@ColinTheMathmo

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So tryptophan. It's an amino acid. (that's a big deal already.)

And it is an aromatic amino acid (more big deal.)

And it is a very large relatively complex looking molecule with formula C11H12N2O2. Tryptophan is one specific structural arrangement out of all those possibilities. (more on that later.)

But why should we care about amino acids in the first place? (and especially, tryptophan).

en.wikipedia.org/wiki/Tryptoph…

chemical compound

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Amino acids are very common molecules, and simple ones have been found in meteorites for a while now. They are small molecules with an amine at one end, and a carboxylic acid at the other end. You can link them up by making amide bonds!

So they are really handy for linking and making little chains.

In between the two linking chains, there is some "stuff". Other molecule parts.

Earth biology uses monosubstituted alpha-amino acids.

Those have the formula H2N-CH(R)-COOH. Where that R bit is the part that can vary.

The simplest alpha-amino acid is called glycine and looks like H2N-CH2-COOH.

The next larger homolog (chemical term where you insert a methylene group) is called alanine. Instead of the H , it has a CH3. So it is H2N-CH(CH3)-COOH.

Each R group can give special properties to that particular amino acid.

You can add neutral space that just bulks up that position (like...valine where R=CH(CH3)2. You can have a tiny neutral R group that just barely locks up that section from rotating around...that is R=CH3 alanine.

(Alanine is a good "Joe-average amino acid")

And you can have tiny little R=H (glycine) in an amino acid chain that lets the chain kinda spin a bit and flex around.

There are other R groups too, like alkylhydroxy, alkylamino, alkylthio.

And the aromatics....

It kinda makes sense that with all the functional molecule pieces lying around, that any biological system would figure how to link them up and create structural proteins or functional catalytic enzymes.

At least, that is the dominant paradigm in #astrobiology.

You might not need to use the exact same set that Earth biology uses.

Heck, a lot of brilliant work by Dieter Seebach on beta-amino acids show that they can do neat structural things, too.

(Fun fact: there is another alpha amino acid with an R group between valine and alanine. The R group is ethyl (R=CH2CH3). The amino acid is called alpha amino butyric acid (AABA). There is a property gap in the terrestrial biology set where AABA could fit right in. And AABA is very common in asteroid samples.

en.wikipedia.org/wiki/%CE%91-A…

BUT EVEN THOUGH THERE IS A GAP AND IT IS COMMON, EARTH BIOLOGY DOESNT USE IT? WHY NOT???

Mystery.....)

Obviously, we've figured work around solutions.....

chemical compound

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So the functionality thing....

Bulky things can control amount of twist, or greasiness of certain areas. Bulk can block stuff from going in. Think of it like filler.

Hydroxy substituents on proteins can be useful for control, and binding.

Side groups like histidine (technically aromatic) are super useful for acylation catalysts

side chains with a thiol (cysteine) can combine across chains and create key structures.

And then there are the aromatics....

Aromatics include phenylalanine, (R=benzenemethyl), tyrosine (R=hydroxybenzene), and tryptophan (R=3-indolemethyl).

Aromatics are bulky and greasy, but they have extra-bonus things they can do too.

The aromatics have a set of delocalized pi-electrons running around. Those can interact with other pi-systems (if the amino acid residues are nearby) to make pi-stacked aromatics, and time-out bonds where the pi-systems are orthogonal - like a time-out hand signal.

These are kinda weak interactions (weaker than hydrogen bonds) but they can still help form structures.

One of my other passions is ice-binding (ice-controlling) proteins. Those have tubes that have tyrosine residues sticking out. The tyrosines on next door tubes interact and make a big tube wall. And that wall (with threonine hydoxy residues) lines up the water molecules for controlling ice crystalization.

Aromatics are cool.

Tryptophan is even cooler.

Tryptophan's aromatic system can make a special bond where the pi-system interacts with a positively charged atom or part of a molecule. This is called a cation-pi interaction.

Cation-pi interactions are STRONGER than H-bond interactions. They are hardcore.

Tryptophan can interact with choline, or small cations in ion channels to help remove the water ligands from the small cation. (The indole substitutes for it.)

Of all the protein structures in the Protein Data Bank (PDB) over a quarter of the tryptophan residues were interacting with a cation.

proteopedia.org/w/Cation-pi_in…

So if you are going to build an alien biochemistry and you have a wish list for those R-groups on an amino acid (not necessarily alpha amino acids), you would like:

Something flexi (glycine, or beta-alanine)
Joe average (alanine)
Bulky greasy things (R=ethyl, propyl, butyl, futile)
something hydroxy
something amino
something acid
something ring constrained you can cis-trans isomerize the peptide amide (proline or pipecolic acid)
maybe something thiol (cross-link)

and definitely some aromatics.

Aromatics are big. As you get bigger and bigger, the relative abundance in meteorites usually falls off. It's hard to make big things.

(There are some things where the synthesis route makes it easier. For example gamma-amino-butyric acid GABA, is very common in meteorites.)

So the paradigm in astrochemistry is that you get a lot of simple things, and very rare amounts of big things.

In biology, all these amino acids are useful. So the belief is that in an active biological system, life will be generating these useful pieces and parts in relative equal abundance.

(There is surprisingly not a lot of literature on this. It is taken as a given. Doing bulk amino acid abundance inventories on different microbes would be very valuable to the #astrobiology community. I give y'all this proposal idea for free. Follow me for more funding ideas!)