Biology 385 CELL BIOLOGY
Fall 2016
Class Times: Lecture: Monday, Wednesday, 12:00 - 12:50 in FSC 16
Lab: Tuesday FSC 132, 8:30-10:30; 11:00-1:00
Required Text: Essential Cell Biology by Alberts et al. 4th edition ISBN # 9780815344544
(hardcover; looseleaf also available at a lower price)
Required
Lab Notebook: Inexpensive graph ruled composition style with sewn binding
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Instructor: Dr. Bill Patrie |
Campus Phone: (717) 477-1400 |
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Office: FSC 152 |
Email:
wjpatr@ship.edu |
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Web Page: http://webspace.ship.edu/wjpatr/ |
Office Hours: Monday 1-3, Tuesday 1-2, Wednesday 1-2:30, Friday 11-1, and by appointment |
General Class Information
The objectives of this course are to become familiar with cell structure and function, to understand some of the current experimental techniques and how to apply them, and to become familiar with some current literature. Topics will include: the structure and function of biological molecules; the structure, function and biogenesis of membranes and organelles; cell signaling pathways; the relationship between cell cycle regulation and cancer; cellular energetics; and genes and gene expression.
PowerPoints for lectures, lab handouts and assignments, and on-line quizzes will be posted on D2L. I will also post your grades on D2L. Please check them periodically to ensure that you are not missing any grades. Let me know ASAP if there are any discrepancies.
Students who require special accommodations
for taking tests or notes should make an appointment to see me so that we can
make appropriate arrangements.
“Shippensburg
University and its faculty are committed to assuring a safe and productive
educational environment for all students. In order to meet this
commitment and to comply with Title IX of the Education Amendments of 1972 and
guidance from the Office of Civil Rights, the University requires faculty
members to report incidents of sexual violence shared by students to the University’s
Title IX Coordinator. The only
exceptions to the faculty member’s reporting obligation are when incidents of
sexual violence are communicated by a student during a classroom discussion, in
a writing assignment for a class, or as part of a University-approved research
project. Information
regarding the reporting of sexual violence and the resources that are available
to victims of sexual violence is set forth as http://www.ship.edu/no_more/.”
The Textbook
Essential Cell Biology, 4th Edition by Bruce Alberts et al. is a readable introductory cell biology text. It is important to read the book. Most of the information in the lectures follows the book quite closely, and most of the figures used correspond to those in the text book, so reading the text will complement and help clarify lecture material. The main differences between text and lecture are the order in chapters presented, applications from current literature, and in some cases depth into details.
The authors include questions throughout and at the end of each chapter to test how well you understand and assimilate important concepts. Try to answer these questions as you read the chapters. Make a good effort to answer them before resorting to the answer key in the back of the book: the act of problem solving is the key to true learning. Looking up answers or "Googling" requires little more than fingers and thumbs.
The
text is accompanied by online animations and interactive exercises illustrating
concepts and techniques described in the text, as well as interactive practice
quizzes. You will find many of these
presentations to be worthwhile, and I will occasionally give assignments based
on them. These appear to be freely
accessible without additional purchase.
(http://garlandscience.com/garlandscience_student/student_home.jsf?landing=student).
On the upper right of the page, select our text from the Go To Textbook
pulldown menu. If you have problems accessing material, please let me
know and I will do my best to provide access.
The animations are good, but of relatively low resolution and not
especially amenable to classroom presentation.
The quizzes/flashcards cover the major concepts and terms of each
chapter.
Labs
The laboratory portion of this class will provide some hands-on
experience with modern cell biological methods. These will include growth
and maintenance of cells in vitro, protein electrophoresis,
immunochemical and immunofluorescent detection of specific proteins, and the
analysis of nucleic acids. Labs will be posted on D2L. Attendance
is mandatory. If you need to miss a lab, get in touch with me and your
lab partner ASAP in order to work something out. Since we meet just one
day a week, it can be difficult to make up or reschedule lab time.
Grades
Exams (350 points): There will be 3 in-class exams (100 points each). The third test will be given during exam week. The tests are cumulative in the sense that the latter chapters build on the concepts of the earlier chapters. Exams will have a mix of short answer, essay, multiple choice, and matching questions. A lab exam (50 points) will be given during the last week of classes that will cover topics related to experiments done in the lab and to a journal article covered in detail during the semester.
Quizzes and Assignments (approximately 150 points): Approximately 12 quizzes and assignments, worth 10- 20 points each, will be given during the semester. Format will include on-line quizzes via D2L, in-class short answer quizzes, take-home problems, and literature reading assignments. In class quizzes will be announced, and I will let you know the format beforehand.
Lab Reports & Lab Notebooks (150 points): You will be expected to keep a detailed laboratory notebook. The notebook will be periodically checked during the semester for completeness and organization and collected for a final grade (50 points). Check with me anytime if you have questions regarding organization, what to include, etc. There will be two formal laboratory reports worth 25 points each (immunofluorescence, western blot), two short group reports (15 points each) and two handouts (10 points each). Details for notebooks and reports will be provided as a separate handout.
The final grade will be based on the percentage of the total (approximately 650) points. I don't typically grade on a curve. Final letter grades will be based on the percentage determined by dividing your point total by the total points in the course. I assign +/- in a favorable manner (e.g., an 89 would likely be a B+ and a 90 an A, not A-)
A= 90 and above; B=80-89; C=70-79; D=60-69; F= less than 60.
Class and
Lab Schedule- Warning! Subject to
change! Last Updated 8/28/2016
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DATE |
TOPIC |
CHAPTER |
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Mon 8/29 |
Overview of Cell Structure and Function |
1 |
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Tues 8/30 |
Lab: Lecture - Chemical Components of Cells |
2 and 3 |
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Wed 8/31 |
DNA, Chromosomes, and Replication |
5 and 6 |
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Mon 9/5 |
Labor Day – no class |
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Tues 9/6 |
Lab # 1 Micropipet Use & BCA Protein Assay Lab Notebook Group report due by 9/13 |
|
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Wed 9/7 |
Gene Expression |
7 and 8 |
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Mon 9/12 |
Gene Expression |
7 and 8 |
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Tues 9/13 |
Lab # 2 Cell Culture Techniques |
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Wed 9/14 |
Protein Structure |
4 |
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Mon 9/19 |
Protein Structure Amino acid quiz |
4 and 1 |
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Tues 9/20 |
Lab # 3 Protein and DNA Sequence Analysis Web Link Handout |
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Wed 9/21 |
Cell and Protein Methods |
4 and 1 |
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Mon 9/26 |
Membrane structure |
11 |
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Tues 9/27 |
Lab # 4 Protein Structure Web Link |
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Wed 9/28 |
Membrane transport |
12 |
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Mon 10/3 |
Membrane transport |
12 |
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Tues 10/4 |
Lab # 5 Immunofluorescence (Formal report) |
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Wed 10/5 |
Exam 1 Chapters 1,2,4, 5-8 |
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Mon 10/10 |
Metabolism- oxphos and photophos |
14 |
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Tues 10/11 |
Lab # 5 continued Immunofluorescence report due by Monday10/24 |
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Wed 10/12 |
Organelle Biogenesis and Vesicular Transport |
14, 15 |
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Mon 10/17 |
Fall Break |
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Tues 10/18 |
Fall Break |
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Wed 10/19 |
Organelle Biogenesis and Vesicular Transport |
15 |
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Mon 10/24 |
Organelle Biogenesis and Vesicular Transport |
15 |
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Tues 10/25 |
Lab # 6 Cell Fractionation/Western Blot (Formal report) |
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Wed 10/26 |
Cytoskeleton |
17 |
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Mon 10/31 |
Cytoskeleton |
17 |
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Tues 11/1 |
Lab # 6 continued |
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Wed 11/2 |
Extracellular matrix and cell junctions |
20 |
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Mon 11/7 |
TBA |
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Tues 11/8 |
Lab # 6 continued formal lab report due by 11/21 |
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Wed 11/9 |
Exam 2 Chapters 11, 12, 14, 15, 17, 20 (ECM, junctions) |
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Mon 11/14 |
Cell Communication |
16 |
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Tues 11/15 |
Lab # 7 Detection of a glioma oncogene by PCR |
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Wed 11/16 |
Cell Communication |
16 |
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Mon 11/21 |
Cell Communication |
16 |
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Tues 11/22 |
Lab # 7 continued; Lecture: nucleic acid techniques |
10 |
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Nov 23 Wed-Sun |
Happy Thanksgiving! |
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Mon 11/28 |
Cell Cycle Control |
18 |
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Tues 11/29 |
Lab # 7 continued |
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Wed 11/30 |
Cell Cycle Control |
18 |
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Mon 12/5 |
Cancer |
20 |
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Tues 12/6 |
Lab Final Lab Notebooks
due 12/7 |
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Wed 12/7 |
Cancer |
20 |
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Exam week |
Final Exam Chapters 16, 10, 18, 20 |