*CHEMISTRY 435
GENERAL BIOCHEMISTRY I
FALL 2012
Instructor: Duane Smith, Jr., Ph.D. Course Section: CHEM 435 – 4 M
Office: Beauregard 134 Meeting Room: BEA 104
Office Hours: MWF 8:30 – 10:30 a.m. Meeting Time: MWF 10:45 – 11:40 a.m.
TR 9:00 a.m. – 12:00 noon; TR 3:00 – 4:30 p.m.
(or as arranged)
Phone: (985) 448-4165 Email:
COURSE DESCRIPTION: *CHEM 435. Biochemistry I. 3-3-0. Prerequisite: CHEM 222. Structure of proteins, nucleic acids, membranes, membrane channels and pumps; kinetics and mechanism of enzyme catalysis; glycolysis, citric acid cycle; and mechanism of oxidative phosphorylation. Fa only. (26.0202)
PRE- & CO-REQUISITES: Prerequisite – Chemistry 222
Recommended – CHEM 437, a laboratory course to accompany CHEM 435
REQUIRED TEXT: Biochemistry: A Short Course, 2th ed., Tymoczko, Berg, and Stryer, 2013, W.H. Freeman Co., New York (ISBN–13: 978-0-4641-0484-8, ISBN-10: 1-4641-0484-0; Student Edition: 1-4292-8360-2; Loose-leaf: 1-4641-0486-7)
The Double Helix, James Watson.
COURSE GOAL: To provide students with an understanding of the basic principles of biochemistry.
STUDENT OUTCOME OBJECTIVES: Upon successful completion of this course, the students will have content knowledge in these general subject areas:
1. Protein structures and functions
2. Protein quantitation, separation and purification techniques
3. Nucleic acids: the molecules of heredity
4. Molecular biology and recombinant DNA technology
* CHEM 435 may be taken for graduate level credit; however to receive graduate level credit, the student must also successfully complete a 10-page research paper over one of the following content areas, and present a class lecture (45 minutes) over that topic area.
COURSE CONTENT:
a. Chemistry and chemical reaction of amino acids, peptides, and proteins
b. Four basic levels of structure in protein architecture
c. Purification of proteins by size, charge, solubility, and binding affinity (column chromatography, affinity chromatography, ion exchange chromatography)
d. Amino acid sequence determined by Edman degradation
e. Proteins can be localized and quantitated using highly specific antibodies (radioimmunoassays, immunocytochemistry, western blot analysis)
f. Protein conformation as assessed using circular dichromism, x-ray crystallography, and nuclear magnetic resonance (NMR)
g. Automated peptide synthesis
h. DNA and the double-stranded helix
i. DNA replication and the flow of genetic information
j. Deciphering the genetic code
k. Restriction enzymes and DNA ligases being key tools in forming recombinant DNA molecules
l. Polymerase chain reaction (PCR) in medical diagnostics, forensics, and molecular evolution
COLLEGE AND CLASSROOM POLICIES:
Absence and Drop/Adds – Absences amounting to the equivalent of 10% of class time, whether consecutive or not, are grounds for the student being dropped from the course. You are expected to be present, prepared, and alert at all sessions. The responsibility for withdrawing from the course, if you decide not to continue, lie completely with the student. Failure to drop a course by the final deadline will result in your receiving a grade of “F”. The last day to drop the course with a “W” is Wednesday, November 7, 2012.
If a student misses a class, he or she is still responsible for the material covered during that class period. If a student misses an exam, a makeup will not be given unless the student notifies the instructor in advance of his or her absence. If no advance notice is given, the student must provide documentation as to the reason for having been absent, such as death of a close family friend (death notice), illness (doctor’s bill), or court appearance (summons).
Please notify the Instructor if you have a disability, so accommodations can be made. If you have a documented disability that requires assistance, you will need to register with the office of Disability Services for coordination of your academic accommodations. The Office of Disability Services is located at 158A Shaver Gym. The phone number is (985) 448-4430 (TDD 449-7002).
ACADEMIC GRIEVANCES: The proper procedure for filing a grade appeal or grievances related to other academic matters is listed in Section 5 of the Code of Student Conduct and at the following link: http://www.nicholls.edu/documents/student_life/code_of_conduct.pdf
CONTINUED LEARNING FOLLOWING AN EXTREME EMERGENCY: In order to make continued learning possible following an extreme emergency, students are responsible for:
· reading regular emergency notification on the NSU website; http://www.nicholls.edu
· knowing how to use and access Moodle (or university designated electronic delivery system);
· being familiar with emergency guidelines;
· evacuating with textbooks and other course materials;
· knowing their Moodle (or designated system) student login and password;
· contacting faculty regarding their intentions for completing the course.
Faculty are responsible for:
· their development in the use of the Moodle (or designated) software;
· having a plan for continuing their courses using only Moodle and email;
· continuing their course in whatever way suits the completion of the course best, and being creative in the continuation of these courses;
· making adjustments or compensations to a student’s progress in special programs with labs, clinical sequences or the like, only in the immediate semester following the emergency.
Academic dishonesty will not be tolerated. The University’s Academic Honesty Policy, as stated in the “Code of Student Conduct” booklet will be followed.
No audible beepers, cellphones, or laptops will be allowed in class. Be sure that these devices are turned off as you enter the classroom. These devices are a distraction to the instructor as well as your classmates. If there is an emergency and you need to respond please let the instructor know of this before the class starts.
Grades will be based on a 10-point grading scale.
90 – 100 A
80 – 89 B
70 – 79 C
60 – 69 D
< 60 F
Grades will be based on the average of four exams and one comprehensive final. Several topic area quizzes may also be given throughout the semester, and the average quiz grade may be counted as an extra exam grade. This grading policy may be amended due to any unforeseen changes in schedule.
THIS SYLLABUS, IN NO WAY, IS TO BE MISCONSTRUED AS A CONTRACT, AND MAY BE AMENDED BY THE INSTRUCTOR AS DEEMED NECESSARY.
OUTLINE OF TOPICS
CHAPTER(S) POINTS
1 Biochemistry and the Unity of Life
2 Water, Weak Bonds, and the Generation of Order out of Chaos
3 Amino Acids
4 Protein Three-Dimensional Structure
EXAM 1 (Fri., Sept. 14) 100
5 Techniques in Protein Biochemistry
6 Basic Concepts and Enzyme Action
7 Kinetics and Regulation
8 Mechanisms and Inhibitors
EXAM 2 (Weds., Oct. 10) 100
9 Hemoglobin, an Allosteric Protein
10 Carbohydrates
11 Lipids
Last day to drop course with a “W” grade is Wednesday, November 7, 2012
EXAM 3 (Mon., Nov. 5) 100
12 Membrane Structure and Function
13 Signal-Transduction Pathways
EXAM 4 (Mon., Dec. 3) 100
FINAL EXAM (TBA) 100
TOTAL POINTS 500
Monday – Wednesday – Friday
Date / Topic / Date / Topic / Date / TopicAug. 20 / Aug. 22 / First Day of Class / Aug. 24
Aug. 27 / Aug. 29 / Aug. 31
Sept. 3 / LABOR DAY
HOLIDAY / Sept. 5 / Sept.7
Sept. 10 / Sept.12 / Sept. 14 / Exam 1
Sept. 17 / Sept. 19 / Sept. 21
Sept. 24 / Sept. 26 / Sept. 28
Oct. 1 / Oct. 3 / Oct. 5
Oct. 8 / Oct.10 / Exam 2 / Oct. 12
Oct. 15 / Oct. 17 / Oct. 19 / FALL BREAK
Oct. 22 / Oct. 24 / Oct. 26
Oct. 29 / Oct. 31 / Nov. 2
Nov. 5 / Exam 3 / Nov. 7 / W / Nov. 9
Nov. 12 / Nov. 14 / Nov. 16
Nov. 19 / THANKSGIVING BREAK / Nov. 21 / THANKSGIVING BREAK / Nov. 23 / THANKSGIVING BREAK
Nov. 26 / Nov. 28 / Nov. 30
Dec. 3 / Exam 4 / Dec. 5 / Study Day
(no classes) / Dec. 7 / FINAL EXAMS
Dec. 10 / FINAL EXAMS / Dec. 12 / FINAL EXAMS / Dec. 13
Thursday / Grades Due 9:00 a.m.