Fall 2013-304 Syllabus-FINAL

Fall 2013 – CHEM 304/504 Biochemistry Lab (1 Credit)
Dr. Lauren Waters
Office: HS-409
Lab: HS-407
Phone: 424-7099
Email: [email protected]
Office Hours: M, T. W from 11:30 a.m. - 12:30 p.m.
Dr. James Paulson
Office: HS-418
Lab: HS-424
Phone: 424-7100
Email: [email protected]
Office Hours: To Be Announced
Dr. Sandra Neuendorf
Office: HS-417
Phone: 424-2039
Email: [email protected]
Office Hours: To Be Announced
Lab Times:
Section 1: Mon 1:50 p.m. – 5:10 p.m. in HS-458
Section 2: Tues 1:10 p.m. – 4:30 p.m. in HS-458
Section 3: Weds 1:50 p.m. – 5:10 p.m. in HS-458
Hardbound Lab Notebook (e.g., composition book)
Lab Safety Goggles
Lab coat optional (If you have one you may keep it on the coat rack in the
lab. Make sure it is marked with your name.)
There is no textbook. Supplementary material will be posted on D2L.
Course overview: This course is specifically designed for students needing practical
experience in the biochemistry laboratory, including Chemistry majors in the Biochemistry and
Biomolecular Science emphases and Medical Technology majors. It is also recommended for
those in other clinically-oriented programs (e.g., pre-med, pre-vet). Techniques include aspects
of spectrophotometry, electrophoresis, chromatography, immunoassays, and fluorescence. A
significant amount of writing is expected. Prerequisite or Co-requisite: Chemistry 303.
Attendance, participation
and lab notebook (5 points/week, 12 weeks)
Pre-labs (11 at 10 points each):
Post-labs (8 at 10 points each):
Formal Lab reports (2 at 30 points each):
Lab quiz
60 points
There will be pre-labs for every lab except Lab #1. Formal Lab Reports are required for the
Enzyme Kinetics and DNA experiments , and post-lab exercises for all other experiments.
Typical minimum percentage grade ranges:
100-90% A/A89-80% B+/B/B79-70% C+/C/C69-60% D+/D/D59-0%
Make-up Labs: Attendance and participation in the laboratory is part of your grade. If you
know in advance that you will miss a lab session for a reason that is recognized by the University
of Wisconsin Oshkosh as legitimate, you may be allowed to attend one of the other lab sections.
If you miss a lab, you should still turn in the pre-lab assignment. You may also be able to get data
from another student and still complete the post-lab or lab report to receive credit for that part
of the grade.
Lab Quizzes: In the case of an unexcused absence, a score of 0% will be assigned. In the case of
an excused absence (e.g., medical problem, death in the family, etc., which must documented in
writing and discussed in person, not through email), the quiz can be dropped or made up at the
discretion of the instructor.
Academic Dishonesty: Any case of academic dishonesty, in any form, will not be tolerated and
will be dealt with according to the University of Wisconsin Oshkosh rules and procedures.
Pre-Labs: These are designed to help you prepare for the lab each week. They must be
completed before class begins.
Lab Notebooks: In addition to simply recording data (your results and observations), a good
laboratory notebook helps you and your colleagues know specifically what you did (your
protocol) and why (your reasoning process). Keeping a lab notebook (or its equivalent, clinical
charts) is an essential skill that any scientist or clinician uses daily in academia, industry, and
You will be required to keep a lab notebook as part of your participation grade. The
notebooks will not be graded for content per se, but you will need the information to complete
post-labs and lab reports. In addition, you will be allowed to refer to your lab notebook during
the lab quiz. The instructors will check your notebooks a few times during the semester to
provide feedback to help you learn to keep an accurate and useful notebook.
Lab notebook guidelines: Remember the goal is accurate information retrieval later on.
 Name and date on every page.
 Title of experiment each week.
 Sub-headings for each section within an experiment, to facilitate locating
information. (It is recommended to underline these so they are easy to find.)
 Aim of experiment or section within an experiment. This is usually a 1-2 paragraph
description of the goal of the upcoming procedure and why you are doing it. For
example, “A purified plasmid was obtained from cells using the miniprep protocol
described above. Now, the concentration of the plasmid will be determined using
absorbance at 260 nm measured in a spectrophotometer. We will also examine the
purity of the plasmid by calculating the ratio of absorbances at 260/280. We need to
know the concentration in order to prepare 1 g of DNA for the next step, which is
digestion with restriction enzymes.”
Protocol. A brief synopsis of what you actually did. You can reference the lab manual
when needed (giving the page number), but for procedures with parameters that vary
(e.g., PCR), you should write this information out so that you can find exactly how it
was carried out. If you repeat a protocol with different steps or change anything from
the lab manual, this must be noted in your lab notebook as well. For example, “No
reaction was observed, even after extended incubation. Repeated protocol, but added
1 mL of Barfoed’s reagent instead of 300 L. Faint pink color after 5 min.” Also note if
you made a mistake or if you notice anything that could be done differently in the
Data and any observations. Record the results of your experiments, as well as any
observations like changes in color, viscosity, precipitation, or other details that you
think are relevant and are not described in the procedure. These can help you
troubleshoot if anything goes wrong. Remember that direct observation is the basis
for all research and science. Often, seemingly random or disconnected observations
by creative researchers sometimes pave the way to important scientific discoveries!
Post-Labs: Most of the labs have a post-lab analysis section, to help you interpret your data
and synthesize the material. They will be due at the beginning of class the following week.
Lab Report(s): There will be two formal lab reports during the semester, after the enzyme
kinetics and DNA labs. Details on the expectations for these reports will be distributed later.
Lab Quiz: There will be one lab quiz at the end of the semester. This will be “open book” to
the extent that you will be able to use your lab notebook.
Graduate Students: Graduate students enrolled in CHEM 504 will be required to demonstrate a
higher level of technical proficiency in the lab, communicate results clearly in lab notebooks, and
be able to apply methods learned in this course to other applications.
As an additional component of the course, graduate students will be required to write and
submit a 10+ page paper on a laboratory method or technical application (worth 30 points) and
give an oral (~10 minute) presentation on it (worth 20 points). Please see Dr. Waters in the first
three weeks for details and topic selection.
Graduate students will also be expected to keep a more detailed lab notebook evincing a clear
understanding of the protocol, technical details, and how actual results differ (if at all) from
expected results. The lab notebook will be graded (worth 50 points).
The final grading will be out of 450 points. The grading scale will also be altered in the case of
any graduate students to be more rigorous. Typical minimum percentage grade ranges:
100-90% A/A89-80% B+/B/B79-70% C+/C
69% or lower will constitute failing the course.
Lab Safety:
You will be required to be familiar with the Laboratory Procedures sheet (to be distributed)
and to sign a form acknowledging that you are familiar with it before you are permitted to do any
lab work. The following points from that sheet are emphasized:
 No food or drink is allowed in the laboratory at any time.
 Lab safety goggles should be worn at all times except when they would be a hindrance to
fine work (e.g., loading gels) or when everyone is merely doing written work. If you do
not already have goggles, you can purchase them at the Chemistry stockroom. It is
recommended that you label them with your name or initials!
 Long hair should be tied back during class.
 Appropriate clothing, consisting of closed-toe shoes and clothing below the knee, must be
worn at all times. For some experiments, a lab coat and latex or nitrile gloves may be
required. You may wish to wear a lab coat and gloves for other experiments as well. Let
your instructor know if you have an allergy to latex!
 Hazardous waste must be disposed properly in the indicated containers.
 Use volatile solvents or strong acids in the hood.
 Report all accidents or injuries to the lab instructor, no matter how minor.
 Note the location of the fire extinguisher, safety shower, and eye wash station. Also note
the exits.
 If there is a fire alarm or other emergency, immediately turn off gas and electrical
equipment and exit the building or proceed to a safe location.
 Broken glass must be disposed of in special sharps containers.
General Policies and Lab Courtesy:
 When e-mailing instructors, please include the subject line “CHEM304” so that we can
prioritize your emails and respond more quickly.
 Please be courteous and provide a good learning environment for yourself and fellow
students. Cell phones must be turned off and put away during class.
 Never stick your personal pipets into community reagent bottles. If your pipet is dirty,
this will contaminate the supply for everyone. Instead, take a small amount of the
reagent to your bench in a small beaker or tube.
 But don’t take more of the chemical or solution than you need! Determine ahead of time
how much you will need and then take just a little more than that.
 Never take a community reagent back to your own bench. One of the most frustrating
things in lab is being unable to find what you need because someone else has it at their
 At the end of the lab, all chemicals and reagents should be put away and any materials to
be kept should be stored in your drawer, the refrigerator, or the -20 °C freezer as
 Every week before leaving, clean your bench area and any equipment and glassware that
you used. The next class may need these things. Your job is not over until the lab is clean
and the equipment is ready to be used by the next class.
Lab Schedule:
Week Date (Week of)
Sept 9
Sept 16
Sept 23
Sept 30
Oct 7
Oct 14
Oct 21
Oct 28
Nov 4
Nov 11
Nov 18
Nov 25
Dec 2
Dec 9
Lab 1
Lab 2
Lab 3
Lab 4
Lab 5
Lab 6
Lab 7
Lab 8
Lab 9
Lab 10
Lab 11
No Class
Lab 12
Lab Quiz
Syllabus, Safety, Pipetting, and Intro to Buffers
Buffers and Dilutions
Protein Quantitation
Protein Purification
SDS-PAGE Gel Electrophoresis and Coomassie Staining
Western Blots
Enzyme Activity Assay and Kinetics 1
Enzyme Activity Assay and Kinetics 2
Carbohydrate Lab
Native Gel Electrophoresis
DNA Lab 1 (PCR and Miniprep)
Thanksgiving Break
DNA Lab 2 (Restriction Digest and Agarose Gel Analysis)
Check Out, Lab Quiz
* Pre-Labs are due at the beginning of the class session listed.
* Post-Labs are due at the beginning of the next class session listed.
* The Enzyme Lab Report is due the week of Nov 4th.
* The DNA Lab Report is due the week of Dec 9th.
Pre-Lab, Post-Lab
Pre-Lab, Post-Lab
Pre-Lab, Post-Lab
Pre-Lab, Post-Lab
Pre-Lab, Post-Lab
Pre-Lab and Report
Pre-Lab, Post-Lab
Pre-Lab, Post-Lab
Pre-Lab and Report
Lab Quiz