Syllabus: Chemistry 429, Spring 2016
Instructor:
Dr. Mette Soendergaard
Office: Currens Hall 540A
Email: m-soendergaard@wiu.edu
Phone: 309-298-1714
Office hours: T, TH 9-11 am; other times by appointment.
Lecture meeting time and place:
Tuesday: 8:00-8:50 am, Currens 202
Lab meeting time and place:
Tuesday: 2:00-4:50 pm, Currens 538
Thursday: 2:00-4:50 pm, Currens 535
Course Credits: 3 semester hours (one 50 min lecture plus two three-hour labs per week).
Prerequisite: Chem. 421 or equivalent.
Objective: The goal of this lab intensive course is to teach students biochemical methods and techniques that
will be useful in their research work.
Recommended Text
"Principles and Techniques of Biochemistry and Molecular Biology” 7th edition by Wilson and Walker;
Cambridge.
Textbook
Home
Page
URL:
http://www.cambridge.org/US/academic/subjects/lifesciences/molecular-biology-biochemistry-and-structural-biology/principles-and-techniques-biochemistry-andmolecular-biology-7th-edition
Other supplemental materials
Lab manuals posted on Western Online
Web links and other materials posted on Western Online
Instructor communication and feedback
Students are encouraged to contact the instructor with questions about the content, grading, etc., of the course.
This can be done by face to face meetings or by email (m-soendergaard@wiu.edu). The instructor will answer
emails within 24 hours during regular business days and hours (M-F, 8:00 am to 5:00 pm), but less frequently
during the weekend or scheduled WIU breaks.
For MMR reports, lab reports and exams, I will provide feedback and assign grades within 2 weeks from their
due date.
Attendance: You are expected to attend ALL of the lab meetings punctually.
If it should be necessary to miss a lab, the instructor must be notified in writing by e-mail, before the fact if
possible. The only acceptable excuses for missing a lab are personal illness, family emergencies or university
sponsored functions (i.e. WIU band trips, field trips in other WIU classes, WIU athletics, etc.). In all cases,
documentation is required, and must be submitted to the instructor in advanced or as soon as possible in case of
emergency. Makeup labs will not be given. In addition, you are allowed only a single (documented) missed lab
per semester (exceptions can be made in some circumstances, such as for athletes, but this needs to be discussed
with the lab instructor well in advance). All other absences, excused or unexcused, will be considered a
“missed” lab period and the student will receive zero points for the missed lab (MMR report and lab report).
Students who show up more than 15 minutes late will be given an unexcused absence and will NOT be
allowed to perform the experiment. The student will receive zero points for the missed lab (MMR report
and lab report).
Instructor’s expectations of students
Regular and punctual class attendance is vitally important to a student's academic achievement. Students are
expected to attend every class (lecture and lab). Special circumstances (personal illness, family emergency or
tragedy, participation in university sponsored trips such as athletics or professional meeting [not sorority/frat, or
other clubs or participation in university sponsored trips]) will be accommodated, but the instructor must be
made aware of these well in advance in writing (by email). Proper documentation must be provided.
Students are expected to use the Online Absence Reporting System (OARS) every time they miss class by
logging onto: http://wiu.edu/oars. The system serves to help students and faculty document absences; it doesn't
excuse students from class. It is the instructor’s discretion on how to use this absence information based on the
attendance policy (see the acceptable excuses above).
Students are expected to come to class/lab on time. If a student misses more than 10 minutes of class/lab by
either arriving late or leaving early, the student will be counted as absent. Missing fewer than 10 minutes of
class is counted as tardy. Three tardies count as one absence.
Students are not to go in and out of the class/lab during lecture/lab/exam unless there is an emergency or the
instructor has given permission. Students leaving the classroom will be counted tardy for missing any time or
absent for missing more than 10 minutes of class time. Students should make arrangements to go to the
restroom between classes, not during class.
Important information is often given during the first minutes of a lecture/lab. Students are responsible for all
information and materials given in class whether you are present or not.
Students are expected to self-motivate themselves and are expected to read ahead, prepare for class and
participate in class discussion.
Please turn off cell phones and put away tablets and laptops (and other devices) while in class. Cell phones and
laptops can be very distracting and cannot be out during an exam! Also, class time is not a social hour. Please
refrain from casual conversation during class time.
Outside work requirements: Students are expected to read, review, and learn all materials discussed in both
lecture and lab. Students are expected to spend significant amount of time on the MMR and lab reports and the
literature searches associated with them.
Materials, Methods and Results (MMR) Reports
Each week an MMR report is due. This report should include a description of the materials and methods, as
well as all data, results and calculations from the experiments performed during the week prior. Each MMR
report will be worth 25 points. MMR reports are to be typed, and are due electronically on Tuesdays at 2 pm the
week after the experiments were performed in lab. Late MMR reports will be deducted by 10% per day. MMR
reports turned in two weeks after the due date or after the last day of classes (May 6th, 2016), whichever comes
first, will not be graded. 5% of the grade for each report will be for writing style and presentation. Make sure
that you use spell checking and that you proofread all reports before submission.
Even though some of the lab work will be done in groups and you collect data in groups, the analysis of your
common data and preparation of your report must be completed independently. Using any part written or done
by others is plagiarism and a form of cheating. It is also cheating if you use a diagram created by someone else
to analyze your data. Using someone else’s data (other than what you have collected in your group) is
considered falsification of data, and is also a form of cheating. Plagiarism and falsification of data, or any other
form of academic dishonesty, will NOT be tolerated. Incidents will results in a grade of zero for the assignment
and failing grade for the whole course. This will happen the first time a student commits an offense of academic
dishonesty. There are no second chances, when it comes to academic dishonesty!
Lab Reports
Two lab reports are due, one for the first half of the semester (Lab 1), and one for the second half of the
semester (Lab 2). Each lab report should include:
Title Page: This should include the title of your report, your name (in bold), your lab partner’s name(s), and
your email address, course number and date.
Abstract: This should be a short version (a summary) of the entire paper. Therefore, it should include a brief
introduction, methods, results, and discussion, expressed in 200-300 words. Basically, from the abstract people
should be able to understand scientific findings without having to read the entire paper. Writing an abstract can
be challenging, as you are trying to summarize your entire paper in a few words. Greatly abbreviating the
methods is usually a good way to start. If you are struggling, look up some recent scientific papers for
inspiration. The abstract should be written in past tense, since it is a summary of what you have already done.
Introduction: This section should describe background information about the scientific problem you are
addressing. Also, you must convey the overall goal of the experiments and the hypothesis tested. Think about
what relevant information is necessary to include, so that someone that did not participate in the experiments are
able to understand the hypothesis and why is it important. What are you hoping to learn from the experiments,
what need to be accomplished?
Materials and Methods: This section should be a brief and concise summary of what you did. It needs to
include enough detail so that any scientist in your field could repeat your work. However, it does not need to be
reported down to the smallest detail. Ask yourself: “Would I be able to repeat my experiment using this
information?” “Have I included too much information to a point where it becomes confusing?” Also, you must
include the source (company) of the reagent and any equipment used, so make sure to take notes during the lab.
Results: This section should be a description of what you did in words, supplemented with figures and tables. It
is not enough to have several figures and tables. Do not merely list results in the text. Instead, explain the
findings and in short fit them into the overall context of the paper. For each experiment consider what you were
doing in the lab and what you were trying to accomplish? Why were you using the methods that you did? And
of course, what were your results? And what do they mean in regard to what you set out to accomplish? You
must briefly summarize how the experiment was performed, what the results were, and how you interpret these
results. Fx. “In order to confirm that the protein purification of enzyme X was successful an SDS-PAGE was
performed using an aliquot from the last purification step. The SDS-PAGE showed (Figure X) that only one
band was present, and that this band corresponded to the expected size of enzyme x (Figure XX). This indicated
that the protein purification was successful since only one protein band was detected. However, this needed to
be further confirmed by Western blotting.”
For reporting numbers in the text, convert the numbers to be easily readable and to have reasonable
values. For example, 1.0014567 mg/μl is not reasonable. Converting the value to 1.46 mg/ml is much easier to
read, and the number of significant figures becomes less excessive. Some of the lab manuals contain questions
that must be answered and included in the lab report. These questions should be answered in a separate section
in the end of the lab report (after the conclusion, but before references and the appendix).
Each figure and table must have a number and a legend that describes what the figure/table means in
enough detail, so that the reader does not need to be searching in the main text for an explanation. Each
figure/table should be referenced in the text as shown in the example above.
Discussion: Begin with a brief summary of what you set out to accomplish with the experiment. What did you
set out to accomplish, and did you accomplish it? What was the hypothesis? Briefly summarize and explain
your results. What did you discover? Were the results expected? Which of your results are interesting? What
can you say about your hypotheses now that you have performed the experiments? Was anything surprising?
Overall, you should answer the question (the hypothesis) that you asked in the introduction. Sometimes the
original hypothesis turned out to be flawed, and then you must propose a new hypothesis to account for your
observations. At other times your original hypothesis is supported by your data, which you must then convince
the reader of. If you have unexpected results, you must explain these with sound biochemical knowledge. Use
research papers to back up your claims.
Conclusion: A brief description of your hypothesis, and whether or not you proved your hypothesis to be
correct and why. Is anything next?
Figures and Tables: In writing a paper, figures and tables, if done correctly, are extremely useful. You must
refer to the figures and tables in the text. For example: “The protein concentration was determined to be 1.02
mg/mL using the Bradford method (Table 2A)”. Again, each figure and table must have a figure/table legend
that describes what the figure or table means in enough detail, so that the reader does not need to be searching in
the main text for an explanation (although it does not have to be in as much detail as in the main text).
References: In the reference section you give proper credit to the originators of the information you are
presenting. Which scientific papers or books did you read to get the information for your introduction and
discussion? In general, every time you present background information, it must be references. Also, where did
your methods come from? (Note that, unless you invented the method, you should always reference the paper
that first described the work. In some cases this will be the lab manual, in others you must find the original
research paper and cite this.)
Appendix: Include your raw data and any calculations that you used to analyze your results in the Appendix
section. In most scientific peer-reviewed papers, the appendix sections are only included for the description of
novel calculations or lengthy methods. However, in this course, the Appendix is included so that your lab
instructor can understand how you calculated and obtained your results.
Lab reports are to be typed. The reports are due electronically as directed by the instructor. Late lab reports will
be docked by 10% per day. Lab reports turned in two weeks after the due date or after the last day of classes
(May 6th, 2016), whichever comes first, will not be graded. 5% of the grade for each report will be for writing
style and presentation. Make sure that you use spell checking and that you proofread all reports before
submission.
Even though some of the lab work will be done in groups and you collect data in groups, the analysis of your
common data and preparation of your report must be completed independently. Using any part written or done
by others is plagiarism and a form of cheating. It is also cheating if you use a diagram created by someone else
to analyze your data. Using someone else’s data (other than what you have collected in your group) is
considered falsification of data, and is also a form of cheating. Plagiarism and falsification of data, or any other
form of academic dishonesty, will NOT be tolerated. Incidents will results in a grade of zero for the assignment
and failing grade for the whole course. This will happen the first time a student commits an offense of academic
dishonesty. There are no second chances, when it comes to academic dishonesty!
Grading
The grade will consist of 60% lab work (MMR reports and lab reports; 600 points) and 40% exams (400
points). There are 1,000 points possible during the semester. Your letter grade will be based on your total
accumulated points. No extra points or assignments will be given at any time.
Points each
MMR reports (12)
25
Lab reports (2)
150
Exams (midterm and final) 200
Points total
300
300
400
Grading Scale (including plus/minus grading) for undergraduate or bridge credits
90.00% and above
86.70 - 89.99%
83.40 - 86.69%
80.00 - 83.39%
76.70 - 79.99%
73.40 - 76.69%
70.00 - 73.39%
66.70 - 69.99%
63.40 - 66.69%
60.00 - 63.39%
56.70 - 59.99%
56.66% and below
A
AB+
B
BC+
C
CD+
D
DF
Grading Scale for graduate credits
90.00 % and above
80.00 - 89.99%
70.00 - 79.99%
60.00 - 69.99%
59.99% and below
A
B
C
D
F
No incompletes will be given to a student with a failing grade in the course unless the student experiences a
documented emergency that takes him/her away from the university for at least two consecutive weeks and/or
causes him/her to miss the an exam. The student must notify the instructor of this emergency before each exam.
Make up exams: The only acceptable excuses for missing an exam will be for personal illness, family
emergency, or university sponsored functions (i.e. WIU band trips, field trips in other WIU classes, WIU
athletics, etc.). In all cases, documentation is required, and must be submitted to the instructor in advance or as
soon as possible in case of emergency. Make-up exams are always designed to be at least as difficult as the
regular exam. Any student who arrives late for an exam loses that amount of time to work on the exam.
Seating will be assigned by the instructor during the exams and/or any other time deemed necessary. Only
simple scientific calculators may be used on exams. Graphing calculators and cell phones/tablets/laptops or
any other electronic devices may NOT be used on exams.
General information

Safety is the first concern in a chemistry lab. Material Safety Data Sheets (MSDS) information about all
chemicals utilized in the laboratory can be found at the following web site http://hazard.com/msds/.
Proper handling of chemicals, especially correct pipetting technique is expected. Safety glasses are to be
worn at all times, and proper attire that covers the entire body including legs and shoulders are to be
worn at all times. Shoes that cover the feet and exposed no skin are to be worn at all times. There will be
no exceptions to these rules. Failure to dress properly and wear safety goggles at all times will result in
dismissal from the lab, and a grade of zero for that lab period.

A bound notebook is required for the daily entry into the lab. Print your name on the front cover and on
the first inside page. Save the first couple pages for a table of contents. All entries are to be in ink, and
errors crossed out rather than erased.

Begin each day's work by entering the date. Following this you may develop an individual style in data
recording, but a suggested pattern is: title, brief description of purpose, protocol, observations, results,
discussion, and conclusions. It is better to write too much information than too little. Remember, you
will have to report everything you have done in lab at a later date, so make sure you can understand it
later in the semester. Have you instructor or TA check your notebook before the end of each lab day.

It is very important that you'll be able to identify your samples throughout the semester. All samples
must be labeled with permanent ink. Labels should include sample ID, your name and date.
Remember where you store your samples.

It is your responsibility to make sure you understand what you are doing, why you are doing it, how to
do it, and what your results mean. Feel free to ask questions if you have any doubt, and please come
prepared!
Statement on Ethics
Western Illinois University, like all communities, functions best when its members treat one another with
honesty,
fairness,
respect,
and
trust.
Students
have
rights
and
responsibilities
(http://www.wiu.edu/provost/students.php). Plagiarism, falsification of data, cheating, and other forms of
academic dishonesty constitute a serious violation of WIU conduct regulations. Students who engage in
dishonesty in any form shall be charged with academic dishonesty. Make sure that you as the student are aware
of the WIU Academic Integrity Policy (http://wiu.edu/policies/acintegrity.php). Please remember that you are
expected to do your own work at all times.
Even though some of the lab work will be done in groups and you collect data in groups, the analysis of your
common data and preparation of your report must be completed independently. Using any part written or done
by others is plagiarism and a form of cheating. It is also cheating if you use a diagram created by someone else
to analyze your data. Using someone else’s data (other than what you have collected in your group) is
considered falsification of data, and is also a form of cheating. Plagiarism, falsification of data, cheating or any
other form of academic dishonesty, will NOT be tolerated. A zero tolerance policy will apply. Incidents will
result in a grade of zero for the assignment and fa ailing grade for the whole course. This will happen the first
time a student commits an offense of academic dishonesty. There are no second chances, when it comes to
academic dishonesty!
Emergency evacuation procedures for the building
If a fire alarm should happen to ring, or if students are ordered to evacuate a lab or classroom by the instructor,
the students should walk to the nearest stairwell (do not use the elevators) and proceed to the ground floor and
out of the building. In the case of a tornado warning, students should gather on the first floor near the elevators
and stay away from any windows or outside doors. Any student on an upper floor who cannot physically
proceed down the stairs should go to the southernmost stairwell and await assistance. If the building should be
evacuated all students and personnel should gather at the southwest corner of the Higgins Parking lot near the
fence (parking lot just outside the building) to wait for further instructions.
Emergency Preparedness
WIU Office of Risk Management and Emergency Preparedness provides resources on how to respond to
emergency
situations.
Please
view
the
video
resources
at
http://www.wiu.edu/vpas/risk_management_and_emergency_preparedness/ref_guide.php.
Students with Disabilities
It is the policy of Western Illinois University to accommodate individuals with disabilities pursuant to federal
law and the university's commitment to equal educational opportunities. It is the responsibility of the student to
inform the instructor of any necessary accommodations at the beginning of the course. Any student requiring
accommodations should contact the Disability Resource Center (DRC).
Holidays and other important dates
Date
January 19
February 12
March 14-18
May 9-13
Event
Classes Begin
Lincoln's Birthday - No Classes
Spring Break - No Classes
Final Exam Week
Tentative lecture schedule
Date
Lecture topic
Readings
(Principles and Techniques of Biochemistry and
Molecular Biology)
1/19/2016
Introduction.
(1.1-1.3, 1.5)
1/26/2016
Manipulation of nucleic
acids.
Recombinant DNA
technology.
Recombinant DNA
technology.
Protein expression and
purification.
Protein measurements.
SDS-PAGE.
Western blot.
Enzyme kinetics.
Enzyme kinetics.
Midterm
Spring break: No class.
Cell culture techniques.
Microscopy.
Immunological techniques.
Drug discovery.
MTT assay.
Dose-response assays.
Cell signaling.
Data analysis.
Review
Finals week
(5.1-5.5)
5.6-5.7, 5.10
(10.1, 10.2)
6.1, 6.2, 6.3, 10.4
6.4-6.6
2/2/2016
2/9/2016
2/16/2016
2/23/2016
3/1/2016
3/8/2016
3/15/2016
3/22/2016
3/29/2016
4/5/2016
4/12/2016
4/19/2016
4/26/2016
5/3/2016
5/10/2016
(8.1-8.2)
6.7, 8.3, 11.8
8.4.1, 8.5.1, 10.3, 7.7, 15.1
15.2
2.1-2.5, 2.8
4.1-4.4, 7.1-7.2, 7.4
18.1-18.3
17.1-17.2
17.3-17.4
Tentative lab schedule
Date
TU 1/19/2016
TH 1/21/2016
TU 1/26/2016
TH 1/28/2016
TU 2/2/2016
TH 2/4/2016
TU 2/9/2016
TH 2/11/2016
TU 2/16/2016
TH 2/18/2016
TU 2/23/2016
TH 2/25/2016
TU 3/1/2016
TH 3/3/2016
TU 3/8/2016
TH 3/10/2016
TU 3/15/2016
TH 3/17/2016
TU 3/22/2016
TH 3/24/2016
TU 3/29/2016
TH 3/31/2016
TU 4/5/2016
TH 4/7/2016
TU 4/12/2016
TH 4/14/2016
TU 4/19/2016
TH 4/21/2016
TU 4/26/2016
TH 4/28/2016
TU 5/3/2016
Lab
Bioinformatics.
i) Plasmid purification.
ii) PCR.
Plasmid purification.
i) Gel electrophoresis: PCR
product and plasmid.
ii) Restriction enzyme
digestion.
iii) Alkaline Phosphatase
digestion.
i) Gel electrophoresis.
ii) Gel purification.
Ligation and transformation.
i) Colony selection.
ii) Colony screening.
i) Grow culture.
ii) Induce protein expression.
iii) Cell harvest.
Protein purification.
Protein measurements:
i) UV280.
ii) Bradford assay.
SDS-PAGE
Western Blot
Enzyme kinetics
Enzyme kinetics
Data analysis
Spring break: No class.
Spring break: No class.
Mammalian tissue culture
technique
Mammalian tissue culture
technique
Mammalian tissue culture
technique
Microscopy
NCI Drug incubation
i) MTT assay.
ii) Microscopy.
Drug incubation.
IC50
Drug incubation
Cell lysates.
2-D gel.
Data analysis
No lab
Due
Readings
(Principles and Techniques of
Biochemistry and Molecular Biology)
5.8
MMR 1.1
MMR 1.2
MMR 1.3
MMR 1.4
MMR 1.5
MMR 1.6
15.2, 15.3
MMR 1.7
Lab report 1
MMR 2.1
MMR 2.2
MMR 2.3
MMR 2.4
MMR 2.5
Lab report 2
TH 5/5/2016
TU 5/10/2016
TH 5/12/2016
Final exam
Finals week
Finals week
Students enrolled in this course are levied a non-refundable laboratory usage fee of $35 to cover the cost
of consumable supplies utilized during the semester.
Supplies to be provided by students
- Safety goggles. Eye protection is required and must be purchased by the student.
- Scientific calculator
- Bound notebook
SYLLABUS IS SUBJECTED TO CHANGE WITH NOTICE
Last Updated January 18, 2016 by Dr. Mette Soendergaard