Saturday, December 19, 2009

RNA, complexity, and a change in the weather

RNAP in action during elongation
Jacinta: Right, now I've shown you the chemical structure of one base, adenine. In base pairing in RNA, adenine pairs with uracil, and guanine pairs with cytosine. According to what I've read in Crick, big pairs with small. In DNA, adenine and guanine are relatively big, thymine [and presumably uracil in RNA?] and cytosine are small. Here's a diagram of the chemical structure of uracil:

Canto: Right, only one ring, less components than adenine, certainly. So how and why do these bases pair off?
Jacinta: In DNA the two big and two small base pairs form a neat hydrogen bond. In RNA it's apparently more complicated - there are in fact other base pair bonds - but for our purposes it's the same story. On your comment about rings, yes, the big double-ring molecules, adenine and guanine, are called purines, and the single-ring molecules are called pyrimidines. I could go on, but I'm not sure if mastering all this detail, supposing we can, will get us far in understanding the organic universe.
Canto: Yes, and no. Obviously Darwin didn't know any of this stuff when puzzling over his barnacles and the diversity of species, but that doesn't mean we don't need to know it, or that it's not helpful to know it.
Jacinta: Well I can tell you it gets more complicated, vastly so.
Canto: Okay let's move away from structure and onto function.
Jacinta: In any case let's try to keep it broad. The DNA into RNA thing. An enzyme called RNA polymerase [RNAP], essential to all living organisms, constructs chains of RNA from DNA. Again, this is by no means a simple process, and it is of necessity highly regulated. For example in E coli,more than 100 transcription factors have been found to regulate the activity of RNAP. This enzyme is responsible for many products, including messenger RNA, the non-coding RNA including transfer RNA and ribosomal RNA, and many other recently discovered RNAs. It's an ongoing, burgeoning field of research. Eukaryotic cells have several different types of this enzyme, so it's hard to know where to begin...
Canto: Okay I get the picture, or I get the idea that we're never going to get the picture. Let's just change the subject completely shall we? I'd like to get on something more topical, like our warming planet.
Jacinta: Later, later, Can. Okay, clearly RNA stuff is getting away from us. What's a nucleic acid?
Canto: Something to do with the nuclei of cells, and an acid has a negative charge, a base has a positive charge.
Jacinta: On the right track. The phosphate groups in DNA in normal conditions have a negative charge, that's what makes it an acid, and yes, it's nuclear, except when there's no nucleus. RNA of course is also an acid, very similar to DNA, but without the missing 'oxy' group. The ribose of both these molecules is a sugar.
Canto: Well thanks, I'm definitely learning something here, and we'll get back to it, but i'm wondering if we can explore this more pressing topic next time. Is the rise of carbon dioxide in our atmosphere, presumably due to human activity, the burning of fossil fuel, deforestation and the like, causing the planet's surface to warm, or is the connection between our emissions and warming unproven, as many sceptics are saying?
Jacinta: Okay, we'll get right onto that one, for the sake of our species and many others.

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