Instructors:
Class:
Mondays, 1-4 pm; Wednesdays 12-4
pm
Office Hours:
By appointment
Text:
Handouts and Web-based
materials.
The following texts are recommended:
Modern Experimental Biochemistry, Boyer,
R.
Dean Fraga, Biology, Mateer 304, x2557, dfraga@wooster.edu
Paul Edmiston, Chemistry, Severance 213, X2113, pedmiston@wooster.edu
Jeffery Myers, Chemistry, Severance 201, x2455, jemyers@wooster.edu
Applied Molecular Genetics. Miesfeld, R. L.
To print out a pdf or doc version of the syllabus click on the appropriate hyperlink.We have decided not to include a copy of the schedule on the web because it is cumbersome to format it using the web management siftware we have.
This laboratory-based course will give students hands-on experience with some experimental methods used in biochemistry and molecular biology. It is organized around a semester-long project in which students will design and work towards specific research goals. This course counts for major credit in Biology and Chemistry.
Prerequisites: Chemistry 112 and Biology 220 (or Biology 201). BMB majors are encouraged to have prior or concurrent enrollment in BMB 331.
Laboratory Spaces
Class discussions will be held in Mateer 305 and in Mateer 308/310 for procedures involving molecular biology techniques. Severance 004 and Mateer 310 will be utilized for procedures involving protein biochemistry.
The course will revolve around a central research project during which important laboratory techniques used in biochemistry and molecular genetics will be learned and performed. The research goal of this year’s course is to explore the evolution of structure function relationships of the phosphagen kinases. The phosphagen kinase family has several family members that can be organized as two large branches, the arginine kinase branch and the creatine kinase branch. There are additional members of this family that map onto these two branches on the basis of structural features and conserved amino acids. These other forms have evolved to be specific for other substrates but still perform the same physiological role. In addition, there are several biochemical features, such as cooperativity and quaternary structure that also map on these two branches in meaningful ways. For example, members in the creatine kinase branch are typically found as multimeric complexes such as dimers or octamers whereas the arginine kinase family members usually function as monomers.
Since we will have essentially two simultaneous versions of the class, we have elected to pursue two different approaches that can broadly fit under the theme of exploring the evolution of structure-function relationships in this family. The question we are trying to answer can be framed as, What are the necessary components for dimerization and negative cooperativity? The first group, Group 1 or THE GENE JOCKEYS, will use bioinformatic techniques to identify conserved regions that may be important for either or both of these two features. The second group, Group 2 or THE MAD MUTATORS OF WOO, will start with a few mutants that have already been made to test a region that may be important in these two processes. This group will purify and characterize these mutants before designing follow-up experiments. In both groups, students will use multiple sequence alignments to determine residues that might be determinants of cooperative ligand binding or dimerization by some phosphagen kinases. These will be or have been mutated using site-directed mutagenesis techniques.
Learning Goals
This course is really about doing science, especially biochemistry and molecular
biological science. The goals listed below are what we hope you will gain
after completing this course.
1. Students will gain a basic understanding of the theory behind bioinformatics approaches and be able to use simple bioinformatics software to query databases, analyze the results and extract useful information.
2. Students will gain a basis understanding of the theory behind simple molecular biological techniques and will be able to design and conduct a typical molecular biological experiment such a site-directed mutagenesis or cloning.
3. Students will gain a basic understanding of the theory behind chromatography and practical understanding of how to use column chromatography to purify proteins.
4. Students will understand the theory behind biochemical analysis and will have gained practical experience in conducting such analyses.
5. Students will be able to keep a properly annotated laboratory notebook.
6. Students will gain additional experience in writing scientific lab reports and simple proposals.
7. Students will gain experience in conducting collaborative experiments.
As mentioned above, due to the size of the class we have divided the class into two large groups. Group 1 will conduct molecular biology experiments first, followed by protein chemistry. Group 2 will conduct protein chemistry first, followed by molecular biology. Students will work individually or in groups of two. The experiments will be performed in a logical order to address the research problem noted above. A tentative timetable is given below. However, since the course is project-oriented, a specific day-to-day timetable of experiments cannot be assigned at the outset. Students will be given several weeks to carry out each experiment. This will allow time for repeating experiments that fail due to “goofs” and periods set aside for experimental design, and discussion.
One faculty member will be the lead person during specific times corresponding to their expertise. Each instructor will lead the class at different times depending on the types of experiments being performed. During these times, the other faculty member may occasionally visit labs and participate in discussions.
Class lectures will be held in Mateer 305. The class will meet in Mateer 308/310 for procedures involving molecular biology and Severance 004 and other research labs for procedures involving protein purification and enzyme kinetics.
You should have one of the above texts (or equivalent) as a reference text. However, design of experiments will be derived from in-lab handbooks, web-based materials, and/or in-class discussions. Much of the procedures and protocols can be found on the web site for the class: www.wooster.edu/biology/wmorgan/bmb303
Grading
Grades will be assigned according to the following weighting scheme:
Quizzes:
40%
Final proposal:
10%
Lab reports (2):
30%
10%
How-to-manual
10%
Quizzes or assignments will be given weekly to test your knowledge of current experiments being performed. Quizzes will examine students’ conceptual understanding of experimental design, methodology and ability to relate weekly results and ideas to the overall research goal. At the completion of both sections (molecular and biochemical) of the course, each student will prepare a formal laboratory report. Students will also keep a laboratory notebook that provides the details for each experiment performed. Guidelines for these assignments are described below and details will follow in handouts provided later in the semester. See the schedule below for deadlines. Throughout the semester, each student team (2 students) will make a presentation to the class. Presentations will require students to explore the scientific literature and place the concepts learned in this course into a larger scientific perspective. More details will be provided later in the semester. These presentations will be given during the first 15 minutes of class.
In place of a final exam each student we are asking that you append a min-proposal to your final lab report. This will be a 2-4 page proposal of what you think the next set of experiments should be and what you might learn from those experiments. The experiments should be sufficient in sscope to occupy a full time graduate student for 1 year. This will be explained in more detail later in the course
Mini-Proposal Guidelines
The scope of this course will be the development of a research project to help understand protein structure and function followed by the performance of relevant experiments to test the hypotheses. The first step in this process is to develop a sound research proposal. This proposal will describe why you are performing the investigation, list the methods that will be used to answer the research questions, defend why these experiments are appropriate, and predict what information may be obtained in the process. The proposal will contain the following sections:
Title. This should be an interesting and concise description of the question to be addressed.
Summary. The project summary should briefly set the context of your research interest, indicate the significance of your research topic, and state the nature of the research problem you wish to examine. This section is generally less than a page.
Background. In the background, you should review the appropriate literature to indicate the significance of your research question, describe any preliminary studies that you've completed, and list the objectives of the research within the context of what is currently known.
Proposed Research. Here you should describe how you will address the research objectives posed in the Summary and Background sections. Indicate what experiments will be carried out and why, anticipate potential difficulties, outline what results you expect to find, and briefly describe how they will be interpreted.
Literature Cited. For instructions on properly citing sources, refer to Pechenik’s A Short Guide to Writing about Biology.
Laboratory Report Guidelines
Two formal laboratory reports will be completed during the course of the semester. These laboratory reports will be organized in a way that is standard to the presentation of scientific work. The sections and the major features expected in each section of your laboratory report are given below. Use third person past tense in your writing. The use of "we" is acceptable, but should be used sparingly. Complete guidelines for the preparation of the lab report are detailed in Pechenik's A Short Guide to Writing about Biology. Published scientific papers will also serve as a good example in how to write and structure your reports.
Title. Spend some time generating a title for your report. A good title should accurately describe the experiment carried out, giving as many specifics as possible in as few words as necessary.
Abstract. The abstract should explain concisely what the goal of the experiment was, what measurements were made, and a summary of the most important results obtained. The abstract must be one paragraph in length.
Introduction. In the Introduction, you should explain why you did the study and provide any necessary background information to explain the significance of the work. Any novel techniques should be explained briefly.
Materials and Methods. In this section, you should describe what you did in sufficient detail so as to permit your experiment to be repeated. However, the writing should be as concise as possible. The key to writing a good methods section is knowing what is an important detail and what is not. For instance, it is necessary to report the composition of the buffer you used, it is not necessary to write that it was prepared using a 500 mL volumetric flask.
Results. In this section, the data is presented using tables, graphs, and words. It is important to point out any particularly interesting trends or data points. Please note that the Results section is:
2. not the place to discuss how the experiment was performed (covered in Methods).
Finally, when appropriate, report the error associated with your data. This can typically be calculated using replicate measurements or other statistical means. Your instructor will point out when this type of analysis should be done.
Discussion. A thorough analysis of the data and conclusions derived from them should be made. The results must be interpreted in the context of the specific questions you set out to address as outlined in the introduction. Questions that should be answered in the Discussion include:
2. How did your results compare with those expected?
3. How might you explain any unexpected results?
4. How might you test these potential explanations?
The Discussion is perhaps the most important section of your laboratory report. Length is not a factor in grading, but depth of thought is critical. Noting other techniques or methods that would be superior or may be helpful in addressing new questions is an example of good information to provide in the discussion.
Acknowledgments. If individuals other than those listed as authors helped in the investigation they should be specifically cited in the Acknowledgment section.
Literature Cited. Cite literature or manuals from which any information or procedures were derived when writing your report or performing the experiments described within.
Lab Notebook Guidelines
For advice on keeping an accurate and informative lab notebook, see "The purpose of laboratory and field notebooks" in Chapter 8, "Writing Laboratory and Other Research Reports," of Pechenik's A Short Guide to Writing about Biology, 4th ed.
For each experiment, your laboratory notebook should include the following as appropriate:
2. experimental design
3. observations and data
4. analysis and interpretation
5. summary statement, including future objectives
Academic Integrity
All students are expected to read and honor the Code of Academic Integrity, which is printed in The Scot's Key. As stated in the preamble, adherence to the Code insures that the College is a community that promotes "the fullest learning by everyone."
The principles of the Code of Academic Integrity are excerpted here:
Under the Code of Academic Integrity, a student will not:
A. give, offer, or receive aid other than that specifically allowed by the professor on any course work or examination;
B. knowingly represent the work of others as his/her own; (This includes, but is not limited to, plagiarism...)
C. falsify data;
D. violate the spirit of the Code expressed in the Preamble.
Plagiarism is defined in the Code of Academic Integrity as follows:
To use or imitate the language, ideas, or thoughts of another person and represent them as one's own is to commit an act of plagiarism. This is true whether the material used is only a brief excerpt or an entire paper or article and whether the original source is the work of another student or some publication.
For a more complete description of plagiarism, consult The Scot's Key and A Short Guide to Writing about Biology. For examples of appropriate and inappropriate paraphrasing, consult A Writer's Reference (3rd ed., p. 261; on reserve in Gault/Andrews Library).
Note that while some assignments may be done in collaboration with a classmate, most should be done individually. If you have any questions about your assignment, plagiarism, or the Code of Academic Integrity, always ask your instructor!