CHEMISTRY 312 GENERAL BIOCHEMISTRY LABORATORY

							                            CHEMISTRY 312
                  GENERAL BIOCHEMISTRY LABORATORY
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                                      Fall 2009 Syllabus
                            W 1:30 to 4:30 pm in 3010 Berndt Hall

Instructor: Les Sommerville                    Office Hours: M W F 10:10 – 11:05 am
Office #: 250 Chemistry Hall                                          F 12:20 – 1:15 pm
Office Phone #: 247-7370                                           Th 11:15 – 12:10 pm
Home Phone #: 385-1849 (before 10 p.m.) You’re welcome to call or drop by my office at other times.
Website: faculty.fortlewis.edu/sommervil%5Fl/. E-mail: sommervil_l@fortlewis.edu
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INTRODUCTION
The purpose of this course is to provide you with a strong foundation in biochemical
experimentation. Experiments during the first few weeks will help you acquire some basic skills
that will help you throughout the remainder of the term. These experiments include investigating
the function of the metabolic enzyme fumarase, carrying out a purification of the enzyme
lysozyme, and learning to carefully acquire kinetic data to understand the catalytic mechanism of
the enzyme β-galactosidase. Through these labs you will gain experience in UV-vis
spectroscopy, NMR, mass spectrometry, computer modeling and curve-fitting.


LAB INSTRUCTIONS
Printed lab instructions will be provided to you on Mondays in Chem 311 lecture. Labs will also
be posted on my website.


GRADING POLICY
Grading:
Grades will be based on a percentage of the total points possible in the course. An A will be
received for 90% or greater of the total points, a B will be received for 80-89% of the total
points, a C will be received for 70-79% of the total points, a D will be received for 60-69% of
the total points, and an F for a percentage of the total points less than 60%.

               Summary of Points Possible
                50 points for Experiment 1 (Check-In)
               200 points for Experiment 2
               100 points for Experiment 3
               200 points for Experiment 4
               150 points for Experiment 5
                25 points for Lab Clean-up (Check-Out)
               725 points total




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Laboratory Reports:
Reports will be written in your laboratory notebook. Half of the report grade will be based on
laboratory participation; 20% will be based on content in your laboratory notebook and the
remaining 30% will be based on completeness and organization of the report.

The general form of the report will be: 1) 1-3 paragraph Introduction, 2) a Materials and
Methods section, 3) a Results section, and 4) a 1-3 paragraph Discussion section; see below for
more information about each of these sections. All reports are to be done in your notebook—the
type of notebook you choose is up to you. All graphs and tables should be generated from Excel
or a similar spreadsheet/graphing program. Note that you may use pencil and you may include
word-processed documents.

Introduction - This section will include a brief statement about the purpose or the hypothesis to
be tested. Some background about the experiment and discussion of theory and technique is also
expected.

Materials and Methods - A neat, complete and concise description of the materials and methods
will be included in this section. When methods are followed exactly as described in the
instructions, then reference the method to the instructions without copying it out of the text. If
modifications are made to the methods described in the instructions, make sure these are fully
described in your report. You should include in this section the make and model of all
instrumentation used during the experiment. You should also list software and other materials
used during the experiment. A flow chart of the entire experiment should be included in this
section.

Results - All results should be presented in graphical or tabular form and be described in the text
of this section.

Discussion - The entire report should be tied together in this section. The significance of the
results should be discussed and how the results lead you to your final conclusions should be
made clear in this section. The final paragraph of this section should be a summary of the
experiment.


Attendance:
Attendance is required! There will be no make-up labs. You will be working in teams. If you
miss a lab each of your teammates will have to do more work. Let me know as early as you can
if you absolutely must miss your scheduled lab time. Come to lab prepared! Prior to lab read the
text/manual, be prepared to ask questions, and know what to do.

Academic Integrity and Dishonesty:
Academic honesty and integrity are essential to the existence and mission of an academic
community. Academic dishonesty in any form (i.e. cheating, aiding in cheating, plagiarism) will
not be tolerated because such dishonesty undermines the entire academic endeavor. During the
lab and data workup you will be expected, and even encouraged, to work together. But, your lab
reports must be written in your own words – not your partners! Any act of academic dishonesty


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will result in a “grade of zero” for the assignment. A second infraction will result in an “F” in
the course. Such an action may warrant referral to the Academic Standards Committee, and
possible dismissal from the College.

COURSE EVALUATIONS
Formal course evaluations will be administered toward the end of the semester. Please make
every effort to complete these evaluations, as they are a valuable resource for me. I take these
very seriously and truly appreciate any constructive comments you might have.

I welcome feedback from you at all times. Please feel free to talk with me at anytime or send
anonymous suggestions if you feel the need. As I get to know each of you better, I can adjust the
course to better meet your needs.


STUDENTS WITH DISABILITIES
Students with disabilities have equal access and equal opportunity in this course. If you require
reasonable accommodations to fully participate in course activities or meet course requirements,
you must register with Disability Services, 280 Noble Hall, 247-7459. If you qualify for
services, bring your letter of accommodation to me as soon as possible.




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   DATE                        EXPERIMENT                        NOTEBOOK

September 3                Experiment #1: Check In
                 Pipetters, Buffers & Intro to Deep View

September 10        Experiment #2: Purification of Lysozyme           Due
                Ion exchange chromatography and activity assay

September 17       Experiment #2: Purification of Lysozyme
                        Protein concentration assays

September 24       Experiment #2: Purification of Lysozyme
                                SDS-PAGE

 October 1         Experiment #2: Purification of Lysozyme
                               LCMS analysis

 October 8             Experiment #3: DNA Unfolding                   Due
                      Helix Stability & Thermodynamics

 October 15            Experiment #3: DNA Unfolding
                          Salt Effects & Deep View

 October 22       Experiment #4: Kinetic Analysis of Lactase          Due
                             Learning the Assay

 October 29       Experiment #4: Kinetic Analysis of Lactase
                         Acquiring ± Inhibitor Data

November 5        Experiment #4: Kinetic Analysis of Lactase
                               Data analysis

November 12         Experiment #5: Investigating Fumarase             Due
               Using NMR to Determine ΔGº and Stereochemistry

November 19         Experiment #5: Investigating Fumarase
                            NMR Data Analysis

December 3         Experiment #5: Investigating Fumarase
                 Determining the pKas of Active Site Residues

December 10         Experiment #5: Investigating Fumarase
                         Deep View of the Active Site
                                                                 Notebook Due Dec 17



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