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BIOCHEMISTRY 3723
Biochemical Laboratory
Syllabus, Fall 2003
Lecture: M, W, 12:30–1:00 PM in 348B NRCLab: M, W, 1:00–4:00 PM in 144 NRC
Instructors:Dr. Sharon Ford 142G NRC, x4-6707Office Hours: M-Th 4:00 p.m.,
email: y appointment,
or stop by my office
Ms. Judy Hall 143 NRC, x4-6204
email:
Prerequisite: BIOC 3653 – If you have not completed BIOC 3653, please tell me right away.
Goals:
1.To familiarize you with properties of biological molecules that can be exploited for their separation, identification, and quantitative determination.
2.To introduce you to the instruments commonly used by biochemists and teach you their usefulness and their limitations.
3.To give you experience using experimental biochemical methods.
4.To develop your analytical reasoning and problem solving skills.
Texts:Rodney F. Boyer, Modern Experimental Biochemistry, 3rd Edition, Benjamin Cummings, 2000. ISBN 0-8053-31111-5
Biochemistry 3723 Lab Manual: Biochemical Laboratory, Fall 2003
If you don’t find the lab manual on the shelf in the Student Union Bookstore, ask for it at the textbook office. A copy will be made for you. It should not take more than one day; be insistent!
Computers: This is a Macintosh department! Computers are available in the Biochemistry Reading Room, 246H NRC, which is open 8 AM-5PM, weekdays. If you want to work there at night, check out a key from the secretary in 246B NRC. Five computers in the teaching laboratory (144 NRC) are available during the day. Biochemistry 3723 material can be accessed three ways:
1.On the web at Not everything is here. More goodies (old exams) can be accessed by method 3 below.
2.On the department server from computer within the department: Go to the Biochem2 server. Log in as Guest and choose FTP. The FTP should appear on the desktop. Open it and find BIOC 3723. This gives the material in Word format.
3.Department FTP serverWeb. This site allows you to download files onto your computer in Word format, which is better than the web-based (html) format: Go to ftp://opbs.biochem.okstate.edu/ftp and open Biochem 3723.
Reading Assignments:
1.I expect you to read and understand the experiments before coming to class. Sometimes calculations must be made before coming to class. I expect you to do these without my telling you. These will usually be collected as quiz grades! If you don't know how to do them, ask for help before they are due.
2.Read material assigned at the beginning of each experiment before coming to class.
3.References listed at the end of experiments are suggestions for your future use.
Teaching Style: I would like to spend less time lecturing and more time problem solving, which is a big part of the exams. I am counting on you to read the material before class and to ask lots of questions both in lecture and in the laboratory. Lecture notes are available on the web and on the FTP. I recommend bringing a hard copy of the notes to class and jotting additions/corrections onto the notes.
Schedule: The schedule of experiments and a calendar are found on pp. 3 – 4 of the lab manual. Copies are attached to this syllabus. Some experiments require work outside of the normally scheduled laboratory time. We have made every effort to keep this extra lab time to a minimum, but until we can find a way make science keep bankers' hours, you will have to do some work at odd times.
Grading:
Lab reports (13 @ various points, see schedule)...... 300
Quizzes and Professional Evaluation...... 40
Exams (3 @ 80 points)...... 240
Total...... 580
1.Lab Reports--are to be written on the forms provided in the lab manual. See p. 5 in the manual for detailed instructions on lab reports. For your convenience, copies of the lab report forms are on the FTP serverWeb.
2.Exams--Three 80-point exams will be given. Every exam is "cumulative". Old exams are available on the web-site and in the FTP and are a good study aid.
3.Quizzes and Professional Evaluation--Unannounced quizzes will be given to determine whether you have come to class prepared to work efficiently and safely. Calculations needed in the lab will usually be collected as a quiz grade. Professional evaluation will be based on preparedness, attitude, cooperation, work habits, etc.
4. Grades: A = ≥ 500 (86%); B = 430 (74%); C = 350 (60%); D = 290 (50%)
5.If more than three lab reports are missing at 5:00 PM on the last day of dead week, Friday, Dec. 5, 2003, an automatic grade of "F" will be given in the course. NO EXCEPTIONS!
Data Verification: In the real world (i.e. industry, government lab, hospital), a laboratory notebook is a legal document. Therefore, it is necessary to have all data verified by having it countersigned by your work supervisor. Data should be recorded in non-erasable ink in a bound notebook. (Actually it should be recorded in duplicate and the two copies stored separately so data isn't lost if something happens to your notebook). In this class you will record data IN INK on the lab report forms in the lab manual. To help you develop good habits, we require you to have your data initialed by the instructor before leaving the lab each day. All raw data must be turned in with each lab report.
Attendance: If you must miss a laboratory session, let the instructor know as soon as possible (by telephone, as email is not always reliable). If possible we will arrange for you to do the experiment at a different time. If the absence is excused, but it is not possible to make up the experiment, you may write the report using your partner's data. This consideration can be given only for one missed lab because the experiments are designed to give you hands-on experience.
Disabilities: If any student feels that s/he has a qualified disability and needs special accommodations, we will work with you and the Office of Disabled Student Services, 326 Student Union, to provide reasonable accommodations to ensure that you have a fair opportunity to perform in this class. Please advise the instructor of such disability and the desired accommodations at some point before, during, or immediately after the first scheduled class period.
BIOCHEMISTRY 3723
Schedule of Experiments, Fall 2003
Date / Experiment / Pts.Aug. 18 / 1 / Pipetting / 10
Aug. 20 / 2 / Preparation of Buffers / 10
Aug. 25 / 3 / Amino Acid Titration / 25
Aug. 27, Sept. 3 / 4 / Radioactivity and Thin Layer Chromatography / 20
Sept. 3, 8 / 5 / Protein Determination by Absorption Spectroscopy / 25
Sept. 10 - 24 / 6 / Purification of Glutamate Oxaloacetate Transaminase (GOT) / 25
Sept.17 - 24 / 7 / Ion Exchange Chromatography of GOT / 25
Oct. 1 / EXAM 1 (Exp. 1-5) / 80
Oct. 1, 6, 15 / 8 / Affinity Chromatography of Soybean Lectin / 25
Oct. 8, 13, 15 / 9 / Polyacrylamide Gel Electrophoresis of Proteins & Immuno-blotting of Soybean Agglutinin / 30
Oct. 20, 22 / 10 / Enzyme Kinetics: Acid Phosphatase from Wheat Germ / 25
Oct. 27, 29, Nov. 3 / 11 / Catabolite Inhibition: Determination of Sugars and
-Galactosidase Activity / 30
Nov. 10 / EXAM 2 (Exp. 1-9) / 80
Nov. 10 - 19 / 12 / Preparation, Isolation and Sequencing of Recombinant DNA Plasmid / 35
Nov. 19, 24 / 13 / PCR Optimization / 15
TBA / EXAM 3 (Exp. 1-13) / 80
Exams:
Wed. Oct. 112:30 p.m.Exam 1 Covers Exp. 1-5
Mon. Nov. 1012:30 p.m.Exam 2Covers Exp. 1-9
TBA Exam 3Covers Exp. 1-13
Grading:
Lab reports (13 @ various points)...... 300
Quizzes and Professional Evaluation...... 40
Exams (3 @ 80 points)...... 240
Total...... 580
Guaranteed grades: A = 500 ; B = 420 ; C = 350 ; D = 290
Note: Friday, Dec. 5, 2003 at 5:00 p.m., is the last time to turn in lab reports.
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BIOCHEM 3723 Calendar, Fall 2003
Wk / Month / SUN / MONDAY /TUE
/ WED /THU
/ FRI / SAT1 / Aug / Aug. 17 / 18
1. Pipetting / 19 / 20
2. Buffers
1
/ 21 / 22 / 232 / 24 / 25
3. AA Titration
1 / 26 / 27
3. & 4. Radioisotopes
2 / 28 / 29 / 30
3 / 31 / Sept. 1
Labor Day
/ 2 / 34. & 5. Protein
3 2 / 4 / 5 / 6
4 / 7 / 8
5. Protein / 9 / 10
6. GOT
4 3 / 11 / 12 / 13
5 /
Sept
/ 14 / 156. GOT
5 / 16 / 17
6. & 7. Ion Exchange
4 / 18 / 19 / 20
6 / 21 / 22
7. Ion Exchange
5 / 23 / 24
6. & 7. / 25 / 26 / 27
7 / 28 / 29
Fall Break
/ 30 / Oct. 1EXAM 1 (Exp. 1-5)
8. Affinity Chrom. / 2 / 3 / 4
8 / 5 / 6
8. Affinity Chrom. / 7 / 8
9. PAGE & Western / 9 / 10 / 11
9 / Oct / 12 / 13
9. PAGE & Western
7 / 14 / 158. & 9. PAGE & Western / 16 / 17 / 18
10 / 19 / 20
10. Kinetics
8 / 21 / 22
10. Kinetics
9 / 23 / 24 / 25
11 / 26 / 27
11. Catab. Inhibition
8 / 28 / 29
11. Catab. Inhibition
10 9 / 30 / 31 / Nov. 1
12 / 2 / 3
11. Catab. Inhibition / 4 / 5
Review for Exam
10 / 6 / 7 / 8
13 / Nov / 9 / 10
EXAM 2 (Exp. 1-9)
12. Plasmid / 11 / 12
12. Plasmid / 13 / 14 / 15
14 / 16 / 17
12. Plasmid
11 / 18 / 19
12 & 13. PCR / 20 / 21 / 22
15 / 23 / 24
13. PCR & Check Out
11 / 25 / 26
No class: Go home for Thanksgiving! / 27 / 28 / 29
16 / 30 / Dec. 1
Dead Week—No lab
12,13 / 2 / 3
Dead Week—No lab
/ 4 / 512, 13 / 6
17 / Dec / 7 / 8
Final Exam: time and date TBA / 9 / 10
Happy Holidays! / 11 / 12 / 13
Key: Experiment – center bold type. Report due date –left, italics. Graded report returned –right, italics.
BIOCHEMISTRY 3723
Spring 2003
NameLocal Phone No. ______
email address : ______
Major Hours completed ______
Advisor's Name/Department:______
Previous chemistry and biochemistry courses:OSU Course Number
(fill in, if taken at OSU)
General Chemistryhours
Analytical Chemistryhours
Organic Chemistryhours
Physical Chemistryhours
General Biochemistryhours
Other Biochemistryhours
Previous biology courses:
General Biologyhours
Zoology, or Botanyhours
Microbiologyhours
Geneticshours
What are your reasons for taking BIOC 3723 (other than that it is required for your major)? Please mention any specific techniques you wish to learn.
If you are working on a research project, describe it briefly.
What are your plans/goals after completing your bachelor's degree?