This project was prepared as part of a BioQUEST faculty development workshop entitled Implementing Bioinformatics in Introductory Undergraduate Biology Courses:
Exploring Microbiology, Molecular Data and Visualization
at San Diego Supercomputing Center in January 2007. The BioQUEST Curriculum Consortium is committed to the reform of undergraduate biology instruction through an emphasis on engaging students in realistic scientific practices. This approach is sometimes characterized as an inquiry driven approach and is captured in BioQUEST's three P's (problem-posing, problem-solving, and peer-persuasion). As part of this workshop groups of faculty were encouraged to initiate innovative curricular projects. We are sharing these works in progress in the hope that they will stimulate further exploration, collaboration and development. Please see the following links for additional information:

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Protein Chronometers
Authors          Audiences          Overview           Materials          Resources           Future Directions



Amy Sprenkle
Salem State College

Marilyn S. Stalzer
Dept of Defense - Puerto Rico- Antilles High School


Possible Audiences:

High School or College Biology  


Brief Overview:

The student will determine the validity of using various well characterized proteins as molecular chronometers to test the validity of the Domain structure of phylogentic relationships. Using the section from Microbes Count! “Proteins: Historians of Life on Earth” use the bioinformatic tools for protein sequence alignment, phylogenetic tree construction and explore the sample molecule. Students first step through a demonstration with the enolase enzyme of glycolysis and then complete their own investigation by comparing and presenting an additional protein molecule. Using a poster format, students prepare for the oral presentation by creating a single PPT screen that includes pictures, alignment sequences, and non-rooted trees. The results of these individual reports will be combined to prepare a class mosaic. The biological relevance of the molecule is discussed in the classroom, and the appropriateness for use in phylogenetic comparisons is evaluated.  


Project Materials:

See attachment below  


Resources and References:

Microbes Count! Biology Workbench Sample Rubric PDB Molecule of the Month  


Future Directions:

The candidate proteins in Table 1 could be analyzed for relevant sized subunits or functional groups, such that the appropriate portions of the molecule can be chosen to make sequence alignment easier (i.e. clean up the data set, and choose sample sequences for alignment) and analysis possible.  



- Microsoft Word - ProjmatWkshp.pdf