Course Specifics:
Instructor: Dr. Jason C. Hurlbert
Office: Sims 301B
Office hours: Wed 12:30-1:20, Fri 11-12 and by appointment
Phone: 323-4928
E-mail: hurlbertj@winthrop.edu
Meeting Times:
All Sections: Prelab Lecture Fridays, 12:30 - 1:20 PM
Section 001 : Laboratory Tuesdays, 2:00 - 4:50 PM
Section 002 : Laboratory Wednesdays, 2:00 - 4:50 PM
Section 003: Laboratory Mondays, 2:00 - 4:50 PM
Credit Hours: 2
Textbook: None. Handouts and Scientific articles will be provided.
Additional Required Materials: Scientific calculator, laboratory notebook, safety goggles
Course Outline:
We will cover recombinant protein production and purification, enzymological analysis and the solution structure of enzymes in several experiments over the course of the semester. As we perform the experiments, I hope you will gain an appreciation of the various techniques performed in modern biochemical research. Upon completion of the course, you will be familiar with many of the basic principles of modern microbiology, protein chemistry and protein bioinformatics. You will also have a much better idea of the databases and software available for use in your own research and studies.
| Week of Monday, |
Topic / Procedure |
| Aug 21 |
No Laboratory Meetings This Week |
| Aug 28 |
Introductory Lecture - Semester Goals and Expectations |
| Sept 4 |
Labor Day - No Class |
| Sept 11 |
Exp 1) Bioinformatics (NCBI Entrez, BLAST and UCSF Chimera) |
| Sept 18 |
Exp 2) Protein Expression and Purification: Cell Lysis |
| Sept 25 |
Exp 3) Protein Expression and Purification: Ion Exchange Chromatography |
| Oct 2 |
Exp 4) Analysis of Protein Purification: SDS-PAGE and Western Blot |
| Oct 9 |
Exp 5) Analysis of Polymer Depolymerization Kinetics by reversed phase HPLC |
| Oct 16 |
Exp 6) Kinetics I: Spectrophotometry I: Influence of [Substrate] on enzymatic reactions |
| Oct 23 |
|
| Oct 30 |
Exp 7) Kinetics II: Spectrophotometry II: Influence of pH on enzymatic reactions |
| Nov 6 |
Exp 8) Protein Denaturation: Influence of Protein Structure on Enzymatic Reactions |
| Nov 13 |
Exp 9) Limited Proteolysis as a Probe of Protein Structure |
| Nov 20 |
Thanksgiving Break |
| Nov 27 |
Manuscript Review |
| Friday, Dec 2 |
Final Exam in Recitation Section
|
| Wednesday, Dec 7 |
Final Report Due in Course Dropbox folder by 5:00 PM |
|
Grading for the Course
Prelab Assignments
Due to the tight schedule we will follow during the semester, you will be given assignments at the conclusion of the Monday afternoon prelab lectures that must be completed before you may begin work on your scheduled laboratory session. This requirement is necessary to ensure that you will be able to perform the myriad tasks that need to be accomplished in the laboratory each week.
Failure to complete the prelab assignments AND bring the completed work to class with you will result in you being barred from the lab for the week. This will, in turn, result in you not being able to complete the assigned work and being unable to complete the Section Writeup which will seriously lower your overall grade.
Take the Prelabs and Assigned readings seriously!
Section Writeups
Four different section writeups will be due during the semester. These writeups will be due at the start of the lab period indicated on the detailed course schedule. Each weekly writeup must include the following sections: 1) Materials and Methods, 2) Results and Discussion, 3) Conclusions and 4) References. The Results and Discussion section will contain all necessary Figures and Tables in addition to scientific explanations of the data. All Figures and Tables must be prepared in accordance to the guidelines provided to authors in the Journal of Biological Chemistry (
www.jbc.org).
Final Report
A final report will be due on the Friday, December 5. This report will be a compilation of the corrected section writeups you turned in during the semester with Abstract and Introduction sections. The entire report must be formatted in the style of an article from the Journal of Biological Chemistry. Despite the fact that much of the material will already be written, you will need to construct a laboratory report that is coherent, logical and accurately describes what you have done during the semester.
Laboratory Notebook
A laboratory notebook is one of most important tools a scientist has and is just as important in this class. You must carefully document all of the procedures and reagents you use as well as the data you collect during the semester. Any of your peers should be able to pick up your lab notebook and be able to reproduce what you did without any problem. Keep this in mind should you have any questions about what you should enter into your notebook. We will discuss how to properly keep a notebook in the first prelab session and examples will be provided.
Final Exam
A cumulative final exam will be given on the final week of the semester and it will cover the background material, theories and practices covered during the semester.
Final Grade
Prelab Assignments: 9 x 10 pts = 90 points
Section Writeups: 4 x 30 pts = 120 points
Homework Assignments: 2 x 20 pts = 40 points
Final Paper: 50 points
Laboratory Notebook: 20 points
Final Exam: 30 points
Total: 350 points
Grading Scale:
A: >90% of the total Points
B+: 87 - 89.9% of the total Points, B: 80 - 86% of the total Points
C+: 77 - 79.9% of the total Points, C: 70 - 76.9% of the total Points
D: 60 - 69.9% of the total Points
F: <60% of the total Points
No late assignments will be accepted without prior permission or, in the case of unplanned emergencies, medical or judicial documentation. Consult the syllabus for a detailed explanation of this policy. This policy will be strictly adhered to and no exceptions will be made.
Technology in the Classroom
You will need to make certain that you bring a scientific calculator to the lab each session, and, more importantly, you must know how to use the linear regression mode of you calculator. No laptop computers or cellular phones may be used in the laboratory when class is meeting as the distractions they cause present a significant safety hazard. Anyone caught using these devices during class without prior permission will immediately be asked to leave the laboratory.
Student Code of Conduct
As noted in the Student Conduct Code: “Responsibility for good conduct rests with students as adult individuals.” The policy on student academic misconduct is outlined in the “Student Conduct Code Academic Misconduct Policy” in the online Student Handbook.
Students with Disabilities
Students with Disabilities
Winthrop University is dedicated to providing access to education. If you have a disability and require specific accommodations to complete this course, contact the Office of Disability Services (ODS) at 323-3290. Once you have your official notice of accommodations from the Office of Disability Services, please inform me as early as possible in the semester.