Projects
Biology | Biochemistry | General Chemistry | Mathematics
| Physical Chemistry | Physics
Biology
A
mixture of undergraduate and high school students worked
on a project
to genetically alter the DNA polymerase from Thermus aquaticus
to
enhance its ability to utilize RNA as a template and therefore
have
reverse transcriptase activity. They started with a clone
of the native
DNA polymerase and decided to try site directed mutagenesis
as one of
several methods of accomplishing their goal.
In order to determine the sites to modify, they utilized
RasMol, a three
dimensional molecular imaging program available free via
the internet.
This allowed them to visualize and determine which amino
acids where
interacting with the DNA and therefore might be likely candidates
to
genetically alter. Similar structures of enzymes with native
reverse
transcriptase activity were compared to the Thermus aquaticus
DNA
polymerase.
Since not all of the students were familiar with RasMol,
we set up a web
site with Chime tutorials. Chime scripts allow us to utilize
the
interactive three dimensional aspects of RasMol with a directed
script
for the students to be guided in the right direction. The
students find
the visualization of ?invisible? molecules very enlightening,
and the
interactive capabilities of the software allow them to alter
the images
and rotate them to better grasp their three dimensional
nature.
The students found it helpful to have several Chime tutorials
to help
them visualize and understand molecular aspects of DNA,
proteins, and
the lipid bilayer structure as well as the DNA polymerase
interactions
described above. The students successfully created a modified
DNA
polymerase that demonstrated reverse transcriptase activity
by the end
of the course. see webpage = www.thermagen.net
Biochemistry
Structural
Analysis of a Metabolic Enzyme: This activity provides
an introduction to viewing protein structures with the program
Protein Explorer. Students answer questions about protein
structural elements as well as active site interactions
with the substrate. file to download = bchenzyme
Amino
Acids Structures and Properties:
Students
discover amino acid structures using the program PC Spartan
Plus. Students are introduced only to the basic structure
of an amino acid prior to this exercise. Placing this
activity prior to the discussion of amino acid function
emphasizes the three-dimensional structures and chemical
reactivities of the amino acids. file to download = bchaas
Polarity
and Intermolecular Interactions: This activity is meant
as a review during the first week of Biochemistry. Students
view previously constructed potential surfaces of a variety
of small molecules. Solubility and intermolecular interactions
are also briefly reviewed. file to download = bchpolarity
General
Chemistry
Molecular
Modeling and Periodic Table Live: In
this first-semester General Chemistry laboratory, students
use Spartan to examine molecular structure and shape and
then carry out exercises with the Periodic Table Live CD.
file to download = chem101model
An
Introduction to IR Spectroscopy: Students
use the IR Tutor program to discover the basic principles
of IR spectroscopy. The IR Tutor program and group frequencies
are also used to identify a solid and liquid unknown. file
to download = chem101ir
An
Introduction to Oxidation-Reduction Reactions: Spartan
electron density surfaces are used to introduce first-semester
General Chemistry students to oxidation-reduction reactions.
By examining how the electron density around the atoms change
from reactants to products, the electron transfer process
can be understood. file to download = chem101redox
Molecular
Modeling in Second Semester General Chemistry: An
extensive Spartan exercise is used to illustrate concepts
of electronegativity, orbital hybridization, molecular shape,
and resonance. This exercise was adapted from: G.P. Shusterman
and A.J. Shusterman, Journal of Chemical Education,
Vol. 74, No. 7, (1997). file to download = chem102model
Melting
Points and Intermolecular Interactions: Second
semester General Chemistry students build organic molecules
in Spartan and also measure their melting points. Students
also complete a short guided inquiry exercise on intermolecular
interactions. This exercise was adapted from: T. Poon,
S.A. Bodolosky, and C.M Norris, Journal of Chemical Education,
1999, 76, 983. file to download = chem102mp
Hydrogen
Bonding in DNA: In
this end of the semester independent project, second semester
General Chemistry students use Spartan to investigate the
hydrogen bonding interactions between base pairs in DNA.
file to download = chem102project
Mathematics
The
mathematics students at Carthage use the CVL to solve open-ended
calculus and linear algebra projects. These projects require
the students to use critical thinking skills and are exploratory
and visual in nature with many different solutions/results
possible. Each project results in a written report and/or
presentation. The projects are completed individually or
in a group based upon the type of project and/or class size.
The projects include:
Polar
Tesselation Tiles: file
to download = PolarProject
Roller
Coaster/Ski Slope Theme Park: file
to download = CurvatureProject
Quadric
Surface Design: file
to download = QuadricProject
Container
Design: file
to download = ContainerProject
Related
Rate Presentation: file
to download = Related
Linear
Algebra Project: file
to download =
Physical
Chemistry
An
Introduction to Mathcad: The following exercise is
completed during the first lab period of Physical Chemistry
I. The exercise introduces the students to the graphing
and numerical analysis capabilities of Mathcad. Important
ideas from Calculus and Physics are also reviewed. file
to download = pchemlab
First
Semester Physical Chemistry: This
document contains six Mathcad problems appropriate for first
semester Physical Chemistry. The problems concentrate
on material covered early in the semester.file to download
= pchem1
Second
Semester Physical Chemistry: The following document
contains 19 second semester physical chemistry problems.
Eighteen of the problems involve using Mathcad to graph,
differentiate, or integrate functions. One of the problems
asks students to calculate moments of inertia from the results
of a Spartan calculation. file
to download = pchem2
Physics
Spectral
Classification of Stars: This project uses a Java applet
to produce emission spectra of a range of main-sequence
star. file to download = spectra
Sky
Coordinates: This worksheet uses Starry Night software
to explore equatorial coordinates in a simulated night sky.
file to download = coordinates_wksht
Note1:
Many of the existing astronomy labs at Carthage have been
replaced or supplemented by CLEA (Contemporary Laboratory
Exercises in Astronomy) software labs that take place in
the CVL. The CLEA suite of activities was developed at Gettysburg
College: http://www.gettysburg.edu/academics/physics/clea/CLEAhome.html
Crash:
This worksheet is used in conjunction with Interactive Physics
software in PHYS201/104. It explores the forces and accelerations
of body parts during a simulated car crash with and without
seatbelts.file to download = crash
Projectiles:
This worksheet is used in conjunction with Interactive Physics
software in PHYS201/203. Projectiles allows students to
simulate 2-d projectile motion in an interactive vide-game
format. file to download = projectiles
Launch:
This worksheet is similar to the one given above, but concerns
the acceleration profile of the space shuttle during the
first two minutes of launch. file to download = launch
Ramp:
This project simulates a standard Physics 201-202 homework
problem. file to dowload = ramp
Falling
Apples: This project simulates Newton 's Thought Experiments
on falling apples and orbiting moons.file to download =
wksht1
Orbits:
This workshheet simulates the effect of posigrade and retrograde
thrusts on spacecraft in orbit about Earth. file to download
= wksht2
Hohmann:
This project simulates the Hohmann transfer orbit dynamics
for spacecraft traveling from Earth to Mars. file to download
= wksht3
Note
2: The
java applets needed to
complete some of the above exercises are available here:
http://www2.carthage.edu/departments/physics/
. Click on Webphysics
and login as "student" password: "physics"
to see the applets.
