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
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.
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.
|
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.
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%
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 |