BIOC-41000 Experimental Biochemistry

Spring 2011

Lecture: Wednesday 1-1:50, CNS 302

Discussion: Wednesday 2-4:50, CNS 302

On Reserve in Lab:

• Short protocols in Molecular Biology
• Fundamental Laboratory Approaches for Biochemistry and Biotechnology

Required texts

• A Short Guide to Writing about Biology, by Jan Pechinik (7th Edition)
• Laboratory Notebook (not a spiral bound piece of crap)

Experimental Biochemistry is a new course to expose you to a variety of experimental techniques in biochemistry, team-taught with Professor Maki Inada.  In the first section with me, we will cover protein expression, purification and enzymology.  Emphasis will be on learning techniques and learning how to design meaningful experiments using those techniques.

Your responsibilities as a student in Experimental Biochemistry:

1. Keep a detailed record of your experiments.  Everything that you do should be written down in a lab notebook.  If you did something but didn’t write it down, you didn’t do it.  You will need good records to write the reports required for each lab.  Avoid writing anything on loose scraps of paper, instead write down everything in your lab notebook.  I will help you to set up a good notebook and there is an informative section in the required text,  A Short Guide to Writing about Biology.
   
   
2. Complete worksheets on the experiment/concept of each lab. These assignments will cover background material, help you critically analyze experimental design and anticipate and avoid mistakes.
   
   
3. Write up a formal lab report for each of the two sets of experiments.  Using a Biochemistry paper as a guide, it should be written up as short “journal article” in that style.  Again, the required text, A Short Guide to Writing about Biology will be invaluable.  The second of the two experiments will involve quite a bit of analysis, combing through the literature, and examination of crystal structures to analyze the data we will generate.
   
   
4. Prepare a presentation describing a key experimental technique in biochemistry  To expose you to more biochemical methods, I’ll ask each of you to prepare a 15 min presentation on a modern method not covered in our experiments. 

I expect you to learn several things:  First, I expect you to be able to competently use equipment and instrumentation, such as pipettes, spectrophotometers, the pH meter, centrifuges, etc.  When learning how to use such things for the first time, keep notes on how they operate in the back of your notebook for reference later.  Second, I expect you to develop the capacity to plan and execute a meaningful experiment.  This means understanding how to include appropriate controls, and how to extract data which is meaningful.  Third, I expect you to become proficient at communicating the results of your experiments in written form.  You should learn how to write an introduction, discuss data in an exact way, how to compose an experimental section.  You are required to purchase the book A Short Guide to Writing about Biology, by Jan Pechinik (7th Edition), which will be a valuable resource to help you prepare papers, talks, posters, resumes and cover letters and science manuscripts for publication.

For each experiment, I’ll hand out materials that describe the goal, describe techniques needed, and how to prepare the reagents required.  Due to the small class size, we’ll work collaboratively to plan and execute the experiments, with the assumption that you will become independent over the course of the semester.

Experiments:

 Beta-galactosidase- purification and kinetics (4-5 classes)

            Purification of Beta-Galactosidase from lacI- E. coli using affinity chromatography,

            Assessment of the purity and concentration of enzyme using SDS-PAGE,

            Measuring Vmax, Km and kcat of B-Gal using the colorimetric substrate ONPG

            Using B-Gal as a reporter gene: bacterial quorum sensing in Agrobacterium tumefaciens    

The Abl oncogene and its inhibition by the human cancer drug Gleevec (2-3 classes)

            Working out a coupled assay for measuring the catalytic activity of Abl

            Measuring the effect of Gleevec on the catalytic rate of Abl – determining the mechanism of inhibition.

            Expression and purification of a clinically derived drug-resistant Abl mutant, measurement of the   inhibitory effects of Gleevec and a second generation drug, Dasatinib

Grading:

Students with disabilities:

In compliance with Section 504 of the Rehabilitation Act of 1973 and the Americans with Disabilities Act, reasonable accommodation will be provided to students with documented disabilities on a case-by-case basis. Students must register with Student Disability Services with the Office of Academic Support Services (607-274-1005, TDD 607-274-7319, acssd@ithaca.edu) and provide appropriate documentation to Ithaca College before any academic adjustment will be provided. 

Academic Honesty:

All the work in this class must be your own, unless stated otherwise.  For many of the assignments, it is expected that you will discuss ideas with your classmates.  Nevertheless, the final work must be your own, and must reflect your own analysis and interpretation. 

Confirmed instances of academic misconduct will result in a zero for that assignment/quiz and referral to the school judiciary system.  Please refer to the Student Handbook for a detailed description of the policies regarding student academic conduct.  If you have a question about what constitutes plagiarism, refer to the following web site:  http://www.ithaca.edu/library/htmls/plagiarism.htm

Course Evaluations: 

Student input is highly valued and is important to maintain high quality instruction.  Course evaluations are mandatory.  You may get a ZERO for a homework assignment or an INCOMPLETE IN THE COURSE if not completed by the due date.  The evaluation will be submitted to the department Administrative Assistant.