Biology 307: Cell and Molecular Biology

Individual cells are able to grow, divide, and respond to stimuli. Because unicellular organisms are able to carry out all the chemical reactions that are consistent with life, an individual cell can be considered the fundamental unit of life. To understand life, therefore, we must understand the molecular assemblies that carry out cellular processes in unicellular and multicellular organisms. The astounding rate at which new information in molecular biology has been accumulating guarantees that only some areas of molecular biology can be discussed in this course. We start by examining how the genetic information is maintained and replicated. We then discuss the molecular assemblies that utilize DNA in the synthesis of biologically-active RNA and protein molecules, and examine how these processes are regulated. Next, we will study membrane structure, the movement of solutes across cellular membranes, and protein and vesicle trafficking within and between cells. Lastly, we will examine how cells communicate with each other, and how the cell cycle is regulated. Prerequisites: Biol 207.

The information below was updated for Spring 2008

I. Course policies

MWF 12:00 – 12:50, Parker 106

Office hours

My official office hours are M 1-2, W 1-3, and F 10-12 and 1-2.

I will be happy to arrange for a different time to meet with you. To do that you may stop by my office and leave a note if I’m not there, send me an email, or leave me a telephone message.

Office 230 Parker Hall; email zpasman@ic.edu; phone 245-3435.

Learning goals

Consistent with the Illinois College and the Biology Department mission statements (see the Illinois College catalog), you are expected to accomplish three broad learning goals in this course. First, you will learn fundamental concepts of biology on the cellular level. Second, you will design, conduct, and interpret experimental results in order to apply the scientific method to solve research problems. Third, you will clearly and effectively present biological information both written and oral in a manner appropriate to the relevant audience.

Textbook

The recommended textbook is Molecular biology of the cell by Bruce Alberts et al., 5th edition. The 4th edition of this text may be used as well. There are many excellent books that cover the same topics, and you are certainly welcome to use them if you wish. Molecular cell biology by Lodish et al., 5th edition, is recommended as well.

Lecture notes.

The lecture notes will be available on the web at the Biol 307 area at http://www2.ic.edu/pasman/. The lecture notes will be provided as .pdf files.

Assignments

There will be four take-home exams (dates indicated on the syllabus), each worth 100 points. The lab grade will be 25% of the final grade for the course. You will have 24-28 hours to complete each take-home exam.

Grading

90-100% A

80-89% B

70-79% C

60-69% D

I do not anticipate using a curve, but I will do so if necessary. I will curve “up” but not “down.” A “+” or “-“ can be used to modify the grades.

Attendance and Participation

You are expected to attend the lectures regularly. Material on the exams will be drawn heavily from the material covered in class, and, in general, those who attend class regularly benefit more from the course. Class participation is expected in the form of debating and answering questions regularly. You are encouraged to ask questions during lectures.

Academic Honesty

I will prosecute any case of academic fraud or dishonesty that I can document. Academic dishonesty, simply put, is representing work as your own when it is not. Also, see the Illinois College honor code. If, in your judgment, an issue might be subject to academic honesty considerations, ask me for clarification as soon as possible, that is, before you might appear as if you acted dishonestly.

Lab

Lab is mandatory for this class. Lab attendance is mandatory and an unexcused lab absence will result in the removal from the course and assignment of a “W” grade. See lab syllabus and description.

II. Lecture syllabus

Week	Topic	Chapter
1/14	Introduction to molecular biology, DNA structure	1,4
1/21	Chromosome structure	4
1/28	DNA replication	5
2/4	DNA replication	5
	Wednesday 2/13, exam 1, chapters 1,4,5
2/11	Steps in gene expression: transcription	6
2/18	Steps in gene expression: translation; regulation of	6,7
	gene expression
2/25	Regulation of gene expression: transcription	7
3/3	Regulation of gene expression: translation	7
3/10	Membrane structure, transport across membranes	10,11
	Wednesday 3/12, exam 2, chapters 6,7
3/17	Spring break
3/24	Transport across membranes	11
3/31	Transport across membranes, protein trafficking	11,12
	Friday 4/4, exam 3, chapters 10,11
4/7	Protein trafficking	12
4/14	Protein trafficking, vesicle trafficking	12,13
4/21	Vesicle trafficking; cell cycle, programmed cell death	13,17
4/28	Cell cycle, programmed cell death	17
	Wednesday 5/7, exam 4, chapters 12,13,17,

III. Lab description

A note on academic honesty: Because you will be working in groups, your results will be shared among group members. In addition, you are allowed and encouraged to discuss your results with anyone. Also, you may ask someone to proof-read your report. Nevertheless, you are expected to write your lab reports on your own. This means that you may not collaborate with anyone on the written reports.

A. Written lab reports.

You are required to write three lab reports in this course (see lab syllabus for dates). Each lab report should include the entire series of experiments performed since the last report you’ve written. Your report should be typed and include the following sections:

1. A title

The title should be concise and relate the essential findings of the series of experiments you are reporting.

2. Introduction

The Introduction section of the report should set the stage for the experiments. After reading the Introduction your audience should be able to understand:

A. The main problems or the goals addressed by the experiments.

B. How, in general terms, these goals will be achieved. Specific details should be included in the Materials and methods and the Results sections.

C. The rationale of the experimental design.

D. Information, which may not be common knowledge to all students, e.g., the bacterial target of ampicilin, or the structure of the arabinose operon.

3. Materials and Methods

Because we’re not going to use a published lab manual, this section absolutely requires that you take good notes in lab. The Materials and Methods section should be written such that other students with a working knowledge of general chemistry and general biology would be able to follow and repeat the experiments. You may divide this section into sub-sections, each containing the information appropriate for a particular analysis, e.g., plates, bacteria growth, gel electrophoresis, etc. You do not need to write how to make a 1M solution or how you poured plates. You do need to report the amount of medium per plate, final reagent concentrations, temperatures, incubation durations, and plate sizes. When in doubt, remember that to repeat the experiments, students can look up “how to” type information, but not the concentrations and amounts you used.

4. Results

Report all the results you obtained. Here, remind the reader the rationale for your experiments. You should state why each experiment was done, and the results. For example, you may state “To prevent the growth of bacteria that did not take up the plasmid during transformation, cells were plated on LB medium + 50 µg/ml ampicilin.” You may refer to the Materials and Methods section as needed. Remember to include quantitative information here, if known, e.g., the percentage of bacteria that took up the plasmid or the percentage of cells that grew but did not express GFP.

5. Discussion

This section should include your interpretation of the data. You should discuss the data you obtained and presented in the Results section while referring back to the problem(s) or goal(s) presented in the Introduction. The Discussion, as well, may be divided into sub-sections, each containing the information appropriate for a particular experiment or set of experiments. You should include the following points:

A. Were the experimental goals met?

B. Would you consider your strategy successful? How would you improve it?

C. If the goals were not met, provide reasons. Be specific (“human error” is not specific).

Back up your statements with reasons. Provide quantitative arguments whenever possible to further buttress your statements. You may provide your opinions as well, provided you state them as such.

B. Oral presentations

Each group will present one lab report during the semester. The presentation should reflect the written lab report due on that day. Group members should divide the presentation duties roughly equally among themselves. Let me know ahead of time what presentation equipment you’ll need (overhead/slide/LCD projector, etc.). Each student will receive an individual presentation grade.

C. Lab Grading

The lab grade is worth 25% of your final course grade. The lab grade is composed of the three written reports and one oral presentation. The first two written reports are worth 100 points, and the last report is worth 200 points, divided as follows:

1. Title 10%

2. Introduction 20%

3. Materials and Methods 20%

4. Results 25%

5. Discussion 25%

Each presentation is worth 100 points, divided as follows:

1. Contents 45%

2. Clarity 45%

3. Style 10%

IV. Lab syllabus

Week	Title
1/21	Competent cell preparation
1/28	Bacterial plate preparation, transformation
2/4	Lab report 1
2/11	GFP expression
2/18	SDS PAGE of GFP I
2/25	SDS PAGE of GFP II
3/3	Lab report 2
3/10	GFP purification 1: cell lysis
3/17	Spring break
3/24	GFP purification 2: anion chromatography
3/31	GFP purification 3: quantitative SDS gel analysis I
4/7	GFP purification 4: quantitative SDS gel analysis II
4/14	GFP purification 5: Western blot analysis I
4/21	GFP purification 6: Western blot analysis II
4/28	Lab report 3