BIOL344
Molecular
Biology Techniques
2 credit hours
Southwestern Adventist University
Biology Department
Fall 2008
Class Time:
Thursday 2:00 3:00 pm
Lab Time:
Thursday 3 6:50pm
Instructor:
Suzanne Phillips, Ph.D.
Office: Scales Hall # 224B office hours are posted on the
office door
Telephone: ext. 6274
E-mail: suzannephillips@swau.edu
Textbooks:
Molecular Biology
Techniques Lab Manual editor, Suzanne Phillips
Description: Introduction to the techniques used
in modern researching laboratories in DNA manipulation for the purpose of
molecular biology.
Purpose of the course:
Students will learn the theory and practice
of molecular biology to enable them to understand and participate in modern
research.
Students will be able to demonstrate this understanding in appropriate
circumstances.
Attendance:
Attendance is required on a regular basis to lecture and lab. The
University policy, as stated in the Bulletin, allows one absence for each hour
of credit. Absences in excess of this limit are grounds for dismissal
from the class. It is the student's responsibility to catch up on
any material that is missed due to an absence. Due to the nature of the
labs, there will be no make-up labs once the labs in a given week have been
completed. Absences on test days will be excused only for very serious
reasons. If an absence occurs on a test day, the instructor MUST be notified prior to test time.
Letter grades: A = 90% and above
B = 80% -
89%
C = 70% -
79%
D = 60% -
69%
F = 59% and
below
Cheating:
Cheating of any kind will not be tolerated and may result in an F for the
test/assignment/or course and possible dismissal from the class. Don't do
it!
Homework: Homework will be
given at the instructors discretion.
Disabilities:
If you have a disability that may require accommodations to complete the
requirements of this course please do the following: 1. Contact the
Director of Students with Disabilities and Academic Support, Dorie Cruz, Scales
Hall, at ext. 6041 so that she may verify that you are eligible for
accommodations. 2. Please make Dorie Cruz aware of your situation before
the end of the 2nd week of classes so that she might be able to
assist you better. The University complies with the provisions set forth
in Section 504 and the ADA Act of 1990.
Grading:
Lab participation = 25%
Lab
reporting
= 40%
Lab
Quizes
= 35%
Total:
100%
Lab Quizzes: Quizzes will be given
during the first part of lab after lab introduction. They will cover the
current and previous lab. If you arrive late and miss the quiz and will
receive a zero.
Lab Reporting: You will be given
appropriate paper to record you lab work. Reporting for each lab should
include a purpose statement, an introduction, methods and materials (exactly
what you did) and a discussion section. Lab reports will be reviewed and
graded by the instructor during the next lab period.
Methods of instruction:
Lectures and labs
Specific objectives of the course:
To gain an understanding of:
Solution
concentrations
Competent
cells
Plasmids
and their isolation
Polymerase
Chain Reaction (PCR)
Restriction
digests
Primer
design
Cloning
Transformations
Southern
Blotting
SDS-PAGE
Weather:
You may check the following for official delay or closing announcements:
SWAU
switchboard (817) 645-3921 KJCR
88.3FM KXAS TV NBC 5. Announcements are
typically made between 9 and 10:30pm. If it is not determined until early
morning that classes may be delayed or cancelled (or will continue as usual)
the announcement will be made by 6am.
Microbiology lab rules:
1.
NO food or beverages allowed in lab.
2.
Immediately notify lab instructor in case of an accident.
3.
Appropriate footwear must be worn at all times. Sandals and open-toed
shoes are not acceptable. High heeled shoes are not appropriate.
4.
Whenever dealing with anything to will come in contact with DNA, you
MUST wear gloves. At all other times, gloves are not needed.
5.
Cell phones should be off and beepers on silent
6.
Other rules may be added at instructors discretion.
Purpose statement what you are doing
for each experiment. Single sentence
Introduction theory and reasons
for doing the particular experiment. At least one large paragraph, up to
pages of information.
Methods and Materials step by step
outline of what you did. This can include references/citations of
published protocols (Qiagen manuals, etc.) however, if it is a protocol that
you made up, or I have given you, you need to include that in your lab
book. The easiest way to do this is to photocopy the protocol and hole
punch it and include it as a page in your book, or if it is short, cut and tape
it into your lab book. This section
should include every detail you need in order to repeat the experiment!
WITH DATES.
Results/Discussion This section should
be a discussion of what went wrong or was unexpected in the experiment.
For you guys, this section is not really applicable when you are doing
protocols and not checking if they worked (Qiagen prep and then not looking on
the gel to see if you actually got DNA). However, during some of the
experiments we ARE checking you need to
discuss that you got what you expected, or did not get what you expected and
then come up with a reason things did not go
as expected. This section is important in published research
in order to justify your work and
explain how it fits into what is already known about your particular
field. If your work does not agree with the present dogmas, it is in this
section that you explain why you are correct.
Molecular Biology Techniques
Table of Contents
Aug 28........... Lab # 1 Molarities..pg 5
Sept 4............ Lab # 2 Cloning (Step #
1) and Plasmid Preps ...pg 10
Sept 11......... Lab # 3 Polymerase
Chain Reaction (PCR) (Cloning STEP # 2) ..pg 24
Sept 18.......... Lab # 4 Gel Purification,
Digestion and Ligation (Cloning STEP # 3) ..pg 33
Sept 25.......... Lab # 5 Ligations (Cloning
Step # 4) pg 71
Oct 2............. Lab # 6 Transformations
(Cloning Step # 5) pg 76
Oct 9........... Lab # 7
Selecting transformants (Cloning Step # 6) and
Genomic DNA preparation (Southern Step #
1) .pg 88
Oct 16........... Lab # 8 Plasmid Prep and
Digestions (Cloning Step # 7)
and Digestions (Southern Step # 2) . pg 93
Oct 23........... Lab # 9 Run, Prepare and
Transfer Gel (Southern Step # 3) .pg 94
Oct 30............. Lab # 10 Hybridization (Southern Step # 4) and
Plasmid Digests Gel (Cloning
END) .pg 107
Nov 6............ Lab # 11 Wash and Reveal (Southern END)
and Plasmid Digests Gel
(Cloning END) ..pg 119
Nov 13........... Lab # 12 SDS-PAGE .pg 120
Nov 20............Lab MAKE UP