email questions/comments to
ckpark@email.arizona.edu
I botched the story. They were actually working on intermediates for sweeteners. However, the miscommunication seems true. The one researcher was told to 'test' the samples but he heard (and did) 'taste' the samples. See: Sucralose history.
A document on easing into Homology modeling.
Inhibition practice problem.
Paper submissions can be (and are preferred) electronic format. MS Word documents (not docx) with complete figures or PDF format are acceptable. Please save your document files as a Word 2000 or even Word 95 for those of us suffering with old versions. I'm trying not to get any vista on me. I hear it's awful. So be warned that I may ask for your files to be resent as earlier versions. Figures can be included, but also are required to be sent separately as Png, or tiff files. I would also greatly appreciate your pymol scripts that you used to generate your figures.
Finally, your papers are still due Friday, but I won't be checking my email until Saturday morning. In other words, if you need a few more hours and are willing to lose your Friday evening on it, you can send in your paper, via email, by Saturday high noon.
Don't forget to check that you are following the instructions for authors!
Recipe for a great M-M plot:
1 spoonful lyophilized enzyme
add to 2L buffer
dilute this solution by hundredfold (1:100)
measure initial velocity as a function of substrate:
The question, obviously, is: what is the molecular weight of the enzyme?
Arizona Smith has a beginning graduate student who took samples of a cone snail's toxin (Conus tessulatus). Unfortunately, the student didn't keep any sample for N-terminal sequencing of the intact toxin. Instead, he split the sample into two. One sample was digested with trypsin which cuts after arginine and lysine. He got peptides of DARPLTK, SFHGADNANR, ILR, and TLWNLR without DTT. When he added DTT to the sequencing reaction he got two more peptides: GCCEDK and TCCFIG. The second sample was digested with chymotrypsin which cuts after bulky, aromatic, hydrophobic groups, phenylalanine, tryptophan and tyrosine. He obtained the following two peptides: TKDDVPLASF and DNANRILRTLW. When he repeats the chymotrypsin cutting in the presence of DTT he also obtains NLRGCCEDKTCCF. Did you get the same sequence as Prof. Smith's erstwhile student?
Dali Server
From your classmate:
To select a portion of the image with a box, in 3-button viewing, hold shift and drag a box with the left click. To move two proteins around, in 3-button editing, hold shift and drag with the middle button. To rotate a single object, in 3-button editing, hold shift and move with the left click.
To switch between '3-button viewing' and '3-button editing' click on the words '3-button...' in the lower right hand side of the main Pymol window.
Agrp.pml
PyMol Wiki
- Everything you wanted to know about PyMol and more.
A page full of mol. graphics
Protein Synthesis from the 70's.
Tomorrow we'll go over the amino acids, some new Fermi problem, and a thinker question. Don't forget to bring your top three choices for your paper!
Today we meet in the Biochem. computing lab, Room 243, BSW, 12pm - 12:50.
Welcome to Honors 462a. Our first discussion section will be in room 212 Biosciences West (BSW) and at high noon: 12pm - 12:50. See you there!
In the meantime, check out the Proceedings (link at left) where the articles from Fall 2007 are posted and the Fine Art Gallery where you can fine some of the best Pymol figures and scripts from the classs!
Please report any mistakes to Dr. Park!
Biochemistry
462a
Department of Biochemistry and Molecular Biophysics
The University of Arizona
ckpark@email.arizona.edu
All contents copyright © 1998-2008. All rights reserved.
Last revision Aug. 2008
Department of Biochemistry and Molecular Biophysics
The University of Arizona
ckpark@email.arizona.edu
All contents copyright © 1998-2008. All rights reserved.
Last revision Aug. 2008