The Use of Problem Based Learning and Blackboard

1
The Use of Problem Based Learning and Blackboard
in Teaching Undergraduate Biochemistry Michael
A. Deibel1 and Janet S. Russell2,   1Department
of Chemistry, 2Department of Biology, Earlham
College, Richmond, IN
EARLHAM COLLEGE
Abstract
Lab that is More Tightly Linked to Classroom
Example of Open-Ended Case - Toxicology
Example of Structured Case - Prions
You are responsible for setting up regulations
for production/use of and exposure to a
potentially toxic/carcinogenic substance (you
choose the substance after checking the
literature)  Potential Outline and questions to
consider I. Sources (both natural and
anthropogenic) - What are the naturally
occurring levels of this substance? How is this
substance produced/used? How is this substance
released into the environment?  II.
Epidemiological / Laboratory Animal Studies - Is
there evidence that this substance is hazardous
to animals and humans? Is this substance
mutagenic? carcinogenic? At what levels is this
substance toxic/carcinogenic? Are its effects
acute or chronic? III. Chemical Properties and
Mechanism of Action - What is the main route of
exposure? How is this substance metabolized? How
is this substance eliminated from the body? Does
this substance bioaccumulate? Is this substance
toxic or is it metabolized to a toxic substance?
How does this substance cause toxicity/carcinogene
sis? Does it work through a free radical
mechanism? Does it inhibit any enzymes? Does it
cause damage to DNA or cell membranes? Does it
disrupt a biochemical pathway? IV. Measurement
of the toxic substance in the environment and in
the human body - What techniques are used to
measure this substance? What type of sample
preparation is required? What are the detection
limits in environmental samples? in biological
samples?  V. Remediation - How can release of
this substance be prevented? How much will this
cost? How can this substance be removed from the
environment once it is release? Are there
nontoxic substitutes for this substance? How
much will this substitute cost?
1. Shown below are two possible folding
conformations for the prion protein, the normal
form and the scrapie form. Figure
from Cohen and Prusiner What factors
influence how a protein folds? 2. Given the
following energy level diagram Figure
from Cohen and Prusiner a. Which form of the
wild type prion (normal or scrapie) is more
thermodynamically stable? b. Why isnt all
the protein in the more thermodynamically stable
form? 3. Conversion of the normal form to the
scrapie form involves a change from disordered
and a-helix to b-sheet. a. How do each of the
secondary structures arrange their sidechains?
b. How would a disordered segment arrange its
sidechains? c. Would changing secondary
structure lead to a change in sidechain
arrangement with respect to solvent
exposure?   4. What force(s) would cause
dimerization (or polymerization) of proteins?
Which force is the strongest?   5. Given the
above, theorize how the change in secondary
structure might lead to protein aggregation.   6.
What are chaperones? What role might they play
in prion folding? 7. The prion theory, which
has not been conclusively proven, has been quite
controversial because it states that an
improperly folded protein can cause other
proteins to misfold and to cause disease (i.e.
that the prions can transmit information). Why
is this controversial?   8. In the PDB file for
prions, the protein is displayed only for the
parts of the protein past amino acid 125 despite
the fact that the prion protein from 90-230 was
measured by NMR. Why are there no coordinates
for amino acids 90-125? 9. There are no PDB
files for scrapie prion. Explain why no NMR or
crystallographic structure has been
obtained.   10. Mad cow disease (BSE bovine
spongiform encephalopathy) has been a hot topic
in the news, especially in England. What steps
have the British taken to deal with BSE? How does
this compare with what the British have done to
control foot and mouth disease? Were these two
disease treated in the same way? Why or why not?
Our college offers a one-semester biochemistry
course for juniors and seniors. The class is a
mix of science majors so students come with a
varied backgroundi.e. strong in chemistry,
strong in molecular biology, or strong in both.
This has made it challenging to find a textbook
that is appropriate, and to cover topics in a way
that is productive and interesting for all the
students. We are currently implementing a
revision of this course. It was revised from a
lecture/lab course to a problem based learning
(PBL) course that retains the laboratory, and is
augmented on-line via the course management
software, Blackboard. Research indicates that
PBL can help students overcome the boundaries
separating them from one another and from the
concepts outside their majors. We predict the
use of problems will motivate student learning
and reduce the perception of redundancy for
students with a strong molecular biology
background. Augmenting with Blackboard allows
each student to tailor their readings and helps
to overcome our textbook problem. This poster
presents the final design of the course, and
reports on the current status of student
reception.
Goals

•   Pace and Coverage
• Wanted to engage both Chemistry and Biology
  Majors who enter this class with differing
  backgrounds.
•  Lab that is More Tightly Linked to Classroom
• Wanted experiments that would compliment and
  reinforce classroom content and not be seen as
  separate
• More Pertinent Textual Materials
• Wanted a blend of broad and selectively deep
  textual materials
• Resulting Curricular Framework
•  Pace and Coverage
• Shift from traditional lecture-centered to more
  learner-centered classroomaugment mini-lectures
  with exercises and other learning checks
• Organize content and student learning groups
  around PBL cases
• Online quizzes used to free up class time and to
  expose students more to multiple choice format
• Lab that is More Tightly Linked to Classroom
• For each topic/case, a lab was found and adapted
  that would compliment and reinforce the material
  and even aid in the solving of the cases
• The connection of the lab to the classroom was
  emphasized by the inclusion of questions on
  quizzes, case solutions, and exams deliberately
  and overtly pertaining to this connection.
• More Pertinent Textual Materials
• No textbook
• Use primary and secondary sources such as journal
  articles, lecture notes, web-sites

More Pertinent Textual Materials
Using Blackboard The image to the left shows
several screen shots of the web-based course
management software, Blackboard. We used this in
lieu of a textbook. You see here the opening
announcement page, followed by the course
information page which organized all content,
then the page containing all textual material for
one of the cases, and finally a quiz.  
Student responses

• Because the class is ongoing, these results are
  not summative.
• Pace and Coverage
• 7/10 students preferred NOT to do traditional
  lecture mode
• All students preferred working in groups rather
  than alone on PBL cases
• Students overwhelmingly felt the in class
  exercises to be very helpful
• Student QuoteI am having a little trouble
  dealing withPBL. the nature of teaching abroad
  (where I have lived)..is very formal
•  Lab that is More Tightly Linked to Classroom
• Mike?
• More Pertinent Textual Materials
• 8/10 students preferred the web readings to be
  augmented with a textbook
• 7/10 students felt the material of the web
  readings was just right
• All students were comfortable with Blackboard
• Student Quote I like the class design but I
  wish we had an accompanied text.

In class exercise Chymotrypsin
Case study Tyrosine Phosphatase
Net reaction
Net reaction
Substrate in active site
Substrate in active site
Citations Resources
Both mechanisms involve covalent catalysis,
acid/base chemistry, and activation of H2O to
produce a nucleophile
Cases in Biochemistry by Kathleen Cornely, New
York Wiley, 1999 Deep View via Gale Rhodes at
http//www.usm.maine.edu/rhodes/Manifesto/index.h
tm Prion article - Cohen, F.E. Prusiner, S.B.
Ann. Rev. Biochem., 1998, 67793-819. Blackboard
at http//www.blackboard.com/ Phosphatase article
- Barford, D. Das, A.K. Egloff, M.P. Ann. Rev.
Biophys. Biomol. Struct., 1998, 27133-164 The
Power of Problem-based Learning by Duch, Barbara
J., Groh, Susan E., Sterling, Va. Stylus Pub.,
2001 Lab citations?
Homology using Deep View - This example allowed
students to explore the conservation of tertiary
structure compared to the conservation of primary
sequence. Students also were asked to determine
the evolutionary tree based on the primary
sequence homology.
2HHB_A
2DHB_A
2HHB_B
2MM1_1
1MBD_1
Tertiary Structure of these proteins using Deep
View
1GDJ_1
Sequence alignment using PDB through windows
(WPDB)
Acknowledgments
Howard Hughes Medical Institute, Earlham College
Chemistry and Biology Departments, Earlham School
of Religion for the use of Blackboard
Resulting evolutionary tree
Leghemoglobin (yellow lupine-1GDJ_1) Myoglobin
(whale- 1MBD_1) Myoglobin(human-2MM1_1) Hemoglo
bin (a-subunit, horse-2DHB_A) Hemoglobin
(a-subunit, human-2HHB_A) Hemoglobin (b-subunit,
human-2HHB_B)