Course
Overview and Objectives: Welcome to biochemistry
laboratory!!! This practical course is
intended to give you an opportunity to apply knowledge you gained in CH411 (and
CH412) lecture to experimental situations.
·
By
the end of the course you should be familiar
with a number of core biochemical techniques: use of pipettors, balances
and the spectrophotometer; making buffers, methods of protein determination;
analysis of enzyme kinetics; methods of protein purification; electrophoresis,
electroblotting and immunoblotting; plasmid purification, restriction analysis
and polymerase chain reaction.
·
In
addition, you should be able to keep a
quality laboratory notebook and feel comfortable “surfing the web” for
information about your favorite protein.
·
By
the end of the course, you should be acquainted
with scientific paper writing and data presentation.
Student Responsibilities:
·
You
will need to CH413 Laboratory Manual available at the bookstore.
·
You need a notebook
for keeping lab notes. The book should be the carbon-copy type such as is used in CH311-313. You may purchase one in
the Chemistry office.
·
You WILL need to wear eye protection in the biochemistry lab. You can purchase a pair
of safety glasses with side shields at a hardware store or I can help you order
them. Goggles, as were used in gen chem and organic, are acceptable, but not
required (believe me, I KNOW how uncomfortable they are!!!!!). Please see me if
you need help procuring eye protection.
·
You will need to use a computer and/or a calculator and
graph paper to calculate and analyze data for lab reports.
·
Each
student is expected to abide by the safety rules set down in the lab
manual. In addition, each student must
sign the “Laboratory Safety” form, indicating her/his understanding of the
rules and regulations and complete the lab safety map.
Grading Policy: Your final percentage of
possible points earned in this course will be rounded to the nearest 1/10th
of a percent and then grades will be assigned as follows:
|
|
Overall
% |
Grade |
Overall
% |
Grade |
Overall
% |
|
A+ |
100-99.0 |
B |
86.9-83.0 |
C- |
69.9-67.0 |
|
A |
98.9-93.0 |
B- |
82.9-80.0 |
D |
66.9-55.0 |
|
A- |
92.9-90.0 |
C+ |
79.9-76.0 |
F |
<55.0 |
|
B+ |
89.9-87.0 |
C |
75.9-70.0 |
|
|
***PLEASE NOTE: I always reserve the right to use a more lenient scale.***
Your grade will be determined based upon your performance on your lab book, quizzes, reports, assignments and attendance/participation as follows: Lab Book, 15%; Quizzes, 35%: Reports/Assignments, 35%: Attendance/Participation, 15%.
Lab Book: You need to be prepared
for each laboratory session. One way to
prepare is to read through the procedure and write out the procedure in your
lab notebook prior to coming
to class and to review the theory of the procedures to be used. Lack of preparedness will result in lost
points.
Also, an important part of laboratory technique is careful
note taking. This means having your experimental
protocol written out and taking notes as
you are doing the experiment – that is, not after you have finished the
experiment or have left the laboratory. Your lab book should contain a
description of each protocol, data obtained and the calculations done to make
conclusions about the experiment. Where data is generated by computer or other
means, please tape a copy of the data into your lab book. Your lab book should STAND ALONE! The importance of taking good lab notes
cannot be overemphasized! You
must turn in the carbon copies from your lab notebook when you turn in your lab
report. This will serve as
evidence of your attendance, participation and striving to attain this
ideal. NOTE: every person must have his/her own lab notebook.
Quizzes: Three quizzes will be
given during the term. Quizzes will cover the theory and calculations relating
to experiments. The average on quizzes
during the term will count for 50% of your quiz grade and will be given during
weeks #6 and #10. The remaining 50% of
your quiz grade will be from a final take-home quiz given at the end of the
term.
Reports/Assignments: All experiment, article
and computer assignments/reports MUST BE TYPE-WRITTEN and DOUBLE-SPACED. The grade will be lowered significantly if it
is not typed or is messy. Report grades
will be based on scientific content and format, as well as grammar and proper
use of language. Points will be deducted
from late reports. Late reports will not be accepted
after the graded reports for that experiment have been handed back to the
class.
·
Research article assignment: Preparation of formal lab
reports will be evaluated by conformation to biochemistry article style and
format. As a way to prepare for this,
you will be asked to read a primary research article from the Journal of Biological
·
Assignments for experiments #1, #2, #3, #4 and #5: You need only complete
the questions posed at the end of the experiment. These will be due during the
week following completion of the experiment.
·
Formal lab reports for experiments #6 and #7/#8 combined:
These should be prepared in the manner of a scientific article according to the
format as observed in the research article exercise (above) and described in
the section entitled “Lab Report Format”.
They are due in class weeks 7 and
10, respectively.
·
Computer assignment: During week 3 you will be asked to complete an
exercise using computer databases, etc. This assignment will be due during week
4. Instructions will be provided at a later date.
Attendance/Participation: You
are expected to participate in each lab session. There will be no “make-up” labs. Please see the instructor if you must
miss lab. Points will be deducted if you
are not fully participating in the experiment and/or clean-up; for example, if
your partner does most of the work or if you are unable to perform basic lab
techniques.
·
BE ON TIME!! Each lab
period will begin with an important
short lecture. In addition, any changes
in procedures are described and required supplies are distributed at the
beginning of the lab period.
·
Cleanliness, etc. The
students in the lab class are responsible for keeping the equipment and
laboratory neat and tidy. Treat the
equipment with respect – BIOCHEMISTRY IS NOT CHEAP. (For example, pipettors cost $250 each). Glassware will be cleaned by students in
the laboratory before leaving. The
manner by which this labor is to be divided will be discussed in class. Each group is responsible for the equipment
checked out to them for the lab period.
Formal Lab Report Format:
Laboratory
reports MUST be type written and
double-spaced. They will be
graded for scientific content (roughly 55-60%), on style and format – that is,
how it conforms to the norms of biochemistry articles - (roughly 30-35%), and spelling, grammar and
proper use of the English language (the remaining 10-15%).
At
the end of each experiment in the lab manual is a list of questions that
should serve as a guide in preparing the report. The answers to these questions must be incorporated into the proper section of the
lab report (see below). Merely
answering these questions is not acceptable as a lab report!
Each
report should have a cover sheet that includes the number and title of
the experiment, and names of students in the laboratory group. The body of the report will have several
sections: an introduction, methods (when required), results, discussion
literature cited and calculations (if appropriate). Grading emphasis will be on the results and
discussion sections, since this is where you will show your understanding of
the principles of the experiment. The
report should be written in prose and should be concise.
You may find it helpful to
consult articles in a journal such as Biochemistry
or Journal of Biological Chemistry
for an example of style.
Abstract: A brief general background placing the
experiment in the “Big Picture”. Include
a statement of the goal of the experiment that was done, a few sentences
summarizing data, and a brief summary of important conclusions of the
experiment. The abstract should be no
longer than 250 words.
Introduction: The purpose of the experiment should be
clearly stated in no more that one to three sentences – why did you do the
experiment??? Be sure to place the
experiment in the “Big Picture”. Include a description in your own words of the biochemical principles upon which the
experiment is based – information can come from lab lecture, the lab manual,
your text book, etc. Be sure to cite
your references. Also, include a
brief description of how the experiment was performed and any techniques that
were used. You need not go into explicit
detail – rather, provide a clear, concise explanation. Finally, provide one
sentence that summarizes the general conclusion of the experiment. Maximal length of the introduction should
be 1-2 pages.
Materials
and Methods:
The
methods should be a narrative description of the protocols used – not a step by
step procedure. The description should
provide enough detail such that someone else could repeat the procedure. If you used a standard procedure with which
competent scientists in the field are familiar, you may describe it in brief
and be sure to properly reference it.
See published research articles and the Labwrite website for further
information.
Results: Final, analyzed data from your experiments is
included in this section. You should use tables, charts/graphs, descriptions
and even pictures in this section to present your data. Raw data and
calculations should NOT be included in this section – only the analyzed,
final calculated data. Sample
calculations should be included in a “calculations appendix” (see below) and
your raw data will be in your lab book. You
must include a descriptive guide to the data (graphs, tables etc.). Make it as simple as possible for your data
to be understood. If necessary, required
graphs may be hand-drawn on graph paper.
Computer-generated graphs are preferred, provided they include the
individual data points. All tables and
graphs must have a number, a title and a descriptive legend. Each axis and each set of data must be
clearly labeled.
Discussion: This section should include your
interpretations of the data and draw conclusions. You should connect your results with those
that were expected, to those of others and/or to what is already known. Be sure
to connect your results back to the “Big Picture”. Thus, you should expect to use outside
references in writing your discussion. If you obtain unexpected results, provide
plausible explanations. This section
should be the most detailed and include interpretation of ALL of your
data. The discussion should be no
longer than 2-3 pages.
References: It is expected that to
write a good introduction and discussion you will need to consult outside
references. These should be listed at
the end of your report – include author’s names, year of publication, title,
volume number, pages and, if it’s a book, be sure to include the name of the
publisher. List the references in
alphabetical order by author and assign each a number. Then, when references are cited within the
text, insert the number in parentheses.
Calculations
Appendix: At the end of the report,
following the discussion, include an example of each calculation used and
indicate into which table or graph the numbers were placed. Do not type out every calculation, only the
first in a series. Be sure that all
numbers include the proper units.