Mathematics, Thermodynamics, and Modeling to Address Ten Common Misconceptions about Protein Structure, Folding, and Stability

Abstract

To fully understand the roles proteins play in cellular processes, students need to grasp complex ideas about protein structure, folding, and stability. Our current understanding of these topics is based on mathematical models and experimental data. However, protein structure, folding, and stability are often introduced as descriptive, qualitative phenomena in undergraduate classes. In the process of learning about these topics, students often form incorrect ideas. For example, by learning about protein folding in the context of protein synthesis, students may come to an incorrect conclusion that once synthesized on the ribosome, a protein spends its entire cellular life time in its fully folded native confirmation. This is clearly not true; proteins are dynamic structures that undergo both local fluctuations and global unfolding events. To prevent and address such misconceptions, basic concepts of protein science can be introduced in the context of simple mathematical models and hands-on explorations of publicly available data sets. Ten common misconceptions about proteins are presented, along with suggestions for using equations, models, sequence, structure, and thermodynamic data to help students gain a deeper understanding of basic concepts relating to protein structure, folding, and stability.

Designing productively negative experiences with serious game mechanics: Qualitative analysis of game-play and game design in a randomized trial

“…It has been long established that the engagement and learning capacity of games should be models for good instructional design (Dickey, 2005;Gee, 2005;Squire, 2013); we expect that our findings and approach have relevance beyond the realm of serious computer gaming, and could be applied to the design and evaluation of any digital interactive tool. While our interventions were designed to address problems in molecular biology at the undergraduate level, misconceptions are very common in all areas of science-from chemistry, to physics, math, evolution, and climate change-and at all age levels (Odom, 1995;Paz-Y-Miño-C & Espinosa, 2012;Robic, 2010;Rocklöv, 2016;Sanger & Iowa, 2000). The design strategies recommended to facilitate productive negativity might apply to interventions in other domains where misconceptions abound.…”

Identifying and Remediating Student Misconceptions in Introductory Biology via Writing-to-Learn Assignments and Peer Review

“…Introductory biology is an ideal place to identify and remediate misconceptions, as it is a prerequisite for many STEM majors and students pursuing degrees in the health professions. Previous work has identified several areas of student misconceptions in biology, especially at the introductory level ( Robic, 2010 ; Parker et al. , 2012 ).…”

“…Previous literature has reported misconceptions in several areas of biology. Common misconceptions regarding the topics of protein structure involved protein folding, protein stability, and the effects mutations have on protein structure ( Robic, 2010 ; Shi et al. , 2010 ).…”

Creating 3D physical models to probe student understanding of macromolecular structure

“…One of the most challenging concepts for students studying biochemistry is macromolecular structure . Common difficulties students face relate to problematic conceptions about the fundamental forces responsible for the formation and stabilization of these structures . Misconceptions about these forces develop at the general chemistry level and persist through biochemistry courses .…”