Biology 46: Cell Biology
Spring 2016
Dr. Susan Koegel
Office: Barnum 109
Phone: 627-3196
Email: susan.koegel@tufts.edu
Course Hours: Mondays, Wednesdays 10:30-11:45 (E+), Barnum 104
Office Hours: Tuesday 10-11:30, Fridays 2-3:30 & by appointment (email to arrange
time)
TA: Kaylinnette Pinet (Kaylinnette.Pinet@tufts.edu)
TA Office Hours: Mondays 12-1, 200 Boston Ave Suite 4700, 4th floor lobby
Course Description
The cell is a fascinating, complex, and dynamic unit that forms the fundamental basis of
unicellular and multicellular life. Cells are constantly engaging with their environment
and making active decisions, and we will dissect these cellular processes. Topics
include: signal transduction, membrane dynamics, vesicle transport, cytoskeleton
dynamics, cell migration, cell cycle, stem cells, and mechanisms of gene expression
regulation. We will use the study of disease states, including cancer, to explore these
topics and how alterations can lead to disease. In addition, drug therapies will be
discussed as they highlight an understanding of a cellular process. We will use data
from original research papers to drive our study of this discipline. Throughout this
course, there will be an emphasis on developing hypotheses, designing experiments,
and analyzing data.
Course Objectives
By the end of the semester, you should be able to:
• Appreciate and understand the dynamic nature of the cell, including how it
receives and responds to information from its environment.
• Explain and compare different mechanisms for receptor activation and regulation.
• Understand and explain how membrane chemistry and regulation are essential in
cell communication.
• Understand intracellular signaling cascades and their impact on cellular activities,
including cytoskeleton rearrangements, motility and changes in gene expression.
• Understand mechanisms of cell cycle regulation.
• Predict how alterations or given drugs/chemical treatments would impact cellular
behavior.
• Develop testable hypotheses based on provided information, design experiments
to test hypotheses, and interpret provided data.
Biology 46 Cell Biology/Spring 2016/Page 1
Preparing for Class
It is expected that you complete assigned readings and review any posted
sources before attending class.
The required textbook is:
Alberts et al. Molecular Biology of the Cell, 6th edition and other reading materials.
Two copies of the 6th edition will be kept on three-hour reserve in the library.
Additional articles on the reading list will be made available on the course’s Trunk site.
To help you focus your reading, Guided Reading Questions will be posted under
Class Materials on Trunk.
Course Requirements
Grading:
Exams: 70% (two highest exams worth 25% each, lowest worth 20%)
Group Poster Presentation: 20% (90% Dr. Koegel’s evaluation, 10% peerevaluation)
Participation: 10% (learning catalytics questions)
Please note that there will be no extra credit opportunities in this course.
Exams: You will have two in-class exams and a third one hour exam during finals
period. If you are requesting an accommodation for a documented disability, you must
register with the Accessibility Services Office at the beginning of the semester. To do so,
call the Student Services Desk at 617-627-2000 to arrange an appointment.
Group Poster Presentation: You will prepare a presentation and scientific poster that
will focus on the identification and evaluation of a drug target to treat a disease of
interest. This group presentation will count as 20% of your final grade. All members of
the group will receive the same grade.
In-Class Questions: You are expected to actively participate in this course. You will
learn by engaging with the material and your peers; therefore, your participation in this
course is extremely important for everyone’s learning.
We will be using Learning Catalytics (https://learningcatalytics.com/), an automated
classroom response system to provide an opportunity for you to answer questions in
class using a web-enabled device. Your participation in these exercises (not whether or
not you get the correct answer) will contribute towards your final grade. You are
required to complete 90% of the questions asked in class from February 1st to the end
of the semester to receive the full 10% credit (given that you only need to answer 90%
of the questions, credit will NOT be given for absence due to illness or personal
reasons). You cannot make-up missed questions. Learning Catalytics will be used in
every class, and you are responsible for bringing your device to each class.
Biology 46 Cell Biology/Spring 2016/Page 2
To sign up for an account, please follow the directions here:
http://trunkuserguide.screenstepslive.com/s/8335/m/33860/l/480103-getting-startedwith-learning-catalytics-for-arts-science-engineering-students. You should complete
this step before the first day of class. Please use your tufts email address as your
Learning Catalytics username and email address.
I expect you to engage in in-class discussions and offer ideas and questions. Even if
you are unlikely to talk in a large discussion, smaller group discussions will provide
another avenue for participation. Failure to actively participate will negatively affect your
participation grade.
Class Policies
Posting Lectures: I will post slides before each lecture on our course Trunk site that I
encourage you to print and bring to class. Slides with in-class annotations will be
posted within 24 hours after class.
Email Policy: I will try and respond to all emails within 24 hours of receiving them. This
time frame is not guaranteed, especially over weekends or holidays.
Academic Honesty
You will work collaboratively throughout the course to solve problems and work on your
final presentations. Your work on exams should be exclusively your own. Cheating and
plagiarism will not be tolerated and will be reported to the university. You must correctly
cite your sources on your final project (instructions on how to do so will be provided).
Important Dates
• February 10th: Poster presentation group assignments due
• February 18th: Exam 1
• February 24th: Group poster presentation topic due
• March 16th: Exam 2
• March 28th: References due
• April 11th: Poster Summary Due
• April 25th, 27th: Group poster presentations
• May 9th: Exam 3
Biology 46 Cell Biology/Spring 2016/Page 3
Class Schedule
(Subject to Modification)
Date
Topic
Textbook
Jan. 25th
Introduction to Cell Signaling and the
Hallmarks of Cancer
Oncogenes and Tumor Suppressors
1091-1096, 11041105, 155-156,
503-504, 469-470,
813-817
Feb. 1st
Receptor Tyrosine Kinases & Breast Cancer
850-853, 822-823
(Modular
Interaction
Domains Only),
452-455, 489, 487
(Types of Mutations
Box)
Feb. 3rd
G-protein Coupled Receptors
820, 832-836, 848849
Feb. 8th
Membranes, Membrane Potential, and
Transport
597-614
Feb. 10th
Ion Transport and Calcium Signaling
Poster presentation group assignments due
546-547, 655 (Fig
12-15), 836-841
Feb. 15th
No Classes: Presidents’ Day
Jan. 27th
Feb. 17th
Additional
Materials
1
2
695-703,695-703,
705-710,705-710,
730-736 730-736
Vesicle Transport and Endocytosis
Feb. 18th
Tufts
Monday
EXAM 1 (on material through Feb.10th)
Feb 22nd
Familial Hypercholesterolemia & Receptor
Mediated Endocytosis
3, 4*
Biology 46 Cell Biology/Spring 2016/Page 4
543-546, 820, 854857, 1106, 11391140
Feb. 24th
Ras/MAPK Pathways, FRET, and the
Targeting of Intracellular Signaling Pathways
Group poster presentation topic due
Feb. 29th
Actin Cytoskeleton Organization and Cell
Migration
March 2nd
Cell Migration & Metastasis
March 7th
Cell-Cell Interactions and Extracellular Matrix
1035-1042, 10541081
March 9th
Targeting Angiogenesis
1120, 1235-1238
March 14th
Transcriptional Control and the Nuclear Pore
Complex
647-657
March 16th
Exam 2 (on material through March 9th)
889-895, 898-917,
951-960
5, 6*, 7
8
Spring Break: March 19th – March 27th
Discovering Cell Cycle Regulation
References due
488-489, 963-970,
978-979, 980-981,
1012-1013
March 30th
The Mitotic Spindle and the Spindle Assembly
Checkpoint
925-931, 971, 982995
April 4th
Cell Cycle Regulation, p53 and Apoptosis
1014-1017, 10211032
9, 10
April 6th
Ubiquitination and Autophagy
157-158, 357-360,
722-729
11
April 11th
Regulation of Gene Expression by Non-Coding
mRNAs
429-433, 499-501
Poster Summary Due
March 28
th
Biology 46 Cell Biology/Spring 2016/Page 5
868-871, 12171224, 1251-1260
April 13th
Stem Cells
April 18th
No Classes: Patriot’s Day
April 20th
Stem Cells & Cancer
April 25th
Targeted Therapy: Poster Presentations Day 1
April 27th
Targeted Therapy: Poster Presentations Day 2
May 2nd
Bringing it all Together: Cells Inside and Out
May 9th
Exam 3 – 3:30-5:30
12
13
Biology 46 Cell Biology/Spring 2016/Page 6
Non-Textbook Required Reading List (Available on Trunk Under Class Materials)
Additional articles may be added during the course of the semester (* denotes primary
research article)
1
2
3
4
5
6*
7
8
9
10
11
12
13
Borzac K. (2014) Three known unknowns. Nature 509: S69-S71.
Castenada J and Matzuk M. (2015) Toward a rapid and reversible male pill. Science
350: 385-386.
Nair P. (2013) Brown and Goldstein: The Cholesterol Chronicles. PNAS 110: 1482914832.
Brown and Goldstein. (1974) Familial Hypercholesterolemia: Defective binding of
lipoproteins to cultured fibroblasts associated with impaired regulation of 3-hydroxy-3methylglutaryl coenzyme A reductase activity. PNAS 71: 788-792.
Farrell A. (2006) Bloodlines. Nature Milestones Cancer. doi:10.1038/nrc1849
Kim KJ et al. (1993) Inhibition of vascular endothelial growth factor-induced
angiogenesis suppresses tumour growth in vivo. Nature 362: 841-844.
Erez N. (2013) Angiogenic awakening. Nature 500: 37-38.
Underwood E. (2015) Plugged pores may underlie some ALS, dementia cases. Science
349: 911-912.
McCarthy N. (2006) Death Defying. Nature Milestones Cancer. doi:10.1038/nrc1854
Scudellari, M. (2013) Sex, Cancer, and a Virus. Nature. 503: 330-332.
Castro-Obregon S. (2010) The discovery of lysosomes and autophagy. Nature
Education 3: 49.
Suomalainen A. (2015) Asymmetric rejuvenation. Nature 521: 296-297.
Couzin-Frankel J. (2015) The bad luck of cancer. Science 347: 12.
Biology 46 Cell Biology/Spring 2016/Page 7