BIO200: Introduction to Cell and Molecular Genetics


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BIO200: Introduction to Cell and Molecular Genetics

  1. 1. BIO200-001: Introduction to Cell and Molecular Genetics Syllabus Fall Semester 2005 Instructor: 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 Required Text: Karp, G. 2005. Cell and Molecular Biology: concepts and experiments. Fourth Edition. John Wiley & Sons, Inc. N.Y. Description: 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 permanently altered. 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 ( 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. Office Hours: 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. Grading Policy: The grade for the course is based upon your combined performance on (see description below): Three (one-hour) Exams 15% each Two-hour Final Exam 15% Final Paper 10% Oral Presentation 10% Class Participation 5% Article Reviews 5% Quizzes 10%
  2. 2. 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. Class Participation: 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. Article Reviews: 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
  3. 3. 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 DNA cloning DNA Fingerprinting DNA sequencing Electron Microscopy ELISA test Gene Therapy Genetically Engineered Products Immunofluorescence Microscopy Knockout Mice Microarray Technology Microsatellites Pronuclear Microinjection Radioimmunoassay RNAinterference Stem Cell Research Transgenic Animals Western Blot Technique Xenotransplantation 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). Oral Presentation: 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
  4. 4. 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. Quizzes: 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.
  5. 5. 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) -
  6. 6. Journals in the field of Cell and Molecular Biology: Annual Review of Cell and Developmental Annual Review of Genetics Biology Annual Review of Microbiology Annual Review of Plant Physiology & Plant Molecular Biology Biochemistry and Cell Biology Biochemistry and Molecular Biology International Biomembranes Bioscience, Biotechnology, and Biochemistry Biotechniques Blood British Medical Journal Cancer Cancer Research Cell Cellular and Molecular Biology Chromosoma Critical Reviews in Biochemistry and Molecular Current Biology 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 - Biology Animal In Vitro Cellular & Developmental Biology - Journal of Bacteriology Plant Journal of Biochemical and Biophysical Methods Journal of Biochemistry and Molecular Biology 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 Sciences, USA Quarterly Reviews of Biology Review on Biomembranes
  7. 7. 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 Yeast 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 Biochemical Societies International Society of Plant Molecular Biology Society for In Vitro Biology Massachusetts Medical Society The National Academy of Sciences The RNA Society Useful Websites ABCNews Berkeley Lab Science Beat BioMedNet Discover Magazine HUGO Gene Nomenclature Committee Human Chromosome Launchpad HMS Beagle (BioMedNet Magazine) Magazine Art. on Biology & Life Sciences Medical Breakthroughs MSNBC Nature (subscription required) NCBI New York Times PubMedCentral Scholar Science (subscription required) ScienceNews Scirus For scientific information Time Magazine WebMDHealth
  8. 8. Academic Integrity 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 unethical behavior. 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
  9. 9. 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.”