Molecular Biology
Molecular Biology
Biology 304, Fall 2006
Text: Denome, A Synopsis of Genetics, Wm. C. Brown Co.
Instructor: Roger Denome, Associate Professor of Biology
Office hours: M-F 8:30-10:00, and by appointment.
Room 213 Science building. Phone: 565-1196 E-mail: rdenome@stonehill.edu
Web site: http://faculty.stonehill.edu/rdenome/molbio.htm
Class Times: T, Th 11:30-12:45, Room 108 College Center
Lab Time: Lab: 1:30-4:30 Tuesday, room 022 Science Building.
Lecture Schedule
Date Topic Chapter
8/29 Introduction
8/31 Molecular Biology Techniques 14
9/5 Molecular Biology Techniques 14
9/7 Prokaryotic genetics 11
9/12 Prokaryotic genetics 11
9/12 You should have discussed your paper topic with Denome by this point.
9/14 Viral genetics 12
9/19 Viral genetics 12
9/21 Viral genetics 12
9/26 Test. Chapter 11, 14, 12
9/28 Mobile Genetic elements 13
10/3 Mobile Genetic elements 13
10/5 First research paper, Baker and Bell
10/5 You should have an outline of your paper topic for Denome by this point.
10/12 First research paper, Baker and Bell
10/17 First research paper, Baker and Bell
10/19 First research paper, Baker and Bell
10/24 First research paper, Baker and Bell
10/26 Test
10/31 Third research paper, Kadonaga
11/2 Third research paper, Kadonaga. First draft of paper due for Denome
11/7 Third research paper, Kadonaga
11/9 Third research paper, Kadonaga
11/14 Third research paper, Kadonaga
11/16 Third research paper, Kadonaga
11/21 Other topics, to be announced
11/28 Student presentation NOON. Paper due.
11/30 Student presentation
12/5 Student presentation
12/7 Test
12/14 1:30 Final exam
Tests and Written Assignments:
Your grade for this class depends on 3 lecture tests (each worth 100 points), a final exam (100 points), a class presentation of lab results (50 points), class participation (50 points), and 1 paper (worth 100 points; see below.) Lecture tests will emphasize the material covered in the previous section of the course (~8 lectures). The format for the tests and final exam will depend on the material, although standard short-essay questions will make up the bulk of the tests. Part of the test may be a take-home section.
The topic of the paper is some aspect of molecular biology not covered in the class. Everyone should have picked a topic by early October. Your topic should be cleared with me before you really start to do the research (10 points for picking the topic). Once you have a topic, a little bit of reading should allow you to define the basic structure of the paper. I need an outline of the paper by the middle of October so that we can make any mid-course corrections that are necessary (10 points for the outline). At any point in this process, I will gladly go over a first draft of the paper with you so that we have no surprises. I need at least one draft to review by 11/2 (10 points for the first draft). The last 70 points will be awarded on the merit of the writing. A few possible topics to start thinking about for the paper include:
Cell cycle control
Specific diseases
Isolation and characterization of a specific gene
Use of molecular biology in population genetics
Genome projects
New sequencing technologies
Comparitive genomics
Specific genetic regulatory systems
Drug development based on genetic information
All of these are too broad. They are given just to get you thinking. You should pick a small topic where reading 5-10 papers from the primary literature will bring you up to speed. This paper should be word-processed and conform to standard rules of English spelling and grammar. Significant deviations from this format may result in up to 20% deduction in points.
The Lab project.
The first 2-3 weeks of lab will involve you getting good at a basic set of technical skills; you will then take on a basic project in molecular biology. It may be in gene expression, population genetics, molecular analysis of pedigrees, development of a technique that we don't have working in the lab right now, or some other project that seems to be worth while. We'll just have to talk it out, to figure out what you are going to do. At the end of the semester, you will present the topic and the results to the class. My guess is it will involve a 15-20 minute presentation. This isn't high drama; it's basic science. I'm more worried that you learn a lot about molecular biology than I am worried that you have a polished presentation.
Grading
540-600 points (90-100%) = A
480-539.5 points (80-89.9%) = B
420-479.5 points (70-79.9%) = C
360-419.5 points (60-69.9%) = D
< 360 points (below 60%) = F
Everything but this grade distribution is appealable. If you have a problem with something having to do with grades (or anything else), let me know and we will figure out a solution.
Notes on plagiarism.
You may discuss written assignments with each other. However, it is essential that the final product of the written assignments be individual projects. Please note the following rules for plagiarism.
1. Make sure that you are responsible for your wording. It is your responsibility to make sure that you put concepts in your own words, not those of a common study group or text. Similar wording and sentence structure are indicators of plagiarism. Copying, then altering a passage slightly so that the wording is not exactly the same as the original is still plagiarism.
2. Give credit to sources. If you do use wording or a significant body of ideas from another source, you must give credit to that source. This means including correct references and page numbers for the source. You can't use the instructor, another student or the textbook as a source. Using someone's work without giving credit is plagiarism.
Don't depend extensively on quotes from other sources. Written assignments are to see if you understand the material. If all you do is quote from outside sources, you haven't shown me that you understand the material. Work to express your answers in your own words.
There are only so many ways to describe many phenomena. The use of jargon words and phrases in genetics is not plagiarism. Plagiarism is the use of significant sections (a sentence or more) from another source without giving credit to the person who produced the original.
3. Response to plagiarism. If I encounter written assignments that seem to be plagiarism, the students involved will be given the opportunity to explain. If the explanation is not satisfactory to all parties involved, an independent member of the science faculty will review the material. If the material is deemed plagiarism, then all of the papers involved will be given a score of 0 (zero). In addition, college rules for dealing with plagiarism will be enforced. This involves reporting the infraction to the Academic Review Board. A second offense will result in a grade of “F” for the course.
Early papers.
I will look at first drafts of papers up until 2 days before the paper is due. The closer to the due date, the less information you will get back from me. This is a simple matter of time. As the due date gets closer, the number of students asking for input increases; I have less time to review each paper. In any event, I will point out where there are problems with a paper and possibly suggest where to go to get the solutions to these problems. I will try my best to catch all of the problems, but given time constraints, I may miss some. Don't assume that I have caught everything. It's your paper, not mine. It's your responsibility to make sure everything is in it that you want in it.
Late papers.
My policy for late papers is: 20% of the maximum point total for the paper will be deducted from the score for each day that the paper is late. (A paper is one day late if it is from 1 minute to 24 hours late.) Getting the paper in on time makes sense. The assignments and due dates for papers are announced long in advance. It is difficult to imagine an excuse that would justify submitting a paper late. It is conceivable that such an excuse is out there. If you think that you have such an excuse, let me know and we'll discuss it. I might waive or reduce the 20% deduction.
Late tests.
The only sure excuse for taking a test late is a death of self or immediate family. Everything else you need to discuss with me. In all cases I need some sort of independent confirmation of the excuse. This may be a doctor's appointment slip or some other “paper” confirmation. If the issue causing you to miss a test is too private to discuss with me, then I will depend on another member of the faculty at Stonehill to confirm your excuse. Just let me know who to talk to. Various deans, members of the counseling center and other faculty members have been helpful in the past.
A makeup test will cover the same material a the original test, although the format may change. The test must be given as close to the date of the original as possible. When I grade a makeup test, I try to keep the grading on a par with the original. However, since the formats of the test may be different, it may be impossible to prove that the grading is comparable. This is just one of the problems with makeup test.
Students with documented disabilities.
If you are seeking classroom accommodations under the Americans with Disabilities Act, you are required to register with the Center for Academic Achievement, located in Duffy 109. To receive academic accommodations for this class, please request an accommodation letter from the Center for Academic Achievement and meet with me at the beginning of the semester.