.

RNA-based life (without proteins or DNA) is thought to have preceded life as we know it today.

https://en.wikipedia.org/wiki/RNA_world

The RNA world is a hypothetical stage in the evolutionary history of life on Earth, in which self-replicating RNA molecules proliferated before the evolution of DNA and proteins... Alexander Rich first proposed the concept of the RNA world in 1962, and Walter Gilbert coined the term in 1986. Alternative chemical paths to life have been proposed, and RNA-based life may not have been the first life to exist. Even so, the evidence for an RNA world is strong enough that the hypothesis has gained wide acceptance.

Like DNA, RNA can store and replicate genetic information; like protein enzymes, RNA enzymes (ribozymes) can catalyze (start or accelerate) chemical reactions that are critical for life. One of the most critical components of cells, the ribosome, is composed primarily of RNA. Ribonucleotide moieties in many coenzymes, such as Acetyl-CoA, NADH, FADH and F420, may be surviving remnants of covalently bound coenzymes in an RNA world.

If the RNA world existed, it was probably followed by an age characterized by the evolution of ribonucleoproteins (RNP world),[2] which in turn ushered in the era of DNA and longer proteins.

So no scifi: a real, existing alternative to amino acids and protein polymers.

Answer 3

Thiolins might work.

Thiolins are a complex range or organic polymers thought to exist on the surface of Titan and other astronomical bodies.

Tholins are disordered polymer-like materials made of repeating chains of linked subunits and complex combinations of functional groups. The properties of tholins will depend on the energy source used and the initial abundances of precursors.

There are probably a large number of alternatives that could be used as the scope of chemistry is huge and humanity is aware of only a tiny fraction of the vast array of possible chemical permutations and combinations.

https://en.wikipedia.org/wiki/Tholin

Answer 4

Heres my analysis: As was mentioned before, natural systems make use of amino acids almost exclusively to make stuff that does stuff.

Why the particular 20 that they do?

Well, its biology we are talking about here so partly due to dumb chance. Apart from that- you need the side chains to perform certain functions that allow your enzymes to work and structural proteins and whatnot to do the same: you need acidic bits and alkaline bits (ideally of differing strengths as well). You need hydrophobic bits to make parts of your proteins despise their surroundings and bunch together. You need sulfurous and other (eg. imidazole) bits as ligands to bind metals for catalysis, redox reactions etc, disulfide bridge formation (or an equivalent kinda strongish covalent interaction) is a nice bonus. Some do side hustles, like histidine being able to take a proton from one side and release another on the other side (acting like a hydrogen shuttle)... and the fewer side groups, ie specific building blocks, you are going to achieve all the required functionality with, the more efficient and simple your system will be- which are good things.

As for the backbone itself, the current design (the amino and acid bits themselves, and the amide bond they form)....

well youd probably want the alternative to be as stable as possible (would not trust the aforementioned thio compounds with that), capable of forming a strong non-covalent interaction with itself (hydrogen bonds are the tried and true method, halogen bonds and pi-pi interactions seem like possible alternatives)- and all that in as small a package as possible (to get the best atom economy, the lightest overall system...).

I am not sure as for the rigidity of the backbone- most single bonds can be freely rotated about, the CO-NH peptide bond being an exception.

Something like a CR2-NH-CR2- repeating unit would form H bonds, would have even better atom economy than amino acids and would be significantly more stable chemically (capable of operating in strongly alkaline conditions) but might be too floppy for reliable folding. A poly pyrimidine ether or amine would make for a rigid backbone, high chemical and radiation resistance, and possibly strong H bonds, but might bee too rigid or bulky for proper folding itself...

all in all any polymeric backbone could be made to work: nucleic acids, polysacharides, polyamides... you could just use polyethylene and stick side chains that do the directed bonding on it instead. The question then is how straightforward, efficient and capable you want your system to be.