The central dogma of biology is difficult to learn because its microscopic processes cannot be visualized. This study aimed to devise two inquiry activities: 'Button Code' and 'Beaded Bracelet Making,' involving the concepts of DNA replication and protein synthesis based on the Metacognitive Learning Cycle (MLC) for students, and to explore the effectiveness of concept learning of the central dogma, how students' metacognition may be expressed, and students' perceptions of their inquiry performance. We developed a 'Concept journal' including metacognitive scaffolds, and employed the 'Central Dogma Achievement Test' as a tool for the above purpose. A total of 18 junior high school students participated in this inquiry course instructed by two of the authors. The results showed that students' achievement performance was significantly improved on the whole, the students' metacognition was expressed during the process of inquiry with scaffolding, and most students gave positive responses about their learning performance. According to the results, this inquiry course could develop students' comprehension of the central dogma concept, and give students opportunities to practice metacognition that might lead to effective learning in inquiry activities. The implications and expandability of this course are discussed.