BMB 335: Laboratory in Molecular Genetics
Centre College
Fall 2008
Instructor: Dr. Peggy Richey, Y214, Ext 5319

For the current BMB 335 syllabus, log on to my BMB 335 Moodle page (login required)


Guidelines, Ground Rules, and Grading

The purpose of this lab is to introduce you to basic molecular genetic research techniques. You will be performing experiments which are standard in this field: DNA and mRNA isolation, plasmid purification, restriction enzyme digestion, DNA ligation, bacterial transformation, polymerase chain reactions, Southern blots, DNA hybridization analyses, and DNA sequencing bioinformatics analysis

This lab is scheduled to meet in Y207 on Thursdays from 12:40-3:40 p.m. Due to the nature of the experiments, it will be necessary for you to be in the lab at other times during the week. When and how long you will be in the lab will depend upon how you execute your experiments. Count on being in lab for at least three hours every Thursday and 1-3 hours per week on other days. College policy states that only one "excused" absence is allowed per student in a laboratory course. An excused absence is one that has the written approval of the College (Dean, Associate Dean, Wellness Centre, Director of Athletics). All other absences in this laboratory, including more than one excused absence, will be considered "unexcused". Each unexcused absence will result in a 10% reduction in your general lab performance grade.

You will be working primarily in a group of two and occasionally with another group. You are expected to cooperate and communicate closely with all other students in the class. Efforts should be made to divide group responsibilities so that each person participates fully and equally. You are expected to be familiar with each step in your experiments even if you are not the person who performed the step. I will give instructions for each day's work at the beginning of lab and I expect you to pay close attention to these instructions and ask questions at that time if you are unsure of anything. I have very little patience for students who do not pay attention or who do not do their work with a complete understanding of it.

Cleanliness and order in our laboratory are crucial to the success of this course. You are expected to remove dirty glassware and to keep up with general housekeeping duties throughout the term. Your contribution will be evaluated as part of your "lab performance" (see grading).

We will not be using radioactive materials in the laboratory, however we will be using chemicals and reagents that are very labile and expensive(!), therefore it is extremely important that you wear gloves at all times in the lab, that you use sterile (autoclaved or filter sterilized) supplies and solutions, and that you are very careful in your work. "Raiding" other labs or cubicles is specifically forbidden. Don't do it. Similarly, no materials from this lab are to be removed for use elsewhere without my specific permission.


GRADING

Lab journal: 35%
Final Exam (oral): 30%
General lab performance: 35%


Lab journal: Each student is expected to keep a complete and up-to-date lab notebook. A 3-ring binder is required for this notebook. We will often be working on more than one experiment in the same lab, therefore I recommend that you organize your notebook by experiment. Your lab notes should be written on loose-leaf paper and contained within your binder. Write with a blue or black ball point pen. Information not found in your text will be provided to you as handouts. These handouts should be contained within your binder in sequence with your notes for each experiment. Each page, including the handouts, should be numbered for unambiguous cross reference. By reading this lab notebook, an ordinary person off of the street should be able to perform the experiments exactly as you did-- they should be that clear and detailed. Notes for each experiment should include 1) the purpose of each experiment and each day's activities, 2) the procedures for each experiment in your own words--do not copy from the handouts or the text, 3) the results of each experiment, and 4) a complete analysis of the results of each experiment. Remember that all data should be kept in the notebook and clearly labeled, and you are responsible for including information about procedures that others in your lab group performed for your experiments. I will collect and grade your lab journals on Thursday, October 9 and when you have your final exam on December 9 .

Final Exam: This will be a written exam based on the material covered in BMB 335.

General lab performance: This will be based equally on attitude, lab skills and understanding. Your attitude means your effort, consistency, cooperativeness, enthusiasm, and determination. It also means paying attention, following directions and lab rules and not asking "Is this lab going to take the whole 3 hours?" ( that is an example of a bad attitude). Your lab skills means your neatness, dexterity, caution, accuracy, organization, efficiency and ability to successfully complete your work. Your understanding means your apparent preparation before lab, grasp of theory and familiarity with the protocols, and ingenuity and analytical insight in dealing with unforeseen problems. This is worth a large chunk of your grade and I will be stringent in my evaluation. I will give you a mid-term lab performance grade, when I return your lab journals at mid-term, as well as at the end of the term.

FINAL NOTE: Please feel free to talk to me about any concerns, questions or problems that you may have with this course. It is your responsibility to notify me in the event that a "crisis" prevents you from meeting a deadline, taking a test, or performing a function in lab. Each crisis will be dealt with on an individual basis. If this crisis affects your participation in an experiment, it up to you, not me, to let your lab partners know.

Office Hours: MWF 10:20-11:20 a.m.
TR: 9:00-10:00 a.m.

BMB 335
Fall 2008
Laboratory Schedule  

Lab

Date

Experiments

1

9/4

•  Introduction; Safety

•  VNTR Human DNA Typing experiment (VNTR expt.): isolation of cheek DNA and PCR

•  Store VNTR PCR rxns @ -20 o C on 9/5

 

2

9/11

•  Finish VNTR expt: agarose gel of amplified cheek DNA (Edvo 22, 26)

•  Begin Southern Blot experiment (So. Blot expt): restriction enzyme digestion of genome samples

•  Store restriction digests @ -20 o C on 9/12

 

3

9/18

 

•  Continue So. Blot expt: agarose gel electrophoresis of genome digests, Southern blot of gel

•  Store So. Blots on 9/19

 

4

9/25

 

•  Pre-hybridization & hybridization will be done on Wednesday, September 24.

•  Finish So. Blot expt: pre-hybridization, hybridization & detection

 

5

10/2

•  Begin Cloning Experiment ( Rvt Cloning expt): PCR amplification of Rvt

•  Store PCR rxns @ -20 o C on 10/3

 

6

10/9

 

•  Continue Rvt Cloning expt: Rvt purification & electrophoresis

•  Lab notebook due

 

7

10/23

•  Continue Rvt Cloning expt: ligation

•  Begin mRNA experiment (mRNA expt): total RNA isolation

 

8

10/30

•  Make competent cells in a.m. on 10/30

•  Continue Rvt Cloning expt: transformation

•  Continue mRNA expt: RNA quantification

 

9

11/6

•  Start plasmid prep cultures on 11/5

•  Continue Rvt Cloning expt: plasmid prep, gel and sequencing PCR

•  Store PCR rxns @ -20 o C on 11/7

 

10

11/13

•  Continue Rvt Cloning expt: agarose gel of PCR products

•  Continue mRNA expt: polyA RNA isolation

 

11

11/20

•  Continue Rvt Cloning expt: DNA sequencing reactions

•  Continue mRNA expt: finish polyA isolation, quantify, RT-PCR

•  Store PCR rxns @ -20 o C on 11/21

 

12

11/25

•  Finish mRNA expt: agarose gel of RT-PCR products

 

13

12/4

•  Finish Rvt Cloning expt: DNA sequence data/bioinformatics

 

 

12/9

•  Final exam (1:30-4: 3 0 p.m.) ; lab notebook due

 

email me: richey@centre.edu

last updated July 22, 2010

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