CHEM 351, Fall 2008 Page 1 of 8 CHEMISTRY 351: BIOCHEMISTRY Term: Prerequisites: Class time: Class location: Instructor: Inst. Office: Inst. Office hours: Inst. Phone: Inst. E-mail: Course Objective: Fall, 2008. Two semesters of Organic chemistry (CHEM 201 and 202). Quantitative chemistry (CHEM 250 from CSUSM or equivalent courses from another collage) with a minimum grade of C (grade point 2.0). 10 a.m. - 11.15 a.m. Mondays and Wednesdays. MARK 101. S. Jayasinghe (Jay), Ph.D. Sci II, 229. Monday and Wednesday from 11:30 a.m. - 12:30 p.m. or by appointment. 760-750-8075 E-mail communication will be via WebCT. E-mails sent to the instructor s campus e-mail address will NOT be returned (unless in the case of an emergency). Use the instructor s campus e-mail (sjayasin@csusm.edu) only in the case of an emergency. Intended for the science major the object of this course is to introduce the student to the fundamental concepts and language of biochemistry, and to the principles that govern the structure and behavior of biological macromolecules. Student Learning Outcomes: Upon completion of this course students should be able to demonstrate their knowledge regarding: 1. the various forces that help maintain the structure of biological macromolecules. 2. the structure and function of the important biological macromolecules: proteins, Carbohydrates, Lipids (and Nucleic acids). With regards to proteins students are expected to demonstrate: a. a detailed understanding of the different structural levels of proteins. b. their knowledge of the forces that contribute to the formation of a proteins unique three-dimensional structure c. their knowledge of methods utilized in protein purification d. their ability to use computational tools to gather information regarding the structure and function of proteins. 3. enzyme kinetics, enzyme specificity, the mechanisms of enzyme action, and enzyme regulation.
CHEM 351, Fall 2008 Page 2 of 8 4. the basic principles of thermodynamics as they apply to biochemical processes and how high energy molecules are utilized to provide the energy requirements of biological systems. These are general learning outcomes. Students are responsible for everything we discuss in class and available to you through your textbook or class notes. Textbook (Required): WebCT: Biochemistry by R.H. Garrett and C. M. Grisham., 3 rd Edition, Thompson, Books/Cole publishing. The course website can be accessed via the campus WebCT system. The following will be available or done through the WebCT site: 1. Posting of all assignments (including the term paper). 2. Submission of all assignments and the return of graded assignments (also see below). 3. E-mail communication with the instructor and receiving notices from the instructor. 4. A calendar tool indicating important course/assignment dates. 5. The syllabus. 6. Lecture slides (also see below). 7. Links to worthwhile biochemistry related web sites. If you are not already familiar with the use of WebCT (version 6) please consult the IITS help desk or the instructor as soon as possible. Lecture Notes: PDF files of lecture slides are available online via webct. It is highly suggested that you print a copy of these files and bring it to class with you. Some lectures contain upwards to 40-50 slides,and therefore, it may be beneficial to print more than one slide per page (4-6 slides per page works well). These lecture notes should NOT be considered as a substitute for attending class. These slides are not comprehensive lecture notes. They are intended to serve as a starting point for taking your own notes. You will notice that the notes contain more questions than answers.
CHEM 351, Fall 2008 Page 3 of 8 Topic List: Unless otherwise noted all chapters refer to the course textbook. Given below is the topic list for CHEM 351 for the fall semester of 2008. This schedule and topic list applies to the Monday/Wednesday section only. Although every attempt will be made to adhere to this list the instructor reserve the right to adjust the time spent on each topic as well as the order of the topics. Read the relevant chapters in the textbook before the lecture. Date Topic Readings Assignments Suggested Homework 8/25/08-8/27/08 Chemistry is the logic of biological phenomena All of chapter 1 2, 3d, 6-8, 10, 12, 13 8/27/08- Thermodynamics of All of chapter 3 1-4, 12, 14 9/3/08 Biological Systems 9/3/08-9/10/08 Water: the medium of life All of chapter 2 1, 2b, 2f, 5, 12, 14, 16, 17 9/10/08-9/17/08 Amino acids All of chapter 4 1, 2, 4, 5, 7, 13, 14 9/17/08- Proteins: Their Primary All of chapter 5 including 2, 10, 11, 13, 9/24/08 Structure and Biological appendix 14, 15 Functions 9/29/08 First Mid-Semester Examination 10/1/08- Proteins: Secondary, All of chapter 6 3, 4, 7, 8, 15, 10/8/08 Tertiray, and Quaternary Structure 10/15/08 Writing assignment 1. (Due 1 week after we finish chapter 6) 10/8/08-10/20/08 Enzymes: Kinetics and Specificity Chapter 13.1-13.4, 13.6,13.7 1, 2, 4, 5, 11, 16, 17. 10/22/08 Web based assignment. Due two weeks after we complete chapter 6. 10/20/08- Mechanisms of Enzyme Chapter 14.1-14.7. In section 1, 8, 9, 10, 11, 11/3/08 Action 14.7 we will only discuss (and therefore you are responsible for) serine proteases. 12, 14, 15 10/27/08 Second Mid-Semester Examination 11/3/08-11/10/08 Enzyme Regulation Chapter 15.1-15.3. In section 15.3 we will only discuss (and therefore you are responsible for) headings on page 483. 11/17/08 Writing assignment 2. (Due 1 week after we finish chapter 15) 1, 2, 13 11/12/08-11/19/08 Lipids Chapter 8.1-8.3, 8.7 1, 3, 4, 6, 11, 16, 17 11/24/08 Membranes and Chapter 9.1 and 9.2 4, 5, 12, 13, Membrane Transport 14 11/26/08 Third Mid-Semester Examination 12/1/08 Writing assignment 3. (Due 1 week after we finish chapter 9) 12/1/08-12/4/08 Carbohydrates and the Glycoconjugates of Cell Surfaces Chapter 7.1-7.4 1, 4, 5b, 6, 16
CHEM 351, Fall 2008 Page 4 of 8 Homework: Exams: Suggested homework problems are given alongside the topic list. These problems will not be collected nor graded. It is, however, highly suggested that you do these problems. It is entirely possible that some exams questions will be based on these homework problems (or may even be the exactly the same). There will be three (3) mid-semester exams and a final examination. The mid-semester exams will be one hour in length. The three mid-semester exams are scheduled as follows: 1 st mid-semester exam Monday, September 29, 2007 2 nd mid-semester exam Monday, October 27, 2007 3 rd mid-semester exam Wednesday, November 26, 2007 The final examination is comprehensive, and is scheduled for Wednesday, 10 th December 2008, from 9:15 a.m. to 11:15 a.m. The final exam is two hours in length. of NOTE: The time of the final is NOT the same as regular class time. Make up examinations will only be given if the student has a valid excuse (severe illness, death in the family, etc.) and notifies the instructor prior to test time (if possible). No make-up examination will be given unless the instructor is notified of the emergency within two (2) days of the test. Exams will contain multiple choice, short answer, and essay type questions. Please bring a scantron. Web Based Assignments: As a biochemists/chemists/biologists/health care professionals you will need to be familiar and comfortable using online databases and tools to mine information relevant to your field. In order to develop some of these skills you will complete a web-based assignments that deal with mining information about protein structure and function. This assignment is available via WebCT. The due date is posted on WebCT (and is also shown above). Although you may work in groups to complete this assignment, all submitted work must be your own. All assignments must be submitted as PDF files through the course web site on WebCT. The assignment is worth 10 points. Late submission will be assessed a 2 point penalty per day of lateness. Web-based Assignment Grading Criteria: The web-based assignment will be graded for completeness and correctness. A completed assignment in which all questions/steps in the assignment have been answered will be awarded 10 points. 1-2 points will be deducted for each question/step that has not been completed or is incorrect. Writing Assignments: In your future careers as a biochemist/chemist/biologist/health care professional you will have to read and interpret primary literature and communicate your understanding through effectively written reports. In order to develop this skill you will complete three (3) writing assignments during the semester. Due dates are posted on WebCT ( and are also shown above).
CHEM 351, Fall 2008 Page 5 of 8 Writing Assignment Grading Criteria: For each assignment two articles from the primary literature will be made available to you via webct. Your task will be to read one of these articles carefully, and critically, and to write a three to four page summary of the overall importance of the study, hypothesis tested, methods used, findings and their impact on the field, and any future work needed. This is not an exercise in paraphrasing. The summary must be written in your own words. It is expected that you will have to do some additional reading of the primary literature and your textbook to successfully complete this task. Your final submission must contain: a. A cover page which should include your name, information (title and name of authors) about the article you are reviewing, date of submission, and course abbreviation (i.e. CHEM 351). b. A properly formatted reference page, which should include any other sources that you used to help review the article. References should be formatted in the style used by either the (journal) Biochemistry, or the Journal of Biological Chemistry. Cover and reference pages do not count towards the page limit. The science librarian will be able to help you carry out your literature search using medline or pubmed. If you are not sure how to summarize information in the article, or are not clear what you should summarize, please see contact the instructor prior to spending significant time writing. Some journals may not be available at CSUSM. Get started on the literature search early so that you can obtain your articles through interlibrary loan in a timely manner. Your papers should be type written (using 12 point Times font), single spaced documents with 1- inch margins. Papers must be submitted via WebCT using the Writing Assignment 1/2/3 link found on the course content page. You should use the file upload method to submit your paper. Each writing assignment is worth 10 points. Late submission will be assessed a 2 point penalty per day of lateness. Points Assessment Criteria 10 Excellent The paper is well written (spelling, grammar, etc.) and conveys the student s understanding of the material presented in the research article. The student has consulted, and incorporated appropriately, additional references to help clarify the material in the article. 8 Very good The paper is well written (spelling, grammar, etc.) and conveys the student s understanding of the material presented in the research article. 6 Good The paper conveys the student s understanding of the material presented in the research article. However, the student has failed to summarize one of the required sections. 4 Fair The student has not adequately summarized the research article or has made a major error in interpreting and summarizing its contents 2 Poor The summary does not convey the student s understanding of the material presented in the research article. 0 Assignment was not turned in, was turned in too late or there were serious concerns of plagiarism. Web and Writing Assignment Submission: Web and writing assignments must be submitted via WebCT. Please DO NOT submit hard copies of your work.
CHEM 351, Fall 2008 Page 6 of 8 Assignments and the Term paper should be properly paginated and should contain 1-inch margins. Reading-based Assignment: After the conclusion of each chapter you will be given a 5-minute in-class writing assignment. Your task will be to answer one question based on the reading material. You will be given 1 minute to look at the question and formulate an answer. You will then be given 5 minutes to write as much as you can in answer to the given question. Grading (points): These assignments will be given at the beginning of class on the day following the conclusion of the chapter. Each assignment is worth 2 points. Each completed assignment will be awarded full points as long as the answer pertains to the question given. No make-up assignments will be given. Type of Assessment Points Percentage of Total 3 mid-semester examinations 150 54 Web based assignment 10 3 Writing assignments 30 11 Reading-based assignments (10 of 12) 20 7 Final examination 70 25 Total 280 100% Letter grades: Letter grades will be assigned based on the following cutoff values: Percentage Grade 90% and above A 88 89.9% B+ 82.1 87.9% B 80 82% B- 78 79.9% C+ 72.1 77.9% C 70 72% C- 68 69.9% D+ 62.1 67.9% D 60 62% D- 59.9% and below F Writing Requirement: Students with Disabilities: The University Writing Requirement will be satisfied upon completion of the web based and writing assignments. Students with disabilities who require accommodation must be approved by the Office of Disabled Student Services (DSS). Please contact this office as soon as possible and should meet with the instructor during office hours (or at some other mutually agreeable time). The DSS office is located in Craven hall 5205. Their telephone number is (760) 750-4905 or TTY (760) 750-4909.
CHEM 351, Fall 2008 Page 7 of 8 Academic Honesty: All students are expected to maintain academic honesty. This is especially true with regards to the completion of all writing assignments. All submitted work must be your own and must be written in your own words. Use of Plagiarism Detection Software: All students should be familiar with the university policies and procedures concerning academic honesty as detailed in the university catalog. An online version of these polices and procedures can also be found at: http://lynx.csusm.edu/policies/procedure_online.asp?id=187 Cheating, plagiarism, and other forms of academic dishonesty will not be tolerated. If you are caught cheating on an exam you will receive a grade of zero. All cases of academic dishonesty will be reported to the dean of students for appropriate action. Where appropriate the instructor will use software (TURNITIN) for the detection of plagiarism. All writing assignments submitted via webct are automatically checked for plagiarism. Plagiarized work will not be graded (also see above). Classroom Behavior and Student Code of Conduct: Students are expected to respect and follow standards of student conduct while in class and on the campus. As your instructor, I have the following expectations concerning your behavior in this class: 1. Promote a courteous learning atmosphere by exhibiting mutual respect and consideration of the feelings, ideas, and contributions of others. 2. Practice consideration for others by maintaining a clean and orderly classroom. 3. Recognize everyone s opportunity to contribute information in a relevant and meaningful manner by not monopolizing discussions, interrupting, interjecting irrelevant, illogical or inappropriate questions or comments. 4. Do not dominate class discussion give others a chance to contribute! 5. If you must eat in class do so discreetly. Use of Electronic Devices: The use of cell phones, PDAs, or any other electronic device during exams is not allowed. Scientific calculators are permitted. Use of Cellular Phones: All cellular phones must be set to the silent mode. Please refrain from using your cellular phone during class. If you must answer your phone, due to an emergency, please leave the classroom. HOW TO STUDY CHEMISTRY IN ORDER TO EARN A GRADE OF A, B, OR C. 1. Take good lecture notes. You are responsible for everything that I write or project on the board (except videos). Make use of the PDF files of my slides (see above) to reduce the amount of writing you have to do in class. 2. Make flash cards of definitions, concepts, reactions, structures, and nomenclature that are covered in lecture notes. 3. Use your lecture notes/flash cards as a guide to your reading in the textbook. Read the relevant chapter (or chapter section) before coming to the lecture and after attending the lecture (yes, twice).
CHEM 351, Fall 2008 Page 8 of 8 4. Solve the homework problems. Some of the answers are in the back of the textbook. One of the best ways of learning is to find a study partner or to form a study group and work on the problems together. Doing the homework problems is how you develop the analytical/critical thinking skills to do well on exams. 5. Attend class. 6. If you have questions, ask. Make use of the instructor s office hours.