Previous studies have shown that students often ignore molecular mechanisms when describing genetic phenomena. Specifically, students tend to directly link genes to their encoded traits, ignoring the role of proteins as mediators in this process. We tested the ability of 10th grade students to connect genes to traits through proteins, using concept maps and reasoning questions. The context of this study was a computational learning environment developed specifically to foster this ability. This environment presents proteins as the mechanism-mediating genetic phenomena. We found that students' ability to connect genes, proteins, and traits, or to reason using this connection, was initially poor. However, significant improvement was obtained when using the learning environment. Our results suggest that visual representations of proteins' functions in the context of a specific trait contributed to this improvement. One significant aspect of these results is the indication that 10th graders are capable of accurately describing genetic phenomena and their underlying mechanisms, a task that has been shown to raise difficulties, even in higher grades of high school.