Curricular Resources and Projects in the CVL
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
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
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 =
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
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