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. Bio/Chem136 is an extension of first semester biochemistry (Bio/Chem135). This course covers selected biochemistry topics in depth and places significant emphasis on reading and discussing biochemistry research articles. The format of Chem136 will primarily consist of student-led group problems and discussion of readings from texts, review articles and research articles.

This semester the Chem136 lab features a semester long project on the purification and spectroscopic analysis of the enzyme lysozyme. Each student will gain direct, individual experience developing a purification scheme, performing kinetic analysis, and investigating the structure using several advanced fluorescence techniques.

 Course Information

Class Format Presentations Testing Writing Assignments  Grading General Outcomes
 Writing Outcomes   CWAC advising  Library support  Disability Services

Professor
Jeffrey A. Sigman, Ph.D.Schedule2018
312 Brouseeau Hall
This email address is being protected from spambots. You need JavaScript enabled to view it.
925-268-0970

Meeting Times
Lecture: Mon/Wed/Fri 915am-1020am
Room: BROH 314
Lab*: Tue 115pm-515pm and scheduled instrumentation time
Room: BROH 329

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 2,535 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 3,120 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 (6th or 7th edition)

Writing Research Papers Across the Curriculum, by Susan M. Hubbuch
Write like a chemist [electronic resource]: a guide and resource byMarin S. Robinson 

Supplemental reading
Biochemistry, Voet, 4th ed.
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 Bio/Chem135 (or equivalent)
C- or better in Engl-005

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 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. It will be graded. 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. 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 the research review 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 2 one-hour long exams during the semester and a quiz every other week. Exams may include a take-home component.

Exam Dates
Exam #1 March 14th
Exam #2 April  23rd
Final Exam Wed May 20th 8-10am

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

Writing Assignments

Research Review article: The paper will be written in the form of a review article in a biochemisry journal (examples will be distributed in class) and will derive from primary research. Primary research studies can include experimental research published in journal articles and patents.  Books, reference handbooks, review articles and textbooks may be used to develop a basic understanding, and to discover the primary research studies.

The purpose of this assignment is to investigate, understand and communicate about a specific drug – drug target interaction by reading and compiling into a coherent summary at least ten primary research studies. Possible areas to explore include the structure of the target, the structure of the drug, a comparison of the drug and the native substrate, the nature of the drug-target interaction, the mechanism of action, the metabolic process and/or chemical reaction that is interrupted, and the technique and process by which the drug was discovered, such as combinatorial, natural product research, and structure-based drug design. RUBRIC

Schedule (for more details see the course calendar):

Mandatory Library Workshops
Prior to Week 4: Explore the resources in the assignment and your textbook and identify at least 1-3 drug-drug target interactions as possible topics to research.
Prior to Week 7: Complete Research Study File reports for at least 5 primary resources.

Understanding Scientific Writing
Prior to Week 7: Read Section 1, Module1 from How to Write Like a Chemist
Prior to Week 11: Read Section 2 Graphics, References, and Final Stages of Writing

Drafts
Prior to Week 10: First draft of paper due
(1) You must schedule to an individual meeting with your professor to discuss your first draft and the writing rubric
(2) Each student will read two peer papers (randomly assigned with names removed) and evaluate it using the rubic.

Prior to Finals Week: Final Draft of paper due

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

  • two exams (125 points each) and one final exam (150 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]
  • review article writing assignment (150 pts)
  • oral presentation (35 pts)
  • pre-class assignments (3-5 points each, 75 pts max)
  • quizzes (50 points)
  • modeling projects (40 pts)
  • lab will be worth 250 points (approximately 25% of your total grade). Lab grades will be calculated based on notebook pages (75%) and the research project paper (25%).

1000 total points (~60% evaluation of written work)


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
  • enzyme kinetics, mechanism, and inhibition
  • carbohydrate structure and function
  • lipid structure and function
  • organization and operation of cell membranes
  • biochemical signal transduction
  • metabolic pathways and their regulation

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 circular dichroism spectroscopy

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)

Written and Oral Communication (these will build off of what you learned in English 5)

Students will be able to:

  • Recognize and write about biochemical topics in clear, well-constructed sentences and logical paragraphs using appropriate scientific language (exams, review article, notebook)
  • Understand and effectively communicate scientific information for peer scientists in the format of research and review articles and laboratory notebooks
  • Analyze data and construct evidence so as to provide clear support of a hypothesis or exploratory question (applies to the lab notebook and formal writing assignment)
  • Use the process of writing (formulation of a hypotheses, discussion and representation of data, drawing conclusions, brainstorming, collaborating, outlining, researching, drafting, revising, and reflecting) to enhance understanding of the biochemical concepts (this particularly applies to the lab notebook and formal writing assignment).

Information Evaluation and Research Practices  (these will build off of what you learned in English 5 and Chem Lit)

Students will be able to:

  • Explore a topic and search for relevant material in handbooks and journal articles using the library biochemistry subject guide, databases and search engines (Web of Science, PubMed, Patent Database)
  • Understand different types of resources (Primary Research Article*, Patent*, Review Article, Handbook and evaluate the references for a incorporation in a scientfic paper
  • Integrate and cite evidence using the ACS style guidelines
  • Understand the concept of intellectual property and practice academic honesty

 

 

Free Writing Advising at the Center for Writing Across the Curriculum

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.

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.