for SYLLABUS CHEMISTRY 365 BIOCHEMISTRY Fall 2002
INSTRUCTOR Dr. Thomas M. Zamis I. Course Description A. Biochemistry (Prerequisites: Chem 248, 326, 328)
Introduction to Biochemistry includes the chemistry of living cell components, and the nature and mechanism of cellular reactions. The chemical structures and biological functions of the most common small biomolecules, molecular assemblies and polymers of living organisms - including carbohydrates, proteins (enzymes), lipids, nucleic acids, coenzymes, and intermediate metabolites are covered. The reaction mechanisms, enzyme catalysts and regulation of the fundamental metabolic pathways are discussed - including glycogenesis, glycogenolysis, gluconeogenesis, glycolysis, the pentose phosphate pathway, fatty acid metabolism, the citric acid cycle, the electron transport system, oxidative phosphorylation, amino acid metabolism, the urea cycle and nucleotide metabolism. Biological information flow is outlined - including DNA replication and repair; RNA transcription, processing and control of gene expression; and protein biosynthesis. The focus of the laboratory portion of the course is on techniques for analysis of small biomolecule mixtures, biopolymer characterization, and enzyme isolation and kinetic analysis. Techniques include computer spreadsheet and word processing, uv-vis and colorimetric spectrophotometry, thin layer chromatography, gel permeation chromatography, gasliquid chromatography, specific activity and kinetic assay, and electrophoresis. B. Information for Spring Semester TIMES: Lecture 1 Lab 1 Lab 2 T,R,F R T 9:00 - 9:50 11:00 - 13:50 14:00 - 16:50 Room Science A107 Science D118 Science D118
REQUIRED MATERIALS TEXTBOOK: McKee, Trudy; McKee, James R. Biochemistry: an Introduction 2nd ed.; WCB/McGraw-Hill: Boston, 1999. INSTRUCTOR: Dr. Tom Zamis Office B135 Phone [phone] e-mail: [e-mail]
Office Hours: T 12:00; W 11:00; R 8:00, 14:00 ; F 10:00 or other times by appointment.
II.
Course Outline Dates 9/3 - 9/6 9/10 - 9/13 9/17 - 9/20 9/24 - 9/27 10/1 - 10/4 10/8 - 10/11 10/15 - 10/18 10/22 - 10/25 10/29 - 11/1 2 1 Exam # Topics Biomolecule Structures Water: The Medium of Life Bioenergetics Amino Acids; Peptides; Proteins Protein Biosynthesis; Enzymes Enzymes Carbohydrates Carbohydrate Metabolism; Glycogen Carbohydrate Metabolism; Glycolysis and Gluconeogenesis Carbohydrate Metabolism; Pentose Phosphate Pathway Lipids, Membranes, Transport; Fatty Acid Metabolism 3 Aerobic Metabolism Citric Acid Cycle Aerobic Metabolism Electron Transport System Nitrogen Metabolism: Amino Acid Degradation and Synthesis Nitrogen Metabolism: Urea Cycle, Nucleotide Biosynthesis
Week # 1 2 3 4 5 6 7 8 9
10
11/5 - 11/8
11
11/12 - 11/15
12 13
11/19 11/22 11/26
14
12/3 - 12/6
15
12/10 - 12/13
Exam 4
Thursday December 19, 14:45 16:45
III.
Principal Assignments
A. Reading - McKee, Trudy; McKee, James R. Biochemistry: an Introduction 2nd ed.; 1999. CHAPTER 1 3 4 5 6 7 8 9 10 11 13 14 16 TOPICS Cells, organic functional groups, biomolecule classes, reaction types Solvent, ionization properties of water Thermodynamics, free energy and coupled reactions Amino acids, peptides and proteins Enzymes: catalytic mechanism and regulation Monosaccharides, disaccharides, polysaccharides Glycogen metabolism, glucose metabolism Lipid classes and membrane structure Fatty acid beta-oxidation and biosynthesis Citric acid cycle, electron transport and oxidative phosphorylation Non-essential amino acid biosynthesis, one carbon reactions Amino acid and nucleotide catabolism DNA, RNA SECTIONS 1 - 3; Box1.1 1 - 6; Box 3.1 1 - 3 1 - 3 1, 2, 4 1 - 4 1 - 4 (11.4) 1, 2 1 1 - 3; Box 11.1 2, 3, Box 13.2 & 3 1, 3 1, 2
B. Supplementary Material Handouts of lecture material may be obtained from your instructor, or the Chem 365 Web page, for easy reference and note-taking in class. You are allowed to prepare, and bring with you to exams, a one page (8 1/2 x 11) study sheet. These are prepared by you, and contain handwritten or typed summaries of your notes. These may not contain any photocopies of handouts or book material. Your instructor will also make available, on the Chem 365 Web page, all course materials from lecture and discussion, and locations on the World Wide Web that have useful instructional materials. IV. Conduct and Evaluation Procedures A. Attendance Attendance is not required for lecture, however the majority of the material that you will be responsible for is presented in lecture. Be sure to obtain notes from your peers on those rare occasions that you miss lecture. Attendance is required for examinations and laboratory. An excused absence requires that verifiable arrangements be made with your instructor in advance for things like off-campus or trips personal appointments; or following an emergency or illness, a written note from a physician or university administrator is presented upon returning.
B.
Student Conduct The following are from the University publication "Community Rights and Responsibilities". The full document is available from the UWSP Web Page under Student Life.
Nearly 10,000 students, staff, faculty and visitors descend on our one square mile campus each day of the academic year. It is apparent that as a learning community, we need standards or codes of conduct which clarify the behavioral expectations for our academic and nonacademic environments. The policies and procedures spelled out in our Community Rights and Responsibilities publication provide for a sense of order for all while respecting the dignity and rights of individuals. Through these policies, civility within our learning community is affirmed, diversity is pursued, the importance of each person is honored and well defined procedures guide behavior for the common good.
UWSP 14.01 STATEMENT OF PRINCIPLES. The board of regents, administrators, faculty, academic staff and students of the University of Wisconsin system believe that academic honesty and integrity are fundamental to the mission of higher education and of the University of Wisconsin system. The university has a responsibility to promote academic honesty and integrity and to develop procedures to deal effectively with instances of academic dishonesty. Students are responsible for the honest completion and representation of their work, for the appropriate citation of sources, and for respect of others' academic endeavors. Students who violate these standards must be confronted and must accept the consequences of their actions. See Section, UWSP 14.03 ACADEMIC MISCONDUCT SUBJECT TO DISCIPLINARY ACTION, for specific examples of academic standard violations. C. Grading Policy
Exams will be held Fridays and will last from 8:55 until 9:55 AM. If you have a conflict with the scheduled exam time, please make arrangements with me for a makeup in advance. A makeup exam will be arranged for any excused absences. Your final grade will be based on the total points earned out of 1000. The distribution of points is as follows: Hour Exams (4 @ 160 pts) Lab Reports Notebook Deportment/Instructor Deportment/Team 640 points 305 points 15 points 20 points 20 points
The tentative levels of achievement required for letter grades are: "A" 900 points "B" 800 points "C" 700 points "D" 620 points.
These levels will not be raised.
V.
Course Objectives
My teaching philosophy for this course has three components. First, one must master the fundamentals. Precise, biochemical definitions for terminology, and biomolecule names and Lewis structures must be learned. Chemical properties ...