A common problem with courses that build on each other is that students have difficulty transferring the skills from one course to another. To increase learning independence, student skill base, knowledge retention, and critical thinking we have developed a bioanalytical lab course that first guides students through analytical laboratory skills, then applies these skills to a protein isolation, followed by a third phase that allows students to use the isolated protein as a peroxidase. This course is an option that can replace separate analytical chemistry and biochemistry lab requirements. The course design includes a multi-level scaffolding that is systematically removed as the semester progresses intended to produce more independent learners. Results of student confidence in learning, lab skills, and attitudes as the course progresses will be presented from the initial offering in fall 2009. Lessons learned after the first offering and adjustments to the course will also be discussed.