Field of Science

That Time Of The Year

Well, I am back now in the land of fast Internet, and doing that thing that happens when exams loom which is try to remember how the hell information is supposed to get from large numbers of bits of paper into your head.

I'm currently revising transcription, which I first encountered in AS level (aged 16 for those not familiar with the English schooling system). I've been taught it almost every year since as well, and over the years the process seems to have become more complex and less certain (along with everything else, strangely enough).

Transcription is the first step for making proteins inside the cell. The information for creating proteins is stored in DNA (...mostly..more on that maybe later), with every three base-pairs of the DNA coding for one protein amino-acid. DNA is made of a string of base pairs held in place by a sugar-phosphate backbone, and proteins are made of strings of amino-acids all folded up so it works quite well.

However the cell doesn't just make protein from the DNA template, it goes through an intermediate step first, making an RNA template of the DNA (known as messenger RNA, mRNA). This is the process of transcription (link leads to a nice animation). The RNA then leaves the nucleus and is used for a template to make the protein.

One thing you get taught in AS levels is about promoters. Promoters are regions of DNA that specify the start sites of transcription, the place all the transcription machinery binds too, before trundling off along the gene. You get told that they have a things called a TATA box, ten base pairs away from the start; essentially a conserved sequence of bases that bind to the transcription machinery very well; and conserved (ish) bases around the start site called the INR box. This makes sense (especially when they tell you how the machinery actually works) and specifies exactly where the mRNA should start being made from. Here's a paper.

Except it turns out that these TATA box promoters are a really rare form of promoter. Most promoters are a lot less precise, very fuzzy, and the start site can be anywhere within about 20 base pairs. The mRNA that comes out frequently has extra bases at the front end, because the start point is not well defined.

This is mentioned very briefly, and then they tell you everything and more about TATA box promoters all over again. This is because people know about TATA box sites, because most if not all of the research is done on them, and that is because all of the focus is on them. Also getting ideas out of scientists is a lot, lot harder than getting them in, and the nice preciseness of the TATA box promoter is a lovely idea. It's just not the one the cell uses the most.

Hehe. Science is crazy fun sometimes. Good luck to everyone else out there hitting exams as well. :)

1 comment:

Anonymous said...

Promoters are AWESOME! Seriously, though, sometimes you have to go 500 bps upstream to get all the TF binding sites, and even then it isn't guaranteed. And then there's splicing. Ahhh, the deeps of biochemistry! :)

Good luck revising. I'm sporadically doing protein structure right now, and it's sapping my will to live. Not that Ramachandran plots aren't cool, but I'm getting sick of every sentence ending with "except for glycine."