BIOL 312L: Molecular Biology Laboratory

Spring 2011

Course meeting times: Tuesdays 2:00 – 5:00 PM in RLHSC 222.

Instructor: Prof. Andrew M. Shedlock

Email: ShedlockBIOL312@gmail.com
Use the above gmail address instead of my COFC account for all course-related correspondence.
Office: Rita Liddy Hollings Science Center Room 216B
Voice Mail (less efficient than using my BIOL312-dedicated gmail): 3-7638
Office hours: Thursdays 1:00 – 3:00 PM or by appointment, RLHSC 216B.

Requirements: You must either be co-enrolled in or have previously completed BIOL 312 Molecular
Biology. There is no textbook or specific manual required for this course, however you must supply
your own laboratory notebook.

Laboratory: During the semester, you will perform multi-session laboratory projects that will
complement the lecture material in BIOL 312 and teach techniques utilized in the molecular biology
laboratory. Students will complete three experimental modules of approximately equal duration that
are investigator-driven, integrate a broad cross section of basic concepts, sampling design and
analytical skills, and promote critical thinking, problem solving and modern research methods
presently used in the field of molecular biology:

Module 1: Identification, characterization, transformation, expression, purification and quantification

of jellyfish GFP protein.
Module 2: DNA fingerprinting and statistical analysis of human genetic variation using hypervariable
microsatellite loci.
Module 3: Self DNA purification, amplification, sequencing, informatics and evolutionary analysis of
coding and non-coding genomic loci.

Lab reports: The laboratory background information and protocols will be available on the BIOL 312L
course website posted on OAKS prior to the lab. Please print and read your laboratory handouts ahead
of time. Bring handouts and any required pre-lab exercises with you to class. You will be required to
submit post-lab assignments as part of lab reports that present, describe, summarize and interpret your
results. Be sure to record notes about protocols and results during the lab itself. You are encouraged
to discuss the laboratory assignments with your lab partner or study group, however, your assignments
must be your own: they should be written by you (in your own words) and reflect your own thinking.

Problem sets: In addition to lab reports, three problem sets will be assigned and made available on the
“problems” portion of the course web site posted on OAKS. These will be related to methods and
concepts being employed to complete your experimental investigations outlined above and are focused
on experimental design, data analysis and interpretation of molecular results. You will hand in your
completed assignments at the beginning of lab on the due dates posted in the syllabus. Late problem
sets will not be accepted.

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Oral presentation: A fourth assignment will involve selecting a method used in BIOL 312 that was
also employed in a peer reviewed journal article from the scientific literature. You will be asked to
review and interpret the results of this method in the context of both the published study and its
importance to the field during a short oral presentation to the class.

In-class quizzes: Throughout the semester, we will occasionally have a quiz at the beginning of class
based on the protocols, concepts and laboratory methods being employed for a particular line of
investigation. Quizzes  will  occur  at  unannounced  times  throughout  the  semester,  so  it  is  
important  that  you  come  to  class  on  time  and  prepared  to  answer  questions  based  on  the  
material  covered  weekly  in  the  course.    Because  quizzes  are  administered  in-­‐class,  there  will  be  
no  make-­‐ups.

Laboratory Notebook: Keeping a detailed lab notebook is essential for completing a molecular study,
recording protocols and sample information, designing experiments and displaying raw data and
interpreting/summarizing primary results. Be proud of your notebook: it is your scientific diary, and
is generally considered a legal document in the professional research community. As such it provides
critical continuity for you and others to evaluate, repeat and expand upon your work in the near and
distant future. Notebooks will be reviewed and graded for their clarity, organization, completeness and
overall quality as a detailed, comprehensive record of your research activities during the course.

Attendance and Participation: Attendance is required and will be recorded weekly. Students must
provide a valid and documented excuse from the Undergraduate Dean’s Office for missing class.
Acceptable excuses include illness, personal tragedy or circumstances beyond the student’s control.
Because of the continuity required for completing experimental research it will be impossible to make
up labs and in-class quizzes and exercises after each week of investigation has been completed. All
graded quizzes and assignments due for that week based on in-class work will receive a zero grade.
Active participation is also expected in all aspects of the course, including asking questions,
participating in discussions, and functioning safely and cooperatively in the laboratory, including
keeping a clean bench space and helping maintain common equipment, supplies and work areas.

Safety matters: It is imperative that everyone adheres to the safety guidelines and procedures
established for use of the molecular laboratory. General safety issues and those specific to certain
equipment, chemicals, procedures and protocols used will be reviewed and highlighted prior to
completing weekly experiments. A comprehensive summary of safety precautions and regulations
entitled “BIOL 312L Lab Safety Handout” has been prepared by Dr. Stephanie Dellis, a long-term
instructor of this course, and is available as a pdf file on the course website in OAKS. Be sure to read
this safety handout completely and carefully before we begin our experiments. Working in a safe,
considerate and responsible manner in the laboratory throughout the semester will be incorporated into
your grade for participation.

OAKS Website: Keep a daily eye on the BIOL 312L OAKS web page accessible with your student
login credentials through MyCharleston for important course information, including announcements,
lab protocols, handouts, problem sets, supplemental readings, software tools and study aides. The page
will also link to course-related animations and videos. Because of the dynamic nature of many
processes covered in molecular biology, you will find animations a valuable tool in helping you to
grasp quickly the main concepts on the topics presented.

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 Exams and Grading
BIOL 312L will be graded out of a total of 700 points. There is no curve in this class and grades will
be assigned based on the total points you have accumulated. You can earn points according to the
following formula:

Grading Formula:
Lab reports (3 @ 100 pts each): 300 pts
Problem sets (3 @ 50 pts each): 150 pts
Literature review and oral presentation 100 pts
Quizzes 50 pts
Lab notebook 50 pts
Safety and participation 50 pts
Total: 700 pts