Again, it works inside the story, though I tend to agree with you otherwise.
I think it’s been said, but just to be sure, I’ll say it. Optical activity is not an indicator of absolute stereochemistry in and of itself. This is especially true in any natural product, with many many stereocenters and lots of possible diastereomers (even though none of them will exist in nature.)
Arthur C. Clarke wrote a short story called “Technical Error” synopsis here if you’re interested.
You misunderstand my point. This explains why individual amino acids would all have the same chirality, but not why all the different amino acids have to have the same chirality. AFAIK, you can make peptide bonds between amino acids of different chirality, although the side chains will be on different “sides” of the chain. I am not clear why you couldn’t build a protein using D-alanine, L-leucine, L-glycine, and D-cysteine, for example.
Colibri, using artificial means of synthesis you can make proteins using amino acids of different chirality. It’s just that earth DNA won’t. All the different amino acids are labeled with the same chirality expressly because they are the set that earth DNA codes for.
The set that DNA codes for is not a result of the labelled chirality, the labelled chirality is a result of which set the DNA codes for.
From here.
Sure. But this does not explain why DNA codes for only one kind of chirality.
Actually, in looking into this a little further, I think I have found the reason. All the rest of the amino acids are synthesized from glutamate. Therefore, if the primordial glutamate happened by chance to be L, this explains why all the rest now follow suit.
Earth DNA does not determine the chirality of amino acids. It merely provides the information which the cell’s translation apparatus uses to construct peptide chains. On earth those chains happen to be made of 20 different L-amino acids, but there’s no reason the same DNA sequence couldn’t serve as the directions for chains comprised of 40 different types of D-amino acids.
Incidentally, D-amino acids do appear in a variety of earthly peptides and peptidoglycans. These isomers are usually proceed by Posttranslational modification of pre-existing L-peptides.
The preference for L over D is probably an artifact of the evolution of Aminoacyl-tRNA synthetases, the enzymes which hook amino acids onto transfer RNAs. In the beginning there were probably only 1 or 2 different versions of this protein, with a chance preference for L isomers of some amino acid. Since the chemistry depends on the position of the amino group within the enzyme’s binding pocket, rather than the position the side chains, mutations to the amino group binding region are more likely to be deleterious than mutations to the side chain binding region. Switching the substrate from D to L requires such movement of the amino group binding region.
That’s a terrible article.
The actual story of amino acid synthesis is much more complex.
OK. But to what extent are the 20 amino acids synthesized from the a limited number of precursor molecules? (It’s a bit difficult to wade through the link to sort this out, but it appears that there are only a few, even if glutamate is not the only one.)
If many of the amino acids are derived from the same precursors, this would be a partial explanation of their common chirality, together with your own point concerning the tRNA synthetases. As per Roog’s cite, perhaps stability issues of mixed D and L proteins could be involved as well.
There’s like 5 or 6 different main pathways, and a bunch of little ones that aren’t major contributors as things happened to evolve, but could have been. You’re right that the production of chiral centers via a limited number of paths will contribute to an overall bias towards D or L. But just as with the aminoacyl-TRNA synthetase story, an improbable mutation back at the dawn of life could have given us a mixed DL world, regardless of what the DNA (see OP) looks like.
That depends on how different you consider to be “different”. You could certainly swap out a few base pairs in a nucleic acid-like molecule: We even see this to some extent on Earth. One of the bases in RNA is different from the corresponding base in DNA. Given that one possible substitution exists, I see no reason to doubt that there could be others. One might have a long ladder-shaped molecule which had an entirely different set of building blocks than Earthly DNA, or a different number of them.
But there are going to be some commonalities. Anything describable as “life” would have to have some way to store the information which tells it how it’s supposed to fit together, which pretty much means an aperiodic polymer of some sort. And this information-molecule is going to have to be easily replicable. I’m sure there are other ways of doing this, but I don’t know of any simpler methods than the ladder-shape used by DNA. For instance, if you made your genetic molecule out of two matching sheets stuck together, rather than two strands, it’s going to be hard to get at the information stored in the middle.
For example, you could build your genetic coding molecule around peptide nucleic acids.
Why? There are different amino acid translation schemes on Earth: why can’t there be an amino acid translation scheme that results in some of them having opposite chirality? It might have to involve a process unlike tRNA due to chirality constraints, but the evolutionary advantage would be enormous for the first adopters considering that others would not be able to eat them nutritiously.
One other thing to consider is that the ribosome, which translates mRNA into protein, excepts amino acids of the same chirality. The entire translation machinery that holds the mRNA, guides in the tRNA, and proofreads is huge and complicated, but the subenzyme which actually creates the peptide bonds doesn’t care about nucleotide sequence and all that. It does however care about amino acids with the correct chirality.
Evolution won’t change everything at once at start from scratch with new proteins for every purpose. So what you’d see would be an organism which incorporated a novel amino acid (not necessarily a dexter one; there are many “amino acids” which aren’t used much or at all in terrestrial life) in a few places in a few proteins. The other proteins in the organism would still be entirely digestible, and even the modified ones would still be mostly digestible. Eventually, you might see an organism evolving to use more and more novel AAs, but that would take a long time, and give the predators time to adapt to eating them, so it wouldn’t be all that huge an advantage.
So they’re advanced enough to colonize another planet, but not advanced enough to do a little organic chemistry and convert some of that planet’s amino acids to isomers we can use? Why didn’t they just genetically engineer bacteria or plants to do this for them before they left earth?
I think it’s more than just a “little organic chemistry;” you would essentially have to break the amino acid apart to rearrange it. Probably a rather expensive process.
That’s not really possible for reasons already explained: Earth life is not set up to handle the opposite chirality at all.