Chemistry 136 - Advanced Biochemistry

Chemistry Department

Saint Mary's College of California

 

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Homology modeling, protein folding, misfolding diseases such as Alzheimer's disease, spectroscopic tools for structural characterization, carbohydrates and their role in cell signaling and drug design are few of the topics that will be covered in this course. Chem136 is an extension of first semester biochemistry (Bio/Chem135), however, it is different from most second semester biochemistry courses that focus solely on metabolism. Instead, the course covers a select few topics in depth and offer the chance for students to pursue a certain aspects of a topic through individual investigation and presentation to the class.

The format of Chem136 will primarily consist of student-led group problems and discussion of readings from texts, review articles and research articles. Lecture will form a minor portion of the course format. In order to accommodate diverse student interests, twice during the semester each student will give 15 minute presentation on a research article that covers an aspect of the a topic of interest to them that we did not have time to cover in detail during class.

For a more detailed look at the course see the Calendar list of topics.

 

 
Prof. Jeffrey Sigman
Gatehouse 312
(925) 631-8222
jsigman@stmarys-ca.edu
 
email is my preferred method of contact
 
 
 
         

  Course Information    
   
   
        Office Hours
   

Meeting Times Mon/Wed/Fri 1130am-1230pm. BROH 314 (Computer Room)

Texts Biochemistry Berg, Tymoczko, Stryer 6th ed.

Other texts Research and Review articles
Biochemistry
Voet and Voet 3rd ed.
Biochemistry Berg, Tymoczko, Stryer 5th ed.
Proteins Whitford 1st ed.

Prerequisite Bio/Chem135 (or equivalent).

Homework Homework will be assigned on a daily basis. Please check the Calendar for daily assignments. There will be some assigned problems as well as reading which must be completed BEFORE coming to class. In addition, some material and resources and activities are only available through the website. It is ESSENTIAL that you come to class prepared and have read the assigned material. Otherwise it will impossible to participate in the discussion. You are responsible for any additional background reading and research to understand key terms and concepts from the reading (especially if research and review articles). I will be available during office hours and via email to go over any difficulties from the assigned reading. You are also encouraged to consult with your peers.

Discussion. When applicable you will be graded discussion of review and research articles. I will keep a detailed notebook of the class discussion. Each day in which we discuss a review or research article you will be given a score of 0 - 4 based on your performance in the discussion. 0 = absent, 1 = present but did not participate and 2-4 depending on your level of participation. You will assessed both the quantity and quality of your questions and comments.

Presentations Each student is required to give two formal (10 to 15-min.) presentation during normal class time. The focus of the presentations will be on one research article selected by the student and approved by the instructor. Although the presentation is to focus on one article, you are still responsible for doing the appropriate background research to assist in your understanding of the article and to help you to answer questions at the end of the talk. You may use the WEB, Powerpoint, handouts or other formats to aid your presentation.

Additional guidlines --------- Peer Review sheets

Testing There will be 2 one-hour long exams during the semester.

Exam Dates

Exam #1 TBD

Exam #2 TBD

Final Exam (See final exam schedule)

Alternate exam arrangements will be considered only for excused absences with prior notification.

Grading Your grade will be based on your performance on two exams (100 points each) and two presentations (100 points), group work and in-class discussion (25-50 points). Lab will be worth 100 points (approximately 25% of your total grade). Lab grades will be calculated based on notebook pages (60%) and the end of semester project and presentation (40%).

Final letter grades will be assigned according to the percentage of points that you accumulate during the semester. The approximate ranges for letter grades will be:

A = 100-85% B = 84-70% C = 69-55% D = 54-40%

Your exact letter grade will be determined by a number of factors, including your performance on the final exam, the consistency of your performance during the term, and class participation.

Academic Honesty Students are expected to do their own work on all exams and quizzes. Violations of this policy will be vigorously prosecuted according to SMC Academic Honesty Procedures.

Tips for Success Keep up with the work! Assignments will be updated on a weekly basis. Check our website after each lecture for the assignments due before the next class.

Most reading material will be distibuted via email. Additional handouts will be given out in lecture or be available in the box outside my office. I cannot emphasis enough the importance of keeping up with the assignments. The material builds upon itself as the semester proceeds, so you must learn the early concepts to understand the later material.

Also, you are here at SMC to get the best possible education. Take advantage of the small class size and individual attention that a small liberal arts school can provide. Work together on assignments, and see me in my office as often as possible.

Outcomes

  1. apply the principles and perspectives of both biology and chemistry to:
    • protein structure and function
    • enzyme kinetics, mechanism, and inhibition
    • spectrocopic methods for structure and mechanistic investigations
    • carbohydrate structure and function
    • lipid structure and function
    • organization and operation of cell membranes
    • biochemical signal transduction
    • metabolic pathways and their regulation
  2. grow in their ability to generate, analyze, and interpret experimental evidence by
    • gaining experience in the design of experiments and understanding the limitations of experimental approaches
    • learning how to acquire representative samples free from interferences
    • appropriate techniques for handling and manipulating protein samples
    • practicing good quantitative skills—the ability to accurately and reproducibly prepare reagents and measure various quantities with high precision
    • using and understanding the operation of modern instruments, including pH meters, spectrometers, and HPLC
    • work safely in the laboratory
    • conducting experimental work in an organized and observant manner and developing excellent record-keeping practices
    • analyzing their results using statistical, graphical, and other methods; assessing the reliability and significance of results; and designing appropriate follow-up experiments
    • interpret their data, drawing reasonable and appropriate conclusions
  3. develop the ability to converse and collaborate with scientific peers in the appropriate “language” by
    • using oral, written, and visual presentations to share their work
    • accessing, reading, comprehending, and extracting relevant information and ideas from the primary and secondary  literature
    • working with peers on laboratory experiments and classroom presentations

 

 

 
Mon 1:00 - 3:00pm
Tue 9:30 - 11:00am
Fri 12:30-1:30pm
 
Additional Office hours

by appointment