BIO 305, Cell & Molecular Biology, Fall 2012 CRN 14303
11:00– 12:15pm Tue & Thurs, 175 Mark Jefferson
Instructor:
Dr. Anne Casper
anne.casper@emich.edu
http://people.emich.edu/acasper2
Office:
Office phone:
Office hours:
401S Mark Jefferson
487-0212
2:30-4:30 Tuesdays
Noon-2:00 Wednesdays
Other times by appointment
Class web site:
Required supplies:
On EMU-Online
Essential Cell Biology, 3rd edition, Bruce Alberts (Garland Science Publishers)
i>clicker (either version of the clicker shown in the photo below is OK)
Course Description
This is a lecture course that examines the basic unit of structure and function in life, the cell. The course
uses concepts of molecular biology to survey aspects of cellular function, such as metabolism,
intercellular communication and cell division.
Prerequisite: CHEM123/124 and C or better in BIO301
Course Objectives
Students will investigate the structure and function of cells and organelles via lecture, discussion and
review of the primary literature. At the completion of this course a student will be able to:
• Demonstrate a basic understanding of fundamental cell biology topics such as cell membranes, cell
signaling, the flow of energy in a cell.
• Effectively read and comprehend scientific literature and demonstrate this knowledge in the form of an
annotated bibliography.
Course Requirements
Prerequisites – The pre-requisite for this course is a C or better in Genetics (BIO 301). I expect that
you understand the material taught in Biology 110, Intro Chemistry and Genetics. I suggest that you
review basic chemistry in the beginning chapters of Essential Cell Biology, specifically, pages 39-49.
Attendance – Students are responsible for all material presented in class, including announcements
about changes in course procedures. Outlines and slide presentations for the lectures will be available for
downloading from EMU-Online. Always print out the outline for a lecture before coming to class. On
planning your time, a fair calculation should take into account the need to spend at least 2 hours of study
for each hour spent in class. An absence (whether excused or unexcused) does not release you from any
assigned work or due dates. Collection of missed class materials is your responsibility.
Textbook –Essential Cell Biology: An Introduction to the Molecular Biology of the Cell (3rd edition)
Authors: Bruce Alberts, Keith Roberts, Julian Lewis, Karen Hopkin, Alexander Johnson, Peter Walter,
Martin Raff, Dennis Bray
Publisher: Garland Pub, 2010 ISBN 978-0-8153-4129-1 (hardcover) OR 978-0-8153-4130-7 (paperback)
Use the emphasis that I place on material in lecture as a guide to the extent of detail you should
focus upon in the text. You are expected to read the assigned chapters or chapter sections
before each class.
Clicker – An i>clicker is required. Bring your clicker to every lecture. I ask questions in class
that can only be answered with your clicker. I will ask several questions in each lecture, and two
of the questions from each lecture will be selected for grading. Each graded question is worth 0.5
point. Clicker points start accumulating on Sept 11. Prior to Sept 11, you must register your
clicker online. To register, go to www.iclicker.com. In the clicker registration, enter your E# as
your Student ID. There are no make-up clicker questions.
Exams – Four exams worth 100 points each are offered and three of these exams MUST be
taken. No make-up exams will be given.
Grading
Extra Credit – If you attend an approved seminar (see last page of the syllabus) and write me a
paragraph about what you learned (minimum length 250 words, maximum length one page), I will award
you up to 3 extra credit points. Fewer points may be awarded based on the quality of the paragraph you
write. The maximum number of extra credit points that you can earn is 15.
Grading –The contributions of each aspect of the course to your final grade are as listed below:
Exams (4 given, best three counted)
Annotated bibliography
i>clicker questions
Total
300
25
25
350
When checking ‘gradebook’ in EMU Online, pay no attention to the calculation of ‘course
average to date’. Since I sum only the best three exam scores, this average may be incorrect.
Be sure to calculate your own course average.
GRADING SCALE FOR BIOLOGY 305
A
AB+
B
B-
92% and above
90 - 91%
88 – 89%
82 – 87%
80 – 81%
C+
C
CD+
D
78 – 79%
73 – 77%
70 – 72%
68 – 69%
62 – 67%
Course Policies
Cell phones and pagers – All cell phones and pages must be turned off and put away during class
time.
E-mail, EMU-Online, and computer use – I expect you to check your EMU e-mail and the
course EMU-Online website on a regular basis for course-related messages and assignments.
Grades will be posted on EMU-Online. This syllabus, lecture outlines and PowerPoint images may
be downloaded from EMU Online.
Academic Honesty – I take academic honesty very seriously. All work must be your own. Students
found cheating or plagiarizing will earn a grade of zero on that particular exam or assignment, and may
receive a failing grade for the course. A permanent record of any incident will be filed with the EMU
Office of Student Judicial Services. Please review the EMU Student Conduct Code
(www.emich.edu/policies/chapter8/8-1.html) for more details. If you are unsure whether a particular
action constitutes academic dishonesty, please discuss with me.
** Important dates **
(Mark these on your calendar early in the semester!)
• Exam schedule:
Exam 1:
Exam 2:
Exam 3:
Final Exam:
Oct 2, 2012
Oct 30, 2012
Nov 20, 2012
Dec 18, 2012
• Annotated bibliography by Nov 20, 2012 must be uploaded to Turnitin.com and an identical hardcopy submitted to me
FERPA— All files, records, and academic work completed within this course are protected under the
Family Educational Rights and Privacy Act. Any materials you submit in this course, as well as your name
and other identifying information, will not be viewable by guests or other individuals permitted access to
the course. The exception will be only when you have given explicit, written, signed consent.
SPECIAL NEEDS – If you wish to be accommodated for your disability, policy #8.3 of the EMU Board of
Regents requires that you must first be registered with the Disability Resource Center (DRC)) in room
240-K Student Center (telephone 734.487.2470). You are encouraged to register promptly, as you will
only be accommodated from the date you register forward.
The Student and Exchange VISitor Statement (SEVIS) requires students with F and J visas to report the following to the Office of
International Student, 229 King Hall within ten days of the event:
Changes in your name, local address, major field of study, or source of funding
Changes in your degree-completion date
Changes in your degree level
Intent to transfer to another school
Prior permission from OIS is needed for the following:
Dropping all courses as well as carrying or dropping below minimum credit hours
Employment on or off-campus
Registering for more than one online course per term (F visa only)
Endorsing I-20 or DS-2019 for re-entry into the US
Failure to report may result in the termination of your SEVIS record and even arrest and deportation.
Annotated bibliography assignment
Cell biology is one of the most active and growing fields in the life sciences. The purpose of this annotated
bibliography assignment is to provide you with an opportunity to explore the scientific literature that has been written
about a cell biology topic of your choice.
While you may not be familiar with the annotated bibliography format, it is frequently used to provide the starting
place for someone wishing to explore the scientific literature on a certain topic. This critical skill of identifying and briefly
summarizing the relevant literature will suffice to meet the course goal of introducing you to the scientific literature in cell
biology.
Your annotated bibliography should include a brief summary to introduce the topic you have chosen, and a summary
and analysis of three articles from the peer-reviewed scientific literature. At least two of these articles must have been
published since 2009. Review articles, if they are published in a peer-reviewed scientific journal, are permissible. Be sure
that you understand the distinction between a peer-reviewed article (which has been read and approved of by experts)
and a literature review (which is a summary and may or may not have been peer-reviewed). Just putting "review
[publication type]” in your search in PubMed will not guarantee a peer-reviewed article. It will guarantee a literature
review. If you have questions about the acceptability of a reference, please ask. For full-text, pdfs of medically-oriented
articles, try “Pub Med Central” or Google Scholar for a variety of peer reviewed literature.
If you would like assistance with writing, I recommend you visit the EMU University Writing Center. You can learn
more about the writing center and their services online at http://www.emich.edu/english/writing-center.
Brief summary (150 words max) (3pt)
• States what the topic of your annotated bibliography is
• Highlights what are the important findings in this topic
• Indicates which articles in your annotated bibliography support which important findings
References (6pt)
• Includes three references
• All references must be from peer-reviewed scientific journals
• Two of the references are recent (published since 2009)
• All articles are relevant to the topic of the bibliography
Formatting (3pt)
• For each annotation, you should first provide the full citation for the article. Be sure to include the authors’ last names
and first and middle initials, the year of publication, the title of the article, the name of the journal, the volume, and the
page numbers. Be consistent with the punctuation/format of all of your citations.
Summary and analysis of each article (each 150 words max)(10pt)
• Includes 2 or 3 main points of article
• Effectively describes why each article is appropriate for inclusion in the bibliography
• Explains what information this article adds that is not present in the other articles that you annotated
First page of each reference (3pt)
• Submit a hard-copy of the first page for each article
Spelling and grammar (-5pt)
• I may deduct up to 5 points from your total score for poor spelling or grammar.
TOTAL (25 Points Possible)
This assignment is due to Turnitin and to me on or before November 20, 2012. Note that a hard-copy of the
assignment and a printout of the first page of each article is due to me by that date as well. A late penalty of 5pt/day will
be assessed. This late penalty applies to both the hard-copy version for me AND the electronic submission
to Turnitin.com.
I recommend that you upload your first effort of the annotated bibliography to Turnitin.com a few days before the due
date. This will allow you to determine if any of the report is judged to be plagiarized by Turnitin.com. Revise your
bibliography to eliminate any plagiarism and re-submit it to Turnitin.com.
BIO 305 use of Turnitin.com
Plagiarism is a common problem for students writing papers. While students are often confused
about what constitutes plagiarism, as a student, it is your responsibility to be aware of plagiarism and
how to avoid it. EMU has a web page dedicated to the subject: www.emich.edu/halle/plagiarism.html.
This page has many links that provide different definitions and perspectives, and describes the
consequences of plagiarism should it be processed through Student Judicial Services.
With the increasing use of electronic file access and the ease of cutting and pasting from other
sources, students sometimes inadvertently or deliberately engage in plagiarism. In an effort to educate
students and to prevent plagiarism, EMU has subscribed to a plagiarism assessment service called
turnitin.com. This service checks for originality by comparing submitted work with other entries in its
extensive database.
When a paper is submitted to turnitin.com for originality assessment, several things happen. First, a
report is generated for both the instructor and the student that highlights passages with a high degree of
wording similarity to other entries in the database. It is the student’s responsibility to make sure that any
plagiarism identified (highlighted sections) is thoroughly revised, and paraphrased using his/her own
words. Second, the submission becomes a part of the database and will be used in the assessment of
future submissions. It is worth noting that student name/identity is not disclosed in any future
assessments.
I recommend that you submit a working draft of your annotated bibliography to turnitin.com for
originality assessment several days prior (at least!) to the due date. This allows plenty of time for
revisions, in the event that plagiarism is detected. Because each writing assignment will be submitted
twice, it is very likely that the originality assessment service will find a high degree of similarity between
the final version and the draft, do not worry about that. It takes time for the originality assessment to
run, so try not to wait until the last minute and make sure to allocate at least 30 minutes for this process.
Once the writing assignment has been revised, and is ready to be graded, the final version must also
be submitted to turnitin.com. The final version submitted to turnitin.com must exactly match the final
version submitted in hardcopy to me for grading.
How to access Turnitin.com
You may be familiar with turnitin.com through use of this tool in other courses, and therefore already
have an account. If not, registration is simple. To register for access to turnitin.com, visit the following
URL: www.turnitin.com. To enroll, follow the “Create Account” link near the upper right-hand corner of
the screen. On the next screen, select “Student” and enter the requested information. You will need the
Class ID and Class enrollment password:
class ID:
5482814
class enrollment password:
biology
In order to create a new account, you will also need to enter your e-mail address and enter your own
personal password.
Course schedule
The following is a general ordering of lecture topics. It is subject to additions and deletions. You are responsible
for keeping up with any changes that may be made.
LECTURE TOPICS
Case Study: Take Two and Call Me in the Morning
ASSIGNED READINGS from
Essential Cell Biology 3rd edition,
Alberts et al.
11-25
Proteins
structure, function
119-141; 166-167
Energetics
Enzymes
regulation
Energy flow in cells
photosynthesis overview
glycolysis, Citric acid cycle, ETC
Article: COX deficiency
Membranes
membrane structure
membrane proteins
cell-to-cell junctions
Cellular signaling
hormones, neurotransmitters
second messengers, response cascades
Article: Isolated Growth Hormone Deficiency
Case Study: The Campus Coffee Shop
Membrane Transport
channels and carriers
nerve transmission
Case Study: Bad Fish
Traffic inside the cell
protein modification and sorting
cytoskeleton and molecular motors
Article: Cystic Fibrosis
Cell division
cell cycle
protein kinases and cyclins
Mitosis
Cytokinesis
Apoptosis
Cancer and metastasis
Article: Retinoblastoma
82-88
89-95; 104-105
149-155
476-486
453-466
Primary Literature Article #1
363-372
372-384
700-707
531- 539
539- 559
Primary Literature Article #2
387-406
407-420
500-521
571-598
Primary Literature Article #3
609-613
613-625
625-634
634-638
638-646
717-728
Primary Literature Article #4
Pre-approved seminars for extra credit
Other seminars may be approved, but only if you contact me at least two days in advance of the seminar, and send me
sufficient information to make a decision on whether the talk is relevant to this class.
EMU Biology Department Seminar Series
Talks are at 3:30pm, Mark Jefferson Science Complex room 154
Date
Sep 19
Speaker
Alexis Garland
Victoria University of Wellington, NZ
Cognition research on birds
Sep 26
Kathy Spindler
University of Michigan
Virus-host interactions
Oct 3
Anne Danielson Francois
University of Michigan – Dearborn
Spider mating behavoir
Oct 10
Bill Taylor
University of Toledo
Control of cell division
Oct 17
Brian Ohsowsi
University of British Columbia – Okanagan
Grassland restoration
Oct 24
Mike Henshaw
Grand Valley State University
Cooperation in social insects
Nov 7
Greg Dick
University of Michigan
Microbial communities in deep sea hydothermal plumes
Nov 14
Beronda Montgomery
Michigan State University
Responses of plants to changes in light
Nov 28
Andrea Benedict
Hugo W. Moser Research Institute
UV radiation-induced skin tumors
Dec 5
Eric Krukonis
University of Michigan
Mechanism of cholera and plague virus infections
EMU Honors College Star Lecture Series
Talks are at 7:00pm, Halle Library Auditorium
Date
Oct 16
Speaker
Harriet Lindsay
EMU Chemistry Department
If we can, should we? Ethics and Science
Nov 13
Michael Scoville
EMU History and Philosophy Department
If we can, should we? Ethics and the Global Environment