Course Outline for Biology 366

Spring Semester 2007 TR, Period B (9:40 am-11:00 am) Fischman 103 Office Phone: X5394

Instructor: H. Itagaki Office: 107 Higley Email: itagaki@kenyon.edu Home Phone: 614-433-0165

Text: Lodish, H.; Berk, A.; Matsudaira, P.; Kaiser, C.A.; Krieger, M.; Scott, M.P.; Zipursky, S.L.; Darnell, J. (2003) Molecular Cell Biology. W.H. Freeman, New York. 973pp.

Plus outside reading assignments on reserve in ERES or linked to course website.

Date		Subject	Readings
		Introduction
Jan.	16	Overview of Cell Biology, Introduction to Biochemistry	Ch. 1,2
	18	Chemical Bonds, Biological Molecules, Carbohydrates, Lipids, Nucleic Acids, Amino Acids and Proteins	Ch. 2
	23	Protein Structure and Function	Ch. 3; ERES
		Membranes and Transport Processes
	25	Membranes and Organelles; Lipid Rafts	Ch. 5; ERES
	30	Membrane Transport Processes I	Ch. 7
Feb.	1	Membrane Transport Processes II	Ch. 7 (cont'd)
		Energy Conversion in the Cell
	6	Glycolysis and the TCA Cycle I	Ch. 8
	8	Glycolysis and the TCA Cycle II (Grant Proposal Topic Due)	Ch. 8 (cont'd)
	13	Class Cancelled due to Snow
		Material Processing in the Cell
	15	Oxidative Phosphorylation (First take-home exam handed out)	Ch. 8 (cont'd)
	20	Photosynthesis	Ch. 8 (cont'd)
	22	Protein Packaging and Transport I (First take-home exam due)	Ch. 16; Ch. 12.3
	27	Protein Packaging and Transport II	Ch.16 (cont'd); Ch. 17
Mar.	1	Lipid Transport	Ch. 18
	3-18	Spring Break
		Cytoskeleton and Cell Motility
	20	The Cytoskeleton I	Ch. 19
	22	The Cytoskeleton II/Motor Proteins (Grant outline and references due)	Ch. 20
		Cellular Communications and Control Systems
	27	Signals, Receptors and Second Messengers I	Ch. 13
	29	Signals, Receptors and Second Messengers II (Second Take-Home Handed Out)	Ch. 14
Apr.	3	Cell-Matrix Interactions I	Ch. 6
	5	Cell-Matrix Interactions II	Ch. 6 (cont'd)
	10	(No class due to Honors Day)(Second Take-Home Due)
	12	Regulation of the Cell Cycle/Cancer I	Ch.21
	17	No Class
	19	Regulation of the Cell Cycle/Cancer II (First Draft of Grant Proposals Due)	Ch.22
	24	Regulation of the Cell Cycle/Cancer III (Review Grant Proposals This Week)	Ch. 23
	26	Regulation of the Cell Cycle/Cancer IV	Ch. 23, ERES
May	1	Special Topic I (H5N1 Flu)	ERES
	3	Special Topic II (H5N1 Flu) (Final Draft of Grant Proposal Due; Third Take-Home Exam Handed Out)	ERES
	11	Third Take-Home Exam Due, 4:30pm

Biology 366: Cell Biology

Course Outline

Spring Semester 2007 TR, Period B (9:40 am-11:00 am) Fischman 103 Office Phone: X5394

Instructor: H. Itagaki Office: 107 Higley Email: itagaki@kenyon.edu Home Phone: 614-433-0165

Text: Lodish, H.; Berk, A.; Matsudaira, P.; Kaiser, C.A.; Krieger, M.; Scott, M.P.; Zipursky, S.L.; Darnell, J. (2003) Molecular Cell Biology. W.H. Freeman, New York. 973pp.

Plus outside reading assignments on reserve in ERES or linked to course website..

About the Course: This course is designed to be an upper-level introduction to one of the pivotal fields in modern biology. It complements Biology 363 (Molecular Biology) in content, concentrating on the non-genomic aspects of cell function. We will cover topics such as biological membranes and ion channels; various aspects of material transport and regulation; regulation of cell energetics; and cell growth and communication. Aside from the main text, supplemental readings made up of original papers and reviews will be assigned.

Prerequisites: Biology 113 and 114

Grading: There will be 3 take-home exams, each of which constitutes 15% of the grade. A grant proposal (of approx. 20 pages of text plus figures and references) on a topic of your choice will constitute 30% of your grade. One page reviews of 3-4 grants from others in the class will constitute 12.5% of your grade. Class participation/attendance will be 12.5% of your grade. There will be no final exam. A 1/3 grade point penalty will assessed for each day an assignment is late.

The Exams: There will be 3 take-home exams during the course of the semester. They are open-book and open notes and will ask you to apply your knowledge to new situations and problems. They will be predominantly essay questions. One part of each of the exams may entail reading and critiquing a recent short journal article. You will be given one week to complete the take-home exams.

Test Dates: First exam handed out 13 February, due 20 February

Second exam handed out 29 March, due 10 April

Third exam handed out 3 May, due 11 May

The Grant Proposal: The grant proposal is to be on any topic in cell biology that is of interest to you. The topic of the proposal has to be cleared with the instructor. The proposal will be composed of a critical summary of a field in cell biology followed by a proposal of a series of experiments that would answer questions based on the materials in the summary. The entire text should be about 20 pages in length, with references and figures appended to the end. It must be written in the language of a biological scientific paper with proper citations and references in the standard format used in biology. Copies of past grant proposals for reference will be placed on reserve in the Bio Reading Room and in Olin.

Peer reviews of proposals will be conducted double-blind, and will be done on a draft of the proposal during the week of 16 April. A final draft incorporating the referees' comments will be submitted after the review process. Your grade on the proposal will be based on the final draft, rather than on the preliminary draft.

Grant Proposal Schedule: Grant proposal topic due 8 February

Grant proposal outline and references due 22 March

Draft of grant proposal due 19 April

Review panels meet the week of 23 April

Final draft of grant proposal due 3 May.

Academic Honesty: Plagiarism and other forms of academic dishonesty will not be tolerated. Please make sure that you have read carefully the Academic Honesty Guidelines in the 2006-2007 Course of Study, pp. 26-29. If you have any questions, please see the instructor!

Disabilities: If you have a hidden or visible disability which may require classroom or test accommodations please see me as soon as possible during a scheduled office hour. If you have not already done so, you must register with the Coordinator of Disability Services (Erin Salva, salvae@kenyon.edu, x5145), who is the individual responsible for coordinating accommodations and services for students with disabilities. All information and documentation of disability is strictly confidential. No accommodations will be granted in this course without notification from the Office of Disability Services.

Biology 366: Cell Biology

Spring Semester 2007 TR, Period B (9:40 am-11:00 am) Fischman 103 Office Phone: X5394

Instructor: H. Itagaki Office: 107 Higley Email: itagaki@kenyon.edu Home Phone: 614-433-0165

The Grant Proposal and Review Process:

Aside from the writing of articles for publication and peer-review, the other major place where scientists put their ideas to the test is in applying for funding to do the next series of experiments that they want to do over the next 3 years (the typical duration of a grant). This process really tests our abilities to summarize previous work and to outline what we believe are interesting lines of investigation. In essence, we're trying to make a sales pitch for our ideas and our work in the space of about 10-12 single-spaced pages.

These proposals are submitted to one of the funding agencies (for cell biology, typically NIH) by a certain deadline. They are sorted by the field of inquiry and assigned to different "programs", which are subdivisions of the fields. In my case, I send my grants to NIH to the Chemical Senses Program of the National Institute of Deafness and Communicative Diseases (NIDCD), while at NSF, they go to the Integrative Biology Program. Once in the programs, the proposals are assigned to different grants panels, which are groups of specialists from different universities and institutes who pass judgement on the different proposals. In many cases, outside opinion from experts not on the panel will be solicited as well.

For each proposal, panel members and the outside reviewers read it critically to see: if the scientific ideas follow logically from the background information; if the work is interesting and useful and doable in the time frame; if the investigator has the background to be able to do the work; if the investigator has the equipment to be able to do the work; if the amount of money requested is reasonable for the proposed work; and if the investigator has been productive in the past. Each panel member and outside reviewer then writes a one-page, single-spaced assessment of the proposal touching upon what they consider to be the good aspects and the bad aspects of the proposal. Then, they each rank the proposal as being Excellent; Very Good; Good; Fair; or Poor. These scores are tabulated, and the highest scoring proposals are proposed for funding. Typically, in recent years, about 1/10 of the proposals are funded, depending on how well-funded the field is and the stiffness of the competition.

The Assignments:

The Grant Proposal: As writing a proposal really tests one's ability to understand a field and to think about the next series of interesting experiments, it's really a great way to challenge your understanding of biology and your ability to think creatively about it.

The assignment is to write a 20-page double-spaced proposal (equal to a 10 page single-spaced proposal) on any topic in cell biology that interests you. The proposal should be divided up in the following way:

Cover Page: Has the name of the investigator, the title of the proposal, and name of the research institution. This will not count in the 20 page limit.

Summary or Abstract: About 200 words summarizing the background and the proposed experiments and the approach(es) that will be taken in the work. This will not count in the 20 page limit.

Introduction: About a 10 page introduction into the field, with enough detail to be able to put the field into context. This section lays down the background for the proposed work, so if your background is shaky, then it undermines the rest of the proposal. Use subheadings to divide this section into discrete topics.

Research Methods: The rest of the proposal (approx. 10 pages) will deal with outlining the question you will ask, and the experiments that you propose to do to answer the questions, and how you will go about doing the work. This is the place where the proposal will be judged on how reasonable your experiments are, and if they are doable; and if they will answer the questions posed earlier. This part should have the following sections: an overview of the research; details of the techniques and the protocols to be used; data analysis; possible problems that could be encountered, and how these problems will be overcome; and what you believe will be the sequence of the experiments.

Appendices: Figures and the list of references are appended at the end. These will not count in the 20 page limit.

The writing should be in standard non-jargon English as much as possible. The citation format should be the standard Dept. of Biology format used in Biol 109-110. If you are having problems with organizing this assignment, see me and the copies of grants on reserve in Olin or in the Bio Reading Room. As in much of life, neatness and precision counts in writing a grant proposal: sloppy proposals with misspellings, bad grammar, errors of fact, etc. do not make it very far.

The Grant Reviews: Each student will be assigned to a grant panel that will review blind 3 draft proposals from other students in the class. Each student will be asked to write a 1-page summary of each proposal reviewed by the panel, and give each proposal a grade. The reviews will be graded by the instructor.

The grant reviews, with the name of the reviewer deleted, will be given back to the investigator (the student) for incorporation into the final draft of the proposal that will be graded by the instructor.