Molecular Cell Biology at Linfield College
Course Overview Molecular Cell Biology BIOL400
Everything that an organism can do or experience is mediated by the activities of individual cells. In this course, we will explore the structure and function of cells, with an emphasis on the experimental designs and techniques currently used in modern cell and molecular biology labs. Our exploration of cellular structure and function will reveal what we know, and what we do not yet know, about the key biological processes that are fundamental to life.
In this course, we will cover a great many topics in cell biology. While you are expected to acquire a significant amount of “cell biology information”, your primary responsibility is to learn to think like a cell biologist. At the conclusion of this course, you should be familiar with our current understanding of cell structure and function, you should be able to evaluate and design experiments that reveal fundamental properties of cells, and you should be able to competently perform several techniques currently used in laboratories engaged in cell biology research. After the course, you should be in a good position to understand and carry out scientific research that adds to the current state of our knowledge of cells and of biology in general.
To help you to assimilate the principles of molecular cell biology, it is my intention that you will be actively engaged in reading, writing and giving formal and informal oral presentations throughout the semester, in order to familiarize yourself with conventions of scientific communication and to learn to think like a cell biologist. Because we are covering a great deal of information in this course, I expect that you will read the assigned readings before attending class. The work that we do in our class sessions will require that you have knowledge of the material from the readings, especially the Pechenik readings and the primary literature readings. Periodic quizzes and exams will be given so that you can practice assimilating and applying the material that we cover in class. In this course, you will also practice reading, presenting and critiquing primary scientific literature. In the lab, you will carry out original research projects and present your work using the “formats, conventions, and habits of mind appropriate to the major’s disciplinary investigations”, in keeping with the stated goals of Linfield’s MWI courses as described in the course catalog.
I introduced a 4 week, 12 hour genome annotation GEP laboratory module to the existing Molecular Cell Biology BIOL400 course at Linfield College in Fall 2012. Students annotated a region of the D. biarmipes dot chromosome following an introduction to BLAST and the UCSC genome browser, as well as practice with annotating a previously characterized sequence of the dot chromosome of D. grimshawi. Following completion of their gene models based on the D. biarmipes sequence, students presented their results informally to the laboratory group.
After students in the laboratory completed their independent genome annotation projects, the lab transitioned to a 4 week molecular genetics and cell biology module. The purpose of this transition was to allow students to pursue an experimental question that would require them to use annotated genomic information similar to the kind of information that they themselves had just generated, so that they could see the utility of their work directly.
To accomplish this, students first analyzed wild type Saccharomyces cerevisiae and a mutant strain of Saccharomyces that demonstrated sensitivity to high temperature and an endoplasmic reticulum morphology defect that students visualized with a fluorescent fusion protein. Students subsequently generated a yeast genomic library and discussed the ways in which a genomic library can be used to identify a gene of interest in the lab through the process of a genetic rescue (in this case, to identify the gene responsible for the temperature sensitive and ER morphology phenotypes of the mutant strain of yeast). Finally, students chose one representative genomic library clone that they had generated to analyze further. Students performed restriction enzyme digests of the plasmid and DNA sequencing of the genomic insert to analyze their representative genomic library clone. Once students received their sequencing data, they used information and tools from the Saccharomyces Genome Database to characterize the region of yeast genomic DNA contained in their representative genomic library clone.
Students achieve significant understanding of the interrelatedness of investigators' work when these two modules are paired. Students generate relevant annotated genomic data in the course of annotating the D. biarmipes dot chromosome, and then pursue a project that depends upon their utilizing an annotated genome. Ideally, students learn by their participation in these labs that 1) the work of investigators is highly interrelated and interdependent, and 2) that they have made an authentic contribution to original research that is relevant to the scientific community, which uses genomic information in many different ways.