Project-based (research-driven) laboratory courses stimulate student involvement, improve critical thinking and initiate cooperative learning. To this end, a 7-week laboratory project was designed for a sophomore cell biology course to reinforce the fundamental relationship between genotype and phenotype using yeast alcohol dehydrogenase I (ADH1). Working in pairs, students used site-directed mutagenesis to create a H44R mutation in the ADH1 gene sequence inserted into a YEp13 shuttle vector. These plasmids were propagated in E. coli, sequenced, and reintroduced into a yeast strain expressing no ADH1 activity. The growth patterns on selective media were determined. As the mutation allows for growth in the presence of allyl alcohol, students make the connection between DNA sequence and protein function. Student performance was assessed with pre- and post-tests, with improvement observed across all learning objectives. In addition to meeting the learning outcomes, 98% of the students thought that this experience allowed them to see how the scientific process can encompass multiple techniques to answer a single question. Eighty-four percent of the students thought that this experience was more engaging than other lab experiences they have had. Our multi-week laboratory examining the phenotypic changes in yeast alcohol metabolism successfully developed students' understanding of the scientific process, knowledge of molecular techniques and the relationship of gene sequence to protein function in an engaging manner.