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Improvement of student understanding of how kinetic data facilitates the determination of amino acid catalytic function through an alkaline phosphatase structure/mechanism bioinformatics exercise
Author(s) -
Grunwald Sandra K.,
Krueger Katherine J.
Publication year - 2008
Publication title -
biochemistry and molecular biology education
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.34
H-Index - 39
eISSN - 1539-3429
pISSN - 1470-8175
DOI - 10.1002/bmb.120
Subject(s) - alkaline phosphatase , enzyme , function (biology) , kinetics , biochemistry , phosphatase , acid phosphatase , amino acid residue , enzyme kinetics , active site , mechanism (biology) , catalytic efficiency , chemistry , catalysis , biology , peptide sequence , microbiology and biotechnology , physics , quantum mechanics , gene
Laboratory exercises, which utilize alkaline phosphatase as a model enzyme, have been developed and used extensively in undergraduate biochemistry courses to illustrate enzyme steady‐state kinetics. A bioinformatics laboratory exercise for the biochemistry laboratory, which complements the traditional alkaline phosphatase kinetics exercise, was developed and implemented. In this exercise, students examine the structure of alkaline phosphatase using the free, on‐line bioinformatics protein‐modeling program Protein Explorer. Specifically, students examine the active site residues of alkaline phosphatase and propose functions for these residues. Furthermore, by examining the mechanism of alkaline phosphatase and by using the published kinetic data, students propose specific roles for several active‐site residues. Paired t ‐test analysis of pre‐ versus postexercise assessment data shows that the completion of the exercise improves student's ability to use kinetic data correctly thereby determining a probable catalytic function for an active site amino acid.