Syllabus - Fall 2009

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Course Home Page | Laboratory Schedule

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Grading | Prerequisites | Computers | Attendance and Exam Policies |Honor Code | Learning Objectives

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Course Home Page: http://csm.jmu.edu/biology/courses/bio480_580/home.html

Instructor:  Dr. Terrie Rife
Office Number: 208 Burruss
Phone Number: 568-3343
Email: rifetk@jmu.edu
Office Hours: T 9:30 a.m. - 11: 30 a.m., W 1- 3 p.m. and F 10 - 11 a.m. by appointment

Lectures:.  MWF 9:05- 9:55 a.m. in Burruss 238.
Text:  Lodish et al. 2007.  Molecular Cell Biology, 6th ed.  Freeman
Laboratory: Burruss 328 - Section 1: Monday - 1:25-5:15 p.m., Section 2: Tuesday- 1:30 p.m.- 5:20 p.m.
Lab Text:  All written materials needed for the laboaratory are available on the internet.  You can link to the materials from the course home page.

• Laboratory Procedures. Available online. Prior to each laboratory meeting print out the laboratory procedure(s) that will be conducted that day and bring them to lab.

Grading (1000 pts) TR>

Item	Date Scheduled	Points
Lecture Quizzes (three total- two will count - 10 pts. each)	To be determined in advance	40
Lecture Exam 1	Friday, September 11	80
Lecture Exam 2	Friday, October 9	100
Lecture Exam 3	Friday, November 6	100
Final Exam	Monday, Dec. 7, 8 a.m. - 10 a.m.	120
Midterm Lab Report	Friday, October 23	120
Midterm Oral Report	Friday, October 23	50
Midterm Lab Exam	Friday, October 30	120
Assignments (Lecture (60 pts.) and Lab (90 pts.))	Throughout Semester	150
Final Lab Report	Friday, Dec. 4 by Noon.	120

Prerequisites

Students enrolled in this course should have satisfactorily completed four semesters of chemistry, including organic chemistry, BIO 214, Cell and Molecular Biology and BIO 224, Genetics and Development. Students who have not completed these courses should understand that the instructor will assume that all students have such a background.

During this course you will be required to use the internet to obtain information. You will need access to a computer which allows you to use e-mail and the World Wide Web. A list of campus facilities for students can be found in the "Computing Reference" guide which is available at the Help Desk, located in Frye Hall.

Attendance will be taken only on specified lecture days where class participation is required. Students will be informed of these days in advance. Attendance and participation in these class periods will count toward the lecture assignment grade. Students who miss the mandatory class days may write three to five page papers on the subjects missed or another approved topic to make up the point values.  Note that students who attend lecture regularly do much better than students who miss several lectures.
Attendance in laboratory is mandatory.

Students are required to take examinations and turn in assignments at the scheduled times (see above). Only under extenuating circumstances will a student be permitted to make up an examination or turn in a late exam. These are limited to severe illness and family emergency. Such instances must be documented. In the case of severe illness, acceptable documentation is limited to a signed note from a doctor indicating that the student was too ill to sit the exam or a verifiable record of visit to the JMU Health Center on the day of the exam. In the case of family emergency, acceptable documentation is limited to a signed note from a parent or guardian stating that a family emergency prevented the student from sitting the exam. It is not necessary that the instructor be told the nature of the illness or family emergency which prevented the student from sitting the exam.

If a student wishes to appeal an exam or report grade, they must present their case to the instructor within one week of receiving the graded exam. After one week, no appeals will be accepted, regardless of their merit.

Assignments and Take-Home Examinations will be docked 10% for every day they are late.

JMU Disability Policy

Students with disabilities who require reasonable accommodations to fully participate in course activities and/or meet course requirements must register with the Office of Disability Services (ODS) and contact me to discuss access issues. ODS will provide you with an Access Plan Letter that will verify your need for services and make recommendations for accommodations to be used in my classroom.  ODS is located in the Wilson Learning Center, Room 107; Phone: 568-6705

JMU Honor Code

Students are referred to the current student handbook for a description of the university honor system. All provisions of the honor system are applicable in this course, including the violations listed in the handbook. The collaborative nature of the laboratory encourages students to work together, however, and collaborative work such as preparation of the posters and planning and execution of laboratory experiments are not considered violations of the honor code.

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Class Registration Information

Students are responsible for registering for classes and for verifying their class schedules on e-campus. The deadline for adding a Fall Semester class without instructor and academic unit head signatures is Tuesday, September 1, 2009. Between Tuesday, September 1, 2009 and Thursday, September 10, 2009, instructor and academic unit head signatures are required to add a class for Fall Semester 2008. No student will be allowed to register for a Fall Semester class after Thursday, September 10, 2009. No exceptions will be made to these deadlines.

BIO 580 Requirements

In addtion to the items listed here, BIO 580 students are asked to complete additonal requirements see http://csm.jmu.edu/biology/courses/bio480_580/mlab/BIO5 80 requirements.html or 580 requirements.

I. The Basics of Molecular Biology (Lodish Chapters 2-5)

• Objective 1: The Chemistry of Life: a review of chemical bonding and molecular interactions in aqueous solutions.
• Objective 2: Understand the molecular structure of proteins, amino acids, nucleotides, nucleic acids,  and genes, and the dependence of function on structure.

II. The Molecular Processes: Transcription, Translation and Replication (Lodish Chapters 4,7-8, 20,21,22)

• Objective 3: Learn the general biochemistry of transcription and understand the general process transcription initiation control in both prokaryotes and eukaryotes.
• Objective 4: Understand the biochemistry of translation
• Objective 5: Learn the fundamental processes of genome replication and repair
• Objective 6: Understand the detailed mechanisms of transcriptional and post-transcriptional processing in eukaryotes and the role of these process in control of gene expression.

III. Molecular Biology at the Genomic Level (Chapter 6 and 24)

• Objective 7: Understand genome organization at the molecular level
• Objective 8: Become Familiar with Basic Genomic Data Bases and how to use them
• Objective 9: Become Familiar with Genomic Methods For Analysis of Protein, RNA and DNA Structure and Function

IV. The Science of Molecular Biology

• Objective 10:  Be able to articulate fundamental scientific, social, political and ethical issues in biotechnology and its application in the fields of medicine, agriculture and forensic science.
• Objective 11: Understand some of the major methods used by molecular biologists and study their application through several case studies.