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Biology Labs

This collaboration has advanced from the creation of classroom teaching/explanation tools to the creation of tools that can be used for student directed learning and to provide authentic assessment of concepts.

The earliest of these was the Protein Purification Lab which allows the instructor to provide the student with a virtual lab experience where they can be given a unique solution in a beaker and asked to develop a purification scheme to obtain some protein in its pure form. The results of their work can be submitted to the instructor for grading.

In addition, we are developing simulation environments that facilitate multiple, linked representations of concepts to be used in different learning contexts. They will allow guided inquiry as well as student directed experimentation and data analysis. These environments can be used as stand alone teaching tools as well as becoming part of the interactive components of an online Modern Biology being created in the OLI system.

Materials listed by category


Protein Purification Practice Lab

protein purification This virtual lab provides the student with a virtual lab experience where they can be given a unique solution in a beaker and asked to develop a purification scheme to obtain some protein in its pure form. (The classroom version allows the results of their work to be submitted to the instructor for grading).

Protein Folding

protein foldingThis is an experiment to study the effect of temperature on protein stability. Alter the temperature using the slider bar and record the experimental fraction unfolded that is presented in the output box. From this data you need to determine the ∆S and ∆H for unfolding using van't Hoft plot.

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Molecular Interactions

Dissociation of Weak Electrolytes

endocytosis Some molecules are weak electrolytes and exist in a reversible equilibrium between the starting molecule and its dissociated parts. For molecules that are weak electrolytes and act as acids (proton donors), the ratio of the products of the dissociated parts and the parent molecule is a constant (K) in neutral water for each separate molecular structure.

Equilibrium of MO complex formation

macro/pinocytosis Equilibrium state as determined by protein and ligand concentrations: This simulation allows you to explore the equilibrium between free protein, ligand, and the complex, and how ligand concentration affects the equilibrium.

Ligand Binding

replication Ligand Binding

Enzyme Catalysis

replication Enzymes bind to substrates in a manner similar to the way myoglobin binds oxygen or the estradiol binds to the estrogen receptor, but enzymes can go one step further. In this case the ligand is specifically referred to as the substrate (the molecule that the enzyme will convert to product) and it binds to a specific binding region of the enzyme referred to as the active site. Once bound, the ligand, or substrate, can either simply reversibly come off the enzyme, or it can be converted into a new compound or product.

Currently Unavailable

Membrane Permeability

transcription The introduction of a cell or liposome to the solution places a barrier to the molecules. As three different molecules diffuse to equilibrium in the following simulation, they encounter the lipid bilayer depicted by the horizontal membrane across the center of the stage. Note that one type of molecule passes freely through the lipid bilayer while the second type of molecule only occasionally passes into the membrane and is trapped within. The lipid bilayer is totally impermeable to the third type of molecule. These molecules move through the membranes via passive diffusion.

Osmosis: Isotonic Equilibrium

protein synthesis Cells continually encounter changes in their external ionic environment and will spontaneously respond by attempting to equalize the concentration of ions on the inside and outside of the cell. Because the plasma membrane (lipid bilayer) is significantly less permeable to ions than water, the establishment of an equal concentration of the ions on either side of the membrane is accomplished by the net movement of water toward the higher concentration of ions to reduce the concentration. This movement of water in response to an imbalance of solute (ion) is referred to as osmosis.

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Future work:

Protein Purification Turorial

The current Protein Purification Lab is used to test the students mastery of designing protein purification schemes to accomplish certain optimal outcomes. The Lab does not instruct the students in the various concepts necessary to successfully complete the Lab.

Simulation Tools

We are working on our Simulation Environment to allow it to model more molecular behaviours. In addition, we are working on the external interface and documentation so that others can author their own student activities within the environment.

Funded by:
Howard Hughes Medical Institute
The William and Flora Hewlett Foundation
The National Science Foundation
Office of Technology for Education, Carnegie Mellon