Terpenes, replisomes and sliding clamps

[tarigwaemir]

Lowell House on the Feast of Ste. Catherine of Avila

First chemistry hourly down, two more to go before the end of the semester. Ugh, stupid terpene biosynthesis question! Judging by the number of questions I failed to answer, the highest score I can receive is an 85. Knowing that if I do complete all the questions in an exam, I usually get about two-thirds correct, I must conclude that my most likely grade is a...57. ::sighs:: Unfortunately, that's probably a pretty good chemistry grade for me. Thank goodness for resurrection finals and grade inflation. This exam was much better than the ones we took last semester, which can be interpreted optimistically as "I've improved my understanding of organic chemistry," and pessimistically as "Professor Evans gives easier exams." >_> Anyway, in honor of the horrible terpene problem, my blockmate and I have created a facebook group called "Down With Terpenes!"

Biology cheered me up, however, with its awesome, awesome animation of the DNA polymerase holoenzyme (also known as a replisome) complex. That has countered the bad miasma left over from the chemistry exam and then some. ^_^ Professor Losick also showed us an X-ray crystallographic image of the sliding clamp, which is a protein that holds DNA polymerase to the template strand and is shaped like a donut that fits around the DNA helix. I've found a JPG file (from the cover of a past issue of Cell) that shows it here. (Careful, dialup users, it's a little big.) The sliding clamp has two subunits that basically look like half-toruses, and there's a clamp loader protein that snaps the two subunits together around the DNA, like closing a bangle around your wrist. The outside consists of pleated sheets, but the inside surface (the part that faces the DNA) consists mostly of alpha helices. I bet the residues involved in the helical domains are positively charged/Lewis acidic/electrophilic (to interact with the phosphate backbone). I don't think the side-chains would extend into the major and minor grooves since the clamp fits loosely around the helix (in order to allow the DNA polymerase to move quickly down the template strand), and besides, the sliding clamp shouldn't be sequence-specific.

I wonder why symmetry is so aesthetically pleasing? (Sociobiologists will mutter things about symmetry as sign of healthiness, sexual selection, etc., but I'm not sure how seriously to take sociobiology.) Anyway, after looking at that structure (do go and look, even if you're on dialup--unless, of course, you've already seen it), who wouldn't be happy? All right, I concede the fact that I am an utter biology geek, but I still think that anyone would be able to appreciate that structure.

Too bad I have no way of linking to the replisome animation...;_;

That reminds me, if I ever get around to putting up Lynne Truss quotes, I should probably put up some Stephen Jay Gould ones too. (Am three-quarters of the way through Hen's Teeth and Horse's Toes.)

Yours &c.

Post-script: Oh right, meme! From pornkings: "Ask me three things. Anything. Go for it. I will ask you three things in return and then you can ask other people to ask you, and so on." (Um, just don't ask me any terpene biosynthesis questions because obviously I'll be unable to answer. Down with terpenes!)

Comments

[team7.livejournal.com]

Yay!

1) Have you always wanted to study biology? (specifically in Harvard? I mean, was it ever really a goal you worked towards?)

2) The premise of a novel you will never write. XD

3) How would you characterize yourself? (I understand that this is fairly obscure, but humor me please XD).

[troisroyaumes]

1) I've always known I wanted to study science, but I think I slowly narrowed it down to biology during middle school and high school. I remember doing a research project on DNA in fifth grade, learning about replication, transcription and translation, and it was probably around then that I unconsciously decided I wanted to be a molecular biologist. Then during high school, I remember reading many books that began with grand illuminations of the "purpose" and "philosophy" of science, and I decided that if science is an art of constructing systems out of observations, I would want to help construct the most elaborate system of all. Life as highest level of organization in the universe and all that. It sounds horribly romantic and a bit arrogant, but that was the way I tended to think in high school (and probably still do, actually...^_^;;). Harvard was chosen as a consequence; it's not so much that I wanted to study biology at Harvard, but that once I decided to study biology, I looked for schools with strong research programs in that department and came up with Harvard. It helped of course that my parents were pleased with my choice. >_> Actually, Caltech probably has a better undergrad science program, and I really wanted to go there, but it's so far off in California that I was discouraged from thinking too much about it. >_< Maybe in grad school...

2) Hm, I don't know about novels...but once my friend and I came up with a K-drama screenplay that would be set in a futuristic world where there is a World Government, and an cold, hard, ruthless, ambitious Korean girl (young of course) would maneuver her way to the top with a circle of equally brilliant and power-hungry people. We came up with a whole cast too, exercising all the clichés! The older brother figure, who would control the largest media corporation; the older brother's quiet love interest, who would be a vicious lawyer in the courtroom but meek and gentle outside; the heroine's love interest, who would be the rich, dashing son of her main political rival. We decided that they'd hate each other at first but then fall in love under cherry blossoms. XD But as she gets more and more absorbed in her political career, she starts to suspect everyone around her and becomes paranoid that her lover is betraying her. And then! In a dramatic climax, she kills her lover herself, with a pistol shot, only to discover as he expires that he was innocent after all. It's an enormous setback to her power, of course, and she takes a while to return to her position as the Ruler of the World! Ahahaha...and then we planned a second season where she falls in love with a much younger man who looks exactly like her first love but has a completely different personality (he happens to be innocent and naive, unlike her sophisticated and cynical first love). She swears to protect him from all harm, but his sister, who is one of those would-be muckraker journalists, tries to use him to dig up dirt on the Ruler of the World. And then more paranoia, and more insanity, until it all ends in suicide and blood on cherry blossom petals...

The sad thing is, if I ever wrote it (which I never will, hopefully), it would be so popular in Korea: lack of plausible plot, plenty of tragic moments, all the usual devices...all we need is an amnesiac moment, and we'd have covered all our bases.

3) Hm, what a difficult question. I'd probably call myself a dork extraordinaire, since that seems to cover all the bases.