SZUBA-DISSERTATION-2021.pdf (131.49 MB)
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A Comprehensive Investigation and Intervention for Understanding Structure, Forces, and Representations

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posted on 01.05.2021, 00:00 by Anna B Szuba
Much of biochemical inquiry deals with the structure, functions and interactions of biological macromolecules. Studies have shown that students struggle with these concepts in biochemistry but researchers have not analyzed this from a knowledge-in-pieces framework and have not provided effective examples of interventions to help students understand structure and representations. This dissertation investigates how students assemble knowledge related to protein structure, noncovalent interactions, and representations in the biochemistry classroom and how an intervention with visualization tools enhances student understanding of these topics. I introduce design protocols that involve the implementation of clinical interviews and development of an intervention using PyMOL and hand-models of secondary structures. Analysis of results showed that during the interviews, participants possessed various ideas of what noncovalent interactions, specifically hydrogen bonding, were involved in the formation of a protein structure. Furthermore, their knowledge of protein structure and the representations used to define these structures was fragmented. The intervention created sought to respond to this fragmented knowledge that students had of these biochemistry concepts. The results from the intervention revealed that when given a specific learning environment in which students are able to use molecular visualization software and hand models, student understanding of hydrogen bonds, structure, and representation was much less fragmented. When compared to interview participants, intervention participants could better understand the purpose of representations and the detailed groups and atoms involved in hydrogen bonding. These findings are further supported by surveys where students indicate that the model kit allowed them to see a physical model of secondary structures and hydrogen bonding between specific atoms, while PyMOL helped them better understand the similarities and differences of representations. The results from both studies present a direction for current educators to teach biochemistry. By asking students to not only explain, but also draw their explanations, educators can identify where students show fragmentation in their understanding. In addition to asking students to draw, educators should provide students with different learning tools during their biochemistry course to promote a concrete understanding of these biochemistry concepts which students can use to succeed in their continuing education or future careers.



Stieff, Mike


Stieff, Mike



Degree Grantor

University of Illinois at Chicago

Degree Level


Degree name

PhD, Doctor of Philosophy

Committee Member

Wink, Donald Fung, Leslie Yang, Xiaojing Towns, Marcy

Submitted date

May 2021

Thesis type




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