Undergraduate Chemistry and Biology Students’ Use of Causal Mechanistic Reasoning to Explain and Predict Preferential Protein–Ligand Binding Activity

Abstract

There is emerging recognition that mechanistic reasoning about scientific phenomena as well as developing an interdisciplinary understanding of science are valuable for student success. Our team of chemistry, biology, and teacher education researchers strives to support students in their interdisciplinary learning and engage them in causal mechanistic reasoning (CMR), a thinking strategy that involves identifying underlying entities and their properties and linking these ideas to explain or predict a target phenomenon. We aim to help students build connections between their undergraduate chemistry and biology courses through engagement with carefully developed activities, which can be administered in a range of courses. In this study, we explored how students in 7 different chemistry, biology, or biochemistry courses engaged in CMR about preferential protein−ligand binding, a biological phenomenon that requires an understanding of core chemistry ideas like atomic properties and electrostatics. Explanations varied from noncausal mechanistic to fully causal mechanistic across all courses; however, students co-enrolled in molecular biology and second semester general chemistry did not differ in their engagement in CMR when situated in each course. Student responses provided evidence of activation of different conceptual resources, including charge, polarity, and space, to explain this phenomenon. Lastly, correct predictions about the preferred binding site were highly correlated with fully engaged CMR, showing compelling evidence for the power of this thinking strategy. This task effectively elicits CMR in both chemistry and biology courses, thus making it a potential tool for helping students build connections across disciplinary silos they experience in undergraduate science curricula.

A Framework for the Integration of Green and Sustainable Chemistry into the Undergraduate Curriculum: Greening Our Practice with Scientific and Engineering Practices

“…Specifically, this scaffolding is composed of prompts for a definition of the problem and an evaluation or design of a solution separately and iteratively, with intermediate prompts to push students to consider specific stakeholders and the criteria and constraints related to that set of stakeholders. In our experience, scaffolding of complex tasks is much more likely to elicit evidence that students are connecting and using their knowledge appropriately. , Lack of guidance to students tends to result in confusion and less productive responses that discuss surface level ideas such as descriptions rather than explanations about causal factors …”

Molecular storytelling: a conceptual framework for teaching and learning with molecular case studies

“…In biology education and research, explanations about proteins often describe methods, analogies, contexts, theories, and 'how' the mechanism works (Trujillo et al, 2015) and integrate thermodynamics and kinetics when considering protein-folding and dynamics (Jeffery et al, 2018). Biology and chemistry educators strive to help students (a) reason through visual representations Anderson, 2006, 2009;Offerdahl et al, 2017); (b) relate causal factors in biomolecular phenomena (Schwarz et al, 2020); (c) trace cellular and molecular activities through time and space (Machamer et al, 2000;van Mil et al, 2013van Mil et al, , 2016, and (d) apply all of these skills to discuss protein-ligand binding (Trujillo et al, 2015(Trujillo et al, , 2016aFranovic et al, 2023). To effectively teach with MCSs, educators must support students in learning biology and chemistry concepts and the various conceptual and discipline-specific representations of biomolecules (see Supplementary Tables S1A,B).…”