BISC411
EXPERIMENTAL MOLECULAR BIOLOGY
Schedule:
The course begins the week of Feb. 7
Week One (Feb. 8): Introduction to the laboratory and safety considerations; Review of mini-prep protocol and plasmids; Lysozyme as a model organism; Assignment of groups; Introduction to the PDB exercise: Finding the lysozyme structure and examining it. Assignment: Research T4 lysozyme and write a 5-6 page summary paper about what you have learned. Be prepared to briefly discuss your paper next week. (5% of final grade)
Week Two (Feb. 14): Summaries due (5% of course grade). Discussion of lysozyme summaries; Mini-prep procedures done; discussion of competent cell preparation and bacterial transformation protocol for next week; Plasmid sequences and research papers distributed. Assignment: Read the papers and be prepared to discuss them next week. Refer to the questions posted on our course website.
Week Three (Feb. 21): Competent cells prepared; T4 expressing plasmid transformed into the competent cells and plated; Paper and restriction enzyme protocol discussed. Note: At least one group member must come down to 020 McKinly the following morning to get their plates out of the incubator, count the number of transformants on each plate, and store the plates in the refrigerator.
Week Four (Feb. 28): Between 3 and 4 of the afternoon before the lab, at least one group member must come to 021 McKinly to inoculate a culture. This will require about 30 minutes maximum. One nice colony from the transformant plates will be selected and one loop of this bacteria will be used to inoculate a 10 ml culture. The culture will be shaken at 37oC overnight. The next day (usual lab day) the culture will be used to prepare plasmid once again as was done in week 2; Final discussion of restriction enzyme patterns; Begin to organize for oral presentation (week 8); Assignment: Read the background information on restriction maps on our course website and do the pencil exercise, answering all questions posed there. This will be included with your first lab report.
Week Five (Mar. 7): Restriction digests done. Agarose gels prepared. Gels loaded and run. Gels analyzed using the documentation system. Assignment: Read protocol for lysozyme standardization assay that you will perform next week.
Week Six (Mar. 14): Discussion of cutting pattern results and pencil exercise. Discussion of lysozyme assays and use of the spectrophotometers; Lysozyme standardization assay done. Groups organize for oral presentation (done in wek 8). Assignment: Lab Report 1, worth 20% of course grade. Due week 9.
Week Seven (Mar. 21): First exam (worth 15% of course grade). Discussion of induction protocol, use of sonicator, and dialysis for week 8. Groups continue to plan oral presentation 2. Final review of requirements for lab report 1, due in week 9.
Spring Break Week
Week Eight (April 4): Oral presentation. (10% of the course grade;. Batch induction; Sonication and clarification of samples for columns; Loading dialysis tubing; During the induction period each group will present their oral presentation.
Week Nine (April 11): Lab Report 1 due (20% of course grade). Columns run. Lysozyme assays run on column samples. Samples set aside for protein concentration (biuret reactions) and protein gel analysis later.
Week Ten (April 18): BSA standard curve. Protein concentrations read on column samples (biuret assay). Discussion of requirements for lab report 2. Assignment: Lab Report 2 (worth 20% of course grade). Due week 13..
Week Eleven (April 25): Discussion of protein purification results. Discussion of polyacrylamide gel electrophoresis. Preparation of gel samples and standards. Discussion of requirements for lab report 3.
Week Twelve (May 2): Polyacrylamide gels run. Gels stained and analyzed. Assignment: Lab Report 3, worth 10% of grade.
Week Thirteen (May 9): Second exam. (worth 15% of course grade). Lab Report 2 due. Discuss polyacrylamide gel results. Review Lab Report 3 requirements again.
Lab Report 3 (10% of course grade) will be due on T, May 17 for section 10 and on R, May 19 for section 11. Note that the report is worth only 10%, not the 20% of the two previous reports. This is because it consists only of the protein gel electrophoresis procedure and therefore is far shorter than the previous reports. You will be instructed where to submit the final report.
Summary of the grading criteria for the course
First lysozyme review paper:
5%
2 long laboratory reports:
20% each
1 shorter laboratory report:
10%
1 oral presentation with summary: 10%
2 exams
15% each
Professionalism:
5%
Oral Presentations
Each group will present one oral presentations with writen summary as part of the requirements for the final course grade. The oral presentation should take 20 minutes and can be presented using visual aids such as powerpoint or overhead projector slides. This, however, is not required. A written summary of the presentation must also be submitted. It is not a research paper but is an outline of the major facts and conclusions from the presentation. The presentation/summary is worth 10% towards the course grade. 70% of this will come from the oral presentation and 30% from the written summary.
Presentation topic: Each group should select a research paper published within the last 5 years that contains procedures using expression plasmids to study protein structure or function, similar to what we will be doing this semester.
A list of research journals is published on-line by the University Library and is a good place to start looking for your paper.
Professionalism
5% of the final course grade is awarded for Professionalism. This reflects the
attitudes and behaviors that each of you display throughout the course. I
assume that everyone will get 100% for this component. The % will lower if I
observe the following:
A. Tardiness. Coming to class late; leaving early.
B. Lack of Cooperativity. Not fulfilling
your part of the group responsibilities.
C. Disrespect. Taking phone calls and text
messaging during class time. Bringing food or
beverages into the laboratory room. Any other
disruptive or inappropriate behaviors that inhibit the class from learning.
You are not only learning the factual and practical aspects of science in this
course but also the expectations of the scientific culture. Therefore we expect
that you will display integrity, maturity, and a sense of responsibility.
Exams
Since the emphasis of the course is on the writing about, speaking about,
analysis and performance of sciencetific processes in
the laboratory, there are only two exams. Each
will consist of objective questions or very short answers related to the
procedures you have performed and any other discussions we have had. Each exam
contributes 15% towards the course grade. There will be no review sessions
or review sheets provided for these exams so read your protocols carefully
and take notes during our lab discussions.
Laboratory
Reports
The 3 laboratory reports you will write will contribute a total of 50% of
the course grade. They are to be individually written. You must
construct your own graphs, data tables, etc. Do not share your work with
your group members. That is academic dishonesty and will be taken to
the student judicial system if it happens.Of course,
the data generated that is used in the reports is obtained as a group and is
shared data. Consult the link on the course website for more details about the
reports. Also, we will spend considerable time as a class reviewing what should
be included in each report and analyzing the results of the procedures before
you actually write your report. We will follow the University regulations
regarding academic dishonesty.