One of the crosscutting concepts in science is cause and effect. A disease model can provide understanding of cause and effect, as teachers scaffold student thinking from molecular changes in the DNA to visible traits in the organism. The project described in this article uses Pompe disease, a rare recessive disorder, as a model of cause and effect. The topics of DNA, protein structure and function, enzymes, genetics, and human disease can all be addressed through the story of Pompe disease. Students have to think like research and clinical scientists while learning the basics of this disease and considering how it might be treated.