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.

 Course Information

Class Format Presentations Testing Grading General Outcomes
 Lab Notebook Library support  Disability Services

Professor
Jeffrey A. Sigman, Ph.D.
312 Brouseeau Hall
This email address is being protected from spambots. You need JavaScript enabled to view it.
925-268-0970

Office Hours
Mon 230-430pm (Oct 14, 28, Nov 4, 18, 25)
Mon 5-6pm (Oct 7, 2, Nov 11)
Tue (all day by apppointment via Zoom)
Wed (430-630pm)
By appintment

Meeting Times
Lecture: Mon/Wed/Fri 1030am-1135am
Room: Galilieo Hall, Room 107
Lab*: Thu (130-530pm) and Fri (115pm-515pm) and scheduled instrumentation time
Room: BROH 309

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.

Texts
Lehninger Principles of Biochemistry, by Nelson, Cox (7th edition)

Supplemental reading
Biochemistry, Berg, Tymoczko, Stryer 5th ed. (online at pubmed books)
Proteins: Structure and Function, Whitford
Crystallography Made Crystal Clear, Rhodes (eText)
Research and Review articles

Prerequisites
C- or better in Chem106 (or equivalent)

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.
Peer Review sheets


Testing

There will be three one-hour long exams during the semester and a quiz every other week. Exams may include a take-home component.

Exam Dates
Exam #1 Wed Sept 25th
Exam #2 Wed Oct 23rd
Exam #3 Mon Nov 25th
Final Exam Mon Dec 9th 1030-1230am

Exams will consist three broad question categories:
1) short answer, multiple choice, and matching etc based on the reading.
2) Worked problems based on the assigned homework.
3) In depth problems (worked or short paragraph or data analysis) based on the worksheets and discussion from class.

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

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
Prior to Week 8 (Spr Break): Lab notebooks on purification of hen egg white lysozyme due
Prior to Finals Week: Three lab experiments on physical characterization of an enzyme and the lab pages on final independent project are due


Grading

Your grade will be based on your performance on

  • three exams (100 points each) and one final exam (175 points) [Note: Exams will be a combination of multiple choice, matching, and short answer (ie 2-7 sentences). At least 50-70% of the points on the exams will be short answer]
  • oral presentation (35 pts)
  • pre-class assignments (3-5 points each, 50 pts max)
  • quizzes and graded problems (75 points)
  • modeling project I (35 pts)
  • other modeling (15 pts)
  • lab will be worth 225 points (approximately 25% of your total grade). Lab grades will be calculated based on notebook pages (75%) and the lab exams (25%).

900 total points


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, your formal and lab notebook writing, and class participation.


Outcomes

Biochemical Concepts

Students should be able to comprehend and discuss the following topics in depth using the principles biology and chemistry:

  • protein structure and function
  • DNA/RNA structure and function
  • enzyme kinetics, mechanism, and inhibition
  • carbohydrate structure and function
  • lipid structure and function
  • organization and operation of cell membranes
  • biochemical signal transduction

Students will understand the basic theory of and application of the following tools towards enzyme structure determination and mechanistic investigations

  • X-ray crystallography
  • Molecular modeling and bioinformatics
  • UV-vis, fluoresecence, and NMR
  • Isothermal Titration Calorimetry

Lab Skills

Students will develop an increased ability to

  • generate, analyze, and interpret experimental evidence
  • design experiments and understand the limitations of experimental approaches
  • use appropriate techniques for handling and manipulating protein samples
  • apply quantitative skills—the ability to accurately and reproducibly prepare reagents and measure various quantities with high precision
  • use and understanding the operation of modern instruments, including pH meters, UV-vis and fluorescence spectrometers, UV-vis plate readers, and HPLC
  • work safely in the laboratory
  • conduct experimental work in an organized and observant manner and developing excellent record-keeping practices
  • analyze results using statistical, graphical, and other methods
  • assess the reliability and significance of results and designing appropriate follow-up experiments
  • interpret laboratoty data, drawing reasonable and appropriate conclusions
  • converse and collaborate with scientific peers in the appropriate “language” by using oral, written, and visual presentations
  • access, read, comprehend, and extract relevant information and ideas from the primary and secondary literature
  • work collaboratively with peers (on laboratory experiments)

 

Ask a librarian!

Need library sources but don't know where to start? Searching for a book, article, or data to support your argument? Not sure how to cite a source in your bibliography? Ask a librarian! 

Research help is available in person at the Reference Desk, by phone at 925-631-4624, and during reference hours you can even text a librarian at 925-235-4762 or chat with us live via the Library's website. Check the Library’s Ask Us page for details. (http://www.stmarys-ca.edu/library/ask-us)

Extended assistance by appointment is also available with Linda WobbeLinda is available at the Reference Desk Sunday's 2-5 pm and 6-8:30 pm. 

Library Subject page: Biochemistry

Disability Services

Reasonable and appropriate accommodations, that take into account the context of the course and its essential elements, for individuals with qualifying disabilities, are extended through the office of Student Disability Services. Students with disabilities are encouraged to contact the Student Disability Services Coordinator at (925) 631-4164 to set up a confidential appointment to discuss accommodation guidelines and available services. Additional information regarding the services available may be found on the Saint Mary’s website.

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.