Prerequisites: Chemistry 215, 333, and 335, all with a grade of C or better as of Spring 2006. If you took the courses before spring 2006 and have a C-, you may take Chemistry 340, but be aware that you are going to find it challenging. If you completed the prerequisites at another institution, you must show an unofficial transcript that documents your grades in order to be admitted into the course.

Required: Biochemistry, 4^{t h} edition, by Nelson and Cox; scientific calculator

Admission into the class: No students will be added until Sept. 4. On that day students who have satisfied the prerequisites, met with me, and attended all previous classes will be admitted with preference based as follows:

1. Registered students, including students on the waiting list.
2. Open University students
3. Others

Registered students who have not satisfied the prerequisites or attended all previous classes will be dropped on Sept. 4 unless they have prior made arrangements with me.

Helpful: Basic Concepts in Biochemistry: A Student's Survival Guide , 2^nd edition, by Gilbert (publisher McGraw-Hill, ISBN 0-07-135657-6). This is a summary text; that is, it presents an overview that helps in organizing the mass of information presented in biochemistry. Students who have used this have recommended it as a study guide.

Course description and objectives: This course is intended to provide students majoring in chemistry, biochemistry, and cell biology with an understanding of protein structure and function, enzyme structure and function, and the metabolism of carbohydrates in humans, including electron transport and oxidative phosphorylation. Because this is a course for majors, students are expected to understand relevant research.

Biochemistry involves learning vocabulary, chemical structures, and concepts. This means that memorization is required in order to know vocabulary and structures. Understanding is also required, because the vocabulary and structures are then used to illustrate and describe the concepts. Biochemistry is a logical science, which means that the concepts make sense. If something doesn't make sense or isn't consistent with courses you have taken in the past, you should ask questions. If you don't ask questions, I assume you understand the material and it all makes sense.

At the end of the course, students should be able to do the following:

1. Name and draw all twenty amino acids, and draw the structure of a peptide whose sequence is specified with one-letter abbreviations.

2. Understand the basis of protein structure, recognize important components of protein structure, and be able to describe the significance of changes in protein conformation for protein function.

3. Describe enzyme function using thermodynamics, kinetics, and mechanisms. Be familiar with the six classes of enzymes and be able to determine the type of enzyme that catalyzes any given biochemical reaction.

4. Have a basic understanding of membrane structure and function. Be able to describe the components and function of a G protein pathway.

5. Be able to describe glycolysis, gluconeogenesis, glycogen metabolism, the citric acid cycle, and oxidative phosphorylation using objectives 2-4.

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Studying and Evaluation
Reading and vocabulary: The textbook readings are selections that expand upon the major points in the lectures. The text also includes a list of key terms at the end of each chapter; students are expected to be able to use appropriately all key terms included in the reading. In other words, know this vocabulary. To some extent, learning biochemistry involves learning a language.

Homework: The schedule lists end of chapter problems that students should be able to solve. I expect to post additional problems and information on iLearn (http://ilearn.sfsu.edu) later in the semester. In order to have access to iLearn, students must be registered in the course. Once registration is clear, students are expected to check the iLearn site regularly as part of class participation. Answers to problems are not collected, but I expect students to work them in a timely manner as part of class participation.

Quizzes: Because I think students who fail to study biochemistry often will fall behind and do poorly, I give regular 10-point quizzes in class. These always cover material from previous classes and are scheduled for the end of class so that students who are late to class don't miss them. The three lowest quiz grades at the end of the semester are dropped, which allows students to miss a quiz or two. The best preparation, again, involves studying for every quiz. The total point value for quizzes is 90 points (9 quizzes x 10 points each).

In-class Problems: Biochemistry requires applying concepts in addition to memorizing information. As part of learning to apply concepts, I regularly give problems in class which must be worked and turned in at the end of the class. Students should work cooperatively to complete these problems, which are worth 2 points each. Five of the problems are required, and the remaining problems allow students to earn bonus points. There is no other extra credit available in the class. The total point value for in-class problems is 10 points.

Assignments: Part of learning about biochemistry involves relating what you have learned to recent advances in scientific understanding. Five times during the semester I will post an assignment on ilearn that requires reading an abstract or paper on the web and answering questions about it. The assignment will be due at the beginning of the next class. Each assignment is worth 5 points, so the total point value for assignments is 25 points.

Attendance: There is no credit for attendance, but students are expected to attend class. A record is kept of quiz and in-class problem grades, and the graded papers are returned in the next class period. Students are expected to collect their graded papers promptly as part of receiving feed-back on what they have learned. I assume that uncollected papers indicate student absence from lecture.

Exams: There are four exams in the course including the final. All exams are required ; that is, no exam grade is dropped at the end of the semester. In-class exams are about 60% multiple choice, matching, and other short answer questions. The remainder of the exam consists of short essay questions and problems, usually with multiple parts. Scantrons are not needed in order to take these exams. Any student who misses an exam is responsible for arranging to take a make-up exam as soon as possible, preferably within 7 calendar days.
Sometimes a student will take an in-class exam and feel strongly that the exam grade does not truly reflect knowledge of the material. One time during the semester , a student in that situation may take a make-up exam over the same material. I will count only the better grade. This option expires two days before the next midterm and is not available for the final exam. For example, the last date to make up Exam 1 is Oct. 16, because Exam 2 is Oct. 18. All make-up exams are given in my office at my convenience.
Make-up exams consist entirely of essay questions and problems; they are not returned but are kept in my office for the rest of the semester.
The final exam is semi-cumulative. Part of the exam will be a mid-term on the most recent material, and the rest will be questions about major concepts and significant material that was not mastered on the midterm exams. The questions will be different from questions on the midterm exams.
The total point value for exams is 460 = 3 midterms (100 points each) + 1 final (160 points).

Keys: Quiz keys, problem answers, and answers to exam essay and problem questions will be posted on the iLearn web site. There are no make-up quizzes or make-up problems.

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Support: There is currently only one workshop available for both sections of Chemistry 340, and it is full. I strongly recommend forming study groups that meet regularly.

Curves and Grades: Exams are curved as needed if the mean is lower than C+. Quizzes are not curved, and neither are the final grades.

I strongly encourage students to keep a record of their grades and to talk with me or send me an e-mail if they have concerns or questions about grades. Grades are based upon the percent of total points (600) as follows:

IMPORTANT INFORMATION: The College of Science and Engineering has set the policy on withdrawals and incompletes. After a certain date, published each semester, withdrawal from a course is allowed only in case of major health problems that arose during the semester, an unavoidable change in job hours, or a major family emergency. Incompletes require completion of at least 70% of the course with a grade of C.

All course deadlines are noted in the schedule. It is the responsibility of each student to be aware of deadlines and act appropriately.

Office hours: I hold posted office hours each week. I also answer questions by e-mail.

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