Connecting common genetic polymorphisms to protein function: A modular project sequence for lecture or lab.
Single nucleotide polymorphisms (SNPs) in DNA can result in phenotypes where the biochemical basis may not be clear due to the lack of protein structures. With the growing number of modeling and simulation software available on the internet, students can now participate in determining how small changes in genetic information impact cellular protein structure and function. We have developed a modular series of activities to engage lab or lecture students in examining the basis for common phenotypes. The activities range from basic phenotype testing/observation to DNA sequencing and simulation of protein structure and dynamics. We provide as an example study of the bitterness receptor TAS2R38 and PTC tasting, however these activities are applicable to other SNPs or genomic variants with a direct connection to an observable phenotype. These activities are modular and can be mixed to meet the student capabilities and infrastructure availability. The complete sequence of activities will demonstrate the direct connection between gene structure, protein structure and organism function. © 2016 by The International Union of Biochemistry and Molecular Biology, 44(6):526-536, 2016.
Department of Chemistry and Biochemistry, James Madison University, Virginia.|Center for Genome and Metagenome Studies, James Madison University, Virginia.
Christopher E
CE
Berndsen
Department of Chemistry and Biochemistry, James Madison University, Virginia.
Byron H
BH
Young
Department of Biology, James Madison University, Virginia.
Quinlin J
QJ
McCormick
Center for Genome and Metagenome Studies, James Madison University, Virginia.|Department of Biology, James Madison University, Virginia.
Raymond A
RA
Enke
D001483:Base Sequence; D035843:Biomedical Research / Q000193:education*; D019295:Computational Biology / Q000193:education*; D003479:Curriculum; D004521:Educational Measurement; D023281:Genomics / Q000379:methods; D006801:Humans; D007753:Laboratories; D008954:Models, Biological; D008958:Models, Molecular; D008967:Molecular Biology / Q000193:education*; D056004:Molecular Dynamics Simulation; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D018794:Problem-Based Learning / Q000379:methods*; D011487:Protein Conformation; D043562:Receptors, G-Protein-Coupled / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D017422:Sequence Analysis, DNA / Q000379:methods; D012689:Sequence Homology, Nucleic Acid; D012984:Software; D013329:Structure-Activity Relationship; D013334:Students / Q000523:psychology; D055697:Taste Perception / Q000502:physiology; D013663:Teaching; D000098706:Taste Receptors, Type 2
D043562:Receptors, G-Protein-Coupled; D000098706:Taste Receptors, Type 2
genomics proteomics bioinformatics; molecular biology; protein structure function and folding; using simulation and internet resources for teaching