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

The high degree of complexity of macromolecular structure is extremely difficult for students to process. Students struggle to translate the simplified two‐dimensional representations commonly used in biochemistry instruction to three‐dimensional aspects crucial in understanding structure–property relationships. We designed four different physical models to address student understanding of electrostatics and noncovalent interactions and their relationship to macromolecular structure. In this study, we have tested these models in classroom settings to determine if these models are effective in engaging students at an appropriate level of difficulty and focusing student attention on the principles of electrostatic attractions. This article describes how to create these unique models for four targeted areas related to macromolecular structure: protein secondary structure, protein tertiary structure, membrane protein solubility, and DNA structure. We also provide evidence that merits their use in classroom settings based on the analysis of assembled models and a behavioral assessment of students enrolled in an introductory biochemistry course. By providing students with three‐dimensional models that can be physically manipulated, barriers to understanding representations of these complex structures can be lowered and the focus shifted to addressing the foundational concepts behind these properties. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(6):491–500, 2017.

[1]  Colin Berry,et al.  Inside protein structures: Teaching in three dimensions , 2010, Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology.

[2]  Jeffrey R. Raker,et al.  The biochemistry tetrahedron and the development of the taxonomy of biochemistry external representations (TOBER) , 2012 .

[3]  Carl-Johan Rundgren,et al.  CRITICAL FEATURES OF VISUALIZATIONS OF TRANSPORT THROUGH THE CELL MEMBRANE—AN EMPIRICAL STUDY OF UPPER SECONDARY AND TERTIARY STUDENTS’ MEANING-MAKING OF A STILL IMAGE AND AN ANIMATION , 2010 .

[4]  Jennifer Loertscher,et al.  Development and analysis of an instrument to assess student understanding of foundational concepts before biochemistry coursework * , 2011, Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology.

[5]  I. Shimada,et al.  Three-dimensional solution structure of the B domain of staphylococcal protein A: comparisons of the solution and crystal structures. , 1992, Biochemistry.

[6]  Geeta Selvarajah,et al.  Model building to facilitate understanding of holliday junction and heteroduplex formation, and holliday junction resolution , 2016, Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology.

[7]  Eric Hagedorn,et al.  Physical models enhance molecular three‐dimensional literacy in an introductory biochemistry course * , 2005, Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology.

[8]  N. Guex,et al.  SWISS‐MODEL and the Swiss‐Pdb Viewer: An environment for comparative protein modeling , 1997, Electrophoresis.

[9]  Riccardo Porta,et al.  Three Dimensional (3D) Printing : a Straightforward, User-Friendly Protocol To Convert Virtual Chemical Models to Real-Life Objects , 2015 .

[10]  Marcus D. Hanwell,et al.  Avogadro: an advanced semantic chemical editor, visualization, and analysis platform , 2012, Journal of Cheminformatics.

[11]  David F. Treagust,et al.  Grade-12 students' misconceptions of covalent bonding and structure , 1989 .

[12]  Arthur J. Olson,et al.  3D Printing of Molecular Models , 2016, The Journal of biocommunication.

[13]  M. Hegarty,et al.  Model Manipulation and Learning: Fostering Representational Competence With Virtual and Concrete Models. , 2016 .

[14]  Stacey Lowery Bretz,et al.  Development of the Bonding Representations Inventory to Identify Student Misconceptions about Covalent and Ionic Bonding Representations. , 2014 .

[15]  Conrad C. Huang,et al.  UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..

[16]  Using simple manipulatives to improve student comprehension of a complex biological process: Protein synthesis , 2012, Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology.

[17]  Anveshna Srivastava.  Building mental models by dissecting physical models , 2016, Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology.

[18]  Protein Structure and Function: An Interdisciplinary Multimedia-Based Guided-Inquiry Education Module for the High School Science Classroom. , 2014 .

[19]  B. van den Berg.  Structural Basis for Outer Membrane Sugar Uptake in Pseudomonads* , 2012, The Journal of Biological Chemistry.

[20]  M. Hegarty,et al.  Representational Translation With Concrete Models in Organic Chemistry , 2012 .

[21]  R. Bertram,et al.  Backbone structure of the amantadine-blocked trans-membrane domain M2 proton channel from Influenza A virus. , 2007, Biophysical journal.

[22]  Jennifer Morris,et al.  A combination of hand-held models and computer imaging programs helps students answer oral questions about molecular structure and function: a controlled investigation of student learning. , 2009, CBE life sciences education.

[23]  W. Robinson,et al.  An Inventory for Alternate Conceptions among First-Semester General Chemistry Students , 2002 .

[24]  B. Panijpan,et al.  Making ordered DNA and protein structures from computer‐printed transparency film cut‐outs , 2009, Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology.

[25]  Sachel M. Villafañe,et al.  Uncovering students' incorrect ideas about foundational concepts for biochemistry , 2011 .

[26]  C. Larsson,et al.  Challenging Students’ Intuitions—the Influence of a Tangible Model of Virus Assembly on Students’ Conceptual Reasoning About the Process of Self-Assembly , 2014, Research in Science Education.

[27]  Miri Barak,et al.  Integrating Model-Based Learning and Animations for Enhancing Students’ Understanding of Proteins Structure and Function , 2013 .

[28]  Margaret A Franzen,et al.  Tactile teaching: Exploring protein structure/function using physical models * , 2006, Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology.

[29]  Vincent F. Scalfani,et al.  3D Printed Molecules and Extended Solid Models for Teaching Symmetry and Point Groups , 2014 .

[30]  Promita Chakraborty,et al.  Coarse-grained, foldable, physical model of the polypeptide chain , 2013, Proceedings of the National Academy of Sciences.

[31]  Stacey Lowery Bretz,et al.  Biochemistry students' ideas about shape and charge in enzyme–substrate interactions , 2014, Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology.

[32]  Marissa Harle,et al.  Students' understanding of external representations of the potassium ion channel protein part II: Structure–function relationships and fragmented knowledge , 2012, Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology.

[33]  Sachel M. Villafañe,et al.  Probing and improving student's understanding of protein α‐helix structure using targeted assessment and classroom interventions in collaboration with a faculty community of practice , 2014, Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology.

[34]  Sheila S Jaswal,et al.  Multimedia in Biochemistry and Molecular Biology Education , 2013 .

[35]  Marissa Harle,et al.  Students' understanding of external representations of the potassium ion channel protein, part I: Affordances and limitations of ribbon diagrams, vines, and hydrophobic/polar representations , 2012, Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology.

[36]  Konrad J. Schönborn,et al.  A Model of Factors Determining Students’ Ability to Interpret External Representations in Biochemistry , 2009 .

[37]  Srebrenka Robic,et al.  Mathematics, Thermodynamics, and Modeling to Address Ten Common Misconceptions about Protein Structure, Folding, and Stability , 2010, CBE life sciences education.

[39]  Julia Khodor,et al.  A hierarchical biology concept framework: a tool for course design. , 2004, Cell biology education.

[40]  Beyond textbook illustrations: Hand‐held models of ordered DNA and protein structures as 3D supplements to enhance student learning of helical biopolymers , 2010, Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology.

[41]  Alipaşa Ayas,et al.  A review of chemical bonding studies: needs, aims, methods of exploring students’ conceptions, general knowledge claims and students’ alternative conceptions , 2006 .

[42]  IJsbrand M. Kramer,et al.  Education Catching Up with Science: Preparing Students for Three-Dimensional Literacy in Cell Biology , 2012, CBE life sciences education.

[43]  Jodie Jenkinson,et al.  Visualizing Protein Interactions and Dynamics: Evolving a Visual Language for Molecular Animation , 2012, CBE life sciences education.

[44]  Keir H. Fogarty,et al.  Do-It-Yourself: 3D Models of Hydrogenic Orbitals through 3D Printing , 2016 .

[45]  S. Meyer.  3D Printing of Protein Models in an Undergraduate Laboratory: Leucine Zippers , 2015 .

[46]  Julian F. Tyson,et al.  Fostering spatial skill acquisition by general chemistry students , 2015 .