Thursday, July 29, 2010

A self-replicating RNA

When I first learned about evolution, I thought a fish grew lungs and legs and became a lizard. I didn't understand that these changes occurred over many generations and many years, that each individual represented an incremental step between fish and lizard, and no one animal acquired new capabilities during its lifetime. (Or if it did, it didn't pass them on to its offspring-- that would be Lamarckian evolution, which is false.) For many years this was a conundrum to me, of how a fish could suddenly change into a lizard. I'd never seen anything like that happen, so it seemed preposterous. (One of the rules of science is that something that happened once has probably happened before and will probably happen again.) I still accepted evolution, but this was one of the parts I didn't understand until I got older and studied a bit more.

Likewise, I learned about the RNA world and wondered what kind of RNA could replicate itself? I imagined a long string of nucleotides floating around, pairing up with other nucleotides willy-nilly, until magically, there were two! Of course, they'd be complementary, not identical, and there wouldn't be any reason the new nucleotides would react to form a chain, but I could accept that there were parts of this hypothesis I didn't quite understand.

Unlike DNA, RNA is single-stranded and has the propensity to fold up into all sorts of complex structures. You can think of it like a knotted ball of string. The self-splicing intron forms a complex structure, as does any other functional RNA. To have a function, it must have a structure. But to be copied, it must be linear. And this was my main problem: if an RNA is replicating itself, it must be linear and structured at the same time.

But what if there were more than one?

Two RNAs with the same sequence, but one is folded, and the other is linear. The folded one could have the function of reading the sequence on the linear RNA, and synthesizing its complement. The synthesis would be catalyzed by the folded RNA, putting the right molecules in the right position in the active site, so that it can break and make bonds in the new complementary RNA.

Then what do you do with that complementary RNA (which probably doesn't fold and function like the original)? You use it as a template to make another folded functional RNA. And now you have another self-replicating RNA. In fact, once you have a folded RNA and a complementary RNA, they can make many more folded RNAs just by repeating the second step over and over again.

A folded RNA can use its twin as a template to synthesize a complementary strand. Then it can use the complementary strand to synthesize another copy of itself.

But where did the first two come from?

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