CHEMISTRY 135 GENERAL BIOCHEMISTRY (Code 40238) Dr.

Peter Nemes Fall 2013 Office: DH 608 (924-4967; email: peter.nemes@sjsu.edu Office Hours: MW 1300-1500, (DH 608) Please make an appointment if you would like to see me at times other than those posted. CLASS MEETING TIME AND FINAL EXAM TIME: MW 1630 - 1820 Sci 142 Final: Thurs. Dec. 12, 1445-1700 REQUIRED TEXTS: 1. Horton, H.R., et al. (2012), Principles of Biochemistry, 5th ed. Prentice Hall 2. Scism, A. J. (2012), The Biochemistry Student Companion, 5th ed. Prentice Hall RECOMMENDED TEXT: 1. Segel, I.H. (1976), Biochemical Calculations, 2nd ed. Wiley PREREQUISITES: Biol 3 (with a grade of C or better), Chem 112B (can be taken concurrently) COURSE DESCRIPTION: This is a one semester, four-unit survey course in biochemistry. Major topics include protein structure and function, intermediary metabolism (bioenergetics, anabolic and catabolic pathways), and both local as well as global control of molecular physiology (e.g. modulation of enzyme activities, intercellular signaling, signal transduction). Reference will be made throughout to the methodologies used to obtain information about the structure, function, and interactions of biomolecules. COURSE LEARNING OBJECTIVES The Course Learning Objectives for Chem 135 are as follows: Students will learn about acid/base equilibrium and its relevance to biochemical systems, the structural features of amino acids and proteins, the kinetics and mechanisms of enzyme catalyzed reactions, the structural features of biomembranes and the manner in which they mediate the transport of solutes, and the nature and regulation of a variety of metabolic pathways. DROPPING AND ADDING: Students are responsible for understanding the policies and procedures about add/drops, academic renewal, etc. Instructions for adding or dropping a class are available at: http://my.sjsu.edu/students/student_tutorials/index.html. The deadlines for adding or dropping a class are available at http://www.sjsu.edu/registrar/calendar/2132/index.html. Information about late drops is available at: http://www.sjsu.edu/aars/policies/latedrops/ Students should be aware of the current deadlines and penalties for adding and dropping classes. EXAMS:

There will be three midterms and a final exam (see Tentative Schedule for dates). Each of the exams will cover approximately a fourth of the course material. It is expected that all students will take each midterm and the final; make-up midterms will not be given. If a student misses a midterm due to an excusable absence, suitable arrangements will have to be made with the instructor. (Medical excuses must be documented by a physician.) The final exam must be taken in order to pass the course. ACADEMIC INTEGRITY Your own commitment to learning, as evidenced by your enrollment at San Jose State University, and the Universitys Academic Integrity Policy requires you to be honest in all your academic course work. Faculty is required to report all infractions to the Office of Student Conduct and Ethical Development. The policy on academic integrity can be found at http://sa.sjsu.edu/student_conduct. Your own commitment to learning (as evidenced by your enrollment at San Jose State University) and the Universitys integrity policy require you to be honest in all your academic course work. Faculty members are required to report all infractions to the office of Student Conduct and Ethical Development. Instances of dishonesty will not be tolerated. Cheating and/or plagiarism will result in a failing grade and sanctions by the University. Note that plagiarism is defined as representing the work of another as ones own without giving appropriate credit, regardless of how that work was obtained, and/or submitting it to fulfill academic requirements. COURSE GRADE: Each midterm will comprise 25% of the final grade, the final exam contributing an additional 25%. The Midterms and the Final Exam will each receive a raw score and a scaled score. The raw score will be the number of points earned for correct answers on a particular exam, while the scaled score will reflect your performance on the material compared with that of your classmates. The maximum scaled score on any exam cannot exceed 100. The method of scaling can only elevate the value of the raw score-raw scores will never be scaled down. The final grade for the course will be determined by averaging the four scaled scores and the total score for the assigned homework problems that were collected and graded. The course grade will be determined from the resulting average as follows: Scaled Score Average 98-100 93-97 90-92 88-89 83-87 80-82 78-79 73-77 70-72 68-69 63-67 60-62 < 60 Final Course Grade A+ A AB+ B BC+ C CD+ D DF

Exams will be accepted for regrading up to two weeks from the date of their return.

If you need course adaptations or accommodations because of a disability, or if you need special arrangements in case the building must be evacuated, please make an appointment with me as soon as possible, or see me during office hours. Presidential Directive 97-03 requires that students with disabilities register with DRC to establish a record of their disability. You are responsible for understanding the policies and procedures about add/drops, academic renewal, withdrawal, etc. Make sure that you are familiar with all of the administrative policies/deadlines that pertain to this course as outlined in the SJSU Catalog. Note that according to the Chemistry Department Drop Policy, only documented medical or similar emergencies constitute a valid reason for dropping a course after the end of the administratively designated drop period.

READING ASSIGNMENTS/PROBLEM SOLVING: There is a reading assignment associated with each of the lectures (see Tentative Schedule; additional reading assignments in the Segal text will be provided in class). It would be prudent to do the readings prior to the lectures for which they are designed. In some cases only certain portions of a particular chapter will be discussed - if this is the case, the relevant sections will be pointed out prior to the lecture. Lectures are designed to both clarify and supplement the material presented in the text - you are responsible for topics covered in the reading assignments as well as those arising during class discussion. Although many homework problems will be assigned, they will not be collected or graded. Each of the chapters in the text has a number of associated problems in the Students Companion, along with a complete set of solutions. It is to your advantage to solve as many problems as you can - there is no better way to check your comprehension of the subject. Do not make the mistake of looking immediately at the solution before attempting the problem; the effort invested in grappling with material you find difficult will maximize both your overall comprehension and your ability to develop creative solutions. (It should be stressed that this course covers a very large volume of material - the pace will be quite rapid, and it could prove disastrous to fall behind.) In addition to the problems mentioned above, one additional homework problem will be passed out once every ten days. These problems typify the kind of questions you will be asked to answer on exams, so it is to your benefit to learn how to do them. I encourage you to ask (both each other and/or the instructor) for guidance if you have difficulty arriving at a solution.

UNIVERSITY, COLLEGE AND DEPARTMENT POLICIES Students in this course are expected to be familiar with and follow various policies developed by the University and the Chemistry Department. The important policies are:

Academic Integrity

Campus Policy in Compliance with the Americans with Disabilities Act Emergencies and Evacuations Chemical Safety Expected Workload One final note: make your participation in this course as enjoyable as possible - you are getting a glimpse of the magically beautiful and staggeringly intricate molecular design of life - it is a privilege indeed to be able to consciously appreciate it.

TENTATIVE SCHEDULE - CHEMISTRY 135 Date Aug 21 26 28 Sep 4 9 11 16 18 23 25 30 Oct 2 7 9 14 16 21 23 28 Nov. 4 6 13 Topic Introduction to course Intermolecular Forces; pH, Buffers Amino Acids Amino acids; Peptides Protein Purification; Sequencing Protein Structure: Three-Dimensional Aspects Protein Folding; Collagen Protein Function: Ligand Binding (Hb, Mb) Protein Function: Ligand Binding, etc. Midterm 1 Enzymes: Introduction, Kinetics Enzymes: Kinetics, Inhibition, Modification Enzymes: Mechanism of Action Enzymes: Mechanism of Action Enzymes: Regulation of Activity Coenzymes and Vitamins, Carbohydrates Lipids: Biomembranes Biomembranes: Structure Biomembranes: Structure, Transport Midterm 2 Biomembranes: Transport Bioenergetics; Introduction to Metabolism Glycolysis 9(11,12) 10 11(1-5) 9(7-10) 5(7-9) 6(1-6) 6(7,8) 5(10,11), 7, 8 9(1-6) 3(1-5) 3(6-10) 4(1-8) 4(9-11) 4(12,13) 4(13,14) 5(1-6) Reading (Ch, Sec) 1 2

Date 18 20 25 27 Dec 2 4 9 12

Topic Glycolysis TCA Cycle (Citric Acid Cycle) Glycogen Metabolism Other Carbohydrate related Pathways Electron Transport Oxidative Phosphorylation Midterm 3 Electron Transport Oxidative Phosphorylation Oxidative Phosphorylation Final Exam (1445-1700)

Reading (Ch, Sec) 11(6,7) 12(1-8) 13 14(1-8)

14(1-8) 14(9-17)