BMB 400: "Molecular Biology of the Gene"

Fall 2002

209S Henderson South, 12:20-1:10 p.m., MWF

Instructor: Ross Hardison, 206 Althouse Lab

Phone: 3-0113; e-mail: rch8@psu.edu

This course will survey the biochemical mechanisms for major genetic phenomena. Part One will discuss the nature of genes, genomes and chromosomes - the repositories of genetic information. Part Two will cover how that genetic information is perpetuated, starting with the mechanics of DNA synthesis and genome replication, followed by discussions on repair, recombination and transposition. Part Three will cover the pathway of gene expression - transcription, RNA processing, and translation. Part Four delves into mechanisms of regulating that pathway, with special emphasis on transcriptional control. Prokaryotic and eukaryotic systems will be integrated into the basic topics, hopefully illustrating the unifying concepts.

In addition to the primary text (listed above), you will benefit from additional readings in a supplemental text. These readings in the supplemental texts are intended to provide a broader overview of the topics, whereas virtually all the class coverage and examination material will be from the primary text. Any of several texts will work as a supplement. Some that are also used in other courses (and hence it is likely that you already have one or more) include: Genes VII by Benjamin Lewin, Principles of Biochemistry by Lehninger et al., and Molecular Biology of the Cell by Alberts et al.

I expect the students to read the material and to work the problems. Working the problems will greatly increase your understanding of the material and will also provide excellent preparation for the exams. To aid you in getting the most out of the class sessions, I have provided in the textbook most of the material covered and figures used as slides. I recommend that you bring this text with you to the class so your note taking will supplement and highlight what is provided, rather than trying to re-copy what is already there.

Your grade will be determined by your performance on several exams. There will be 4 major, scheduled exams. The three midterm exams cover (respectively) the material in Parts One, Two and Three. They will be given during the class period (50 min) and will count 80 points each. The final exam (which lasts 110 min) will count 160 points. 80 points will cover the material in Part Four, and the other 80 points will be comprehensive over the entire course material.

You will also be assigned a project using a few genomics resources on the web to explore the structure, function and conservation of a mammalian gene. This report is worth 100 points. The points for required work total 500.

For extra credit, of the order of 4 unannounced quizzes may be given in class at various times during the semester. These will be worth 5 points each. Points from these unannounced quizzes will be added to your point total for the course. Some additional web-based projects will be available for extra credit as well.

Summary of the scoring scheme: Points

Midterm Exam 1 80

Midterm Exam 2 80

Midterm Exam 3 80

Final Exam 160

Required Project Report 100

Total required 500

Extra credit (quizzes) 25

Additional projects 60

Final Total 585 maximum

Letter grades are assigned based on a "curve". For example, the class mean for many of my exams in the past has been roughly 65-70%. I use the mean to set the mid-point of the "B" range, and I assign other letter grade cutoffs based on that (this is a "B-centered curve").

I will use only the scores from the required work (maximum of 500 points) to define the cut-offs for the letter grades. Then I will assign your letter grade based on the combined points from the required work (exam plus required project) and the extra credit (quizzes plus additional projects). Thus your letter grade can only improve from the addition of these extra credit points.

No make-ups will be offered for the unannounced quizzes. Make-up EXAMS can be scheduled for students who must miss the exam. You must clear the excuse with me before the exam; examples of acceptable excuses are illness or a death in the immediate family. The makeup exam will be essay and problem-solving, either written or oral.

All Penn State policies regarding ethics and honorable behavior apply to this course (see links below for policy statements). Academic integrity is the pursuit of scholarly activity free from fraud and deception and is an educational requirement of this institution. All University policies regarding academic integrity apply to this course. Academic dishonesty includes, but is not limited to, cheating, plagiarizing, fabricating of information or citations, facilitating acts of academic dishonesty by others, having unauthorized possession of examinations, submitting work of another person or work previously used without informing the instructor, or tampering with the academic work of other students. For any material or ideas obtained from other sources, such as the text or things you see on the web, in the library, etc., a source reference must be given. Direct quotes from any source must be identified as such. All exam answers must be your own, and you must not provide any assistance to other students during exams. Any instances of academic dishonesty will be pursued under the University and Eberly College of Science regulations concerning academic integrity. Academic dishonesty can result in assignment of "F" by the course instructors or "XF" by Judicial Affairs as the final grade for the student.

Refer to the following URLs for further details on the academic integrity policies of the Eberly College of Science and the University: