In molecular life science phenomena exist on a sub-micro scale and are not readily accessible for learners. Here tools, as external representations and metaphorical language, become essential for students’ learning. Metaphorical language is often used to relate abstract concepts to more familiar ideas from everyday life. For successful meaning-making students need to be familiar with the concepts being compared and know which characteristics of the metaphor are relevant and should be conveyed to the conceptual domain. There is a need for students to interpret and focus on certain given aspects and also on deviances between the two domains. Students’ prior knowledge of the real life domain as well as the scientific domain, then becomes the foundation for students’ learning. Furthermore, the metaphor itself mediates new meaning and new ways to interpret the natural world in interaction with learners, and this has an impact on students’ conceptualization of the concept the metaphor is describing. The objective of this study was, i) to explore which metaphors students tend to use while interacting with two external representations of dynamic molecular processes, and ii) to describe what connections between the scientific concept and the identified metaphors students made, both useful connections and potential pitfalls. The first representation is an animation visualizing the formation of Adenosine triphosphate (ATP) in a metabolic process in the cell. The second is a physical model of self-assembly of a virus capsid. The empirical material analysed consisted of ten audio-recorded group discussions with university students (n=59). The students had completed basic courses in chemistry and molecular biology. A pre-formulated discussion guideline was used and the students had access to the external representation during the whole session. A qualitative analysis was performed using an inductive analytical model. The preliminary analysis showed that students used several metaphors, for example water mill, paddle wheel, ball, and chief, to create meaning to the scientific concepts while interacting with the two representations. The following analysis will examine to what degree the metaphors possess characteristics that can mislead and tempt students to use parts of the iconographic representation that are not relevant for understanding the represented phenomenon. With these results we can clarify how far the metaphors, and thereby the representations, reach and thus make valuable implications for education.