Course Information Laboratory Schedule Molecular Graphics Exams

BECUR (Undergraduate Research Conference) website: Information on the conference, abstract submission, and speakers.

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Special Research Project.pdf: instructions for the project you will do at the end of November. A mass spectrometry project will be added to this list, the details of which are still be worked out. Project Deadline: by Oct. 29 ALL groups must inform Dr. H what project they will do during the week of Nov. 17 - 19. There will be limitations to how many groups can do each experiment, therefore the projects are first come, first served! REINCARNATION: a comical and metaphysical observation with a Western flair. Molecular Graphics Gallery is now up and running. The grading Rubric and Score Sheet can be downloaded from this page. Molecular Graphics Project information has been moved. Molecular Graphics Important Dates and Deadlines: Sept. 14, 15, and 16 in BSW 243 (computer lab) from 6 pm to 8 pm: Workshops for initial instruction on Jmol and developing a Jmol webpage:   The same material will be covered in each of these workshops, so only attend one due to limited seating.  A sign up sheet will be provided in class. By Oct. 2: meet with Dr. H to decide what protein will be subject of Jmol webpage. By Oct. 16: meet with Dr. H to show progress on Jmol script development. Nov. 6: all Jmol webpages, scripts, and jpegs must be submitted to Dr. H. Nov. 9: Jmol gallery will be created on course website. Dec. 4: submit grades for class mates Jmol webpages to Dr. H as a group. As you can see, you will need to begin working on this project right away, do not put it off!   For those looking a laboratory in which you can do your Senior Thesis project, check out these two resources: Olivia Mendoza sent out an email about a central information portal for undergrads looking for research labs: http://www.ur.arizona.edu For more assistance Prof. Marc Tischler has put the following information together: http://www.biochem.arizona.edu/dept/dgre/res_advice.html Examine these two sources of information, let me know if you need more information. A word to the wise, THIS IS NOT AN EASY PROCESS, BETTER TO START NOW!!!!!!!! Rooms and Times Section 1: Shantz 242E @ 8 am for lecture Section 2: Forbes 206@ 1 pm for lecture Sections 1 & 2: Koffler 540 after lecture.   Instructor Room and Phone Number Email Office Hours Dr. James T. Hazzard (Course Coordinator)   BSW 342A, 621-7118 Koffler 540, 621-9989 jhazzard@email.arizona.edu Friday, 9 - 12 noon(BSW 342A) (M, T, W, Th : usually can be found in Koffler 540). Daniel Martinez tba danielm1@email.arizona.edu tba Deboleena Sarkar tba. dsarkar@email.arizona.edu tba Katie White tba ktwhite@email.arizona.edu. tba Zach Miles tba zmiles@arizona.edu tba Dario Pasalic . Preceptor contact information is at the discretion of the individual By appt only tba . Preceptor contact information is at the discretion of the individual By appt only Molecular Graphics Websites Instructions for the JAVA/JMOL installation. BIOC 462a JMOL scripts NCBI Home NCBI/Structure Home VAST Home

Tuesday, Nov. 17 and Thursday, Nov. 19 Special Research Project Morning class meet in Koffler 540 at 8 am Afternoon class meet in Koffler 540 at 1 pm The first thing we need to do is determine the appropriate concentration of BME or TCEP (CD expts) to render AP catalytically inactive. We also must determine the best buffer to do the CD, fluorescence, activity assays which involve taking the enzyme up to 85 C and rapidly bringing it back to room temp. Mass Spec people, my apologies but we will not be able to begin dialyzing your protein until Tuesday due to unforeseen problems with receiving the AMBIC and DTT and some personal issues. Please make sure you have spoken with Linda Breci so we can figure out what we need to do for both the MALDI-TOF and Tandem expt.   General tips for composing ones thoughts prior to writing your lab report can be found at Lab_Report.pdf. Detailed information for what is to be included in the first lab report can be found at the end of the Protocol along with supplimental questions that will also be turned in. A general guide for scientific writing can be obtained at : BMB_Sci_Writing.pdf. For subsequent lab reports, "Instructions to Authors" for the journal Biochemistry will be handed out and rigorously adhered to when writing your "manuscripts". The following links will be used as the semester progresses: Youtube video on pouring gels, check it out!: http://www.youtube.com/view_play_list?p=0DF3730B1D55C58B Mass Spec links:http://www.chem.arizona.edu/facilities/msf/index.html www.chem.arizona.edu/facilities/msf/BiochemLab/exercises.html End of the semester assignments: edta_ap.pdf. ap_massspec_data.pdf . ap_structure_exercise.pdf. Molecular Graphics Exercises. Miscellaneous Material: Old exams can be accessed at: exam.html beta-gal activity assay.pdf Molecular Graphics for Ligand Binding Experiment.pdf Molecular Biology Homework Transport across membrane: Processing_AP.pdf. Formation of Disulfide bonds: DsbB-DsbA.pdf Mass Spec/Proteomics material: http://www.chem.arizona.edu/facilities/msf/index.html www.chem.arizona.edu/facilities/msf/BiochemLab/exercises.html Go to the bottom left of the page and click on the links there. Mass Spec and Proteomics Homework.pdf Literature References for Mass Spec and Proteomics: (1) Hanash, S.M. (2000) Electrophoresis 21 (6): 1202-1209: Biomedical applications of two-dimensional electrophoresis using immobilized pH gradients: Current status. (2)Aebersold, R. and Mann, M. (2003)NATURE* 422 (6928): 198-207: Mass spectrometry-based proteomics. *There are several very stimulating articles in this issue of Nature.

Section #	Lecture	Lab
1	8 - 8:50 a.m. in Shantz 242E	9 - 11:50 a.m. in Koffler 540
2	1 - 1:50 p.m. in Forbes 206	2 - 4:50 p.m. in Koffler 540