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Biochemistry education relies heavily on students' abilities to conceptualize abstract cellular and molecular processes, mechanisms, and components. From a constructivist standpoint, students build their understandings of these abstract processes by connecting, expanding, or revising their prior conceptions and experiences. As such, biochemistry instructors often use analogies to teach difficult or hard-to-visualize topics to their classes by relating these target concepts to more commonplace analogs with which their students may already be familiar. For example, the binding of an enzyme to its substrate is often compared to a lock and a key; and ATP is frequently referred to as a cellular energy currency in discussions of metabolism and reaction coupling. Although the use of analogies in biochemistry classrooms is fairly common, the specific ways biochemistry instructors use analogies differ from instructor to instructor and class to class. In this article, we discuss biochemistry instructors' perceptions of the use of analogies in their classroom instruction. Specifically, we discuss (1) biochemistry instructors' objectives for using analogies, (2) their perceptions of the potential disadvantages associated with analogy use, (3) the sources of the analogies they use in their classes, and (4) the ways they perceive that analogies should be presented in class to promote student learning of biochemical concepts.

Biochemistry instructors often use external representations—ranging from static diagrams to dynamic animations and from simplistic, stylized illustrations to more complex, realistic presentations—to help their students visualize abstract cellular and molecular processes, mechanisms, and components. However, relatively little is known about how students use and interpret external representations in biochemistry courses. In the current study, variation theory was used to explore the potential for student learning about protein translation from a stylized, dynamic animation. The results of this study indicate that students learned from this animation, in that they noticed many critical features of the animation and integrated those features into their understandings of protein translation. However, many students also focused on a particular feature of the animation, the Shine–Dalgarno sequence, that their instructors did not feel was critical to promote an overall understanding of this metabolic process. Student attention was focused on this feature because of the design of the animation, which cued students to notice this feature by significantly varying the appearance of the Shine–Dalgarno sequence.