Field of Science

I'm sure I should feel happier...

Well...I handed my dissertation in. I'm sort of waiting for a nice happy heartfelt rush of relief, or some kind of feeling. Something other than cold and tired would be nice.

It did look all professional though; bound up properly with some nice results, pretty pictures and surprisingly meaningful graphs. And I think I'll probably feel better tomorrow, when I hand my lab book back to my supervisor in the safe knowledge that she's continuing with the work we were doing, and may yet find something even more interesting. At the moment though I'm kind of oscillating between oh-my-ghod-so-much-revision and well-there-goes-10%.

So if you want some interesting science go here for snails that ride on other snails, and other easy-to-understand scientific awesomeness from Ed Yong.

And if you want some mind-knotting philosophy go here for a discussion of induction that I feel so proud to actually understand (eventually and after much discussion)

(and if you want general fun, go to xkcd because it's always good)

Translocon structure

Well, I'm still busy with revision but, miraculously, I seem to have almost achieved my crazy aim of writing all of first terms lectures notes in a week *dies theatrically*. I still don't actually know any of the stuff, but at least I now have notes to work from, and I understand it all, which is important.

Topic of the day today was protein targeting within cells, specifically targeting secreted proteins to the inside of the endoplasmic reticulum; a network of internal membranes which modifies secreted proteins and then exports them out of the cell.

Best story in all this is about the discovery of the structure of the translocon; the channel the protein goes through to get into the endoplasmic reticulum (through a membrane). When they first started looking at the structure of the translocon, they saw it was usually found in the form of four proteins very close together, so the first idea was that these formed a ring, with a nice wide hole in the centre for the protein to travel down. It made sense; but unfortunately it only made sense in that specific biological way where the idea is nice but it doesn't fit in with biology.

Because from the cells point of view (if it has one) a large channel like that is a very unhelpful thing to create. You can't regulate it; it needs a filter, or a cap, or some mechanism to prevent just anything going through. Also, a closer look at the translocon showed that it wasn't always found with four proteins close together; sometimes there were three, or two, which would make the channel even less specific or (in the case of only two) almost non-existent.

So the current model (with a lot more supporting evidence) is that there is a little channel down the middle of each individual protein, shaped a bit like an hourglass, which secreted proteins travel through to enter the endoplasmic reticulum. This model works better, especially as the middle bit of the hourglass can expand and change shape; allowing protein folding inside the channel. This also allows for proteins that want to stay in the membrane to be released, there's a little exit space near the middle of the hourglass (alpha helix two of Sec61 for those who are interested) that allows the protein to escape from the translocon into the membrane before it enters the endoplasmic reticulum.

But of course every new model leaves questions behind that were answered by the old model. The thing now, is nobody is quite sure why the proteins cluster together in groups of (mostly) four. If they have a channel through each protein, why not be all separate? Why form specifically numbered groups? It has been suggested that one protein is used for recognition while the other is actually used for the channel but it's all a bit uncertain at the moment.

*sigh* I miss lab work. I miss blogging about lab work. Revision is like forcing yourself to eat when you're already full, I want to get onto some new stuff.

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. :)

Slow internet should DIE

I'm overseas at the moment, which means that although I am surrounded by palm trees, the weather is warm and I am practically living in the swimming pool, unfortunately I am reduced to dial-up Internet.

Which is very...very...slow.

So there will probably be a short break from blogging, as I'll be using the computer infrequently (although I am determined to message a Certain Special Someone every single day, even if they don't message back :p )

On the plus side, the lack of Internet means that I'm doing about six times as much work as normal. Which hopefully (hopefully!) should help with exams next term.

On Conferencing

I spent most of last week at a conference. The Society of General Microbiology conference to be precise, up in Harrogate. It was my first conference, so I was pretty excited about it, and it certainly lived up to expectations. It was fun, exciting, and I learnt a whole lot of stuff. Some of it was even about science.

But the most amazing thing? Julian Davies was there. The same Julian Davies I spent the last blog post ranting about; with the papers about how sub-inhibitory antibiotics acted as signalling molecules. Best of all, I had a chance to talk to him as well. After the initial slight embarrassment of me being slightly uncertain of how to introduce myself (mostly I was desperately attempting not to gush as him in an 'I've-read-all-your-papers-and-omg-they're-amazing' way) I finally talked a little about my research.

He actually seemed interested! It turns out all his work has been on soil bacteria, so he was quite interested in my work, which was on an antibiotic-producing bacteria. We chatted for a bit, then someone else came up and I politely scarpered out the way feeling a little wobbly around the knees. Gushing mostly avoided. Serious scientific talk achieved :) It was a good feeling.

One thing I didn't realise about conferences was just how much the evenings play a part. During the day there are talks and lectures and poster displays and promotional stalls for various companies that sell scientific equipment. So there is nothing official planned for the evenings (I even brought some revision along for then. hah. Like that happened). But the evenings, it turns out, are all about going out with the people you've met at the conference; getting to know people, talking with them, sharing experiences and ideas and having the most amazing conversations about scientific things with people who pretty much think along the same lines as you. And nobody rolls their eyes and tries to change the subject. It was amazing.

So that was my first conference. Hopefully, it will be the first of many.