AP Biology Capstone Project

Contributed by
Dan Shannon

Duration: One week
Level: Intermediate/High School Seniors
Requirements: Internet Access for students, a molecular modeling/editing program  (We use the free "Jmol" )

Over the course of the past year, we have studied Hemoglobin, Diabetes, and AIDS by looking at the evolutionary, genetic, molecular, and ecological aspects of each. You and a partner will choose one molecule that has been depicted as a molecule of the month by the Protein Data Bank Website and present a poster and a 3D representation detailing its evolutionary, genetic, molecular, and ecological aspect.

Directions:

1. Refer to the “Molecule of the Month from the Protein Data Bank site (look year by year)

2. Download your molecule into

2. Choose one molecule and tell its story.

a. What is your molecules structure and function (phenotype)?

1. What is the significant region of your molecule that allows it to function (active site/binding region/allosteric region

b. Does your molecule have a historical significance?

1. Did organism with/without your molecule have a competitive advantage?

c. Is this molecule involved/have a role in a disease?

1. Were organism protected or hurt by having your molecule?

d. Are there selection pressures for or against your molecule?

1. How did the environment affect organisms with your molecule

e. Are there groups of organisms relying on the proper/improper functioning of your molecule?

1. Were organism protected or hurt by having your molecule?

3. Create a poster to tell the story of your molecule.

4. Create a 3D structure that tells the story of your molecule.

5. Present your poster and 3D structure to the class.


Grading Rubric and Due dates
Molecule Choice 5/11
3D print coordinates 5/11
Poster Due 5/15
Poster Presentation 5/17

Poster (40 points)
Explanation of the structure and function of your molecule - 10
Title and Appearance - 10
Scientific Accuracy – 10
References – 10

3D Structure (30 points)
tells the important aspect (story) of the molecule - 15
It highlight the significance of the molecule. - 15

Presentation  (30 points)
Explains the way that the poster and the 3D structure display the significance of the molecular structure.

  • Clarity – 10
  • Scientific accuracy - 10
  • Demonstration of understanding – 10

JMol Directions

  1. Go to X-Drive, Teacher Folders, Shannon, Jmol folder
  2. Open Jmol (described as an executable jar file)
  3. File, Get PDB
  4. Type in code for your molecule

Readying the Molecule for 3D Print

  1. Open file, console
  2. In console view

    a. type “select all”

    b. backbone 1.5

    c. spacefill off

    d. wireframe off

    e. calculate struts

    f. struts 1.0

    g. color struts gray

Saving Molecule

  1. Right click on Molecule on jmol screen, Choose “File, Export”

    a. Export as X3D

  2. Choose location, filename is the PDB code in .x3d

Examples

   

Alcohol Dehydrogenase Model
Alcohol Dehydrogenase Model

   

Alcohol Dehydrogenase
Alcohol Dehydrogenase

   

Fibrinogen-Thrombin Complex
Fibrinogen-Thrombin Complex

   

Fibrinogen-Thrombin Complex
Fibrinogen-Thrombin Complex

   

Reverse Transcriptase Model
Reverse Transcriptase Model

   

Reverse Transcriptase
Reverse Transcriptase

   

Ricin
Ricin

   

Ricin
Ricin

   

Vancomycin Model
Vancomycin Model

   

Vancomycin
Vancomycin

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