Teaching Scenes, Tutorials, and Educators' Pages

All pages in Proteopedia are educational, but some have been designed by teachers (instructors, professors, educators) specifically as slides for projection to illustrate lectures, or as tutorials for classroom use. Below is a list of such pages. Note that pages by students are listed separately at Student Projects.

To Search this page, use your browser's Find function (Windows: Ctrl-F; Mac: Cmd-F). For a more extensive listing than this page, see Proteopedia:Structure Index.

Pages created within a User: domain are protected from edits by others, but their contents may be freely copied and adapted into other pages in Proteopedia, see Help:Page Type.

Pages by Educators

Concepts

See a longer list at About Macromolecular Structure which includes topics of a more technical nature.

• Basics of Protein Structure introduces primary, secondary, tertiary and quaternary structure at an advanced high school or introductory college level.

• Backbone representations introduces standard ways of simplifying the main chain of proteins interactively in JSmol.

• Bonds, non-covalent: see Hydrogen bonds, Salt bridges, Cation-pi interactions.

• Chains. Many students have difficulty explaining what is a macromolecular "chain" and what are its properties. This page will help.

• Four levels of protein structure: slides illustrating primary, secondary, tertiary, and quaternary structure levels. Also in Spanish: Los cuatro niveles estructurales de las proteínas.

• Intrinsically Disordered Protein

• Evolutionary Conservation, Introduction to explains conservation and variation using Rett's Syndrome as an extreme example, multiple sequence alignments and coloring proteins by conservation (ConSurf) using enolase as an example.

• Molecular Visualization, Introduction to: introduces atomic representations (ball and stick, stick, spacefilling), slabbing, backbone representations, disulfide bond representations, and common color schemes.

• Introduction to Protein Structure--a basic introduction to protein structure and includes questions and measurements for students to consider.

• Ozonolysis an example of a chemical reaction.

• Ramachandran Principle and Phi/Psi Angles. This page list several tutorials, some in Spanish. One of the tutorials is available as a narrated YouTube video, and as a slideshow in English or Spanish.

• Readout of DNA minor groove shape is the molecular basis for Hox specificity

• Resolution What is the meaning of resolution in an X-ray structure determination?

• Rossmann fold featured in Biochemistry and Molecular Biology Education.

• Standard Residues and Non-Standard Residues: amino acids and nuceotides.

• Structural templates -- an introductory tutorial on protein structures

• Thermal motion of peptide

Molecules

Within Proteopedia

Many of these pages have been Featured in Biochemistry and Molecular Biology Education.

• Acetylcholinesterase

• Avian Influenza Neuraminidase, Tamiflu and Relenza

• Collagen

• Cytochromes: Drug Metabolism by CYP450 Enzymes A tutorial on the medicinal chemistry of drug metabolism for pharmacy students

• Dipeptidyl peptidase IV

• DNA

• Glutamine synthetase: User:Tom Gluick/glutamine synthetase (University of Maryland, Baltimore County). Includes instructions for using Jmol commands in the Jmol console for advanced scene authoring.

• G protein, ras oncogene: James_D_Watson/Proteins_Intro. (European Bioinformatics Institute.)
• Lac repressor: Introduction, structure, morph of the conversion from non-specific to specific DNA binding, and questions to challenge your understanding.

• Gramicidin Channel in Lipid Bilayer, also in Spanish, Canal de gramicidina en bicapa lipídica. Dramatic illustration of water passing through this channel in a lipid bilayer.

• Hemoglobin
  • See also external Hemoglobin.MolviZ.Org which has challenge questions and a practice quiz.
  • Tutorial:How do we get the oxygen we breathe? for high school students and beginning college students, featured in Biochemistry and Molecular Biology Education.
  • ¿Cómo conseguimos el oxígeno que respiramos?

• HMG-CoA Reductase featured in Biochemistry and Molecular Biology Education.

• Hoogsteen base pairs modulate shape of p53-DNA binding site

• Immunodeficiency virus protease

• Keratins featured in Biochemistry and Molecular Biology Education.

• Neurotensin receptor featured in Biochemistry and Molecular Biology Education.

• Nucleosomes: User:Eric Martz/Nucleosomes: Slides of nucleosome structure designed for, and used in, the majors' biochemistry class (Biochm 524). The same slides were copied into the non-protected page Nucleosomes, where they are freely editable (and the color scheme was improved). (University of Massachusetts, Amherst MA US)

• Pharmaceutical Drugs

• Pharmaceutical Drug Targets and Diseases

• Prion protein

• RNA Polymerase, bacterial, beta-prime subunit

• Ribosome

• Ribosome, large subunit, haloarcula featured in Biochemistry and Molecular Biology Education.

• Phosphoinositide 3-Kinases featured in Biochemistry and Molecular Biology Education.

• Protein Kinsase Catalytic Domain, Eukaryotic

• Recoverin, a calcium-activated myristoyl switch with morph animations.

• Ricin featured in Biochemistry and Molecular Biology Education.

• Serine Proteases A Tutorial of Chymotrypsin, Trypsin and Elastase by User:Amy Kerzmann

External to Proteopedia

• Atlas of Macromolecules with links to view each molecule in Proteopedia or FirstGlance in JSmol.

• BioModel: interactive exploration in JSmol of carbohydrates, lipids, vitamins, proteins, and nucleic acids. English or Spanish or several other languages.

• DNA Structure, a non-linear JSmol tutorial in English, Spanish, and many other languages. Includes quiz questions for students of various ages.

• Hemoglobin Structure, a JSmol tutorial with thought-provoking questions and a Practice Quiz in Proteopedia. Includes secondary structure, amphipathic alpha helices, regulation of oxygen binding with animations, and sickle hemoglobin.

• Water: hydrogen bonds, liquid, ice. Includes an animation and a quiz. English or Spanish.

Syllabi

You are free to copy and adapt syllabi in Proteopedia. See Terms of Service and licenses linked at the bottom of this page.

• User:Eric Martz/Introduction to Structural Bioinformatics Syllabi and report assignments for assessment for undergraduate college students and graduate student groups.

• Protein Structure for Biosci 203, emphasizing secondary structure and an active site: User:J. Shaun Lott/BIOSCI 203. (Univ. Auckland, NZ.)

• Introduction to Proteopedia and Authoring Pages for a work session for Chemistry 791 - Biomolecular Structure (University of Massachusetts at Amherst) so they could do their end-of-the-semester presentations on the protein of their choice using Proteopedia.

• Introduction to Molecular Visualization and Proteopedia Workshop for two two-hour sessions for Biochemistry 642 Advanced Molecular Biology at the University of Massachusetts, Amherst MA US. Students were assigned problem sets that required authoring accompanying scenes in sandbox pages. November, 2009.

Quizzes

• Hemoglobin Quiz

• Ramachandran Principle Quiz

Art

• Proteopedia pages featuring artistic representations of macromolecules, etc. will be found under Art.

Molecule of the Month (MotM) Series

The Molecule of the Month series of tutorials by David Goodsell offers a wealth of molecular structure information, beautifully explained and illustrated, for student and educators. Beginning with the August, 2008 molecule, Goodsell has begun writing Proteopedia pages to complement his articles. For a complete list of Proteopedia pages in this Category see RCSB PDB Molecule of the Month.

See Also

Many excellent educational pages with contributions from students, listed at Student Projects.

• Molecule of the Month
• Student Projects has many excellent educational pages on specific molecules.
• Proteopedia:Structure Index for an extensive list of human-authored articles on specific molecules.
• Adoptions in University Classes
• Teaching Strategies Using Proteopedia
• High school teachers' resources
• Proteopedia:Primer, a guide for teachers making a page in Proteopedia for the first time.
• Molecular modeling and visualization software
• Help:Quiz offers help on how to set up quizzes in Proteopedia.
• Molecular Sculpture

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz, Jaime Prilusky, Wayne Decatur, Eran Hodis, Joel L. Sussman, Ann Taylor, Arthur Cox, Karl Oberholser