
Why does all life use the same 20 amino acids? - respinal
https://www.chemistryworld.com/news/why-does-all-life-use-the-same-20-amino-acids/3010824.article
======
mirimir
As is often the case with titles like this, the answer is that all life
doesn't use the same 20 amino acids.

For example:

Akaogi et al. (2006) Role of non-protein amino acid L-canavanine in
autoimmunity. Autoimmun Rev. 5(6):429-35.
[https://www.ncbi.nlm.nih.gov/pubmed/16890899](https://www.ncbi.nlm.nih.gov/pubmed/16890899)

Nunn et al. (2010) Toxicity of non-protein amino acids to humans and domestic
animals. Nat Prod Commun. 5(3):485-504.
[https://www.ncbi.nlm.nih.gov/pubmed/20420333](https://www.ncbi.nlm.nih.gov/pubmed/20420333)

~~~
Sharlin
> non-protein

The title, of course, refers to the 20 proteinogenic amino acids.

~~~
mirimir
Except that some sorts of life, such as some sprouting plants, _do_
incorporate those "non-proteinogenic" amino acids into proteins.

Which then screw up animals that eat them. Because they, in turn, _also_
incorporate them into proteins. And those tweaked proteins elicit immune
responses, because they weren't present during immune system development. And
some of that immune response cross reacts with the normal host proteins. So
you get autoimmune disease.

~~~
Reelin
This turned out to be an incredibly interesting (and educational) diversion!

It seems these amino acids aren't typically incorporated, but rather appear to
serve as defense
([https://www.ncbi.nlm.nih.gov/pubmed/21529857](https://www.ncbi.nlm.nih.gov/pubmed/21529857))
and signaling molecules
([https://www.ncbi.nlm.nih.gov/pubmed/28218981](https://www.ncbi.nlm.nih.gov/pubmed/28218981)).
Apparently humans do that sometimes as well
([https://www.ncbi.nlm.nih.gov/pubmed/18828673](https://www.ncbi.nlm.nih.gov/pubmed/18828673)).
Sometimes the insects even end up using the toxic compound (in the linked
example the non-protein amino acid L-DOPA) for their own purposes
([https://www.ncbi.nlm.nih.gov/pubmed/27006098](https://www.ncbi.nlm.nih.gov/pubmed/27006098)),
which I find quite amusing.

More than just being eaten, apparently L-DOPA is released into the environment
at an impressive rate in some cases
([https://www.ncbi.nlm.nih.gov/pubmed/24598311](https://www.ncbi.nlm.nih.gov/pubmed/24598311)).

~~~
mirimir
Yes, I was wrong about that. Alfalfa seeds and sprouts don't themselves use
canavanine in their proteins. And yes, plants do seriously get into chemical
warfare.

------
H8crilA
An even bigger question: why is DNA/RNA always expressed in the same way? I.e.
the codon->aminoacid table is constant for all living things. I always found
this very puzzling. Of course, the easiest explanation is that life really did
start from a single cell. But it sounds unlikely that a) there really was that
single origin cell, and not a few that popped up around the same time (on a
geological scale), and b) no organism has drifted in the millions of years of
evolution.

~~~
klmr
> _But it sounds unlikely that a) there really was that single origin cell_

This is just a fact. All life _that we know of_ has the same origin. Common
descent is a core tenet, and one of the best established facts, of modern
biology
([https://doi.org/10.1038%2Fnature09014](https://doi.org/10.1038%2Fnature09014)).
For there to have been multiple distinct ancestors, we would need to see
_some_ relevant differences in the core machinery of life. And the fact is
that, despite minor variations, we simply don’t see any. The odds of there
being multiple distinct ancestors is astronomical, and would fundamentally
impact our understanding of modern biology.

> _and b) no organism has drifted in the millions of years of evolution_

Organisms _have_ drifted. That’s what evolution _is_. But evolution plays by
rules, it can’t just change things willy-nilly. Changes to the core machinery
would presumably either break it outright, or be so strongly detrimental as to
be purified away almost immediately. Of course _many_ genetic changes are
deleterious to some extent but most effects can either be buffered for a short
time because they are minor, or they confer some other advantage. In the core
machinery of the cell this is much (!) less tolerated because even tiny
chemical inefficiencies would immediately be amplified millionfold. Odds are,
the DNA/RNA core machinery of all life sits in a steep local optimum. It’s not
necessarily a _global_ optimum but it’s essentially impossible to evolve out
of because any individual change, or even a handful of coincidental changes,
would leave the organism a lot worse off.

~~~
jyounker
> Common descent is a core tenet...

It's taken that (known) modern organisms descend from a common set of
ancestors, but the tree of life isn't a tree. Organisms diverged and merged
multiple times along the way to the modern world.

It says nothing about how that/those points of common descent came to be.

What originally constituted living things probably weren't very good at living
by modern standards. They probably leaked like sieves, and they probably
traded RNA, polypeptides, and other small molecules back and forth.

When was this soup alive, and when wasn't it? I suspect it's just a continuum,
and that complicated soup probably went back and forth across that grey zone
of living-nonliving many times.

~~~
klmr
> _but the tree of life isn 't a tree_

That’s correct but I don’t see what this has to do with my comment. It’s still
a fact that all modern life, at some point, came through the same individual
organism (EDIT: this should be _population_ ) which, furthermore, already
possessed the fundamental machinery of DNA replication, RNA transcription and
protein synthesis (amongst other things).

EDIT: I misunderstood. Yes, you’re right: due to lateral gene/molecule
transfer, it’s not certain that the last universal common ancestor was an
_individual cell_ , and at that time the label “individual” probably didn’t
make much sense (although the paper I linked argues strongly that it _was_ in
fact one single cell).

~~~
ejstronge
> That’s correct but I don’t see what this has to do with my comment. It’s
> still a fact that all modern life, at some point, came through the same
> individual organism which, furthermore, already possessed the fundamental
> machinery of DNA replication, RNA transcription and protein synthesis
> (amongst other things)

This is a contentious statement that I don't think is established - a fact
that the grandparent comment is trying to raise.

~~~
klmr
I misunderstood both your and the grandparent comment. You’re right. I’ve
amended my other comment.

------
dnautics
Pardon my ignorance, but hasn't it been trivially known why orninthine and DAB
don't make proteins? This was a test question in undergrad bioorganic
chemistrty class 15 years ago. Ornithine can self-cyclize to make a six
membered lactam, and DAB will self-cyclize to make a five membered lactam,
which are energetically favorable, and thus chain termination compete with
chain extension polymerization, making them unsuitable for proteinogenesis.

edit: read the paper carefully. They came to the same conclusion. But... Is
this new?

------
apo
> ‘We thought that, in general, all of these amino acids would react similarly
> because they are structurally similar,’ says Leman. But while almost all the
> experiments did produce oligomers, the three proteinogenic amino acids
> reacted more efficiently and produced fewer side products compared with
> their non-proteinogenic counterparts. ‘That came as a real surprise. We
> thought “Is this for real?”,’ Leman says.

Looking at the structures, I would not expect similar reactivity:

[https://www.pnas.org/content/pnas/116/33/16338/F1.large.jpg?...](https://www.pnas.org/content/pnas/116/33/16338/F1.large.jpg?width=800&height=600&carousel=1)

They differ in both size and shape. More importantly, they differ in the
length of the tether to the positively charged group which could easily play a
role in carbonyl activation by this unit, either in the forward direction
(peptide formation) or reverse (peptide hydrolysis).

The paper doesn't mention autocatalysis (catalysis of external amino acids or
short peptides themselves), but this is also a possibility. There's a large
body of synthetic chemistry in which amino acids and short peptides show
remarkable catalytic activity.

But the main problem with this study is that peptides are made biologically
through catalysis. What we observe in isolated system reactivity has no reason
to translate into what's seen in nature because enzymes offer lower-energy
transition states.

------
petjuh
The translation system's universality is the best proof that there is a LUCA.

[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1894784/](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1894784/)

~~~
sokoloff
LUCA = Last Universal Common Ancestor

------
gus_massa
Note that the paper gives a hint about why 3 of the 20 amino acids were
selected, it is not clear that the same rule can be applied to the other 17
amino acids and why the number is 20 (or approximately 20).

From a comment in a previous post:

In the research paper they analyzed a few amino acids like Lysine. Lysine is
an amino acid that has the usual amino group and the usual acid group in one
side, and it has an additional amino group in the other side. In the study
they compared Lysine with Lysine-like amino acids that are shorter and the
additional amino group are closer to the usual amino group and the usual acid
group. For example
[https://en.wikipedia.org/wiki/Ornithine](https://en.wikipedia.org/wiki/Ornithine)

They found that the usual amino acids like Lysine are better to form
spontaneously protein-like chains than the shorter versions when they are in a
solution that gets dried. I'm not sure if this is enough to explain why Lysine
is used in proteins but it's an interesting result anyway.

In the more optimistic case, the research article "explain" why the 3 usual
amino acids that they used are better than the 3 shorter variants that they
used. It doesn't "explain" why the other 17 amino acids where selected.

In particular they used amino acids with an additional amino group, so the
polymerization can get "confused" and instead of using the usual amino group
use the other group, so instead of a nice chain, you get some other structure.
There are 17 of the other usual amino acids that don't have an additional
amino group, so the polymerization process can't get confused.

------
bayesian_horse
Never change a running system!

There has probably been a lot of evolution, maybe one or two billions of years
since the last common ancestor of all known life on earth. And that LCA had
that system. It's a bit like ASCII.

------
pfdietz
Another possibility: life came to Earth already well formed (panspermia), and
that single ancestral introduction rapidly filled the terrestrial biosphere so
no further introductions could take hold.

~~~
thehappypm
Panspermia is such a plausible theory. We know that life spreads like crazy if
you let it -- try to keep something sterile and life always finds a way in,
even into our sealed jars and cans, volcanoes, the bottom of the ocean, etc. I
wouldn't be surprised if one day we find that Mars is teeming with bacteria
that hitched a ride on one of our rovers and adapted.

~~~
pfdietz
Almost certainly Mars would have been seeded billions of years ago, w.
bacteria hitching rides on ejected debris from asteroid impacts, when
conditions were much more hospitable there. And of course it could have gone
in the other direction also. Even autopanspermia -- where ejecta from a
planet-sterilizing megaimpact later comes back to the cooled off world -- is a
possibility.

------
DaveWalk
No offense to the good discussions here, but this article is no more than a
press release. It doesn't even directly address the question in the title!

Again no disrespect to the talk here, but this is a Stack Exchange kind of
question, and lo there is an SE answer:
[https://biology.stackexchange.com/questions/653/why-20-amino...](https://biology.stackexchange.com/questions/653/why-20-amino-
acids-instead-of-64)

------
api
Why is almost everything written in C if you go down enough levels? Why does
everything run on Unix-heritage OSes?

Answer: because it's built on stuff that was built on stuff that...

------
dredmorbius
Is the frequency / preponderance distribution of amino acids known?

If so, is it known _over time_ to any extent?

(I'm going to presume that to a meaningful extent it is _not_ as any potential
samples are going to be largely recent -- past few thousand years, maybe tens
of thousands given frozen samples. Amber possibly excluded.)

What does that distribution look like? Zipf? Normal? Other?

------
tzs
This isn't an important distinction presently, but keep in mind this is for
Earth life. If we someday encounter alien life, they may be different, which
could lead to some trouble if people are not careful [1].

[1]
[https://www.youtube.com/watch?v=eEeLhqNLhZw](https://www.youtube.com/watch?v=eEeLhqNLhZw)

------
mrfusion
So where are the essential amino acids actually produced?

And to follow on to that how could life get started without being able to
produce amino acids? It doesn’t seem like something early life could evolve
gradually. Are they then naturally occurring?

~~~
klmr
“Essential” amino acids are those that _humans_ can’t synthesise. Other life
forms can, which is why we ingest them with our food.

As for how early life started, presumably with a strongly reduced set of amino
acids. Some of these are simple enough chemicals which form spontaneously
given the right conditions (technically all of them can, but probably at very
low rates). This was famous established by the Miller–Urey experiment
([https://en.wikipedia.org/wiki/Miller–Urey_experiment](https://en.wikipedia.org/wiki/Miller–Urey_experiment)).

------
Medicalidiot
We are carbon based life forms, but researchers have hypothesized that there
are probably sulfur based lifeforms out in the universe.

If I remember correctly, there's over a hundred various amino acids. For
humans, we have only 20.

~~~
mixmastamyk
Have heard that Silicon and Germanium have 4 bonds like Carbon does. Follow
the periodic table down.

~~~
JumpCrisscross
> _Have heard that Silicon and Germanium have 4 bonds like Carbon does_

This is true of all group 14 elements.

Carbon is the lightest and thus most-common group 14 element. Carbon and
silicon are the only two group 14 elements lighter than iron, which means
they're the only ones produced by stellar burning. (Everything heavier than
iron is produced exotically, _e.g._ by supernovae and neutron star
collisions.)

Most (chemical) life is thus probably carbon based, with a minority running on
silicon. If germanium-based life exists, it's near a supermassive black hole.

~~~
small_fish
Uller Uprising, H. Beam Piper

Sci-fi novel based on the Sepoy Mutiny. Life on Uller is based on silicon.

------
bregma
Perhaps because it was designed by someone with a great deal of intelligence
but not a whole lot of imagination?

I mean, if your greatest creation is something made in your own image, how
does that demonstrate imagination?

~~~
taneq
I am far more amused than I should be by your implication that God is made of
protein, and probably edible.

~~~
tsomctl
So God created man in his own image, in the image of God he created him; male
and female he created them. (Genesis 1:27)

~~~
DataGata
But was it a jpeg? A gif? What type of image file?

~~~
bregma
Obviously a GIF, but with its name pronounced correctly.

------
maga
So, tl;dr answer is that it's because those amino acids are more eager to
react/polymerize.

I wonder what it means for exobiology, is this true only in Earth conditions
or in general, i.e. can we expect life elsewhere to use the same 20 amino
acids? Also, if not, how toxic/dangerous would that life be for humans?

~~~
gus_massa
They only analyzed 3 of the 20 amino acid, and they found a reason that
perhaps explain why they are used. It's only a (good?) reason, but it's not a
definitive proof. The conditions are quite simple, something like a small pond
that can be desiccated and collect some water again later. When the "soup" is
almos desiccated it is easier that the amino acid form small proteins-like
chains.

About life in other planets, nobody knows, so it's guessing time:

The 20 amino acids are some of the ones that get formed spontaneously in the
prebiotic conditions, so it's probably that they exist in other planets. In
some proteins, the amino acids are modified after the protein is produced, so
a few additional amino acids may be a nice feature. Some amino acids of the
proteins are quite similar and perhaps we can live without them. So will
independent life in other planets:

* use the same 20 amino acids: Probably no. Unofficially: No way.

* use the exactly 20 amino acids: Probably no. It's a hard question, there are some paper that try to justify the number 20 or a similar number, but I'm not convinced. I guess that something between 15 and 30 amino acids.

* Use some set of amino acid similar to our 20 amino acids: Probably. I guess yes.

* Use the same L variants as us, or use the specular D variants: Let's say 50%.

* Use proteins at all: Another hard guess, I'd say yes. Proteins are very versatile and easy to build in different configurations. It's hard to guess a replacement.

------
mixmastamyk
Tldr: Those 20 work more efficiently than the others.

------
mapcars
Because they work :D

~~~
firstbabylonian
while others??

~~~
mapcars
Don't fit the job

~~~
firstbabylonian
but isn't it surprising that such a strict subset is maintained across _all_
life?

~~~
rleigh
Not at all. It would be surprising if it _wasn 't_ maintained.

Evolution can progress very rapidly, but the core machinery which drives life
is very conservative.

A good analogy would be to look at other codes. In the computer world,
consider ASCII. Each number maps to control code, letter, number or symbol.
This encoding is _entrenched_. Imagine how hard it would be to change a single
letter of ASCII to mean something else. Most of the hardware and software on
the planet would require updating. It's not just that interoperability is
important. It's that every piece of software on a single computer system would
require updating, in lockstep, to transition from the old to the new encoding.
This would be an almost impossible feat.

The same constraint applies to DNA encoding of protein (and other) sequences.
There are multiple pieces of the machinery which would require changing _in
synchrony_ for the result to work and result in a viable living organism. A
triplet coding system change would require almost all instances of that coding
triplet changing to retain existing structure and function in every protein
using it, new enzymes to synthesise the new amino acid and tRNA, along with
all of the associated regulatory and control systems. Only at that point could
you start using the new amino acid triplet sequence in a new or modified
protein. Evolution works by single small changes and natural selection. Making
several big changes is extraordinarily unlikely.

It's easier to make such a fundamental change in simpler organisms where the
scope of the change is limited. And this is likely why the small number of
variations we see in genetic encodings are both in the lowest forms of life,
and are largely superficial. The current encoding is entrenched as a result.

------
stevenalowe
No others were available?

~~~
firstbabylonian
at a certain evolutionary point in time?

