Prerequisites

Students enrolled in this course should have satisfactorily completed Organic Chemistry (Chem 241 or 342) and Genetics and Development (BIO 224). Students who have not completed these courses should understand that the instructor will assume that all students have such a background.

Laboratory
Attendance in laboratory is mandatory. Failure to attend a laboratory session or extreme tardiness without a documented excuse for an illness or family emergency presented to the instructor will result in a 10% reduction of the lab portion of the grade for each lab day missed. In the case of an 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. Exceptions may only be made with prior instructor permission, see the general policies section below.

Moreover, Molecular experiments often require time outside of the scheduled lab. As often as possible students will be informed in advance of expectations outside of class for a given weeks experiment.

Lecture
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 laboratory assignment grade. Students who miss the mandatory class days may write three- to five- page papers on the subjects missed to make up the points missed.   Note that students who attend lecture regularly do much better than students who miss several lectures.

Note: Students and instructor together will choose five lecture classes to skip to make up for the extra-long lab times.

Examinations, Quizzes and Assignment Points
Students are required to take examinations at scheduled times. Only under extenuating circumstances such as a severe illness or family emergency will a student be permitted to make up an examination. Such instances must be documented and the instructor should be contacted as soon as possible after a missed exam. Exceptions may only be made with prior instructor permission, see the general policies section below. Quizzes cannot be made up although the lowest quiz grade for each student will be dropped. Daily Assignment Points cannot be made up. These points can be earned by correctly answering daily questions in lecture, presenting on timely journal or news article to the class with prior permission from the instructor, or participating in a designated lecture activity. Students will be given at least 50 points worth of daily questions throughout the semester so students attending regularly will have ample opportunity to earn the required 40 points even if they miss a day or two of lecture or a question or two.

All lab assignments and the take-home examination will be docked 10% for every day late.

General Policies
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.

Exceptions to scheduling of exams or a request to miss a mandatory lab must be made either during the first week of class or at least three weeks prior to the exam or lab to be missed. Requests should be made in person and must be reasonable. Reasonable requests include missing because of a verifiable reason such as a religious observance, school sponsored outing, or giving a presentation at a scientific conference.

Adverse Weather Event

In the case of an adverse weather event that causes a cancellation of a a lab, students will be required to make up the lab on the University scheduled make-up day.

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

Academic Honesty

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.

Making references to the work of others strengthens your own work by granting you greater authority and by showing that you are part of a discussion located within an intellectual community. When you make references to the ideas of others, it is essential to provide proper attribution and citation. Failing to do so is considered academically dishonest, as is copying or paraphrasing someone else’s work. The consequences of such behavior will lead to consequences ranging from failure on an assignment to failure in the course to dismissal from the university. Because collaborative work is valued, you will be encouraged to share ideas and to include the ideas of others in papers, but please ask if you are in doubt about the use of a citation. Honest mistakes can be prevented.

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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 September 6. Between Tuesday, September 6, 2011 and Thursday, September 15, instructor and academic unit head signatures are required to add a class for Fall Semester 2011. No student will be allowed to register for a Fall Semester class after Thursday, September 15, 2011. No exceptions will be made to these deadlines.

Course Description: Cellular constitutes and genetics are emphasized at the molecular level. This course builds upon basic molecular knowledge previously learned in BIO 214 and BIO 224.

Learning Goals for the Lecture:

Knowledge Objectives

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.
• Objective 3: Become familiar with the history of molecular research.
• Objective 4:  Be able to articulate how molecular biology is applied in the fields of medicine, agriculture and forensic science and some of the ethical concerns of its use.

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

• Objective 5: Learn the general biochemistry of transcription and understand the general process transcription initiation control in both prokaryotes and eukaryotes.
• Objective 6: Understand the biochemistry of translation.
• Objective 7: Learn the fundamental processes of genome replication and repair.
• Objective 8: Understand the detailed mechanisms of transcriptional and post-transcriptional processing in eukaryotes and the role of these processes in control of gene expression.

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

• Objective 9: Understand genome organization at the molecular level.

Skills Objectives

IV. Applying The Science of Molecular Biology

• Objective 10: Be able to apply molecular knowledge to analyze and criticize scientific data.
• Objective 11: Be able to design experiments to test hypotheses using molecular knowledge.
• Objective 12: Be able to utilize Basic Genomic Data Bases such as BLAST.

More Detailed objectives for Individual LECTURE EXAMS and QUIZZES can be found at: http://csm.jmu.edu/biology/courses/bio480_580/Objectives/objectives.html

Learning Goals for the Laboratory:

1. Formulate a hypothesis and identify relevant variables necessary to test that hypothesis.
2. Design and execute experiments to test hypothesis.
3. Obtain and organize Molecular data.
4. Analyze and interpret Molecular data.
5. Use effective professional communication in posters.
6. Use effective professional communication in oral reports.
7. Use mathematics to understand and analyze biological phenomena
8. Synthesize information and concepts, and apply that knowledge to new situations.
9. Experience working “at the bench” in a controlled environment.
10. Be able to perform several molecular techniques including microarray analysis, real time PCR, Western Blotting, protein, RNA and DNA isolation.

BIO 580 students will also gain experience in writing grant proposals.