BIOCHEMISTRY I

Course Overview: Welcome to Biochemistry II!! You have endured the pace of Biochemistry I, and signed on for yet another term – I think it’s the reward. This course is intended to help you learn biochemistry on your own. The course will include a mixture of lecture, discussion and student involvement. During the first part of the term we will cover a number of topics I think are important or particularly timely. Then, toward the end of the term, we will learn about topics you find interesting.

Course Objectives: Students should…

1. Understand the biochemistry of gene expression and its regulation.

2. Develop skills for interpretation and assessment of journal articles from primary literature in the field of biochemistry.

3. Gain experience in sharing new knowledge with others.

Course Content: We will continue to use Essentials of Biochemistry by Pratt and Cornely. In addition, review articles and readings of primary literature will also be assigned. Reading assignments will be accompanied by questions that you should answer before coming to class, as your participation in discussion is an important portion of your grade. You should consider your textbook as a background reference for understanding the articles and answering the questions I pose. Topics to be covered in class and the relevant readings from the text are listed below:

Amino acid metabolism Chapter 15 (pp. 463-475)

Proteolysis TBA

Protein interaction domains & Signal transduction TBA & Chapter 16 (pp. 503-515)

Nucleotide metabolism TBA & Chapter 3& 15 (pp. 475-482)

DNA replication Chapter 17

DNA repair and recombination Chapter 18

Transcription and RNA processing Chapter 19

Translation Chapter 20

Regulation of gene expression TBA

Genomics, proteomics and bioinformatics TBA

Mystery week TBA

Grading Policies: Your grade will be determined based upon your performance on two exams, in-class participation, an in-class presentation and the final exam with the following distribution:

Grade	Overall %	Grade	Overall %
A+	100-99.0	C+	79.9-77.0
A	98.9-93.0	C	76.9-72.0
A-	92.9-90.0	C-	71.9-67.0
B+	89.9-88.0
B	87.9-83.0	D	66.9-55.0
B-	82.9-80.0	F	<55.0

Exams	40%
In-class participation	25%
Presentation	20%
Final Exam	15%

Final percentages will be rounded to the nearest 0.1 percentage point and then grades will be assigned as follows:

Exams: There will be two exams. Although there will be some “memory” work required, the exam questions will stress problem-solving. So, memorizing without understanding is not sufficient. Tentative exam dates are: Exam #1 on January 11^th,2008 and Exam #2 on February 15^th, 2008.

In-Class Participation: Participation is a vital part of this course, as we will have a discussion period nearly every Friday throughout the term. If you read the assigned material, complete the suggested study questions and get involved in class discussion, you should do well in this component of the course. However, remember that just opening your mouth is not enough.

· Discussion facilitation: A group of students will be assigned as discussion facilitators each week. When you are assigned as a facilitator, I expect that you will be prepared to help lead the discussion. I am looking for informed, well-considered comments and questions – that show you are thinking about the material. I do not expect that you will always understand everything, so will do my best to answer questions. The facilitator schedule will be prepared by the end of week 1.

· Another part of in-class participation will be your attentiveness and involvement during discussion – EVEN IF YOU ARE NOT AN ASSIGNED FACILITATOR!

· Problems from chapters and questions covering articles to be discussed will be assigned. These homework assignments will be collected, but not graded. However, they will be used in determining your participation grade and will be covered on exams.

· In-class presentations: An additional component of in-class participation is your attentiveness and involvement with your fellow students as they present to the class.

Presentations: A major objective for this course is to help you to learn biochemistry on your own and to share your new knowledge with others. You and two other students and choose a recent (within 1 year) journal article in biochemistry and research the background related to the article to present to the class during week 10 of the course. You and your partners will present the information to the class in two ways:

· A short background to the topic: This portion of the talk will be an introduction to new ideas or methods required to follow the research in your article of choice. For example, suppose you chose an article about site-directed mutagenesis of a mitochondrial transporter of a citric acid cycle intermediate in yeast. You would want to explain site-directed mutagenesis and/or membrane transporter function. This is important to provide your audience with important background material for understanding your journal article.

· Journal article presentation: You and your partners will present the journal article you chose. In presenting your journal article to the class, you will explain the goals or objectives of the study, the main figures/data obtained, the conclusions of the study and the future directions and implications of the results. You should point out any shortcomings or oversimplifications.

· You should endeavor to choose your journal article before the Christmas break. To aid you with this deadline, I will require that you turn in a copy of the journal article abstract for instructor approval no later than December 19^th, 2007.

· As you prepare for your presentation, you should plan to read a majority of the papers referenced in your article (usually about 10). Get those articles that must be acquired via interlibrary loan early - DO NOT PROCRASTINATE!

· Grading of presentations: The presentations will be graded on a variety of components including clarity, organization, visual aides and scientific understanding. I will give you a copy of the grading rubric for the presentations later in the term. In addition, I will ask your classmates to assess your performance. These “peer-review” grades will be included as a portion of your grade. Each member of the pair will receive an individual grade – not a “group grade” – so be sure that both of you participate!!! The presentation will make up 20% of your total course grade, or the equivalent of one exam.

Final Exam: A standardized exam in biochemistry produced by the American Chemical Society will serve as the final exam in this course. This is an extremely important chance for you to test your overall biochemical knowledge, and for the department to assess the biochemistry courses. The exam will cover information from Biochemistry I and II. Your grade will be based upon your performance relative to other students in our class rather than national norms. PLEASE NOTE: Our final exam is tentatively scheduled for the multi-sectional exam period on Tuesday, February 26^th, 2007 from 6-8pm.

Course Materials: Lecture slides, class handouts, assignments and other materials will be posted in on Moodle. The URL is http://moodle.augustana.edu/ ; Click on “CH – Chemistry” and then “CH412 Biochemistry II”. The enrollment key for the course is “Biochem Rules!”.

Tentative Schedule:

Week 1 (12/3-12/7)	Amino acid metabolism, Proteolysis
Week 2 (12/10-12/14)	Protein interactions & signal transduction, Nucleic Acids
Week 3 (12/17-12/21)	Nucleotide metabolism Presentation paper abstract due Dec. 19^th
Break	12/22/2007-1/6/2008
Week 4 (1/7-1/11)	DNA replication, repair and recombination EXAM #1 on January 11^th!!!!
Week 5 (1/14-1/18)	Transcription and RNA processing
Week 6 (1/21-1/25)	Translation
Week 7 (1/28-2/1)	Regulation of gene expression
Week 8 (2/4-2/8)	Genomics, proteomics and bioinformatics
Week 9 (2/11-2/15)	Mystery Week EXAM #2 on February 15^th !!!
Week 10 (2/18-2/22)	Student presentations, Final Exam Review
Final Exam	Tuesday, February 26^th, 2008; 6-8pm

Grade