| |
Biochem 651 - Introduction to modern biochemical laboratory techniques.
Fall 2008-2009
Introduction to modern biochemical laboratory techniques. For advanced undergraduates (biochemistry and other majors) and graduate students not majoring in biochemistry. Prerequisites: Chemistry 221 and Biochemistry 501 or equivalent.
| |
|
|
|
|
|
|
|
|
| |
Course Description:
Section 001
(Class Number: 10558
)
| Instructor(s): |
Fox,Brian G. |
| TA(s): |
|
| Credits: |
2
|
| Day: |
MWF
|
|
Time: |
12:05 PM - 12:55 PM
|
| Location: |
Rm 1420 Microbial Science Building
|
|
Website: |
http://www.biochem.wisc.edu/courses/biochem651/
|
|
Description:
BIOCHEMISTRY 651, Biochemical Methods, is an integrated lecture and lab course covering basic theories and techniques used in the experimental life sciences. The course is directed at upper level undergraduate majors in Biochemistry and other interested students. Participants will have the chance to apply a broad range of biochemical, catalytic, molecular biological, and physical techniques that are currently applied in modern biochemical research.
Lectures are primarily scheduled in the early part of the semester, so that theoretical and practical aspects can be introduced before the corresponding lab experiments are undertaken. The laboratory experiments are designed to provide "hands-on" experience with the equipment and techniques that are the foundations for modern biochemical and clinical research. These experiments focus on instrumental techniques such as spectrophotometry, gel electrophoresis, enzyme assays, scintillation counting, and protein chromatography. Students also participate in an extended lab exercise in which they clone and overexpress the gene operon responsible for luminescence in the marine bacterium Vibrio fischeri. This comprehensive exercise introduces new molecular biological methods as well as further refines the techniques introduced earlier in the class.
The lab reports will be graded on the basis of data collection, analysis, and on the clarity, correctness, and completeness of write-up.
Weekly problem sets (self-graded) will be provided.
Two exams will cover the lecture materials and related lab experiments. The content of the exams will be mixed format: multiple choice; short essay; identification of relevant chemical and biochemical structures; identification of the role and importance of biological functional groups; and calculations based on the laboratory exercises are common themes for exam questions.
Lectures and laboratory experiments
* Analytical electrophoresis of proteins and nucleic acid
* UV-visible spectrometry and other forms of spectroscopy in biochemical research
* Assays to monitor enzyme induction
* Molecular cloning of genes responsible for luminescence in marine bacteria
* Chromatographic methods for purification of biological macromolecules
Required supplies
SAFETY EYE PROTECTION IS REQUIRED AT ALL TIMES IN THE LABORATORY. Each student is responsible for acquiring their own eye protection.
Lehninger Principles of Biochemistry, 4th edition. D.L. Nelson and M.M. Cox (2004). Worth Publishers.
Lab manual is available at DoIT Tech Store (near Union South).
Schedule
Please download this pdf file to see the entire semester by date.
Or, you can click on the Calendar tab and click the "View
Calendar as list" link.
Lectures are on Wed/Fri in 1420 Microbial Sciences Bldg (MSB), 12:05 p.m..
Pre-lab Lectures are on Mondays in 1420 Microbial Sciences Bldg (MSB), 12:05 p.m.
Lab Section 301 meets in 2145 Microbial Sciences Building, Mon--1:20 p.m. to 5:00 p.m.
Lab Section 302 meets in 2145 Microbial Sciences Building, Tues--9:55 a.m. to 1:35 p.m.
Lab Section 303 meets in 2145 Microbial Sciences Building, Wed--1:20 p.m. to 5:00 p.m.
Problem Sets and Exams:
Problem sets and answers will be available via the internet on a regular basis.
Two exams will be given.
Important Dates and Point Breakdown
|
Due Date
|
Report or Problem Set
|
Points
|
Return date
|
|
Feb. 15
|
SPY, EZA
|
50
|
Feb. 29
|
|
Feb. 22
|
SPY, EZA |
50
|
Feb. 29 |
|
Feb. 29
|
Exam 1
|
200
|
TBA |
| Mar. 7 |
ING
|
150
|
Mar. 14 |
|
Mar. 15-23
|
Spring Break
|
|
|
|
Mar. 28
|
MBL Parts 1 & 2
|
100
|
Apr. 4 |
|
Apr. 11
|
MBL Parts 3 & 4
|
100
|
Apr. 18 |
|
May 2
|
GPC
|
150
|
May 9 |
|
May 5
|
Late Material
|
|
May 21 |
| TBD |
Exam 2, University Schedule |
200 |
|
Notes:
Lab reports are due by 4:30 pm. Reports will be collected at precisely 4:30 pm on the day they are due. From the dropbox outside the lab door.
In the absence of a previously negotiated agreement with the Professor,
a 10% deduction per day will be made from the absolute score of all late lab
reports. These deductions will begin at 4:30 on the day the report is
due, but will not include weekends or holidays. For example, a report that is due on Friday but not turned in until before 4:30 pm
on Monday will have a 10% deduction.A lab report that is 10 days late will not be graded.
EXAMS and LAB REPORTS WILL NOT BE RE-GRADED.
Discussions/Labs/Other:
|
LAB - 301
(Class Number: 10579
)
|
| Instructor(s): |
Fox,Brian G. |
| TA(s): |
|
| Credits: |
2
|
| Day: |
M
|
| Time: |
01:20 PM - 05:00 PM
|
| Location: |
Rm 2145 MSB
|
|
|
LAB - 302
(Class Number: 10580
)
|
| Instructor(s): |
Fox,Brian G. |
| TA(s): |
|
| Credits: |
2
|
| Day: |
T
|
| Time: |
09:55 AM - 01:35 PM
|
| Location: |
Rm 2145 MSB
|
|
|
LAB - 303
(Class Number: 11838
)
|
| Instructor(s): |
Fox,Brian G. |
| TA(s): |
|
| Credits: |
2
|
| Day: |
W
|
| Time: |
01:20 PM - 05:00 PM
|
| Location: |
Rm 2145 MSB
|
|
View
Calendar as Syllabus
|
NOTE: Only
one(1) color is used to display on the calendar. The event with the
highest importance will be the color of the day. Click on the day or select the
type of event from they key to display ALL items of a particular type.
|
|
|
Thursday, August 07, 2008 (8/7/2008) |
No calendar events for today
|
|
Course Materials
No course materials available.
Lab
Lab Orientation and General Laboratory Procedures
SPY
:
A Spectrophotometric Study of Hemoglobin
EZA
: Development of an Enzyme Assay
ING: Introduction
ING-Part 1:
Induction, Sampling, Growth Measurements
ING-Part 2:
Enzyme Assays plus Denaturing Polyacrylamide Gel Electrophoresis
MBL: Cloning the lux operon from Vibrio fischeri
MBL-Part 1: Isolation of Genomic DNA from V. fischeri
MBL-Part 2: Spectrophotometric Analysis of Genomic and Plasmid DNA
MBL-Part 3: Restriction Digestion of Genomic and Plasmid DNA
MBL-Part 4: Quantitation of DNA by Plate Fluorescence and Agarose Gel Electrophoresis
MBL-Part 5: Ligation of Genomic DNA Restriction Fragments to Vector
MBL-Part 6: Transformation of Competent Escherichia coli DH5¿
MBL-Part 7: Identification and Isolation of Bioluminescent Clones
MBL-Part 8: Plasmid Mini-preps From Lux+ Clones and Restriction
Digestion and Agarose Electrophoresis of Plasmids
MBL-Part 9: Summary
GPC
: Gel Permeation Chromatography of Egg White Protein
Buffer Appendices
General topic reading list
The assigned readings will come from the following:
Principles of Biochemistry, 4th ed., Nelson, D. L. and Cox, M. M. (2004) New York, Worth Publishing.
Supplemental readings come from these, which can be found at Steenbock Library.
1. Ninfa, A.J. and Ballou, D.P. (1999) Fundamental Laboratory Approaches for Biochemistry and Biotechnology. Fitzgerald Scientific Press, Inc.
2. Branden, C. and Tooze, J. (1991) Introduction to Protein Structure, New York, Garland Publishing.
3. Brock, T. D., Madigan, M. T., Martinko, J. M., and Parker, J. (1994) Biology of Microorganisms, 7th ed., Englewood Cliffs, Prentice Hall.
4. Cooper, T. G. (1977) Tools of Biochemistry, New York, John Wiley and Sons.
5. Creighton, T. E. (1994) Proteins: Structure and Molecular Properties, 2nd ed., New York, W. H. Freeman.
6. Deutscher, M. (1991). Guide to Protein Purification. Methods Enzymol., 182, 1-894.
7. Harris, D. C. (1998, 2003) Quantitative Chemical Analysis, 4th ed., New York, W. H. Freeman.
8. Robyt, J. F. and White, B. J. (1987) Biochemical Techniques: Theory and Practice, Chicago, Waveland Press.
9. Sambrook, J., Fritsch, E. F., and Maniatis, T. (1989) Molecular Cloning, A Laboratory Manual, 2nd ed., Cold Spring Harbor, Cold Spring Harbor Laboratory Press.
10. Scopes, R. K. (1994) Protein Purification: Principles and Practice, 3rd ed., New York, Springer-Verlag.
11. Skoog, D. A. and Leary, J. J. (1992) Principles of Instrumental Analysis, 3rd ed., New York, Saunders College Publishing.
Guidelines for preparation of lab reports
1. For each experiment, each student should prepare their own lab report, including plots, data analysis, and answers to questions. You may discuss how to best answer the questions and how to perform sample calculations with other students.
It is absolutely not acceptable for a group of students to print out multiple copies of a joint report for grading purposes.
Please also note that simple rearrangements of clauses and minor phrases that maintain the same overall structure and content can be considered plagarism in some contexts and should be avoided.
The best strategy is to prepare your final written statements independently after discussions are complete.
2. As discussed in class, lab reports should be printed from word processing software or should be typewritten. The report should be prepared with 2.5 cm margins on all sides in a 12 point font such Times Roman, and double line spacing should be used.
Handwritten or other unformatted reports will be considered late and will be returned for revision. Handwritten labels may be used on gels, spectra, and other primary data materials, and complicated equations may be handwritten, however.
3. Correct punctuation, correct spelling, and the use of complete sentences will be expected, and reports that significantly deviate from normal usage will receive deductions in point totals.
4. Answers to questions should be clearly identified by number, and the graders will most appreciate a short, to-the-point answer. In this regard, consider the following quote by the (in)famous author Oscar Wilde
"I would have written a shorter letter, but I didn't have the time."
A short, well-structured answer takes more thought and revision than a stream-of-consciousness deposition. The graders in Biochemistry 651 will be looking for short, well-structured answers.
How to Insert Equations in Microsoft Word
Click here for Jenna's Instructions
No homework assignments are currently due.
|
|
|