Biochem 660 - BIOCHEMICAL TECHNIQUES

Fall 2007-2008

I, 1-3 cr. Survey of modern biochemical techniques. Prerequisites: 2 Semesters organic chemistry, physical chemistry, Biochemistry 601 or concurrent registration and consent of instructor.

	Description		Calendar		Contact
Course Description: Section 001 (Class Number: 20611 ) Instructor(s): Wickens,Marvin P TA(s): Credits: 2 Day: TR   Time: 08:50 AM - 09:40 AM Location: Rm 175 BCHM ADDN   Website: http://www.biochem.wisc.edu/courses/biochem660/ Description: Aims The course will focus on modern and emerging approaches to biochemical problems. We will discuss how the methods work, with an emphasis on their actual practice at the bench — how you do them, what are the pitfalls, and what are the strengths. We will emphasize what is available on campus. Credits: 2 Lecturers Lectures generally will be given by dissertators who volunteer and have expertise in the relevant methods. Dr. Wickens will oversee the course, and work with the lecturers. H. Adam Steinberg of the Media Center will oversee the Graphics and Presentation portion, and Drs. Ann Palmenberg and Jean-Yves Sgro will oversee the Molecular Graphics and Bioinformatics (MGB) portion of the course. We will also have field trips to facilities in the department and on campus. These will take place at the usual class time. Specific meeting arrangements will be discussed in the preceding session. Reading materials Reading will be available from course calendar on the Thursday before the lecture. Some will be required, and some will be optional. Be sure to look for any relevant comments on the web site. Scheduling We will meet on Tuesdays and Thursdays at 8:50 am throughout the semester. During the Molecular Graphics and Bioinformatics Module, class will meet for longer periods, and in the early evening (5 to 7 or 8 pm). Please see the Calendar. Grade There will be three problem sets (see calendar). Together, these will account for 60% of the grade. An oral presentation in the MGB module will be graded (30%). Class participation (10%) will also count toward the final grade. Final Grade Distribution.pdf Web site Check the calendar to: Download required reading (look for any relevant comments about the reading) Download the lecture’s visual aids (i.e., the images for a Power Point presentation) – you should bring these to class.      View Calendar as Syllabus April May 2008 June Sun Mon Tue Wed Thu Fri Sat 27 28 29 30 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 1 2 3 4 5 6 7 NOTE:  Only one(1) color is used to display on the calendar. The event with the highest importance will be the color of the day. Click on the day or select the type of event from they key to display ALL items of a particular type. Key   Class   Lab   Homework   Quiz   Exam   Final   No class Friday, May 16, 2008 (5/16/2008)   No calendar events for today Course Materials     Handout      Cell Culture.pdf      Lecture slides (4/page pdf file) Course Evaluation      Word document for submission Crystallography.pdf      Enzymology !!      4/page pdf of slides Enzymology 1      4 per page pdf of slides Final Grade Distribution.pdf      Final Grade Distribution.pdf      Graphics Evaluation      Word document for submission Immunological Methods 2007.pdf      Lecture slides ( 4/page pdf) Interacting molecules      Lecture slides (4/page pdf file) Mapping Protein-Protein Interactions/PDF Slides; 4/pg      Methods in membrane biochemistry.pdf      Lecture slides (4/page pdf file) Microarrays      - Lecture slides (4/page pdf file) Microscopy 2007.pdf      Lecture slides (4/page pdf file) NMR Spectroscopy      - Lecture slides (4/page pdf file) Protein Purification I      Lecture slides (4/page pdf file) Protein Purification II      Lecture slides (4/page pdf file) Testing Gene Function.pdf      Lecture Slides (4/pg pdf) Thomas Gottler and Dagmar Klostermeier      Same reading as listed for 11/27 lecture Protein Characterization via Mass Spectrometry      Lecture slides (4/page pdf file) Homework      MSMS Data      Mass spectrometry data for homework. Right-click (Windows) or control-click (Mac) "Save link as..." to download to your local machine. Problem Set 1      Problem Set 1 Answer Key      Problem Set 3.1     (Due: 12/13/2007) Word document for submission Problem Set 3.2      Word document for submission Problem set reading 1      I-Jin Lin, et al. 2005 Problem set reading 2      Heike Blad, et al. 2005 Problem set reading 3      Fariba M. Assadi-Porter, et al. 2003 Problem set reading 4      Jocelyne Fiaux, et al. 2002 Problem set reading 5      Kenji Sugase, et al. 2007 Reading      Aebersold & Mann      Mass spectrometry-based proteomics Betzig et al.pdf      Deglon, et al.pdf      Delano: Unraveling Hot Spots... (Recommended)      Flow Cytometry Review.pdf      Garavito & Ferguson-Miller      Detergents as Tools in Membrane Biochemistry Hell et al.pdf      Jose Arnau, et al.      Reading 1: Current strategies for the use of affnity tags and tag removal for the purification of recombinant proteins Mistaken Identity.pdf      Moreira: Hot Spots Review (Required)      Overview of Purification Techniques      Read pages 1-5. Phizicky et al.      Suggested reading: Protein-Protein Interactions: Methods for Detection and Analysis Poulsen.pdf      A brief introduction to NMR spectroscopy of proteins Problem Set 2.doc      Problem Set 2.pdf      Reference HIC      Background reading on hydrophobic-interaction chromatography. Read pages 1-6. Reference IEX      Background reading on Ion-exchange chromatography. Read pages 1-10. Refernce SEC      Background reading on size-exclusion chromatography. Read pages 1-6. Semowegere & Weeks.pdf      The QIAexpressionist      Reading 2: pp. 48-58 (protein expression), pp 63-73 (purification) Thomas Gottler and Dagmar Klostermeier      Tomari et al 2007.pdf      Sorting of Drosophila Small Silencing RNAs Lab             No homework assignments are currently due.         Contact Information: