Instructor: Jamie Havrilak
Spring 2012
Cell Biology
University of Cincinnati
College of Medicine
Instructor
Information:
Course Number: Biol-306
MWF 9:00-9:50am (3 credits)
Email: Havrilja@mail.uc.edu
Phone: 513-636-2937
Office Hours: MWF 10:0011:00a
What is going on in this picture?
The picture above was created using fluorescence microscopy, a
technique you will learn about (and be performing if you take the lab)
in this class. This technique allows us to see the location of various
proteins within a cell by staining them with different fluorescence
labels: microtubules in red (TRITC), DNA in blue (DAPI) and
microfilaments in green (FITC). Can you determine which phase of
mitosis is occurring in the upper-most cell pictured above?
What is this class about?
Daily Syllabus
This course will focus on the structure and function of eukaryotic cells.
We will examine many different areas of cell biology, including
membrane and organelle structure and function, cell-cell
communication and signal transduction, as well as discuss various
scientific techniques used in modern cellular biology research.
Additionally, human diseases will be used as models for understanding
cell function and the effects of the disruption of normal cellular
processes.
Meet your instructor!
Why take this class?
Office Location: CHRF 4503
Links:
Assignments
Prerequisites:
This course is intended as an
upper-level
course
for
majors/minors
in
the
biological sciences, and is not
recommended for non-biology
majors seeking to fulfill their
science requirement.
Required Classes:
BIOL-101 Ecology, Evolution
and Heredity
BIOL-102 Cell and
Organismal Biology
You will not only be gaining a foundational knowledge in this class;
you will be exposed to some of the research that is currently ongoing in
cellular biology, while learning about the various techniques cell
biologists utilize to understand cell structure and function. Whether
you plan to directly enter the workforce or go on to medical or
graduate school, this course will give you some of the information and
skills you will need for your future endeavors.
We will use various human diseases as models for understanding cell
function and what can happen when the normal cellular processes are
disrupted. This will enable you to relate basic science and knowledge
that you have from this course and others to clinically relevant ideas.
Science is a process that requires the constant thought and feedback
from other scientists; group discussions and homework will contribute
to that process. This course is structured for you to have more
opportunities to express and discuss your ideas with others.
S
t
u
BIOL-306 Cell Biology Syllabus
R. Lue & A.
Viel/Harvard
University and J.
Liebler/XVIVO,
LLC
Student Learning Outcomes:
Upon completion of this course students will be able to:
1. Illustrate how the structure of a protein affects its
function.
2. Identify components of the cell and describe their
structure and functions(s).
3. Describe experimental techniques that are used to
analyze cell structure and function.
4. Examine biomembrane structure and function and
distinguish between the various methods of
transmembrane transport/translocation.
Course Materials:
“Clicker”: If you do not already have one, please
purchase one from the bookstore
Lodish, et al. (2008). Molecular Cell Biology, 6th ed.
New York: W.H. Freeman and Company.
5. Compare and contrast the mechanisms used by cells
to transport proteins.
6. Distinguish between the various mechanisms used for
cell movement.
ISBN-13: 978-0-7167-7601-7; ISBN-10: 0-71677601-4.
One of the reasons I chose this text for this class
is because it integrates information about relevant
diseases into each of the chapters.
The book be purchased easily from Amazon.com
or any other online textbook website.
7. Identify the different signaling pathways and illustrate
various mechanisms used by cells in signal transduction.
8. Recognize how disruption in the normal cellular
processes results in specific diseases.
9. Analyze a scientific article.
How will your learning be evaluated?
Exams will account for 75% of your grade. Remember that this is an upper level
course and material from the various chapters will build upon each other, so in this
sense exams will be cumulative.
Exams
75%
Homework
10%
Homework assignments will be 10% of your grade and will be described in detail
on blackboard. See also page 5 for a list of assignments and dates they are due.
Quizzes
10%
IF-AT group quizzes will account for 10% of your grade. Your lowest grade can
be dropped. What is the IF-AT? See page 2.
Participation
5%
The remaining of your grade 5% will come from your participation in class
discussions/journal clubs, group work and clicker questions.
Grading Scale
A
93-100
A90-92
B+
87-89
B
83-86
B80-82
C+
77-79
C
73-76
C70-72
D
60-69
F
<60
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BIOL-306 Cell Biology Syllabus
What is the IF-AT?
This class will utilize the IF-AT testing system as quizzes for each unit. Groups will be given a scratch off card that
correspond to multiple point questions, and you scratch off your answer. If your answer is correct, a symbol will
appear indicating that you have the correct answer. If this answer is wrong, you choose the next answer you
believe to be correct until you get the right answer.
Why use the IF-AT instead of a normal quiz?
The IF-AT provides immediate feedback. It allows you to keep answering until you get the correct answer, which
ensures that you get the right answer immediately (instead of waiting a week for me to grade quizzes). This
immediate feedback facilitates both learning and retention of the material being tested. Plus, its fun!
How will these be graded?
You will get 5 points for getting the correct answer on the first try, so be sure to think about your answer fully
before beginning to scratch-off the letters. After that, 3 points will be given for a correct answer on the second try, 2
points for the third try, and zero for the fourth try.
Class Policies
Attendance
I will not be taking attendance every day, but
remember that participation in lectures (answering
clicker questions) and group work will affect your
grade. Importantly, students will still be responsible for
knowing material covered in any classes they happen to miss
and must make up work that was done and turned in during
class. You cannot make up missed clicker questions,
quizzes or exams. A hard copy of your homework is
due before class starts. If you will be absent from
class, please have a friend or group member hand
your homework in for you.
Late Assignments/ Make-Up Policy
Assignments will be penalized by a 10% reduction in
their grade for every day they are handed in late. IFAT quizzes will be given in class after every unit and
cannot be made up. However, you will be able to
drop your lowest quiz grade.Attendance at the exams
is mandatory. Please look ahead at the scheduled date
for the exams and plan accordingly.
Academic Dishonesty/Plagiarism
The University Rules, including the Student Code of
Conduct, and other documented policies of the
department, college and university related to
academic integrity will be enforced. Any violation of
these regulations, including acts of plagiarism or
cheating, will be dealt with on an individual basis
according to the severity of the misconduct. I take this
issue very seriously. Any violations (cheating, plagiarizing,
etc.) will not be tolerated, and will result in a zero for that
assignment/exam.
Blackboard and Email
Please be sure to check your email and Blackboard
regularly, as I will be communicating with you through
these methods.
Assignments will be posted on
Blackboard, as well as discussed in class, and a hard
copy should be turned in at the beginning of class.
Additionally, feel free to email me with any
question/concerns, or make an appointment to meet
with me in person. Please include your name, course
number and section number in all emails.
Use of Electronic Devices
Clickers will be utilized daily, and therefore you should
bring them to class every day. The use of other
personal electronics is not permitted during class. This
includes but is not limited to laptops, cell phones,
iPads, etc. If there is a class activity that requires the
use of a computer I will inform you ahead of time.
Special Needs Requirements
If you have any special needs related to your
participation in this class, including identified visual
impairment, hearing impairment, physical impairment,
communication disorder, and/or a specific learning
disability that may influence your performance in this
course, you should meet with the instructor to arrange
for reasonable provisions to ensure an equitable
opportunity to meet all the requirements of this course.
At the discretion of the instructor, some
accommodations may require prior approval by
Disability Services.
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BIOL-306 Cell Biology Syllabus
Tips to be
successful in
this class!
Check blackboard
regularly (before and
after class) to check for
the daily wrap-up, as
well as for information
on the topics, readings
and assignments for
next class.
Turn in your
homework on time!
Start your homework
assignments/readings
in advance so that you
have plenty of time to
ask questions.
Participate in
answering clicker
questions! Not only do
they count as part of
your grade, but they
also act as a selfassessment tool you
can use to determine
what areas you may be
having trouble with.
Schedule of Topics, Journal Clubs and Exams
Below is a flexible schedule of what we will cover in class and the homework that is
due. This schedule may change depending on how quickly we move through the
material, and I will notify you of any changes in class and via blackboard. Please read
through the respective chapters before class. Additionally, please bring your clicker to
every lecture.
Unit 1
Life begins with cells
Chemical building blocks of cells
(Chapter 1)
(Chapter 2.2)
Protein structure and Function
(Chapter 3)
Visualizing and culturing cells
Journal Club 1
(Chapter 9)
Biomembrane structure
(Chapter 10)
Transmembrane transport
(Chapter 11)
Unit 2
Unit 3
Unit 4
Unit 5
Unit 6
Moving proteins into membranes and organelles
Journal Club 2
Midterm
Midterm Exam (Date)
Fall break
(Chapter 13)
Unit 7
Vesicular traffic, secretion and endocytosis
(Chapter 14)
Signal transduction
(Chapter 15)
Signaling pathways
Journal Club 3
(Chapter 16)
Cell organization and movement
(Chapter 17)
Microtubules and intermediate filaments
(Chapter 18)
Unit 8
Unit 9
Unit 10
Unit 11
Unit 12
Regulation of cell cycle
Journal Club 4
(Chapter 20)
Cancer
(Chapter 25)
Unit 13
Unit 14
Journal club group presentations/discussions
Final
Final Exam (date)
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BIOL-306 Cell Biology Syllabus
Assignments
Experimental Technique Assignment
Due Feb 15, 2012
For this assignment you will need to find a paper form the primary literature that utilized one of the
experimental techniques we discussed in class. Please provide a copy of the paper when you turn in the
assignment. There is no length requirement for this assignment, but be sure to completely address all of
the points listed below.
To complete this assignment:

Use Pubmed or another search engine (such as science direct) to find an appropriate peer-reviewed
paper. If you are not sure if the paper you have chosen is suitable you can bring me a copy of the
paper to look at. (If you decide to have me look at the paper before hand, please bring it to me no
later than Feb 8th)
 Choose a paper that you can read and understand (and interests you!).
 Be sure it includes one of the techniques discussed in class (such as a Western Blot,
chromatography, immunohistochemistry, cell culture, gel electrophoresis, etc)
 Read the paper and get an overall idea of what the topic and central questions/hypothesize are.
 Include 1-2 paragraphs describing the overall question/hypothesis and why it is important.
 Chose 1 or 2 figures from the paper that utilize 1 or more of the techniques discussed in class.
 Describe the experimental question being addressed in this figure and how this will help answer the
overall question/hypothesis.
 Give a detailed explanation of what technique they are using and why they are using that it.
 Include a summary of their methods and describe the steps for the technique they used. (What
antibodies did they use, what is their model system, etc)
 Explain the results and the conclusions they made based on these results.
 Did the results support their hypothesis?
 What other techniques could they have used to answer the same question (if applicable)?
This assignment will address course SLOs 3 and 9. The purpose of this assignment is for you to describe
(in detail) an experimental technique that we have discussed in class and illustrate a real-world
application. This assignment will also enhance your ability to analyze a scientific article and to think
about why they are using a particular method, what the results mean and how it will help them answer a
specific question.
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BIOL-306 Cell Biology Syllabus
Assignments
Disease Presentation
One of the course learning outcomes is to recognize how disruption in the normal cellular processes
results in specific diseases. Throughout this class we will discuss human diseases as a model for
understanding cell function and the effects of the disruption of normal cellular processes. Now you and
your group will have the opportunity to investigate this in further detail for a disease of your choice.
Topics must be approved by me in advance however, so that each group discusses a different disease.
Groups will present their projects to the class on the assigned days. We will have time in class to discuss
this project and I will answer any questions you may have.
For this assignment you should choose a disease and prepare a detailed power point presentation (15-20
minutes), which includes (but is not limited to) the various aspects discussed below.
You must have at least 6 sources (in addition to the text), which should come from both web sources and
peer-reviewed articles. Remember to include citations throughout the presentation, and a slide with
references at the end.
Please address the following questions in your report:






What proteins, signaling pathways, etc are disrupted in this disease?
How does this disruption results in this diseases? (Is there a misfoleded protein? Is the regulation of
this protein disrupted? How?)
What techniques are used to study this disease? (Do they use immunohistochestry to show a
disruption in the location of this protein? Do they use cell culture techniques? These are questions
that can be answered in the primary literature. )
What is not known about this disease?
Are there any therapies available? If yes, what are they? Are they effective?
Can they treat this disease at the cellular level?
Some other aspects you might address include:



How was the disease discovered?
How many people suffer from this disease?
How do they get this disease? Is it inherited or caused from environmental factors?
It is important that you pay attention and stay engaged while other groups are presenting, as you will be
answering questions based on the presentations.
Groups should submit 3-5 questions to me the day before their due date that the class should be able to
answer based on their presentation. Please provide me with a copy of both the questions and answers.
How will this be graded?
The presentation itself will count for 75%, with both the content and the quality of the presentation (oral
and quality of the slides) being considered.
The quality of questions that your group provides to go along with your presentation will account for 5%
of your grade.
Correctly answering the questions based on the presentations will account for 15% of your grade.
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