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Related Concept Videos

Protein Organization01:24

Protein Organization

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Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
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Molecular Models02:00

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Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
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A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
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Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
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Updated: Mar 8, 2026

Modeling an Enzyme Active Site using Molecular Visualization Freeware
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Using molecular visualization to explore protein structure and function and enhance student facility with

Cassidy R Terrell1, Laura L Listenberger2

  • 1Center of Learning Innovation, University of Minnesota Rochester, 111 S. Broadway Ave #300, Rochester, Minnesota, 55904.

Biochemistry and Molecular Biology Education : a Bimonthly Publication of the International Union of Biochemistry and Molecular Biology
|February 2, 2017
PubMed
Summary

This project enhances biochemistry education by using cyclooxygenase-1 (COX-1) to teach protein structure and computational tools. Students gain confidence in using online databases and molecular visualization software.

Keywords:
Protein structure and functionassessmentmolecular visualizationundergraduate biochemistry

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Area of Science:

  • Biochemistry Education
  • Molecular Biology
  • Computational Chemistry

Background:

  • Undergraduate students benefit from analyzing 3D protein structure and function.
  • Traditional biochemistry curricula may not fully integrate computational tools for molecular analysis.

Purpose of the Study:

  • To develop and assess an inquiry-based molecular visualization project for Biochemistry I students.
  • To enhance student knowledge and confidence in using online databases and computational tools for protein analysis.

Main Methods:

  • Developed a multiweek project using a virtual model of cyclooxygenase-1 (COX-1).
  • Guided students through primary, secondary, tertiary, and quaternary structure analysis.
  • Incorporated inhibitor design, binding energy computation, and mutation modeling (COX-2).
  • Utilized mixed methods pre- and postsurveys to evaluate student learning outcomes.

Main Results:

  • Students demonstrated increased knowledge of online databases and computational tools.
  • Student confidence in using these digital resources significantly improved.
  • The project successfully integrated 3D protein structure analysis into the biochemistry curriculum.

Conclusions:

  • The molecular visualization project effectively improved students' understanding and application of biochemical concepts.
  • Inquiry-based learning combined with computational tools enhances biochemistry education.
  • This project provides a model for incorporating advanced molecular analysis techniques into undergraduate science courses.