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Manual for Chemical Biology Laboratory

Manual for Chemical Biology Laboratory

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Published by: adriana_obr on Sep 02, 2010
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Manual for Chemical Biology LaboratoryChemistry 427bSpring 2004Lab Manual Contents
Course Description(page 2)2.
Semester Schedule(page 2)3.
Course Materials(page 5)4.
Policies(page 6)5.
Lab Faculty, Staff, and Hours(page 6)6.
Lab Safety and Waste Management(page 7)7.
Material Safety Data Sheets(page 10)8.
Writing in your Lab Notebook (page 11)General Guidelines(page 11)Before Lab: Experimental Plan(page 11)During Lab: Recording experiments and data(page 12)9.
Grading Information(page 13)10.
Guidelines for Final Report(page 14)11.
The Research Projects(page 15)Sub-group 1: The
-peptide project(page 17)Sub-group 2: The mini-Bak project(page 23)Sub-group 3: The phage display project(page 29)12.
Keeping up with the Literature(page 35)13.
Protocols for Chemical Biology Laboratory Techniques(page 36)Affinity chromatography (GST fusion)(page 37)Agarose gel electrophoresis(page 44)Bacterial expression of miniature proteins(page 50)Centrifuge usage(page 55)Circular dichroism(page 58)Cloning basics(page 62)DNA technical information(page 74)Fluorescence background and techniques(page 76)Fluorophore labeling of miniature proteins(page 80)HPLC purification(page 85)Mass spectrometry(department MALDI-TOF instrument) (page 91)Phage display: panning against DNA(page 97)Phage display: panning against proteins(page 105)Sample preparation for amino acid analysis(page 108)Sample preparation for sedimentation equilibrium(page 110)Using the lyophilizer(page 111)Using the Phastsystem(page 113)Using the speed-vac(page 118)Ultra-violet visible spectroscopy(page 120)Western blots(page 130)14.
Useful Internet Links(page 136)
1. Course Description (return toContents)
The goal of Chemical Biology Laboratory is to involve undergraduates enrolled inChemical Biology I in the challenge and excitement of independent discovery at an earlystage of their Yale experience, long before such research opportunities would usually beavailable to them. Each student will have an individual project that is a sub-project of amajor funded investigation currently underway in graduate research laboratories at Yale.Since the projects in this course represent novel research, they differ from those in atraditional laboratory course which tend to have pre-determined outcomes. Students inChemical Biology I will share the excitement—and perhaps the frustration—of hands-onexperience with original research.Sub-groups of four students working on related projects will be guided by a TA who isworking on related research in his or her own lab. This feature fosters independence andcommunication, since the students within a particular sub-group will be working onindividual problems but may encounter similar challenges. There will be frequent mini-meetings of the research sub-groups for troubleshooting and discussion of results. Theschedule is designed so that significant milestones can be reached by the end of eachsemester.As students progress through the semester, they will gain experience performing a varietyof indispensable laboratory techniques while they gain exposure to research methods. Bythe end of the semester, students will be expected to analyze their results and proposelogically related future experiments.
2. Semester Schedule (return toContents)
The laboratory classroom is
SCL 168
, with sub-groups meeting from 1 – 5:00 p.m. oneither a Monday-Wednesday or a Tuesday-Thursday schedule. Sub-groups will meetfrom 1 – 1:30 p.m. in
with the TA and/or Dr. Allen for pre-lab discussions onMW or TTh (according to their scheduled laboratory sessions). A 50-minute Fridaylecture will be held from 2 – 2:50 p.m. in
. All Chemical Biology Laboratorystudents are encouraged (though not required) to attend the Schepartz laboratory groupseminars, which are held at 3 p.m. in SCL 201 (the Faculty Lounge). Note: Each sub-group will have distinct schedule guidelines for experimental progress.Because of the inherently open-ended, results-driven nature of research, it is impossibleto provide an exact script of the semester! This is part of the excitement of research, but italso requires students to maintain focus and look to their TA for direction as necessary.Other than how experimental time is organized, the rest of the schedule is identical for allsub-groups. Every student is responsible for attending all scheduled laboratory andlecture periods. If an illness, injury, or family emergency prevents you from fulfilling thisobligation, please email the instructor and your TA
the absence.
 Below is the general schedule that applies to all sub-groups (see next page). Click thelinks that follow to view the specific schedule for your particular sub-group.
Sub-group 1
-peptide project 
: What is the effect of salt bridge structure on14-helix stability?
Sub-group 2
The mini-Bak project 
: How well do miniature proteins distinguish between members of the Bcl-2 superfamily?
Sub-group 3
The phage display project 
: Can we identify miniature proteins that bind human MDM2 with high affinity?

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