Using PyMOL to Explore the Effects of pH on Noncovalent Interactions between Immunoglobulin G and Protein A: A Guided‐Inquiry Biochemistry Activity

Allred, Zahilyn Roche; Tai, Heeyoung; Bretz, Stacey Lowery; Page, Richard C.

doi:10.1002/bmb.21066

Cited by 16 publications

(12 citation statements)

References 35 publications

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“…Third, electrostatic forces play a crucial role in the structure and stability of biological systems, and the interactions between and within biological systems, which has led researchers to identify electrostatic interactions as a threshold concept in biochemistry, 44 meaning that if students do not possess a deep understanding of noncovalent interactions, they will have difficulties gaining a conceptual understanding of ideas taught in more advanced courses like biochemistry. To develop the activity presented herein, we relied on previous research of student understanding of noncovalent interactions and the structure and stability of DNA 45,46 and noncovalent interactions within proteins 47–49 …”

Section: Introductionmentioning

confidence: 99%

Students' use of chemistry core ideas to explain the structure and stability of DNA

Allred

Farias

Kararo

et al. 2020

Biochem Molecular Bio Educ

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Students tend to think of their science courses as isolated and unrelated to each other, making it difficult for them to see connections across disciplines. In addition, many existing science assessments target rote memorization and algorithmic problem‐solving skills. Here, we describe the development, implementation, and evaluation of an activity aimed to help students integrate knowledge across introductory chemistry and biology courses. The activity design and evaluation of students' responses were guided by the Framework for K‐12 Science Education as the understanding of core ideas and crosscutting concepts and the development of scientific practices are essential for students at all levels. In this activity, students are asked to use their understanding of noncovalent interactions to explain (a) why the boiling point differs for two pure substances (chemistry phenomenon) and (b) why temperature and base pair composition affects the stability of DNA (biological phenomenon). The activity was implemented at two different institutions (N = 441) in both introductory chemistry and biology courses. Students' overall performance suggests that they can provide sophisticated responses that incorporate their understanding of noncovalent interactions and energy to explain the chemistry phenomenon, but have difficulties integrating the same knowledge to explain the biological phenomenon. Our findings reinforce the notion that students should be provided with opportunities in the classroom to purposefully practice and support the use and integration of knowledge from multiple disciplines. Students' evaluations of the activity indicated that they found it to be interesting and helpful for making connections across disciplines.

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Section: Introductionmentioning

confidence: 99%

Students' use of chemistry core ideas to explain the structure and stability of DNA

Allred

Farias

Kararo

et al. 2020

Biochem Molecular Bio Educ

Self Cite

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“…The third is promoting students' independent learning. There does not seem to be any need to develop tasks using a molecular viewer for the student to acquire knowledge of proteins, since there are other techniques of learning using molecular models 3–10 . However, the student's involvement in the tasks, which incorporate procedural knowledge P2 regarding the use of software features for high‐school students, may promote independent learning.…”

Section: Discussionmentioning

confidence: 99%

“…Visual literacy in biochemistry can greatly assist experts and students, both of whom use such molecular models to study protein structure and function 1,2 . Most of the curricula for students in tertiary education suggest three main means of displaying visual information using molecular models of proteins: (i) retrieving structure files from the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RSCB‐PDB) and visualizing them using PyMol 3–6 or another molecular viewer 7–10 ; (ii) encouraging the haptic perception of protein structures using tactile molecular models in combination with visualization of molecular models 11–16 ; (iii) using virtual reality or augmented reality in 3D 17–19 . The wide scale use of molecular models as a visualization tool for learning about proteins has prompted the development of frameworks for evaluating visual literacy in biochemistry 1,2,20 for teachers and students in tertiary education 21–26 …”

Section: Introductionmentioning

confidence: 99%

Conceptualizing learning about proteins with a molecular viewer in high school based on the integration of two theoretical frameworks

Levkovich

Yarden

2021

Biochem Molecular Bio Educ

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The use of a molecular viewer to visualize proteins has become more prevalent in high schools in recent years. We relied on the foundations of two theoretical frameworks to analyze questions in two learning tasks designed for 10th‐ to 12th‐grade biotechnology majors that make use of Jmol. The two theoretical frameworks were: (i) classification of scientific knowledge into content, procedural, and epistemic knowledge; and (ii) evaluation of the cognitive skills central to visual literacy in biochemistry. During the analysis, two sub‐elements of procedural knowledge emerged from the data: (i) the visualization of molecular models, and (ii) the use of Jmol software features. Based on the theoretical frameworks and data analysis, we suggest a conceptualization of learning about proteins using a molecular viewer, where the scientific knowledge elements are integrated with the eight cognitive skills central to visual literacy in biochemistry. In addition, a model presenting a hierarchy for the knowledge elements and sub‐elements is suggested. In this model, content knowledge is a basic requirement; without it, the other knowledge elements cannot be used. Moreover, the use of epistemic knowledge or Jmol software features is not possible without visualization of the molecular models, which requires content knowledge. This conceptualization is expected to facilitate the development of learning tasks, decrease the complexity of knowledge acquisition for students; it may also assist the teacher during the teaching process.

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“…Introducing the students to several molecular visualization tools can help the students to develop visualization skills. Visual literacy skill including drawing interpretation of 3D representation to explain concept is important (Roche Allred et al, 2017). Visual literacy can be developed by introducing submicro drawing questions to investigate students' conceptual understanding.…”

Section: Agreementioning

confidence: 99%

Implementation of Molecular Visualization Program for Chemistry Learning

Listyarini

2021

J. Prisma. Sains

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This study aims to investigate the implementation of molecular visualization programs for improving students’ understanding of concepts in chemical bonding. Chemistry learning in chemical bonding was conducted using molecular visualization program ACD/ChemSketch and Avogadro program. Several topics in chemical bonding include molecular geometry, polarity, bond angle, bond length, intermolecular forces and predicting boiling points. This study employs quasi-experimental research One Group Pretest – Posttest design. The subjects of this study were 46 students of undergraduate program in chemistry education department at Universitas Sanata Dharma. This study use test (pretest and pretest) and questionnaire to assess students’ perception of implementation of ACD/ChemSketch and Avogadro in chemistry learning. Implementation of ACD/ChemSketch and Avogadro in chemistry learning of chemical bonding gave an effect on students’ understanding based on paired t-test (sig < 0.05) and Kruskal-Wallis (sig < 0.05) test. The percentage of students is 45% with the medium N-gain category and 65% with the high N-gain category for ACD/ChemSketch program. It is 38.46% with the medium N-gain category and 61.54% with the high N-gain category for Avogadro program. Students show positive response to the implementation of ACD/ChemSketch and Avogadro program regarding their understanding, motivation and prospective skill for becoming teachers. Molecular visualization program helps the students to understand the chemical bonding topic.

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Using PyMOL to Explore the Effects of pH on Noncovalent Interactions between Immunoglobulin G and Protein A: A Guided‐Inquiry Biochemistry Activity

Cited by 16 publications

References 35 publications

Students' use of chemistry core ideas to explain the structure and stability of DNA

Students' use of chemistry core ideas to explain the structure and stability of DNA

Conceptualizing learning about proteins with a molecular viewer in high school based on the integration of two theoretical frameworks

Implementation of Molecular Visualization Program for Chemistry Learning

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