Biology 307: Cell and Molecular Biology
Lecture
MWF 12:00 – 12:50, Parker 107
Lab
M 1-3:50 or H 8-10:50
Office
hours
My
official office hours are M 10-11, T 10-11, W 10-12, H 1-2, and F 10-11.
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 |
|
1/12 |
Introduction
to molecular biology, DNA structure |
1,4 |
|
1/19 |
Chromosome
structure |
4 |
|
1/26 |
DNA replication
|
5 |
|
2/2 |
DNA
replication |
5 |
|
|
Wednesday
2/4, exam 1, chapters 1,4,5 |
|
|
2/9 |
Steps
in gene expression: transcription |
6 |
|
2/16 |
Steps
in gene expression: translation; regulation of |
6,7 |
|
|
gene expression |
|
|
2/23 |
Regulation
of gene expression: transcription |
7 |
|
3/2 |
Regulation
of gene expression: translation |
7 |
|
3/9 |
Membrane
structure, transport across membranes |
10,11 |
|
|
Wednesday
3/11, exam 2, chapters 6,7 |
|
|
3/16 |
Spring
break |
|
|
3/23 |
Transport
across membranes |
11 |
|
3/30 |
Transport
across membranes, protein trafficking |
11,12 |
|
|
Wednesday
4/1, exam 3, chapters 10,11 |
|
|
4/6 |
Protein
trafficking |
12 |
|
4/13 |
Protein
trafficking, vesicle trafficking |
12,13 |
|
4/20 |
Vesicle
trafficking; cell cycle, programmed cell death |
13,17 |
|
4/27 |
Cell cycle, programmed cell
death
|
17 |
|
|
Exam
4, final exam period |
|
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. Your
presentation should be in an electronic format, using software such as
Microsoft PowerPoint or Apple Keynote.
Each student will be awarded an individual presentation grade.
The lab
grade will be 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. Each report will be
graded according to the guidelines above and 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.
The grading rubric will be
A. (10%) Title
1. The title
was descriptive _______
B. (20%) Introduction
2. The
introduction contained a sufficient amount of relevant
background information _______
3. The
introduction identified the question and/or hypothesis
that is/are being addressed in this
study _______
C. (20%) Methods
4. The
methods were described clearly _______
5. The
methods included sufficient detail _______
D. (20%) Results
6. All
relevant data were included _______
7. Graphs
and tables were used appropriately _______
8.
Appropriate conclusions that address the questions/hypothesis
(see item 3 above) were drawn _______
9. The
results were explained (why did your experiments produce
these results?) _______
10. The
presenter exhibited confidence and clear enunciation _______
Week
|
Title
|
|
1/19 |
Bacterial plate
preparation |
|
1/26 |
Competent cell
preparation, transformation |
|
2/2 |
Lab report 1 |
|
2/9 |
GFP expression |
|
2/16 |
SDS PAGE of GFP I |
|
2/23 |
SDS PAGE of GFP II |
|
3/2 |
Lab report 2 |
|
3/9 |
GFP purification 1:
cell lysis |
|
3/16 |
Spring break |
|
3/22 |
GFP purification 2:
anion chromatography |
|
3/30 |
GFP purification 3:
quantitative SDS gel analysis I |
|
4/6 |
GFP purification 4:
quantitative SDS gel analysis II |
|
4/13 |
Easter break |
|
4/20 |
GFP purification 5:
Western blot analysis |
|
4/27 |
Lab report 3 |