Lecture notes
Mar. 8th, 2004 06:31 pm![[personal profile]](https://www.dreamwidth.org/img/silk/identity/user.png){kind=small}
tarigwaemirAd Mundo Exteriore,
I think I really was the only undergraduate student at the Bristol-Myers-Squibb lecture. I recognized several of the chemistry TFs in the audience (including my own section TF), plus a couple of biology TFs from last semester. Actually, my chemistry professor was there too, in the third row. I think the entire chemistry department attended. Naturally, I felt small, insignificant and out-of-place. But! I did get to see Leslie Orgel and Gerald Joyce! Dr. Orgel is a soft-spoken man with a British accent and very consciously old-fashioned. His voice is a little dull, and he's not nearly as charismatic as Dr. Joyce, who is much more energetic and outgoing. Still, you could tell that they were both amazing scientists. I'm afraid that I dozed off during both lectures--they soon reached a point where they were discussing material that went entirely above my head, and it didn't help that I was sleepy from last night/this morning's homework sprint.
Some interesting things I want to note down before I forget:
1. Ribose has dozens of isomers, plus it has the unfortunate advantage of being most likely to revert to its open chain aldehyde form. However, in its open aldehyde form, it can react with cyanamide (a relatively simple compound that one could postulate was present in a prebiotic environment) that will not only sequester it in ring form but also specifically select for the alpha-ribo-furanose isomer, which is the one present in nucleotides. Rather amazing. Also, not only is it most likely to react with cyanamide, but it will also tend to crystallize, unlike the other cyanamide-sugar complexes. Apparently, it has the same diffraction pattern regardless of whether it is racemic or L- or D- form, the significance of which is not yet quite understood. This research hasn't been published yet, but I'm looking forward to the paper. Also, proof that I really do need to do more than survive organic chemistry but actually understand it.
2. The catalytic component of the ribosome is entirely RNA-based. The ribosome's structure was finally elucidated by crystallography in 2000, and the structure shows that the nearest peptide is at least 25 angstroms away from any active site. That means that ribozymes are wholly responsible for catalyzing peptide bond formation, which Dr. Orgel called the "smoking gun" evidence for the "RNA world". We've all heard something along those lines before--that the catalytic function of ribosomes is at least partially RNA-mediated--but never so conclusively and absolutely as all that. Proteins are not involved at all! They should change the textbooks soon. -_- This is what happens when you don't follow the major science journals (the findings were featured on the cover of Science, four years back, and were major news).
3. There are several problems with the likelihood of RNA synthesis in a prebiotic environment, and one of the issues that I was not aware of was that the 5' - 2' phosphodiester bond is more likely to form, rather than the 5' - 3' which we all know and love from those antiparallel DNA strand diagrams. (There are several other bonds that are possible as well.)
4. Dr. Joyce's lab is also working on the problem of developing a "cell"-like environment, and they've constructed this interesting octahedral structure made entirely out of nucleic acid chains. I didn't really follow all the details, but it was a cool concept. I get the feeling that this direction of research--which does not focus so strictly on exploring the actual means by which life arose on earth but rather on the synthesis and artificial evolution of biological molecules--may be the real source of future nanotechnology development. I mean, bucky-balls and nanotubes are all very fine, but I think that it's really this border realm of macromolecules outside of biological systems that has the flexibility for truly complex function and design. Almost ironic, that the mechanisms of selection from a pool of random mutations has the potential to be more precise than synthesis by intelligent design.
All right. I think I'm going to skip section today because (1) I'll probably fall asleep anyway and (2) I need to get more of the problem set done so I can go over it with Jenny later tonight.
...Tari
I think I really was the only undergraduate student at the Bristol-Myers-Squibb lecture. I recognized several of the chemistry TFs in the audience (including my own section TF), plus a couple of biology TFs from last semester. Actually, my chemistry professor was there too, in the third row. I think the entire chemistry department attended. Naturally, I felt small, insignificant and out-of-place. But! I did get to see Leslie Orgel and Gerald Joyce! Dr. Orgel is a soft-spoken man with a British accent and very consciously old-fashioned. His voice is a little dull, and he's not nearly as charismatic as Dr. Joyce, who is much more energetic and outgoing. Still, you could tell that they were both amazing scientists. I'm afraid that I dozed off during both lectures--they soon reached a point where they were discussing material that went entirely above my head, and it didn't help that I was sleepy from last night/this morning's homework sprint.
Some interesting things I want to note down before I forget:
1. Ribose has dozens of isomers, plus it has the unfortunate advantage of being most likely to revert to its open chain aldehyde form. However, in its open aldehyde form, it can react with cyanamide (a relatively simple compound that one could postulate was present in a prebiotic environment) that will not only sequester it in ring form but also specifically select for the alpha-ribo-furanose isomer, which is the one present in nucleotides. Rather amazing. Also, not only is it most likely to react with cyanamide, but it will also tend to crystallize, unlike the other cyanamide-sugar complexes. Apparently, it has the same diffraction pattern regardless of whether it is racemic or L- or D- form, the significance of which is not yet quite understood. This research hasn't been published yet, but I'm looking forward to the paper. Also, proof that I really do need to do more than survive organic chemistry but actually understand it.
2. The catalytic component of the ribosome is entirely RNA-based. The ribosome's structure was finally elucidated by crystallography in 2000, and the structure shows that the nearest peptide is at least 25 angstroms away from any active site. That means that ribozymes are wholly responsible for catalyzing peptide bond formation, which Dr. Orgel called the "smoking gun" evidence for the "RNA world". We've all heard something along those lines before--that the catalytic function of ribosomes is at least partially RNA-mediated--but never so conclusively and absolutely as all that. Proteins are not involved at all! They should change the textbooks soon. -_- This is what happens when you don't follow the major science journals (the findings were featured on the cover of Science, four years back, and were major news).
3. There are several problems with the likelihood of RNA synthesis in a prebiotic environment, and one of the issues that I was not aware of was that the 5' - 2' phosphodiester bond is more likely to form, rather than the 5' - 3' which we all know and love from those antiparallel DNA strand diagrams. (There are several other bonds that are possible as well.)
4. Dr. Joyce's lab is also working on the problem of developing a "cell"-like environment, and they've constructed this interesting octahedral structure made entirely out of nucleic acid chains. I didn't really follow all the details, but it was a cool concept. I get the feeling that this direction of research--which does not focus so strictly on exploring the actual means by which life arose on earth but rather on the synthesis and artificial evolution of biological molecules--may be the real source of future nanotechnology development. I mean, bucky-balls and nanotubes are all very fine, but I think that it's really this border realm of macromolecules outside of biological systems that has the flexibility for truly complex function and design. Almost ironic, that the mechanisms of selection from a pool of random mutations has the potential to be more precise than synthesis by intelligent design.
All right. I think I'm going to skip section today because (1) I'll probably fall asleep anyway and (2) I need to get more of the problem set done so I can go over it with Jenny later tonight.
...Tari
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(no subject)
Date: 2004-03-08 08:46 pm (UTC)Also I don't know if you intended this or come off as anal retentive but I think it's correspondEnt.
(no subject)
Date: 2004-03-08 09:46 pm (UTC)And you're right about "correspondent". I must have written it wrong the first time and never noticed the mistake. >_< Thanks for pointing it out.
...Tari