Biochemical Pathways Biology 361, Spring 2014 Instructor: Office: Office Time: Email: Lecture: Text: Lecture Notes: Course Website: Gregory Johnson, Ph.D. Thompson 257d W, 10:00-11:30 and 1:00-2:00 pm or by appointment gregoryjohnson@pugetsound.edu T&TH, 11:00-12:20 am, TH197 David L. Nelson and Michael M. Cox. Lehninger: Principles of Biochemistry, 6 th edition. W.H. Freeman and Company. 2013. Provided online after class as a PDF on Moodle. A Moodle site will be used to distribute lecture notes and other materials. http://moodle.pugetsound.edu/ Class description Biochemistry is a broad subject that has been touched upon in many of your prerequisite courses. Between Bio 111, The Unity of Life; Bio 212, Cell Biology; and Bio 311, Genetics; you have learned about carbon and water chemistry, biological molecules, conversion of chemical energy to ATP, protein structure and synthesis, enzyme kinetics, nucleotide structure, nucleic acid synthesis, and so on. Biology 361 is a course designed for life-sciences students interested in furthering their study of biochemistry, but who are not Biochemistry or MCB majors. Many of you are interested in a career in the health professions and will need evidence of training in biochemistry in order to proceed to post-graduate training. In order to make this course most useful to you, we will not take a comprehensive approach in studying biochemistry. Instead, in BIOL361, we will concentrate on the biochemistry topics that your prerequisite courses did not cover in detail. Specifically, we will focus on metabolic pathways and their regulation. Of course, since metabolic reactions do not happen in isolation, we will also draw upon knowledge of cell biology and genetics from previous courses. Course format Lecture: Reading: The lecture will include slides. These slides will be made available to you after lecture. However, the slides alone do not constitute complete lecture notes. You must attend class to get a complete picture of what has been presented. We will use the text, Lehninger: Principles of Biochemistry, as the primary supplement to topics presented in lecture. Student Presentations: Clear communication of technical information will be a vital skill in your post-graduate lives. To hone this skill, you will have multiple opportunities to present a topic related to biochemistry to your peers. Assigned presentations include, but may not be limited to, a review
Assessment presentation at the beginning of this semester, metabolic pathway presentation in the middle of the semester, and the literature review at the end of the semester. Time requirements will vary for each presentation, but will not exceed 45 minutes of in class presentation time. Your grade will be based on the following assignments: Exams: There will be three midterm exams. Exams will consist of short answer questions covering material from the lectures, readings, AND student presentations. Presentations: Your presentations will heavily influence your final grade. To promote improvement in your presentation style, the first presentation will be worth fewer points than your final presentation. Writing: For the final presentation project, you must write a mini-review paper covering your chosen topic. This will be graded on its merit alone; the quality of your presentation will not affect my assessment of your paper. Other brief writing assignments will be due throughout the semester. Participation and peer evaluations: There will be many ways for you to participate in our class. One of those ways is through participating in peer evaluations. You will be asked to critique your peer s class presentations. These critiques will be summarized then relayed to the presenters to ensure anonymity. These critiques are invaluable to the presenter as they can help to identify strengths and weaknesses in their presentation skills. Grading and other policies Handing in assignments: If you need to turn something in, turn in a hard copy of the assignment. You must have my permission to submit an assignment via email. If handing in an assignment outside of class, you must either hand it directly to me, or to Carol Curtin (Biology office: Thompson Hall room 223A). Do not put homework assignments in my mailbox or slip them beneath my door. Disputing a test grade: Return tests directly to me with a typed appeal attached to the front of your test. This appeal should indicate (1) which question(s) you would like re-graded and (2) why you are disputing the grade you received. I will also check each exam to ensure that the point total was correctly calculated. I will accept appeals up to one week from the date that the test was returned to you.
Late assignments: I expect assignments to be handed in on time. Coursework handed in after its due date will be graded at a reduced rate; late assignments will be docked 5% of the total points per day (including weekends). Academic Misconduct: Cheating, plagiarism, and any other forms of academic misconduct are serious offenses and will not be tolerated. You are responsible for understanding what constitutes plagiarism. Refer to The Logger (the university s academic handbook) for definitions of, examples of, and penalties for academic misconduct. At minimum you will receive a zero for the assignment/exam/paper in question. At the discretion of the instructor you may also be removed from the course. Grades Below is an approximate breakdown of how each type of assignment will contribute to your final grade. This point distribution may change slightly. Assessment Review presentation Exam 1 Exam 2 Exam 3 Final Presentation Final Paper Final Poster Participation, brief presentations, short writing assignments & critiques Total: Points 40 points 600 points Letter grades will be assigned as follows: Percentage Letter Grade Percentage Letter Grade 93-100 A 73-77 C 90-93 A- 70-73 C- 87-90 B+ 67-70 D+ 83-87 B 63-67 D 80-83 B- 60-63 D- 77-80 C+ <60 F
Tentative Schedule of Course Content (subject to change) The following is an outline of topics, associated chapters in Principles of Biochemistry and student activities, presentations and due dates that we will occur this semester. Topic/Activity Student Presentation / In Class Activities Intended Date Chapters Introduction 1/21 1 1/23 2 Protein structure and folding reviews; Buffering in biological systems and Acidosis Buffering 1/28 3 Enzyme Function and Kinectics 1/30 4 Enzyme kinetics and catalysis mechanisms Enzyme regulation Regulation of Enzyme Activity 3a Chymotrypsin Mechanism (In Class) Regulation of Enzyme Activity 3b 2/4 6 2/6 13 Principles of bioenergetics The Logic of Signal Transduction HIV Protease Activity (In Class) 2/11 Exam 1 2/13 Carbohydrate structure and function Glycolysis and Fermentation 2/18 7 Glycolysis Glycolysis Presentation by Whole Class 2/20 14 Gluconeogenesis The Citric Acid Cycle 2/25 Reciprocal Regulation of Glycolysis and Gluconeogenesis Glycogenolysis and Glycogenesis Citric Acid Cycle; Glyoxylate Cycle Electron Transport and Oxidative Phosphorylation Diagram for Regulation of Glycogenolysis; Diagram for Regulation of Glycogenesis High-Fructose Corn Syrup Papers (In Class Discussion) 2/27 15 3/4 3/6 16 Exam 2 3/11 Conferences in 257D (no lecture on this day) One page summary about Metabolic Pathway Topic 3/13
Spring Break 3/18 Spring Break 3/20 Fatty Acid Catabolism Trans Fat Activity (In Class) 3/25 17 Lipid Biosynthesis 3/27 21 Amino Acid Catabolism Diagram for dietary proteins, gastrointestinal track 4/1 18 Amino Acid Biosynthesis 4/3 22 Paper Due 4/8 Exam 3 4/10 Presentations 1, 2 and 3 4/15 Presentations 4, 5 and 6 4/17 Presentations 7, 8 and 9 4/22 Presentations 10, 11 and 12 4/24 Presentations 13, 14 and 15 4/29 Presentations 16, 17 and 18 5/1 Final Day of Class Take Home Poster Instructions Provided 5/6 Final Exam, 5/15, 12:00-2:00 pm Take Home Poster Due In class poster session 5/15