Experimental courses for undergraduate students majoring in biochemistry or related subjects often do not provide students with systematic and research-based experiences. To help students develop abilities related to laboratory techniques, data analysis, and systematic thought in biology, we performed an exploratory program that employs project-based learning in collaborative groups. The participants (total of 18 students) organized themselves into groups of 2-4 students, and each group researched an enzyme that had not been described previously. The program began with a literature survey of enzyme and bioinformatics analysis. The students cloned the gene encoding the enzyme, purified the enzyme, and, finally, analyzed the enzyme's catalytic characteristics. The students explained the catalytic mechanism, integrating their experimental data and other knowledge. An instructor provided support and training during the process to support effective teamwork and to cultivate a habit of independence that is believed to be useful for the students' future careers. The assessment showed that the pilot program yielded an improvement in the participant' laboratory skills, scientific presentation ability, and experimental design ability. These analyses indicated that the small-scale practice in this study provided benefits to the students and the methods may be popularized to a large extent.