Spider Silk : Examining Biological Sequences (Student)

What is the BioMath Connection (BMC) Project?

BMC was a pioneering project linking biology and mathematics in the high schools. It provided an opportunity for high school teachers, writers, researchers, and others to get in on the ground floor of developing innovative classroom materials. The materials consist of 20 modules that can be flexibly adapted for use in a variety of courses at a variety of grade levels in both biology and mathematics. The project was run by DIMACS at Rutgers University in collaboration with the Consortium for Mathematics and its Applications (COMAP) and Colorado State University (CSU).



This unit asks students to apply knowledge of protein structure and function to pose and answer the fundamental question investigated in this unit, "What alignment of two sequences is biologically most meaningful?" The unit introduces students to the rapidly emerging field of bioinformatics by developing the basic mathematical principles that underlie computer programs used to align amino acids. It also provides instruction on how to use one such resource, Biology Student Workbench. In effect, the students become researchers and should begin to understand how mathematical modeling, computing, and biology can work together to answer important scientific questions.

Topics
Biology: Comparison of amino acid and nucleotide sequences between species, alignment of protein and DNA sequences, use of computers with databases.
Mathematics: Edge-vertex graphs and tree diagrams as models for sequential decisions, numerical scores as measures of similarity between letter sequences, dynamic programming, minimal- and maximal-path algorithm, path-counting algorithm, and combinatorics.

Prerequisites
Biology: Basic ideas behind DNA, RNA, protein composition and synthesis, amino acids, and classification.
Mathematics: Integer arithmetic and ability to select the minimum (or maximum) number from a list of Integers.

Length
This unit consists of 5 lessons and will take 5-6 class periods (45 minutes each. The length may vary depending upon the time you allocate for student explorations on Biology Student Workbench.