Ridiculously oversimplified summary of lectures 1
I don't understand why they can't just introduce us to the concepts early on instead of cramming everything hard into the last year of your degree. They had 2 years to prepare us for the hard bits but noooo... They chose to lull us into a false sense of security with how easy the subject was. Those bastards. Anyway, here's a ridiculously oversimplified summary of what I learnt yesterday.
We are thought to have roughly 30,000 genes but most of it isn't even protein coding genes. Protein coding genes are genes that code for the production of protein, as in, what makes up your body. Instead, DNA is filled with a few other components, some of which don't even have any function. Examples of these are LINES/SINES which are long/short interspersed nuclear element, other short interspersed repeat sequences (for gene fingerprinting), regulatory elements such as promoter and enhancer regions, pseudogenes or silent genes that have been unnecessary and have been mutated silent , chromatin structures such as origin of replication, centromeres and telomeres (essential for packing).
DNA needs those structures, well except pseudogenes, really, in order to regulate transcription for particular genes. Not all genes are active at one point in time, there's a reason why you get different cells in different areas. Like, skin cells outside and liver cells where the liver is. The thing about genes though, is that there are only 4 bases; Adenine, Thymine, Cytosine and Guanine (ATCG). There's only so few combinations that one may have with only 4 bases but that's not the worst thing. C and T are quite similar in structure where C can get methylated for whatever reason and be deaminated to become T. This is a problem because for example, if ACG coded for one amino acid, ATG is a start codon. So you can imagine the problems that can happen with that.
I suppose the main thing to take away from these lectures is about DNA packaging. DNA is normally considered to be roughly 2m long, therefore it would require really efficient packaging in order to fit it all in microscopic nuclei. So, the DNA is wound around a histone (H2a, H2b, H3, H4) making a nucleosome. H5, another histone molecule makes a linker between other nucleosomes. The thing about the histones is that they tightly pack the DNA, making it near impossible for RNA polymerase to do its job. The histones form ionic interactions with the DNA in helix-turn-helix conformation (I think, feel free to correct me) making strong bonds.
All isn't lost, there are chromatin remodelling machinery such as SWI/SNF that loosen the chromatin with ATP (adenosine triphosphate molecule, ie, the holy grail of biochemistry) as SWI/SNF contain bromodomains that recognise acetylised lysine. It also binds and stablises this other molecule, CBP (cAMP response element binding protein) that acetylises lysine. What's with this thing lysine? Well, the acetylation of lysine in the histone has been associated with activation of transcription. That's not the end of the story.
So, you've got the DNA loose, now it's time for the DNA binding protein (which protein is determined by which area of the body you're in. ie, which protein is expressed at whichever area. Eg: GATA in rbc and GTTAAT in liver) to bind onto the DNA and recruit DNA transcription factors (TF) for example NPY (binds CCAAT), Sp1 binds onto CpG boxes, TATA-binding protein (TATA-bp), etc bind onto the loosened DNA and recruits RNA pol (in some cases, basal transcriptional machinery which is also just a platform for RNA pol). There are different types of DNA binding protein in different animals, where the leucine zipper with homeodomains and Zinc fingers are predominant in humans, prokaryotes prefer helix-loop-helix interactions, that sort of thing.
Of course, I was mainly talking about the activators, there are repressors too. But before that, we've initiated mRNA transcription. It's done by looking for that start codon, ATG and RNA polymerase will go along the DNA until it finds a stop codon. Then it'll drop off and everyone will be merry. So, we've stopped making the protein we need and now we want to prevent more from being made. The opposite of the acetylation of lysine is the DEacetylation of lysine, there's also methylation which basically does the same thing. This is too long and I need to start on my other subjects.
Why the HELL did I attempt doing this as a major?
13 comments:
Yes, there is more to come. Much more, but I also major in Neuroscience so you know, that's a hell lot more interesting.
All this through evolution? I find that hard to imagine. Oh, best wishes with the studies. Keep your own neurons from blowing up on you. i.e. remember to relax.
It is amazing to me. I of course don't fully understand it all but I understand enough to be awed by the complexity of even the simplest life forms.
And then if you keep telescoping down, all those DNA bits that you mentioned are composed of specific elements, which are another fascinating world.
If I understand right, someone, theoretically, could actually mess with a helium atom and convert it to say, an atom of lead or of mercury, just by adding atomic pieces. Theoretically, you could take a box of swamp mud and change it into a zebra.
Everything in the universe, from a ham sandwich to Alpha Centauri, from a driblet of cigarette ash to the drool on a baby's bib, from Kim Jong Il to Kate Moss, is built utilizing the same handful of atomic bricks: electrons, protons and neutrons.
Yeah, it's kinda cool but pretty lame to have to memorise.
Squirrel, didn't you do biochem or some molecular bio ish thing?
Ecd, what a frightening thought. It's weird that we're all made of the same basic elements but because of the arrangements of said element, things turn out different. Like diamonds and graphite.
le snob'd~
it's like listening to arts students discussing how their post-soviet impressions of renaisance paintings in a particular 1960's setting can upset the kaos theory.
You chose it, deal with it like everyone else.
PS; chubbyzoid!~ ^^ sif moderate comments, you're as bad as ... Georgie W Bush.
I don't moderate comments, if I did, yours wouldn't make the cut.
Sorry poopsy.
I felt as if something was missing around here lately and I realized what it was today.
You removed the photo of beautiful You that used to grace the top right corner of Your blog.
Might I beg for its return? You are a lovely Woman and beauty should be celebrated however and in whatever ways possible.
Hahaha, it'll be back soon. Well, another picture after I get this weight under control. I might put another one up, depends if I find one worthy enough to grace this blog. Thanks ecd.
we demand chubbazoid photgraphy.
Chubs! Kankles!
No, Morris-whoever-you-are, WE don't. One doesn't demand anything of a Lady. You ask nicely. Or maybe you beg/implore/on your knees. And you certainly don't insult Her with stupid nicknames.
Hahaha, ignore it ecd. It doesn't really bother me. I think I've mentioned this in a post ages ago about stupid insults that have no affect on me and those are one of them.
Thanks for standing up for me though!
Also, the thing is I don't go around posing for photos unless absolutely forced. Hahaha, there's very few pictures I have that are just of myself. So pretty hard to get a good picture, but you know, it'll pop up someday.
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