The CHROM Web applet has been used to create a new active-learning exercise in which students design a purification scheme for a recombinant protein using ion-exchange chromatography (IEC). To successfully complete the exercise, students are challenged to apply elementary concepts from acid-base chemistry as well as protein and amino acid structure to devise a scheme purifying the target recombinant protein from other "Escherichia coli" proteins. By actively applying fundamental principles to solve an unfamiliar problem, students develop higher-level cognitive skills and gain a deeper understanding of key concepts that are difficult to teach effectively through traditional methods. The effectiveness of the exercise in promoting deep learning was assessed by comparing the performance of students in answering questions on acid-base chemistry, amino acid structure, and IEC before and after the completion of the active-learning exercise.