In Structural/Physical Biochemistry students will learn to understand and apply facts and techniques of physical and structural biochemistry. They will build upon and apply knowledge from general chemistry, organic chemistry and introductory biology. The emphasis of this course is on macromolecular structures and biophysical techniques and will cover selected biochemistry topics in depth. Spectroscopic tools for protein structural characterization, protein folding and misfolding, enzyme mechanisms, DNA and RNA structure and function, and lipid and membrane structure are a few of the topics that will be covered in this course. See the attached schedule for a complete list. There will also be emphasis placed on learning to read and discussing biochemistry research articles. The format of the course will primarily consist of student-led group problems and discussion of readings from texts, review articles and research articles.
The laboratory portion of the course will feature two multi-week projects on the purification and analysis of an enzyme, lysozyme. Each student will gain direct, individual experience developing purification schemes, performing kinetic analyses, and investigating structure using several advanced spectroscopic techniques. Students will develop their own protocols and learn to evaluate their results in order to successfully complete experiments.
The start of lab will be reserved only as time to introduce concepts and procedures. Often lab partners will self-schedule a time to work on the lab.
Credit Hours: This course meets for three lecture periods per week for 65 minutes each period. For the 13 week semester, this is a total of 2,470 lecture minutes. In addition, you are expected to devote 6-9 hrs (450-600 minutes) per week outside of class. The lab meets once per week for 4 hours (240 minutes). This is a total of 2,880 lab minutes. In total, this meets or exceeds the contact hour requirement for courses at Saint Mary's College of California.
Class Format: The regular daily format will consist of (1) reading and a pre-class assignment, (2) an in-class activity, and (3) the homework assignments. Some classes will also have a short lecture but the majority of class time will be devoted to student work. The pre-assignment will vary in format but may require you to take an online quiz, produce a reading log (notes), contribute to a discussion board, and/or solve selected problems. The pre-assignments will be available from the course website. The in-class activity will be either student-led group problems or a student-led discussion of research articles. For discussion of research articles each group will elect or be assigned a group leader who will lead the discussion of the article. Groups will be randomized at various times in the semester. You will be evaluated on your participation in class. Homework will be assigned on a daily basis. Please check the daily assignments of homework problems from the text. In addition, some materials, resources and activities are only available through the website or Moodle. I reserve the right to give short quizzes at the start of class and collect homework without prior notice.
Presentations: Each student will give one formal presentation (~10-15 min.) that will be scheduled during normal class time or lab near the last week of classes. Individual presentation dates will be determined by lottery. The focus of the presentations will be on a primary research article selected by the student and approved by the instructor. You may use the WEB, Powerpoint, handouts or other formats to aid your presentation.
There will be three one-hour long exams during the semester and a quiz every other week. Exams may include a take-home component.
Exams will consist three broad question categories:
Lab Notebook: Your lab notebook pages will be collected and graded in two parts. Part one: Purification of hen egg white lysozyme. Part two: Physical characterization of an enzyme.
You must obtain a bound notebook (no spiral notebooks). Your laboratory notebook will build on skills you have developed in general chemistry and organic chemistry. The lab notebooks will be assessed using the following rubric. Please reveiw each area of the rubric (Clarity/Organization, Procedure, Results, Goals, Discussion) to help you in writing your notebook. Your notebook should provide a complete record of eveything you have done in the lab. It is not permissable to record data outside your notebook and then transfer to your notebook later. Instead, all of your rough notes, recording of data, and calculations should be included in your notebook and then rewritten for clarity if necessary. While the notebook is considered informal writing you are still expected to use appropriate biochemical diction.
Schedule (for more details see the course calendar):
Prior to Week 4: Meet with your professor to discuss your lab notebook and address questions about the rubric