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Why does all life use the same 20 amino acids?
- stevenalowe 7y agoNo others were available?
- deleted 7y ago[deleted]
- firstbabylonian 7y agoat a certain evolutionary point in time?
- mixmastamyk 7y agoTldr: Those 20 work more efficiently than the others.
- mirimir 7y agoAs 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
- respinal 7y agoI don’t see your point. Could you elaborate some more?
- mirimir 7y agoPlease see my reply to Sharlin.
- Sharlin 7y ago> non-protein The title, of course, refers to the 20 proteinogenic amino acids.
- mirimir 7y agoExcept 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.
- Catsandkites 7y agoThat makes lots of sense. Do you have any examples of sprouting plants that so this? I'm guessing ones we consider poisonous?
- afarrell 7y agowoah that sounds interesting. Do you have some links to videos or articles which talk more about this?
- krick 7y agoWhile somewhat true, essentially the question of 20 amino acids still holds and trying to answer it is still meaningful (and in the same way article addresses it). Consider this: how old are these plant insecticides (or whatever they are)? Maybe some 150 mln years old? (I'm only assuming, of course, but it seems like a plausible assumption.) Well, the life on Earth itself is about 3.5 bln years old, and as far as we know it mostly utilizes the same set of 20 proteinogenic amino acids it did back then. It is only natural that given time, constantly mutating and evolving organisms would eventually learn to produce whatever amino acids possible, if it is useful (and being insecticide is obviously useful, if you are a plant, and for reasons you mention yourself it is natural to use as insecticide some compound that is not normally utilized in the other organism). The question is how did it occur that these amino acids weren't present during immune system development? Why it was always the same 20?
- appleflaxen 7y agoSuper interesting example! Nevertheless, even the organisms referenced in these papers don't have these amino acids in their DNA structure, and the meaning of the linked research really isn't affected by the point you are raising. Perhaps "non-proteinogenic" is a poor choice, or not exactly correct, but readers generally understand what is meant. It's a bit like responding to an article about "why do all pendulums keep the same frequency as they lose energy" with "but they are neglecting relativity!". It just isn't really relevant to the research question, which is "why are some amino acids present in the DNA code, and why is there consistency across species".
- mirimir 7y agoI'm not sure what you mean by "don't have these amino acids in their DNA structure". There are 64 codons that code for amino acids and start/stop signals. But there are only 20 common amino acids, so multiple codons typically code for the same amino acid. However, just exactly what happens depends on the set of tRNAs that are being expressed. Plus the enzymes that catalyze attachment of amino acids to tRNAs. That is, what's in the DNA is codons, and what amino acids get incorporated depends on tRNAs etc, plus what amino acids are around (synthesized or ingested). Anyway, I get that I was being a little pedantic. But in the paper referenced by TFA, I see that they studied three nonproteinaceous amino acids: ornithine, 2,4-diaminobutyric acid, and 2,3-diaminopropionic acid. Canavanine is much closer to arginine, with a methylene replaced with an ether bridge. I wonder how well it would have polymerized. 0) https://www.pnas.org/content/116/33/16338 https://www.pnas.org/content/116/33/16338 Edit: Upon reflection, "there are just 20 proteinaceous amino acids" and "AS/400 is a database" are ~similar simplifications.
- dekhn 7y agoarticles like this are really talking about a standard that covers 99.9% of cases, not some sort of universal absolute. We know of many special cases which violate the standard (to the extent that 'life' has 'standards') but it's not clear how valuable it is to point out the exceptions here.
- mapcars 7y agoBecause they work :D
- firstbabylonian 7y agowhile others??
- mapcars 7y agoDon't fit the job
- firstbabylonian 7y agobut isn't it surprising that such a strict subset is maintained across all life?
- rleigh 7y agoNot 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.
- H8crilA 7y agoAn 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.
- Sniffnoy 7y agoVariants on the genetic code are known to exist: https://en.wikipedia.org/wiki/Genetic_code#Alternative_genetic_codes https://en.wikipedia.org/wiki/Genetic_code#Alternative_genet... I don't think there are any known to be radically different. Note that it's possible that life arose several times but only the lineage of that one cell survived, perhaps? In any case, it's not like there's been no variation. Now, here's a mystery (AFAIK): Just where is the genetic code stored? I seem to recall reading an article a while back about how while this seems like an easy question it's actually not known. I can't seem to find it at the moment, though. Anyone know more about this?
- fabian2k 7y agoThe mapping between base triplets and amino acids is encoded in the tRNAs. And the tRNAs themselves are of course again encoded in the DNA sequences used to produce them.
- Sniffnoy 7y agoI mean, that's the obvious answer, but I recall reading a thing about why it wasn't actually that simple, how swapping out the tRNAs didn't actually have the effect you would expect. Like, obviously the anticodons match the codons, no problem there, but there was some complicated confusing thing about how the rest of the tRNA matched the amino acid. Trying to find it. Hoping someone knows what I'm talking about.
- 7y ago
- maga 7y agoSo, 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?
- raducu 7y agoThat's the real question! It might be far-fetched, but to me it seems that if carbon life exists elsewhere, it probably uses the same biochemistry that we do.
- gus_massa 7y agoThey 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.
- bayesian_horse 7y agoNever 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.
- lngnmn1 7y agoOh, that's easy. Because it is so happened, that all present life forms have a common ancestor. Why exactly these amino acids? Because it so happen that, after endless process of trial and error, they happen to be abundant in the environment and, it seems, provide variety of stable shapes (via folding). But the general and less wrong answer is "by chance and environmental constraints".
- api 7y agoWhy 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...
- petjuh 7y agoThe 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 7y agoLUCA = Last Universal Common Ancestor
- gus_massa 7y agoNote 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.
- mrfusion 7y agoSo 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 7y ago“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).
- bregma 7y agoPerhaps 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 7y agoI am far more amused than I should be by your implication that God is made of protein, and probably edible.
- tsomctl 7y agoSo God created man in his own image, in the image of God he created him; male and female he created them. (Genesis 1:27)
- pretendscholar 7y agothat explains communion
- chaosbutters 7y agoso the flying spaghetti monster?
- apo 7y ago> ‘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?width=800&height=600&carousel=1 https://www.pnas.org/content/pnas/116/33/16338/F1.large.jpg?... 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.
- pfdietz 7y agoAnother 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 7y agoPanspermia 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 7y agoAlmost 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.
- waserwill 7y agoAssuming that abiogenesis wouldn't happen very frequently (given the right set of conditions, a mean time to happen on the order of thousands to billions of years), a single life-forming event would have the same effect, no? After a foundation is set, the self-replicator starts exploiting existing energy gradients, making any other abiogenesis-event much less likely.
- Medicalidiot 7y agoWe 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 7y agoHave heard that Silicon and Germanium have 4 bonds like Carbon does. Follow the periodic table down.
- JumpCrisscross 7y ago> 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 7y agoUller Uprising, H. Beam Piper Sci-fi novel based on the Sepoy Mutiny. Life on Uller is based on silicon.
- Medicalidiot 7y agoI thought it was sulfur, but it may have been silicon that the researchers had used.
- tzs 7y agoThis 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
- dnautics 7y agoPardon 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?
- DaveWalk 7y agoNo 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-acids-instead-of-64 https://biology.stackexchange.com/questions/653/why-20-amino...
- dredmorbius 7y agoIs 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?