Biology 405…..Cell Biology…..Spring 2005…..T 6-7:50, Th 6-8:50….. Malouf 202
Instructor:
Bonnie K. Baxter, Ph. D., Associate Professor of Biology
bbaxter@westminstercollege.edu
801/832-2345
Office Malouf 208
Office Hours: M 2-3; Tu 8:30-10:30, 12-2
Text:
Alberts, Johnson, Lewis, Raff, Roberts, Walter (2002) Molecular Biology of the Cell 4th ed.
Course Description:
This is intended to be a senior level course for those students who have had general chemistry,
organic chemistry, and genetics. It is a course rich in reading and thinking. Please make sure
that as an enrollee, you have the background, work ethic, and enthusiasm to get the most from
such a challenging class. Students who have had a specialized class, such as Neurobiology,
Developmental, Immunology or Microbiology are assets to our discussion format with
knowledge of specifics, and they often benefit from fitting those specifics into a more general
context. A basic outline of topics follows:
I.
II.
III.
IV.
The Basics
A. Cell Chemistry
B. Evolution of Cells
C. Becoming a Specialized Cell
Methods
A. Isolating/Fractionating Cells
B. Visualizing Cells
Cell Structure/Function
A. Nucleus
B. Membranes
C. Vesicular Transport
D. Organelles of Energy
E. The Cytoskeleton
F. The Cellular Matrix
Cell Regulation
A. Cell Cycle
B. The Meiotic Process
C. Programmed Cell Death
D. Cell Signaling
E. Cancer
Course Objectives:
 Heighten your awareness of the chemical composition of cells and their components.
 Apply an understanding of gene expression and how it affects Cell Biology.
 Develop an understanding of cell structure and function with a molecular perspective.
 Explore complex eukaryotic cell processes and control mechanisms.
 Learn how cell regulation mechanisms are connected to human diseases, especially
cancer.
 Become familiar with reading the primary literature.
 Learn how to apply the scientific method.
Course Requirements:
1. Reading:
We will be reading journal articles, news articles, and the best Cell Biology text available. The
expectation is that you read everything assigned in a timely manner. Our text is simply a
reference, not a book that guides the course. We will take a “chapterless” approach in our
reading that does not adhere to the order prescribed in the book, but will follow the syllabus.
Assignments will be focused on the topic and will take in to account different perspectives
presented in different chapters of the text.
2. Exams:
Exams will be designed to check for understanding of the information we discuss and read. I
will not be checking for memorization, but understanding of concepts, the synthesis and
application of concepts, and critical thinking skills. Therefore do not expect to see questions on
exams that ask you to bring forth minute details from examples in the reading that we did not
cover in our lectures. Do expect to enrich your answers with the reading and discussions from
our classroom. Question “What will be on the exam?” Answer “Everything.”
You are responsible for all reading assignments, activities and lecture material on each exam.
Each exam is cumulative with respect to the material you encounter since the course is designed
for the material to build on basic principals of cell biology. However, none of them are
cumulative in the traditional sense of details pulled from topics studied in the past.
How to study: As you read, listen, and take notes, attempt to build an understanding. Do not list
facts for your self, instead try to link concepts and apply principles. Practice asking yourself
analytical questions about the material or study with a partner who can take turns doing this with
you. If, for example, we are studying cytokinesis, do not simply memorize the steps in the
process. Instead ask yourself or your partner thought-provoking questions, “what would happen
if we restricted ATP,” “What would happen if we did not segregate all of the chromosomes
before the cells split?” I hope my role in your learning will become clear to you as you prepare
for exams: I am your guide through a maze of reading and other learning resources. I will lead
you with questions during lecture. I will model for you methods of approaching material that
you do not understand upon your first encounter. I will be available for clarification of anything
murky.
The exam dates are indicated on the schedule below. Please make note of these dates as you
must be present to take these exams. If you cannot be present because of a legitimate reason,
you must seek approval and reschedule with the instructor prior to the exam date. Vacations are
not excused absences.
3. Journal Club:
Scientists depend on reports in the primary literature for information, not textbooks. We will
learn techniques for reading articles in our journal club. In this format, you will be introduced to
the primary literature in the field of Cell Biology. For each journal club session, which is an in
class discussion, read the article assigned. Then write a (2-3 double-spaced typed pages)
summary which is due in class the day of the scheduled discussion (Late papers will not be
accepted or graded.). The summary should contain the four sections, titled as follows:
1. What was the question being investigated?
Look at the conclusions and determine what the paper is trying to address. Can you
formulate a question that the authors were seeking to answer?
2. What were the results of the authors’ experiments and their conclusions?
List a brief description of the major experiments conducted and the results. What was
concluded from each result? Do not include control experiments, only those that led to
major conclusions. Do include a sketch of the methodology employed for each.
3. What was the key experiment?
Describe the one experiment on which the paper turns. If you feel there are several,
weigh them and determine the one with the most impact. We may disagree on this point,
so make sure that you back up your claim with strong rationale.
4. What is the next experiment?
If you were the authors, what would you do next? If the authors hint at their next move
in the discussion section of the paper, see if you can add an additional possibility to move
this work forward.
You must be succinct, be organized, use proper grammar and spelling, and use proper
referencing. Reading the primary literature is not always easy. Unless you have worked in
research, you may find you have to do some background reading to fully comprehend the subject
matter. Make sure you allow for time to do a thorough job on these assignments. Due dates are
indicated below on the schedule.
4. Laboratory Research:
This class is an integrated lab/lecture course, which means that we will split our block into lab
and lecture as the material demands. Absences can severely impact group-work in lab projects,
and therefore, attendance is part of your lab grade. The most enriching lab experiences are those
which are real. For this reason, we will all be working on research projects during lab times this
semester. We will discuss topics and materials/supplies during the first two weeks of class. You
will be graded based on three products from your group: Interim Lab Report (5% of final grade),
Final Lab Report (5%), and Poster Presentation (5%) (lab attendance will also count for 5% of
your grade). Keep excellent notes to facilitate the process. All of these are described below:
Interim Lab Report
This report must contain:
 Purpose- a clear statement of purpose. Why are you conducting these experiments?
 Hypothesis- predictions about experiments which include rationale: I predict
________because ______.
 Materials and Methods- accurate description of experimental approach, assays and
materials used for the investigations. Include protocols, strains, supplies. Make this
detailed enough that someone could replicate it if you published this report.
 Results- all recorded results, including and visuals necessary to describe your results
(charts/graphs/tables/sketches). Be careful to not include conclusions in the results
section. In this preliminary lab report, please also include experiments that did not work!
This is the place to be comprehensive with your data.
 Conclusions- discussion of results and conclusions drawn from the results described.
 Extensions- future directions, i.e.: next experiment or application of this technique.
Indicate where this work should go.
Your report will be graded for the presence and quality of the sections above, plus these overall
performance criteria:
 Evidence of critical thinking
 Organization, including clear headings
 Neatness and legibility
 Assignment is turned in on time
 Demonstration of an understanding of the scientific process
Final Lab Report
This report should contain the same sections and will be judged by the same performance criteria
listed. However, this report should be polished. Show only your most meaningful data and your
best figures. Leave out those things that did not work unless they were controls. Focus on
whatever conclusions you can draw from your best work. This report must be submitted
electronically.
Poster
Each year in April, the college holds an undergraduate research fair. My expectation is that your
groups will have enough data to contribute a poster to this fair (Apr 15). Your poster will be
graded by me as well as be displayed at the fair, so work hard to make this poster speak for you.
The following are guidelines for making posters:
Content:
Title Board (include the names of coworkers, your prof’s and institution name/address)
Abstract (a concise summary)
Introduction (background and significance)
Materials/Methods and Results (often merged but may be separated, or may be separated
by each figure)
5. Conclusions/Discussion (may be combined with #4 or bulleted at the end)
6. Future Directions, optional (what would you do next?)
1.
2.
3.
4.
Design and Structure:
1. Have an array of visuals to keep the reader interested and attract people to your poster.
2. Keep the words to a minimum. The poster is a visual presentation of information;
therefore, one relies sparingly on verbal print. The presenter must rely on graphs, charts,
tables and pictures to communicate. The verbal text that is used should focus on the main
points of the experimental design, rationale, etc. The poster should NOT be a copy of the
written paper glued onto poster board. Descriptions of complex analyses, etc. are saved
for the complete paper. However, this being said, you need enough text for the poster to
stand alone if it is posted, and you are not in attendance.
3. The reader should be given a map-some visual cue as to how the poster flows. Figures
should be numbered and move them from left to right in general. Boxing figures together
with their legend also helps.
4. Since several viewers may be standing around the poster at one time, the best
organization is in a “panel” format. Start on the left side and move from top to bottom,
then the next set of data should begin at the center-top, flowing to the bottom. The next
set should go top to bottom on the right-most panel. This way each reader may advance
from one side to the next without standing on top of each other.
5. The title should include all of those credited with the work even if they are not at the
presentation. Also, it should show the institutional affiliations, city name, and states.
6. Think BIG. The title banner should be readable from 15 - 20 feet away (72 point or so).
The text should be readable from 3 feet away (24 point or so, headings can be 36 point)
7. If space permits, use first names on title line for authors to facilitate interactions.
8. Refer to your meeting guidelines for more details (size constraints, etc) specific to the
meeting you plan to attend.
Check out this website which has great tips for putting posters together:
http://ublib.buffalo.edu/libraries/units/sel/bio/posters.html
Grade:
Your final grade for the course will be computed with the following weights given to each:
Exams 60% (15% for each of 4 exams), Journal Club 20% (10% for each), Laboratory 20% (5%
each Interim and Final Reports, Poster, attendance).
Schedule:
Date
T Jan 4
Topic
Cell Chemistry
Reading/Assignment Due
Ch 2:pp47-91
Th 6
Evolution of Cells
Ch 1
T 11
Becoming a Specialized Cell
Ch 7:pp375-379, pp415-435,
Ch 21:pp1170-1177
Th 13
Journal Club I
Read assigned journal article
Journal Club Report Due
T 18
Th 20
Academic Monday:
No Class
Exam I
T 25
Isolating/Fractionating Cells
Responsible for all reading
assigned thus far
Ch 8:pp469-481
Th 27
Visualizing Cells
Ch 9
T Feb 1
Nucleus
Ch 4:p197, Ch 6:pp327-335,
pp669-677
Th 3
Membranes
T 8
Exam II
Th 10
Vesicular Transport
Ch 10, Ch 11:pp615-645, Ch
12:pp659-669
Responsible for reading
assigned since the last exam
Ch 12:pp689-709, Ch 13
T 15
Vesicular Transport
Ch 12:pp689-709, Ch 13
Th 17
Organelles of Energy
Ch 14, Ch 12:pp678-686, Ch
2:pp91-108
T 22
Work on Interim Lab Reports
Th 24
Lab Intensive
Feb 28-Mar5
Spring Break
T Mar 8
The Cytoskeleton
Ch 16
Th 10
The Cytoskeleton
Ch 16
T 15
The Cellular Matrix
Ch 19
Th 17
Journal Club II
Read assigned journal article
Journal Club Report Due
Interim Lab Reports Due
T 22
Exam III
Th 24
Cell Cycle
Responsible for reading
assigned since the last exam
Ch 17:pp983-1010, Ch 18
T 29
Cell Cycle
Ch 17:pp983-1010, Ch 18
Th 31
The Meiotic Process
Ch 20
T Apr 5
Th 7
Lab Intensive
Programmed Cell Death
Ch 17:pp1010-1025
T 12
Cell Signaling
Th 14
Cell Signaling
Ch 15, Ch 11:pp645-652
Final Lab Report Due
Ch 15, Ch 11:pp645-652
F 15 *
T 19
UR Poster Session
Cancer
Poster Due
Ch 23
T 26
Final Exam
6:00 PM
Responsible for reading
assigned since the last exam
* note this is not a normal class meeting day; please record on your schedule.