Mo Bio Lab

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Syllabus for BIO 436/536 Molecular Biology Lab Fall 2005

Instructor: Scott Cooper Room 3022 Cowley Hall 785-6983 (work) 857-3615 (home)

We meet Mondays from 11-2:05 (001) or 2:15 to 5:20 (002) in room 355 Cowley Hall. Occasionally students will have to come in at other times to check on cell cultures or harvest bacterial cultures. These times are indicated in italics. Assignments are indicated in bold.

Plan for the semester.

My goal this year is to involve you in two real scientific experiments, one identifying protein/protein interactions using the yeast two-hybrid system, and a second examining specific amino acids involved in protein/protein interactions by site-directed mutagenesis. This means we will be doing things that have never been done before, which is exciting, and why we do science. It also means that some things won’t work, which is why we blow off steam by exercising, eating ice cream or whatever else you do to relax. We will have to do some work out of class because actual experiments rarely fit into a 2-3 hour class period, welcome to the real world. To compensate, I will try to keep our scheduled lab periods as brief as possible, some will run for the full three hours, but some may only be an hour.

Tentative Outline:

I’ve never tried either of these experiments in lab, so the schedule will need to be flexible, but here is the plan…

Week	Topic in lab on Wednesday	Additional research days (usually just 15-30 min.)
1	Bacteriological Techniques
2	*Project I. Detecting protein/protein interactions.* Transform yeast with cDNA library.	Friday, replica plating
3	Make master plate of interacting clones. Bioinformatics of nud-1	Monday, replica cleaning Friday, replica plating
4	X-gal staining of filter	Tuesday, fix yeast to filter Thursday, examine results on filter
5	Miniprep plasmids from yeast, calculate [DNA]	Tuesday, start O/N cultures of yeast
6	Prepare competent bacterial cells, transform Draft of Intro/Materials & Methods due (20 pts)	Thursday, calculate transformation efficiency
7	Miniprep and digest plasmids from bacteria Quiz (25 pts)	Tuesday, start O/N cultures of bacteria
8	Run digested plasmids on gel and sequence DNA
9	Bioinformatics on DNA sequences *Project II. assaying protein/protein interactions.* Examine 3D models of fumarase and MDH Design mutagenesis primers
10	Mutagenize DNA Draft 1 of lab report due/peer review (25 pts)
11	Miniprep and sequence DNA Peer reviews due (20 pts)
12	Thanksgiving – take a break J
13	Sequence analysis and protein expression	Presentations in genetics, cell biology or biochemistry labs.
14	Preliminary activity assays, make freezer stocks
15	Lab final exam (100 pts) Final draft of lab report due (100 pts)

Labs: We meet Wednesday from 11-2:05 (001) or 2:15 to 5:20 (002) in room 355 Cowley Hall.

Exams: (125 points) There will be a lab quiz worth 25 points on basic lab calculations. There will be a lab final worth 100 points. This will cover calculations and theories used in the yeast two hybrid and mutagenesis experiments you did this semester.

Research Paper: (165 points; 20 points for draft of intro and methods, 25 for rough draft, 20 for review, 100 points for final paper). Each student will write research paper on the results from their research project (maximum 6 pages). The paper will be in the format of the Journal of Biological Chemistry. Complete with Introduction, Methods, Results, Discussion. Figures will be attached to the end of the paper, after the References section. This paper will contain the data from the bulk of the work done in this lab. Prior to final submission you will exchange papers with other students for “peer-review”. This is a very important step in getting a paper published. Other scientists review your work and make suggestions and comments. You will then respond to these comments by making some or all of the suggested changes in your paper. Instructions on writing a formal research report can be found on the Communications in the Biological Sciences page.

Oral Presentation: (25 points) Each lab group will give an oral presentation on the results they obtained from their yeast two hybrid experiment. In the past these presentations have been given to students enrolled in genetics, cell biology, or biochemistry labs. This will give you valuable experience in public speaking.

Lab notebook: (10 points) Your lab notebooks will be collected and graded at the end of the semester. This link will give you instructions on writing a lab notebook.

Total points: 325

Grading A 92-100%

AB 88-91%

B 81-87%

BC 77-80%

C 67-76%

D 55-66%

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