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.

starting from the base

adenine

Canto: You know, just as an aside on this earliest forms of life stuff, it's interesting how the pioneers of modern biology were interested in getting down to the smallest, simplest forms of life, and studying them, to see just how far down they could go, in size, and still find life. I mean they were asking, just how small can a living organism be?
Jacinta: Right, and they were no doubt amazed at the complexity of those little critters, once they developed microscopes powerful enough to detect them and look inside them.
Canto: Well you know Darwin took a microscope with him on the Beagle, a state-of-the-art instrument of the time, and his Beagle notes were more about zoophytes than anything else. Zoophytes were sea creatures - the term is obsolete now - that seemed to have the qualities of plants as well as animals. But he was also intrigued by what he called infusoria, another obsolete term, then given to what we now know are diverse forms of largely water-dwelling eukaryotic micro-organisms. And I'm sure his interest in such organisms ran along these 'how small can life be' lines.
Jacinta: And yet the pioneering microbiologist Christian Ehrenberg considered that there were no 'lower' creatures, and that 'the infusorian has the same sum of organisation-systems as a man'. These were the beginnings of heretical ideas, questioning the role of humanity as the pinnacle of the earth's, or God's, creation. Darwin was definitely being influenced by these new lines of thinking.
Canto: So anyway, we were talking about ribosomal RNA as I recall.
Jacinta: Well you know that the ribosome is the protein-making factory of the cell, right?
Canto: Of course. And so ribosomal RNA is - the RNA in ribosomes, right?
Jacinta: No, it's nowhere near as simple as that, mate. First we know that 'DNA makes RNA makes protein', but it's not a simple process. Certainly rRNA is central to that protein-making process, but there are two other forms of RNA, messenger RNA [mRNA] and transfer RNA [tRNA], that need to be understood and differentiated.
Canto: Yeah, I can see this is going to be horribly complex, but let's just do it. How does DNA make RNA and why does it make these three different types?
Jacinta: Well this first step is called transcription or RNA synthesis. We know that both DNA and RNA are nucleic acids.
Canto: Made up of nucleotides. But what's a nucleotide?
Jacinta: Okay, if you're serious, I'll tell you. A nucleotide has three basic components - a nucleobase, a five-carbon sugar, and a phosphate group [or two, or three]. A nucleobase is involved in base pairing in DNA and RNA. They're often called bases for short. The four bases in DNA are cytosine, guanine, adenine and thymine.In RNA the first three are the same, and uracil replaces thymine.
Canto: Fine, you've named some nucleobases, but what are they?
Jacinta: Well, if you want their chemical structure, you'll find all that here. But aren't we getting a little bogged down?
Canto: No, no, there's no use talking of RNA until we understand the basics, and that includes bases. Let's take it slowly, inch by painstaking inch.
Jacinta: Okay, you're the boss.

Source: Rebecca Stott: Darwin and the Barnacle. Faber & Faber, 2003.