Larry Moran has a post up about a new paper that claims to help solve the 'problem' of the origin of biological chirality by showing that amino acids forming in space are not an equal mix of the two 'mirror' isomers but slightly biased towards the L isomers used by living organisms for protein synthesis. [NON-RACEMIC AMINO ACID PRODUCTION BY ULTRAVIOLET IRRADIATION OF ACHIRAL INTERSTELLAR ICE ANALOGS WITH CIRCULARLY POLARIZED LIGHT]. I was going to write a post arguing that the use of only one isomer isn't a problem in need of explanation, but then realized that I'd written such a post several years ago. I haven't seen my argument being made anywhere else, so I'm reposting it below.
Is the origin of biological chirality a no-brainer?
One argument invoked by creationists for a magical origin of life is that the observed homochirality (definition below) of biological molecules could not have arisen without divine intervention. Creationists are notorious for their sloppy reasoning, but I'm a bit puzzled that scientists also see this as a big problem. Here's an example from the Answers in Genesis people, and the blue box in this article is an example from PLoS Biology.
The fundamental argument seems to be that some special forces or factors are needed to explain how and/or why the first living things used only D-sugars and only L-amino acids. It's often claimed that this would not have happened unless the starting abiotic materials had an excess of one enantiomer (definition below) over the other.
I think people have fallen into the error of assuming that, at the molecular level, enantiomers are much more similar to each other than to other related molecules. But it shouldn't be any harder for an asymmetric reactant or catalyst to distinguish D-glucose from L-glucose than from either enantiomer of fructose or galactose. Or to distinguish L-leucine from D-leucine than from D- or L-isoleucine. They may contain the same atoms but they all have entirely different shapes, and so they are all entirely different molecules.
(Here's the same point made about words. The words pacer and recap are palindromes, but most readers have no more trouble telling them apart than telling either from caper.)
Chemists discovered chirality when investigating the bulk properties of pure crystals and solutions. Chemical synthesis of a chiral molecule from simpler non-chiral precursors usually produces equal amounts of both enantiomers, whose identical physical properties make them very difficult to separate. Chemists thus view enantiomers as almost-identical molecules, differing only in their 'handedness'.
But chemists are late arrivals on the evolutionary scene, and the first self-replicating entities would usually have interacted with individual molecules in complex mixtures. Because all but the simplest of biologically relevant molecules are asymmetric, most inter-molecular interactions would always have been between asymmetric participants, each no more likely to confuse their partner with its enantiomer than with any other molecule. The fact that crystals of D-glucose and L-glucose have the same bulk properties (solubility, melting temperature) would have been irrelevant.
We don't need to fuss with defining 'life', but can simply think about the origin of entities capable of evolving by natural selection (having heritable variation causing differential reproduction). Any molecule complex enough to have heritable variation would certainly have been complex enough to be asymmetric. To such molecules, discrimination between enantiomers wouldn't have been any more of a problem than discriminating between other possible reactants.
Although this now seems so obvious to me, I only realized it a couple of years ago. Until then I unquestioningly accepted the general teaching that the origin of biological chirality was a big problem. Am I missing something?
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Definitions of enantiomer and homochirality: Like letters in words, the same combinations of atoms can be put together in different arrangements. Sometimes the arrangements can be mirror-images of each other. Chemists call molecules that contain the same atoms connected in mirror-symmetry arrangements enantiomers of each other. Enantiomers are distinct molecules (like the words speed and deeps), but pure preparations of these chiral molecules have the same bulk physical properties. The molecules found in organisms are usually homochiral: only one of the two enantiomers is used. Our metabolism uses only the D enantiomers of sugars and only the L enantiomers of amino acids.
Simple, atypical but neat estimation of energy released in fission
2 weeks ago in The Curious Wavefunction
I think you are missing something. The soupists seem to think that proteins self-assembled from a mixture of amino acids in the primordial soup. If true, how do you explain the fact that the earliest proteins only formed from L-amino acids? The soupists try to get around this by supposing that there was natural enrichment for L-amino acids over D-amino acids in the soup.
ReplyDeleteAs you know, since you are a microbiologist, it's quite possible to make peptides with a mixture of L- and D-amino acids.
Now let's imagine that the first amino acids weren't delivered by meteorites but instead arose from primitive metabolism. The first one was probably glycine followed by L-alanine—made from pyruvate. L-alanine may have been made by chance instead of D-alanine but subsequent synthesis reactions may have favored the L isomers because of the abundance of L-alanine.
That's a much more plausible scenario, in my opinion, and it fits with your idea.
@Larry
ReplyDeleteIs there any reason to think that pyruvate -> L-alanine is more likely than pyruvate -> D-alanine. If both are equally likely then we are just one more turtle down to the answer
There's no good reason to assume that L-alanine was more likely than D-alanine. It's a frozen accident.
ReplyDeleteNo turtles needed.
Yep! Makes no difference atheist morons! Take 100% LEFT handed amino acids and see if they self assemble into one single protein! Its IMPOSSIBLE! Atheists come up with all these ridiculous chemical assumptions, just so they can always rule out GOD!
DeleteGosh Anonymous! You seem very aggressive. Is something making you feel threatened? Cognitive dissonance, maybe?
DeleteHow does your argument explain that all used sugars are D and all used amino acids are L?
ReplyDeleteWhy not use certain amino acids as L only and others as D only?
I think you got the definition of palindrome wrong.
ReplyDelete@larry: is there any experimental proof that earliest proteins were made from l-aa only? Isn't more reasonable that anything was made out of all possible kind of aa and only after for some reason the l-aa made proteins were selected due to some advantage? This can be totally off, I would be glad if you could explain..
ReplyDeleteC.
I think the reason they used L amino acids for the proteins is that D aminos are used for the cell wall in bacteria.
ReplyDeleteMaybe i am wrong, i´am still doing my a levels, but the using of different enantiomers prevents the depletion through enzyms
enantiomers are having completly different characteristics
ReplyDeleteat example the synthetical flavour of peach and of passion fruits are enantiomers.
Without deeper thinkings i believe using d aminos would change the angle of the bindings and so change the whole secondary and higher structures
In my opinion there isn´t a problem with homochirality at all. Enantiomers are having different characteristics, and a protein formed by d aminos would be completly different.
ReplyDeleteSaying the enantiomers are exchangeable in a protein is like saying you can drink gasoline cause it is liquid.
I miss the time creationists have been in church and scientists have been in lab.
It seems likely that the building blocks of proteins and nucleic acids co-existed together from the very beginning.
ReplyDeleteHence there was probably no "protein world" or "RNA world", but rather a coexistence world - at the very least, that's what eventually happened.
Such associations rely on specific three-dimensional interactions, of course.
It would of course be interesting to visit another world and see if everything was reversed, however.
Makes no difference you atheist morons! Take 100% LEFT handed amino acids and see if they self assemble into one single protein! Its IMPOSSIBLE! You atheists come up with all these ridiculous chemical assumptions, just so you can always rule out GOD!
DeleteAnd again! Blimey!
DeleteI guess the 15 minutes of fame of this blog are over. Good luck for your research, Rosie.
ReplyDeleteComing on this a bit late I thought I'd still add my two aminos. I think Rosie's post would predict a world where all alanine was L and all trptophan was D; all mannose was D, all glucose L, and so on. The odd thing seems to be that all aminos are L and all sugars D. Likewise, it seems that any attempt to argue that (proto)translation or (proto)protein folding works best with homochiral peptides seems doomed to fall on the face of the sugars. The only way such considerations would seem relevant would be if a peptide built from all right-handed (say) subunits was likely to prefer a left-handed molecule in its active site. This seems unlikely to me. And so yes I think homochirality still needs an explanation.
ReplyDeleteSomeone pointed it out already, but it is worth pointing out again. There are D-amino acids in living cells - lots of them! Every bacterium has them, and in fact D-alanine is one of the most important amino acids on earth (it is crucial to the transpeptidase reaction in Peptidoglycan synthesis). So an obvious alternative explanation is that the ancestral population of LUCAS committed to L-amino acids in the ribosome either as a previous commenter said to separate pools of precursors (excuse me if I've paraphrased poorly), or to allow for separate transpeptidase/autolysis reactions and protein turnover. I don't know enough about polysaccharides, but I would imagine a similar "just-so" story makes sense. I imagine that there are some experiments that could be done on deeply diverging bacteria that could shed light on this, but it's the weekend :)
ReplyDeleteI disagree with TIB.
ReplyDeleteThe catalytic machinery that syntheses any polymer can only work if the subunits all have the same core geometry. This seems fairly obvious for homopolymers like starch or cellulose, but it also applies to polymers with differing side chains such as proteins and nucleic acids.
Template-driven protein synthesis could never have evolved if some amino acids were L and some D.
For different reasons, metabolic interconversion of sugars would be impossible if some were L and some D.
Rosie, sorry to be thick but I don't follow. I can indeed see why a racemic mix of, say, alanine, won't work. Anytime the structure needs an alanine then it needs the correct enantiomer. Fine. But let us imagine a soup in which all the alanine is L and all the valine is D, the tryptophan is L and the asparagine is D, and so on. Are you saying that peptides with mixures of L and D aa's could not fold? Could not adopt a specific conformation? I don't follow why that would be. Honestly I am not a good enough chemist to visualize the consequences for L and D aa's in the same peptide, vs all Ls. But it would surprise me to learn tha structures were difficult with mixtures.
ReplyDelete@TIB: I guess the inantiomer issue is really two issues, why any given amino acid is always a single enantiomer, and why all the amino acids are the same enantiomer. You're asking about the second.
ReplyDeleteIf proteins were constructed of some L and some D amino acids, they wouldn't form alpha helices and beta sheets, but that doesn't mean that they couldn't fold into active structures.
One critical question is whether protein synthesis by ribosomes would work well with a mixture of L and D amino acids. Could the ribosome components that move the growing chain of amino acids from the P site onto each loaded tRNA in the A site do this if the amino acids to be joined had different conformations? It would have to deal with four different combinations of D and L (D-D, D-L, L-D and L-L). I don't think this degree of catalytic flexibility could work.
Another issue is the pathways that synthesize the amino acids. Where several amino acids are synthesized by the same pathway, they would all end up with the the same conformation.
I'm a chemist and happened to stumble on the blog... and naturally gravitated towards a chemistry-related entry... Anyway, I may be able to shed some light on this issue. (Hopefully).
ReplyDeleteFirstly, I wholeheartedly agree that a chiral reactant or catalyst would have no problem differentiating enantiomers from each other or from other isomers. The issue is that the chiral reactant/catalyst itself has an enantiomer (which, statistically should exist in the same concentration) and in the absence of some kind of chiral selection process, both enantiomers of the catalyst would act on each of the entatiomers of the substrate at the same time, resulting a the generation of some product at the same rate, with no net chiral amplification.
To use your palindrome example (correctly), consider the word LEVEL. In the absence of any preconditioning a new reader may decide to read from left to right, and give rise to future readers that will also read this word, and eventually other words, from left to right.
However, there is an equal chance (statistically speaking, again in the absence of any preconditioning) that the new reader may decide to the read the word LEVEL from right to left, and having read the same word and derived the same evolutionary advantage of being able to read this word as the previous reader, they should give rise to readers who read all words from right to left.
In a world where there are trillions upon trillions of readers reading words all the time, statistically speaking, there should be an equal number of left-to-right readers as there are right-to-left readers.
But this isn't the case, and so the question is (not WHY; the answer to why is probably just chance) HOW and at what point did everyone only start reading things on one direction?
Hi! Fellow chemist and open minded philosopher here. In my opinion Jon is spot on here in that it is probability that dictated the predominance of L-aa's. L-aa's have also been proven to be *slightly* more common than the D variants due to the fact that D-aa's do indeed degrade more readily in certain UV environments.
ReplyDeleteHere's another analogy that you may find helpful. Imagine the outcomes of L and D aa's binding to form larger helices and sheets are like the outcomes of heads or tails on a coin flip. Except L starts with a slight advantage, let's say 51 to 49. And for each outcome, that outcomes identity increases the odds of the identical outcome. It is likely that the two enantiomers were competing for location, and the side of the coin that formed in the largest structures first won the real estate, which sealed the deal.
As far as D sugars go, I'm assuming it just "fit", and if we were made of aa's with opposite chirality, the same would go for the sugars.
O.o oh really? Don't you see any 'problem' with the homochirality? Great... It's fair easy to speak whatever we want to, yet, when it comes to the pratical, experimental moment, the problem stands still as a redwood :P
ReplyDeleteThe fact is: evolution defenders like to fly in fancy about hypothetical, untestable scenarios, whereas creationists always base their premises on EMPIRICAL STUFF... To which side should we give hears? Which one is more honest and credible?
Your shouldn't leave your personal materialistic agenda influence on your articles, teachings, etc, with the purpose of misleading other people...