BIO200: Introduction to Cell and Molecular GeneticsDocument Transcript
BIO200-001: Introduction to Cell and Molecular Genetics Syllabus
Fall Semester 2005
Dr. Elisabeth Arévalo. Office: Sowa 221 (x 2158); Lab: Hickey 246 (x 2543);
Class Meeting time: Series A: M, T, R 8:30 AM - 9:20 AM. Room: AM 106
Karp, G. 2005. Cell and Molecular Biology: concepts and experiments. Fourth Edition. John
Wiley & Sons, Inc. N.Y.
Cell biology and molecular genetics are certainly among the most exciting frontiers of
modern science. Recent advances in methodology are revolutionizing medicine, agriculture, and
other fields of direct relevance to our daily lives. For this reason an introductory course in
cell/molecular biology is relevant not only as training for scientists, medical practitioners, and
other specialists, but also as a source of information for the general public. Furthermore,
technology is now available to manipulate individual cells, biochemically and genetically, such
that whole organisms may be temporarily modified, or whole populations of organisms
Lectures meet three times weekly. Lecture information will be a main source of exam
questions. It will be very important to attend lectures, and to complete your text reading
assignments in order to do your best in the course.
Note: If you miss four lectures during the semester without a justified cause,
you will automatically get an F for the course.
Most of the lectures will be presented using Microsoft PowerPoint, and the slides
presented in class will be available on the Angel page for the course (http://angel.providence.edu). You
may find it useful to view the presentation BEFORE class and even to print copies of the slides
that will be presented to facilitate your note taking and to study from after class. However, the
PowerPoint notes will not replace the assigned readings from the textbook.
I will be available Monday, Wednesday and Friday from 1:00 – 3:30PM, in my office
(Sowa 221) or in my lab (Hickey 246), and accessible by e-mail or phone. Please email me and
make an appointment if you need to meet with me at a different time.
The grade for the course is based upon your combined performance on (see description
Three (one-hour) Exams 15% each
Two-hour Final Exam 15%
Final Paper 10%
Oral Presentation 10%
Class Participation 5%
Article Reviews 5%
Exams I, II, and III will be given in the classroom during the lecture period. Each exam
will include materials covered since the last exam. The Final Exam will be given in your
classroom, date and time according to your class schedule.
NOTE: Please read this paragraph carefully as it represents firm course policy. Anyone who
misses one of the in-class exams must take the make-up exam or receive a zero for the missed
exam grade. The make-up will substitute for the missed earlier exam. There will be no substitute
exam times or other make-up exams, so do not skip any exam unless absolutely necessary.
Under no circumstances will missed exams be made up unless I am notified prior to the exam, as
a result to an unavoidable situation. The make-up exam is scheduled from 10:00-11:00 AM on the
first day of the reading period at the end of the semester (usually a Saturday morning).
Exam questions will emphasize lecture information, but will also include all the
information from the textbook reading assignments and scientific articles assigned. Exam
questions will be multiple choice, fill-the-blank, or short answers.
Please come to see me as early in the semester as possible if you are having excessive
difficulty in the course. It is usually difficult and often impossible to make corrective adjustments
late in the semester.
At the beginning of every class during the semester, I will select one student and ask
him/her one question in reference to the materials covered the previous class. Another student will
be selected to answer a question about the materials that will be covered during the current class.
Students will be selected randomly. If the selected student cannot answer the question, points will
be deducted from this portion of the class grade. Every student will have at least two chances to
answer a question. Questions posed to presenters at the end of the semester (Oral Presentations, see
below) will also count for this portion of the grade.
Every other week (generally on Thursdays), different articles from the primary literature
(see list attached) will be assigned. Articles will be discussed in class. Two to three students will
be selected randomly to be the leaders in the discussion (participation as a discussion leader will be
considered for the final grade). They will be expected to know the contents of the article, give a
summary of the article and to direct the class discussion. Participation in the discussion will be
considered for fine-tuning of the final grade. A one-page summery of the article will be due prior
the class, by submitting it into a dropbox in the class section of Angel.
NOTE: Attendance during article discussions is expected. If absent for two discussion sessions,
your grade for this portion of the class will be zero. You are expected to read the papers even if
you are not the leader for that specific week and write the summary. Points will be deducted if
selected to answer a question during discussion and does not know the topic.
Final Paper and Oral Presentation:
During the semester we will cover several topics in cell biology and molecular genetics.
Different methodologies are commonly used to study these areas in Biology (e.g. use of the
electron microscope to study the subcellular organelles, or the use of molecular techniques to study
genetic diseases, etc.). For the lecture portion of the class, these methodologies would not be
covered; they will be part of your Final Paper and Oral presentation. For this paper, you should
pick a specific methodology that might interest you (i.e. methods of study the evolution of gene
families), you will have to explain why is it important to study this issue and describe what type of
technique(s) you would recommend to learn more about this topic. Justify why you selected this
technique versus another one, either at the cellular or molecular level. Throughout your textbook
chapters (Karp), different methodologies are explained and applied to different topics (Chapter 18
is exclusively dedicated for this purpose). Write this paper following a professional journal’s
format for a REVIEW article (I recommend looking at your Gen Bio. book: McMillan, Victoria E.
Writing Papers in the Biological Sciences, 3rd Edition, Bedford/St. Martin’s. 2001, to check the
format). This paper should include the different sections as if you were going to submit your paper
for publication: Title, Abstract, Introduction, Discussion and Conclusion and Literature Cited.
During the semester you should schedule an appointment with me to discuss your paper. I will
provide you with some guidelines to follow in your paper.
Examples of Potential Topics for Final Paper
Complementary DNA Libraries
Genetically Engineered Products
Stem Cell Research
Western Blot Technique
You will submit an outline of your paper on Friday 04/08, into Angel’s dropbox. This
outline will consist on a brief description of your methodologies suggested, level of the study
(cellular or molecular level) and a list of potential applications. Upon approval, you will then write
your Individual Research Paper. At least 5 articles from Primary Literature should be
included, using the proper citation format (these references should come from scientific
journals, not from Internet Sites, I will deduct points if the paper has internet references).
The paper should be no longer than 10 pages long (double space), including the references.
More information about the specifics for the final project will be provided later during the
semester. The complete paper is due on the last day of classes (Friday April 29).
Group presentations should consist of two students each, which will be assigned during the
semester. The oral presentations are completed in combination with the Final Paper (see section
above) and will cover specific applications for the specific Methodologies selected for your final
paper (i.e. if you selected DNA sequencing as your final paper’s topic, the two members of the
group, would talk about different applications for DNA sequencing like biomedical purposes
(sequencing a mutated gene that determines a specific disease), for systematic studies (the
phylogenetic relationships of related species), and/or for Conservation studies (sequencing
different individuals of a species in danger of extinction), among other uses).
Presentations will take place at the end of the semester. Two presentations per class, 20
minutes each, including questions (15 minutes presentation, 5 minutes questions). Topics will
be selected during the week after exam 2 (03/15-03/18). Your presentations will be prepared in
PowerPoint format, and will be evaluated by other members of the class and myself. Those
evaluations will determine the grade for the oral presentation.
Biweekly quizzes will include 3-4 questions related to the past and present lectures, to be
completed at the beginning of the lecture. Ten minutes will be provided to complete the quiz.
Readings for class materials (according to schedule) will be included on each quiz.
BIO 200-001: Introduction to Cell and Molecular Genetics
Schedule - Fall 2005
Day/date Lecture topic Chapter (pages)
T 09/06 Introduction – Your expectations and mine -
R 09/08 Introduction to Cells 1 (1-7)
M 09/12 Two Different Classes of Cells 1 (7-25)
T 09/13 Plasma Membrane Function Quiz 1 4 (121-131)
R 09/15 Article Discussion -
M 09/19 Structure and Function of Membrane Proteins 4 (131-141)
T 09/20 Nature and movement of Membrane 4 (141-165)
R 09/22 Interactions between Cells and Environment 7 (243-252)
M 09/26 EXAM 1 -
T 09/27 Interactions with Extracellular Materials 7 (252-258)
R 09/29 Article Discussion -
M 10/03 Interactions Cell/Cell 7 (258-275)
T 10/04 Cytoplasmic Membranes Quiz 2 8 (279-281)
R 10/06 Endoplasmic Reticulum 8 (288-298)
T 10/11 Golgi, Lysosomes and The Endocytic Pathway 8 (299-326)
R 10/13 Article Discussion -
M 10/17 Cytoskeleton: Microtubules Quiz 3 9 (334-344)
T 10/18 Motor Proteins 9 (344-355)
R 10/20 Intermediate and Micro Filaments 9 (364-375)
M 10/24 Cellular Reproduction 14 (578-587)
T 10/25 Mitosis and Cytokinesis 14 (588-607)
R 10/27 Article Discussion, Final Groups Selection -
M 10/31 EXAM 2 -
T 11/01 Meiosis 14 (607-616)
R 11/03 The Cell Nucleus 12 (492-516)
M 11/07 Nature of Genes Quiz 4 10 (397-409)
T 11/08 The Structure of the Genome 10 (410-426)
R 11/10 DNA Replication 13 (550-564)
M 11/14 Replication in Eukaryotes and DNA Repair 13 (564-575)
T 11/15 Gene Expression: Trascription Quiz 5 11 (436-450)
R 11/17 Article Discussion -
M 11/21 Messenger RNAs and Decoding the Codons 11 (451-484)
T 11/22 EXAM 3 -
M 11/28 Control of Gene Expression Outline Final Paper 12 (517-525)
T 11/29 Structure of Transcription Factors 12 (526-545)
R 12/01 Student Presentation -
M 12/05 Student Presentation -
T 12/06 Student Presentation -
R 12/08 Student Presentation Final Paper due -
F 12/16 FINAL EXAM (1 – 3pm) -
Journals in the field of Cell and Molecular Biology:
Annual Review of Cell and Developmental Annual Review of Genetics
Annual Review of Microbiology Annual Review of Plant Physiology & Plant
Biochemistry and Cell Biology Biochemistry and Molecular Biology
Biomembranes Bioscience, Biotechnology, and
British Medical Journal Cancer
Cancer Research Cell
Cellular and Molecular Biology Chromosoma
Critical Reviews in Biochemistry and Molecular Current Biology
Current Opinion in Biotechnology Current Opinion in Cell Biology
Current Opinion in Genetics and Development Current Opinion in Microbiology
EMBO Journal Environmental Health Perspectives
Evolutionary Computation FASEB Journal
Gene Genes & Development
Genetics Genome Research
Genomics Human Molecular Genetics
International Journal of Biochemistry & Cell In Vitro Cellular & Developmental Biology -
In Vitro Cellular & Developmental Biology - Journal of Bacteriology
Journal of Biochemical and Biophysical Methods Journal of Biochemistry and Molecular
Journal of Biomolecular NMR Journal of Biotechnology
Journal of Cell Biology Journal of General Virology
Journal of Heredity Journal of Molecular Biology
Journal of Molecular Neuroscience Journal of NIH Research
Journal of Virology Methods in Cell Biology
Methods in Molecular and Cellular Biology Molecular Basis of Disease
Molecular Biology of the Cell Molecular Biotechnology
Molecular Cell Molecular Cell Research
Molecular & Cellular Biology Molecular Diversity
Molecular Microbiology Molecular Pharmacology
Nature Nature Bio/Technology
Nature Genetics Nature Medicine
New England Journal of Medicine Nucleic Acid Research
Oncogene Plant Molecular Biology
Plasmid Proceedings of the National Academy of
Quarterly Reviews of Biology Review on Biomembranes
Review on Cancer RNA
Science Trends in Biotechnology
Trends in Cell Biology Trends in Ecology & Evolution
Trends in Genetics Trends in Microbiology
Trends in Pharmacological Sciences Virology
Societies: American Association of Cancer Research
American Cancer Society American Society for Cell Biology
American Society of Microbiology Cell Biology International
Federation of American Societies for Genetics Society of America
Experimental Biology Federation of European
International Society of Plant Molecular Biology Society for In Vitro Biology
Massachusetts Medical Society
The National Academy of Sciences The RNA Society
Berkeley Lab Science Beat http://enews.lbl.gov
Discover Magazine http://www.discover.com
HUGO Gene Nomenclature Committee http://www.gene.ucl.ac.uk/nomenclature
Human Chromosome Launchpad http://www.ornl.gov/hgmis/launchpad
HMS Beagle (BioMedNet Magazine) http://news.bmn.com/hmsbeagle
Magazine Art. on Biology & Life Sciences http://magportal.com/c/sci/bio
Medical Breakthroughs http://www.ivanhoe.com
Nature http://www.nature.com/nature (subscription required)
New York Times http://www.nytimes.com
Science http://www.sciencemag.org (subscription required)
Scirus For scientific information http://www.scirus.com
Time Magazine http://www.time.com
As a student at Providence College, you are expected to understand and follow standards of
intellectual and academic integrity. The College and the professors in the Department of Biology
assume that you will be honest and that you will submit only your own work. The faculty requires
that you adhere to the level of honesty as outlined below and refrain from dishonorable or
A. Plagiarism: Plagiarism is taking another person's work and calling it your own.
Plagiarism includes any paraphrasing or summarizing of the works of another person without
recognition, including the submitting of another student's work as your own. Plagiarism can
involve a failure to reference a source of information in a paper or report the quotation of the
paragraphs, sentences, or phrases written by someone else. Any information taken from the
Internet without properly referencing the source (i.e., the URL) is considered plagiarism. You are
responsible for understanding the rules of use for sources, the appropriate ways to reference
sources, and the consequences of plagiarism.
B. Cheating on Exams: Cheating on exams makeup tests or quizzes involves giving or
receiving help during the exam. Examples of such help include the use of notes, computer based
resources, books, or "crib sheets" during an examination (unless specifically approved by a faculty
member), or sharing answers with another student during an exam. Other examples include
allowing another student to view your own exam or quiz.
C. Unauthorized Collaboration: Submission for credit of a report or paper as your own
work, which has been written in collaboration with another individual is not allowed. It is also a
violation of academic honesty knowingly to provide such help. Collaborative work specifically
authorized by a faculty member is allowed.
D. Falsification: It is a wrong to misrepresent or falsify data generated in the laboratory
portion of the class. You are expected to report the date as it is appears regardless of whether it
“fits” into the expected outcomes of the laboratory.
E. Multiple Submissions: It is a violation of academic honesty to submit the same or
substantial portions of the same work for credit more than once unless the faculty member(s) to
whom the material is submitted for additional credit allows it. In cases in which there is a
progression of research in a lab or course, use of prior work may be allowed or required; however
the student is responsible for indicating in writing that the new work is cumulative.
Penalties for failure to adhere to academic policy:
1. Exams or quizzes: For the first offense, the student will receive a zero for the
assignment. If a student aids another student during the exam, both parties will receive a zero. For
the second offense, the student will receive an F for the course.
2. Lab reports or papers: For the first offense, the student will be asked to rewrite the
assignment after a meeting with the appropriate faculty member in the course and will receive a
“late” penalty of one letter grade. For the second offense, the student will receive a zero for the
assignment. For any subsequent offense, the student will receive an F for the course.
Students will be required to submit their papers electronically via Angel in the class site.
Each paper will be screened with plagiarism software so it is in your best interest to write in your
own words and reference the paper correctly. As required by the Dean of Undergraduate Students,
all offenses will be reported to the Dean. In addition, all offenses will be recorded in the
Department of Biology for future reference. Providence College Policy on Academic Honesty:
“Acts of academic dishonesty (plagiarism, collusion, cheating, etc.) are subject to an appropriate
penalty. The grade of “F” may be assigned to students found guilty of such acts. The professor of
the course in which the infraction occurred will inform the Office of the Dean of Undergraduate
Studies of the offense and the action taken. Students who earn a failing grade may petition a
review by the Academic Appeals Committee. In addition, the Dean of Undergraduate Studies may
refer any case of academic dishonesty to the Office of the Vice President of Student Services,
which will judge whether further penalties should be assessed. A second offense against academic
honesty renders students liable to automatic dismissal from the college.”