SYLLABUS |
Biochemical Techniques |
CHEM361 BIOL395 |
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Spring 2005 |
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Professors: Dr. Margaret Jonah (Sci106, x-6900)
Dr. J. Brent Friesen
(Sci304, x-6972)
Class Times:
Tuesday 11:30 to 2:15,
room 220 in
Tuesday 3:15 to 6:00, room 220 in
COURSE SCOPE AND OBJECTIVES
This course is designed to:
1) acquaint the student with the major techniques used in analysis of
biological molecules and
2) give an introduction to some of the techniques used in the study
of living cells.
The theory of each method will be
presented. Practical applications of each method will be described and carried
out during the associated laboratory period or periods. Each of the four major
classes of biomolecules will be studied.
Another objective of this course is to
develop skill in writing formal laboratory reports. The ability to write
accurate and clear reports is important in many of the careers you may choose
in the future. The laboratory reports will use elements of the basic format for
professional research publications.
COURSE
MATERIALS
Reference
and Background Works (Not Required):
Biochemical Techniques: Theory and Practice
J.F. Robyt & B.J. White (1987),
Writing Papers in the Biological Sciences 3rd edition
V.E. McMillan (2001),
Handouts
Course
Webpage: http://domin.dom.edu/faculty/jbfriesen/chem361.htm
LABORATORY
POLICY
Attendance
at each laboratory session is required. It may not be possible to make up
missed labs. Most of the laboratory exercises will involve use of biological
materials and require extensive preparation prior to the laboratory period.
Laboratory procedures, including safety precautions, should be carefully
followed, in order to allow you to collect meaningful data.
Students
will be required to come to the laboratory period prepared. The Pre-lab
assignments are due at the beginning of lab. If you have trouble with a
pre-lab, get help before you come into lab. A pre-lab quiz may be given at the
discretion of the instructors.
A lab missed
for any legitimate and pre-excused reason must be made up within two weeks of
the scheduled lab time. Penalties for late assignments will still apply in the
case of make-up labs.
LABORATORY NOTEBOOKS
In the world of science and medicine, laboratory
notebooks are public, legal documents that can be subpoenaed by the
courts. Each student will be required to keep a laboratory notebook to
record each step of the experimental operations and related observations. The
notebooks may be collected, evaluated, and graded by the instructors at any
point in the course.
Your
laboratory notebook is the primary record of all work done in the
laboratory. Everything relevant to the
experiments you perform should be entered into your notebook as you
proceed. Your procedures should be complete enough so that someone with a
comparable level of proficiency in chemistry could repeat your experiment.
The
following guidelines should help you to know what is expected:
1) The notebook must be bound
so pages cannot be removed.
2) The dates you perform the
experiments should accompany your entries.
3) Pages should be numbered; a
table of contents should precede your first experiment, and each experiment
should be titled.
4) All entries must be permanent, i.e. use ink.
5) Keep all entries legible,
even errors. Cross out mistakes so that the original entries are still easy to
read.
6) Acknowledge partners and
anyone else who has supplied data to you. Cite references where appropriate.
7) Entries,
which can include notes on discussion of theory and methods or experimental
data, must be dated.
8) All data (including units),
graphs, calculations and conclusions should be in your notebook.
Keeping
a proper notebook becomes easier with practice, but if you have any questions,
please don’t hesitate to ask your instructors. Laboratory notebooks will be
collected and/or checked and graded periodically during the semester.
We
will perform approximately 10 different experiments during this course. Each
report will be given points based on a scale of the work performed in the
experiment and for the lab report. Each experiment will have roughly equal
weight in the final point totals. Completion of a lab is defined as both
attendance at the lab and completion of the written report. Failure to complete
a lab will result in a score of zero for that lab. Prelab questions, lab
notebook evaluations and quizzes will be also be a part of the total points for
the course.
No
chemical waste may be disposed of down the drain or in the trash unless
specifically directed to do so. Labeled waste collection containers will be
available for each laboratory exercise.
All
chemicals must be treated with respect, and all necessary precautions should be
observed to avoid exposure to chemicals. However, even under the best
laboratory safety conditions, accidents involving chemical exposures may occur.
Exposure to chemicals is possible through a variety of means, such as chemicals
splashing onto your skin, touching your face with a contaminated hand,
ingestion or inhalation of a chemical or getting stuck with a contaminated
syringe. To ensure that the appropriate actions are taken, any exposure must be
reported.
BLOODBORNE
PATHOGENS
If
you are bleeding you must notify your lab instructor. Fellow students in
lab should avoid assisting in situations involving potentially infectious
materials. The potential for others to be exposed to potentially infectious
materials must be limited. Your lab instructor has been trained to handle these
situations. If you are able, you will be asked to clean up any contaminated
area involved. Again, this is to reduce the potential of others being exposed
to potentially infectious materials. If you
need assistance, security will be called. Be aware that they will put on gloves
to protect themselves and you - please do not take this personally! Any area
contaminated by potentially infectious materials has to be properly disinfected
and all materials used to clean up the area have to be disposed of as
infectious waste. No infectious waste can go into the regular trash.
Students
will be responsible for the maintenance of their laboratory station. This
includes careful attention to the following:
1. Make sure hot plates and other instruments are
unplugged.
2. Make sure the faucets are OFF and positioned
above the sink.
3. Make sure the bench top is wiped down to remove
all chemicals.
BROKEN
AND DAMAGED GLASSWARE AND EQUIPTMENT
Students
are responsible for taking care of the glassware and laboratory equipment they
are using. Any breakage or loss of glassware and laboratory equipment should be
reported. The replacement cost of any glassware and laboratory equipment broken
or lost due to negligence on the part of a student will be charged to that
student’s account.
It
may be necessary for you to come in following your regularly scheduled lab day
in order to perform analyses. You may be required to sign up for instruments
ahead of time. If so, there will be sign-up sheets for you to select a time
during the next morning or early afternoon to do the necessary work. Do not procrastinate on these
determinations. Instruments and materials are available for a limited time.
LAB REPORTS
The text of
all lab reports must be typed. However, tables of data, graphs, and other
figures may be handwritten. The data tables and labels of axes, etc., for
graphs of figures should be written in ink, unless there is good reason to use
pencil.
Lab reports are due one week after completion of the experiment. All deadlines must be adhered to. A failure to hand in lab reports on the proper deadline will result in a 1 to 5 point deduction in the score. Handing in a lab report after the same report has been graded and handed back by the instructors will receive a grade no higher than a “C”. In addition to the above penalties no more than two late assignments will be graded.
Most of the lab reports will
be submitted in an informal question-guided format. However, a few will be
requested in a more formal research paper format.
(This format is found in
Chapter 4 of Writing Papers in the Biological Sciences)
Title
The experiment should be given a clear title that
utilizes the key words of the study.
The abstract is a short
paragraph that summarizes the major elements of the paper: objectives, methods,
results and conclusion.
Introduction
Purpose. This section should only take a couple of sentences.
State why this experiment will be performed and include any relevant background
information.
Theory and Techniques. Include a discussion of all the major theories and
techniques that the experiment is supposed to demonstrate. Don’t rely entirely
on handouts to write your lab reports. Include at least one other reference
(besides the handouts) in the writing of each lab report. Proper citations must
be given in the text of the report for all information taken from references
(See chapter 6 in Writing Papers in the Biological Sciences). The text of the report should be in your own words,
with as little quotation or paraphrasing as possible. Remember also that formal
papers require formal language usage in third person past or present tense.
Materials.
Write a complete list of instruments, glassware, solutions and other materials
that you used for the experiment.
Methods.
Write a step-by-step procedure used for the experiment. This list will be taken
from published procedures. Be sure to include a complete description of any
variations or modifications of the published procedure.
Summary. A short written summary of
the data is presented in this section but the meaning of the data is not
discussed here. All raw data should be taken into account.
Presentation of Data. Data should be put in
tables if at all possible, as it is easier for the reader to digest in this
fashion (see chapter 3 in Writing Papers in the Biological
Sciences).
Each table or graph should have a descriptive title. Be sure to include all the
information for how the data was collected (instrument make and model, solvent,
concentration, IR method, etc). Graphs should be planned to include the full
range of values on each axis. The axes should be clearly labeled including
units of measurement.
Sample Calculations. The results of
calculations would usually be presented in a data table, but you should show
how the values were calculated. Include units in the sample calculation not
only to identify the numbers but also to make sure you are calculating the
correct value.
Discussion:
This section will include a
few paragraphs discussing what the experimental data mean. Discuss the most
important aspects of the experimental data including any problems or unexpected
results. Explain why the problems or unexpected results occurred. Note what
errors may be possible in the experiment and how they were avoided.
Synthesis of ideas and concepts can take place in this section.
Comparison of your data with others in the lab is entirely appropriate, but
other peoples' work should always be given credit (i.e. reference them).
Write a few carefully
constructed sentences describing the most important conclusions that can be
drawn from the experimental data. Don't draw conclusions that aren't supported
by the data. Most of the time conclusions in a well-written report should
reflect back to the purpose of doing the experiment.
Acknowledgments.
See
Chapter 6 in Writing Papers in the Biological Sciences for
the correct format.