When I Heard the Learned Astronomer
Walt Whitman

When I heard the learned astronomer,
When the proofs, the figures, were ranged in columns before me,
When I was shown the charts and diagrams, to add, divide, and measure them,
When I sitting heard the astronomer where he lectured with much applause in the lecture-room,
How soon unaccountable I became tired and sick,
Till rising and gliding out I wandered off by myself,
In the mystical moist night-air, and from time to time,
Looked up in perfect silence at the stars.


Welcome to the 'mystical moist night-air' in the world of Biochemistry. 

Course Syllabus

ANNOUNCEMENTS

 

Get these FREE molecular graphics programs for your home computer. Learn to use them with self-guiding tutorials. They will become an indispensable tool for deepening your understanding of proteins, DNA, and other important biomolecules.
PROTEIN EXPLORER	This program provided free to educators by Eric Martz is the program that will be used for this course.
RASMOL	Widely used graphics viewer for large and small molecules.
CHIME (Plugin)	A Netscape plug-in version of RasMol. Very helpful to have installed on your computer.
DEEP VIEW (aka Swiss-pdb viewer)	The premier graphics program for studying macromolecular structure.
PROTEIN MORPHER	Follow conformational changes in recoverin, integrin, influenza hemaglutinin, calmodulin or cAMP kinase or make your own morph between two protein conformations!
ISIS/Draw	Give your chemistry reports a professional touch with this powerful but easy-to-use program for drawing structural formulas and equations.
WAIT! Before you can view a molecule using any of the above programs, you will need to get the file that contains the structural information on your protein of interest.
THE PROTEIN DATA BANK	The world's repository for protein and other macromolecular structures determined by x-ray crystallography or NMR.
PDB Tutorials	Tutorials on how to search and download files from the protein data bank.
HIC-UP	Where you can find PDB Files of Cofactors, Prosthetic Groups, and Other "Small" Molecules
You will need Chime to follow many of the links below that contain "Chime Scripts" for molecular viewing. You may download Chime from the MDL Website onto your home computer. Alternatively, Chime is installed and working properly on all of the PCs in the computer lab.  Be aware that Chime works best with Netscape 4.x. Internet Explorer 5.x DOES NOT display some Chime scripts properly.
Lesson Plan for Spring 2005 The textbooks for this course will be 1Creighton, T.E. Proteins: Structures and Molecular Properties- 2nd Edition, Freeman and Company, (1993).   and  2Any general biochemistry textbook
Week Lecture Background reading required Lecture-based reading assignment Other materials 1 Web resources and Molecular Viewing tutorials Expasy.org RCSB.org Protein Explorer     Explore the following websites:   www.expasy.org www.rcsb.org www.proteinexplorer.org Homework Assignment: Discovery in Protein Explorer 2-5 Protein structure determination By x-ray crystallography Crystallization Diffraction Electron density map Refinement By other high resolution methods NMR Neutron diffraction By other lower-resolution methods small-angle solution scattering Electron Microscopy   Proteins 5.1 and 5.2 pp. 171-176 ·   conformation vs. configuration ·   peptide unit/ residue- dihedral angles ·   1° 2° 3° and 4° structure ·   The Ramachandran Plot Proteins 6.1 and 6.3  pp. 201-217; 238-244 X-ray Crystallography lecture slides   Krueger_Protein Explorer Presentation   Protein NMR lecture slides 6 Non-covalent forces in proteins Electrostatic Interactions Hydrophobic Interaction Cooperativity   Proteins 1.3 pp. 6-19 ·   Amino acid residues   Proteins 4 pp. 139-167    HW problem set #1   Non-covalent Interactions lecture slides   Low-Barrier H-bonds 7 Biosynthesis/ Protein Expression ·   Protein Engineering ·   Mutagenesis ·   The Ribosome   Proteins 2.1 pp. 49-59 ·   Genes ·   Transcription ·   Translation    HW problem set #2 Proteins 2.2 pp. 59-64     Ribosome lecture slides Read this review of the ribosome structure and the original, if desired: Nissen et al. (2000) Science 289:920 and Ban et al. (2000) Science 289:905   8-9 Protein Purification/ Characterization ·   Detection ·   Size Determination ·   Solubility ·   Hydrodynamic properties ·   Spectral properties     HWproblem set #3   SDS-PAGE      . description      . simulation Proteins 1.4 & 1.5 pp. 20-43 Proteins 7.1 pp. 261-276     This Amersham-Pharmacia web site has an excellent introduction to chromatography including how to set up a protein purification scheme and descriptions of various chromatography media and protocols   Protein purification lecture slides   MIDTERM EXAM       10 Evolution ·   Sequence homology o  Gene o  protein ·   Structural homology   Proteins 3 pp. 105-137     HWproblem set #4     Practice Blast Sequence searching Proteins 6.4 pp. 244-259           Evolution lecture slides Chapter 7 of Stryer 5th edition   Using BLAST sequence search software   Article on gleaning information from a sequence search 11&12 Protein folding/conformational properties ·   Regular Conformation of polypeptides ·   Protein Flexibility/Motions ·  De-/Re-naturation     Proteins 5.1 and 5.2 pp. 171-176 ·   conformation vs. configuration ·   peptide unit/ residue- dihedral angles ·   1° 2° 3° and 4°   Proteins 5.3- 5.4, 6.2, & 7.4 -7.5 pp. 182-193, 217-238, & 287-325       HWproblem set #5   Protein folding lecture slides   Probing the partially folded states of proteins using limited proteolysis        13 & 14 Approaches to deciphering the protein folding problem computational thermodynamics of protein folding differential scanning calorimetry     Deciphering the message of life's assembly   Linus article part 2   Privalov_thermodynamics of protein folding   DSC_lecture slides 15   Philosophical Discourse on Structural Biology   The New Architectonics Final Exam Due Tuesday May 10 at 7p
Journal Club Presentation Schedule

JOURNAL CLUB PRESENTATIONS

(JKK) 1HZW Thymidylate Synthase (TS)	Protein Science 10: 988 (2001) JC #1 Questions
(WK) 1TLL nNitric-Oxide Synthase (nNOS)	JBC 279: 37918 (2004) JC #2 Questions
(CNE) 1T9R, 1T9S, 1TBF Human Phosphodiesterase 5A	JC #3 questions+ Molecular Cell 15:279-286. (2004)
(MBT) 1NWK Monomeric Actin in the ATP state	JBC 278:34172 (2003) JC #4 questions
(JFD) 2GAW and 2GAC glycosylasparaginase	JBC 273:20205 (1998) JC #5 questions
(MSP) 1P8X Ca2+-bound C-terminal half of gelsolin (domains 4- 6)	FEBS Lett. 552:82-85 (2003) JC # 6 questions
(JBO) 1ND1 BaP1 snake venom metalloproteinase	JC #7 questions + Protein Science  12:2273 (2003)