Molecular Biology. 3100: 480/580.001     3 credits   Spring 2003      M,W 3:15-4:30 PM       BCCE 56

 

Instructor.         Dr. Amy Milsted Rm ASEC 279              Phone: 330-972-7976             
e-mail: milsted@uakron.edu

Office hours:                Mon. 2:00-3:00 PM, Wed. 4:30-5:30, or by appointment. 

Biology dept. office phone: 330-972-7155

 

Required text.  "Molecular Cell Biology", Fourth Edition, 1999, by Lodish H,  Berk A,  Zipursky SL, Matsudaira P, Baltimore D, Darnell J.  W.H. Freeman and Company, New York.

For your own benefit you should review the questions at the end of each chapter.

 

Supplementary materials.  Most of these are available for examination in my office.

            There are many good textbooks available.  In addition to the required text I recommend "Molecular Biology of the Cell", Fourth Edition, 2002, by Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P.  Garland Science, New York, NY

            It is often helpful to review a biochemistry text, as well.

            Additional readings from Scientific American and various scientific journals may be recommended during the semester.  For more details on a subject, see the References lists the back of each chapter in the book.

Course Description.

            This course will include the fundamentals of molecular biology including recombinant DNA technology, applications in biotechnology, medicine and genetic engineering.  Much of the course will be geared toward understanding mechanisms of gene regulation.  Areas of genetics, chemistry/biochemistry and cell biology will be touched upon.  While the textbook will be our guide, we will not include everything in the book.

Prerequisites.  genetics, or permission of the instructor

 

Drop dates.
Jan. 27, last day to withdraw without adviser's signature
March 7, last day to withdraw without instructor's signature
April 11, last day to withdraw for Spring 2003 (4:30 PM)

 

Course Goals.

            The emphasis of this course is on applying the material presented in class to problem solving.  This requires that first we learn the basic principles underlying modern molecular biology.  The general principles of each area are more important than memorizing details of each topic.  This will allow students to understand the molecular basis for biological properties such as dominant and recessive alleles in genetics, secretion in cell biology, actions of hormones in development, and the full range of biological processes.  After completing this course the student should have knowledge of the principles of gene therapy and the use of DNA testing in forensics, for example.

 

Course Requirements.

 

            All students are required to give a brief oral presentation of an article, paper or topic to be chosen after consultation with the instructor.  The presentation should last 20-30 minutes and be a summary and review of the material you have chosen.  Handouts will be available to assist you in preparing your presentation.

            Graduate students will also be required to write a paper, on a topic different from their oral presentation.  In consultation with the instructor, chose a primary reference published in a research journal in 2002 and write a short report (at least 6 typed pages), based on the paper.  Include enough background and supplementary material to interpret the data in the primary reference.  Consult a minimum of 3 additional published research papers and correctly reference them.  Your report can be a critical review of a scientific paper, including an analysis of the authors' work compared to studies previously published by other investigators.

 

Course Policies.

            Attendance at all classes is expected.

No cell phones or beepers in use during class.

No use of tobacco products or alcoholic beverages in class.

Lectures may be recorded.

            All visitors to class must be approved in advance.

Any student who has a disability that substantially limits learning in a higher education setting may contact the Office of Accessibility for information regarding his/her eligibility for reasonable accommodations

 

Academic Honesty Policy.

Plagiarism:  Theft of someone else’s work, words or ideas will not be tolerated.  This includes plagiarizing material that is posted on the Internet.  It is also not acceptable to include extensive, direct quotations from another source, even if that material is enclosed in quotation marks.  If you have questions regarding what constitutes plagiarism, consult the Instructor before you submit your paper to be graded.

Any evidence of plagiarism will result in a grade of F, not only for the paper, but also for the entire course.

                                   

Grading.  A course grade of         A                      requires approximately              90-100%

                                                B                                                                                  80-89%

                                                C                                                                                 70-79%

                                                D                                                                                 60-69%

                                                F                                              less than 60% or evidence of plagiarism

 

Course grade for 580.001                                         Course grade for 480.001

            Midterm exam I            20%                                                     Midterm exam I            25%

            Midterm exam II            25%                                                     Midterm exam II            25%

            Paper                          20%                                                     Oral presentation            25%

            Oral presentation            10%                                                     Final exam                25%

            Final exam                25%

 

All exams are essay.  A typical exam consists of 10 questions, 8 of which are selected by each student to answer,

During exams - no radios, tape players or headsets.  No calculators, electronic translators or computers.

 

Make-up exams will be administered only in cases of extreme emergency.  To be eligible for a make-up exam, written documentation of the reason for your absence must be provided.  For example, proof of visit to a doctor's office or emergency room, proof of involvement in an auto accident, etc.  In addition to providing written documentation you must notify the instructor or the Biology Dept. Office by the day of the regularly scheduled exam.  Those phone numbers are listed above.  Make-up exams will be given from 1-7 days after the scheduled exam date.  All make-up exams will be oral and no options for choice of questions to be answered will be available.

 

Tips on how students do well in this course.

Read each chapter before attending class.  If you have questions about the material presented, or if it is not clear, ask questions during class.  No question is too simple to be asked.  If the instructor goes too fast, let her know immediately.

Attend class and take good notes.  You can't take good notes if you have not previously read the book or assigned papers.  Review your notes each day and if you have questions, see the instructor the same or the following day.  Do not wait until the week before the test to talk to your instructor.

Study with other students in the class. 

Tentative Course Calendar.

The exam dates and deadlines for other assignments should be considered definite.  The chapters covered on each exam will be made clear as the course progresses.  The exams are not cumulative, except that to understand the material we will cover later in the course you need to have a good foundation on the basics that we review in the first part of the course.

 

Topic                                                                    Chapter

Introduction and overview                                       1             Read - no lecture

Chemical foundations, Proteins                                   2, 3                  Jan 13, 15

No class (Martin Luther King, Jr. Day)                                      Jan. 20
Nucleic acids                                                               4

Cell membranes and organization                             5

Cell culture                                                                  6

Midterm Exam 1                                                                                   Feb 12

Recombinant DNA and genomics                                 7

Genetic analysis                                                           8

Gene structure                                                            9

Regulation of transcription initiation                                   10

Midterm Exam 2                                                                                   Mar 19

Spring Recess                                                                                     March 24-29
RNA processing, post-transcription control             11

DNA replication                                                        12

Gene control in development                                        14

Student presentations                                                                   April 14, 16, 21, 23

TBA                                                                                                     April 28-30

Final exam                                                                             Wed. May 7, 4-6 PM

 

In addition, throughout the course we will read and discuss classic and new research papers.

 

Due dates for assignments: March 31                                 Graduate students: outline [2 pages]

                                                April 7         All students: selection of journal article or topic for oral presentation

                                                April 14                                    Graduate students: paper due [6-10 pages]       

                                                April 14, 16, 21, 23              All students: oral presentations. 

 

            We may be able to schedule the oral presentations earlier, if desired.  Outlines, papers and topic selection can all be completed before these due dates.

 

 

Listed below are some useful Web sites.

 

http://www.ncbi.nlm.nih.gov/  GenBank, other databases, searches, other tools at NCBI; PubMed

http://www.wi.mit.edu/  Biocomputing, software, other  Whitehead Institute, MIT

http://research.nwfsc.noaa.gov/protocols.html  Molecular Biology Protocols from US Dept Commerce/NOAA/NMFS/NWFSC

http://mcb.harvard.edu/BioLinks.html  Harvard University Dept. of Molecular and Cellular Biology

http://www.hgsc.bcm.tmc.edu/tools/   Database and search tools from Baylor College of Medicine

http://www.metacrawler.com/  Search the search engines - good for everything.  See also the link to Dogpile at the bottom of the page.