View source for 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 [[Help:Protected Pages|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: [[Four levels of protein structure (Spanish)|Los cuatro niveles estructurales de las proteínas]].

* [[Intrinsically Disordered Protein]]

*[[Introduction to Evolutionary Conservation|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.

*[[Introduction to molecular visualization|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.

*[[Dihedral/Index|Ramachandran Principle and Phi/Psi Angles]]. This page list several tutorials, some in Spanish. One of the tutorials is available as a [http://tinyurl.com/RamachandranPrincipleYoutube narrated '''YouTube''' video], and as a slideshow in [http://tinyurl.com/RamachandranPrinciple English] or [http://tinyurl.com/PrincipioRamachandran Spanish].

*[[Group:USC-LCHS|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 [[:Category:Featured in BAMBED|''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 [[:Category:Featured_in_BAMBED|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, [[Gramicidin Channel in Lipid Bilayer (Spanish)|Canal de gramicidina en bicapa lipídica]]. Dramatic illustration of water passing through this channel in a lipid bilayer.

*[[Hemoglobin]]
**See also external [http://hemoglobin.molviz.org 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 [[:Category:Featured in BAMBED|''Biochemistry and Molecular Biology Education]].
**[[Tutorial:How do we get the oxygen we breathe (Spanish)|¿Cómo conseguimos el oxígeno que respiramos?]]

*[[HMG-CoA Reductase]] featured in [[:Category:Featured in BAMBED|''Biochemistry and Molecular Biology Education]].

*[[Group:USC-LCHS|Hoogsteen base pairs modulate shape of p53-DNA binding site]]

*[[Immunodeficiency virus protease]]

*[[Keratins]] featured in [[:Category:Featured in BAMBED|''Biochemistry and Molecular Biology Education]].

*[[Neurotensin receptor]] featured in [[:Category:Featured in BAMBED|''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]]

*[[Beta-Prime Subunit of Bacterial RNA Polymerase|RNA Polymerase, bacterial, beta-prime subunit]]

*[[Ribosome]]

*[[Large Ribosomal Subunit of Haloarcula|Ribosome, large subunit, haloarcula]]  featured in [[:Category:Featured in BAMBED|''Biochemistry and Molecular Biology Education]].

*[[Phosphoinositide 3-Kinases]] featured in [[:Category:Featured in BAMBED|''Biochemistry and Molecular Biology Education]].

*[[Eukaryotic Protein Kinase Catalytic Domain|Protein Kinsase Catalytic Domain, Eukaryotic]]

*[[Recoverin, a calcium-activated myristoyl switch]] with morph animations.

*[[Ricin]] featured in [[:Category:Featured in BAMBED|''Biochemistry and Molecular Biology Education]].

*[[Serine Proteases]] A Tutorial of Chymotrypsin, Trypsin and Elastase by [[User:Amy Kerzmann]]

====External to Proteopedia====

*[http://Atlas.MolviZ.Org 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. [http://biomodel.uah.es/en/inicio.htm English] or [http://biomodel.uah.es/ Spanish] or several other languages.

*[http://DNA.MolviZ.Org DNA Structure], a non-linear JSmol tutorial in English, Spanish, and many other languages. Includes quiz questions for students of various ages.

*[http://Hemoglobin.MolviZ.Org Hemoglobin Structure], a JSmol tutorial with thought-provoking questions and a [[User:Eric_Martz/Hemoglobin_Quiz|Practice Quiz in Proteopedia]]. Includes secondary structure, amphipathic alpha helices, regulation of oxygen binding with animations, and sickle hemoglobin.

*[http://biomodel.uah.es/en/water/index.htm 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.)

*[[User:Wayne Decatur/Chem791A Work Session|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.

*[[User:Wayne Decatur/Biochem642 Molecular Visualization Sessions|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===

*[[User:Eric_Martz/Hemoglobin_Quiz|Hemoglobin Quiz]]

*[[User:Eric_Martz/Ramachandran_Principle_Quiz|Ramachandran Principle Quiz]]

==Art==

*Proteopedia pages featuring artistic representations of macromolecules, etc. will be found under [http://proteopedia.org/wiki/index.php?title=Special%3AAllpages&from=&namespace=212 Art].

==Molecule of the Month (MotM) Series==

The '''[https://pdb101.rcsb.org/motm/motm-by-date Molecule of the Month]''' series of tutorials by [[User:David_S._Goodsell|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 [[:Category:RCSB_PDB_Molecule_of_the_Month|RCSB PDB Molecule of the Month]].

<!-- SINCE THIS TABLE HAS NOT BEEN MAINTAINED SINCE 2009 I AM HIDING IT. ERIC MARTZ JANUARY 2019.

<center><table border="1" cellpadding="5"><tr>
<td>Date</td>
<td>MotM Article</td>
<td>Proteopedia Page</td>

</tr><tr>
<td>June 2009</td>
<td>[http://dx.doi.org/10.2210/rcsb_pdb/mom_2009_06 Vaults]</td>
<td>[[2zuo]],[[2zv4]],[[2zv5]],[[3dkt]],[[2qw7]],[[3bn4]]</td>

</tr><tr>
<td>May 2009</td>
<td>[http://dx.doi.org/10.2210/rcsb_pdb/mom_2009_05 Influenza Neuraminidase]</td>
<td>[[1nn2]],[[3b7e]],[[2hu4]],[[1nca]],[[2bat]],[[3cl0]]</td>

</tr><tr>
<td>April 2009</td>
<td>[http://dx.doi.org/10.2210/rcsb_pdb/mom_2009_04 Oct and Sox Transcription Factors]</td>
<td>[[1gt0]],[[1nkp]],[[2ebt]],[[1o4x]]</td>

</tr><tr>
<td>March 2009</td>
<td>[http://dx.doi.org/10.2210/rcsb_pdb/mom_2009_03 Hydrogenase]</td>
<td>[[2frv]],[[1feh]],[[3dag]],[[3f47]],[[1e08]],[[1hfe]]</td>

</tr><tr>
<td>February 2009</td>
<td>[http://www.pdb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb111_1.html Hydrogenase]</td>
<td>[[1e08]]</td>

</tr><tr>
<td>January 2009</td>
<td>[http://www.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb109_1.html Tobacco Mosaic Virus]</td>
<td>[[2tmv]]</td>
</tr><tr>
<td>October 2008</td>
<td>[http://www.pdb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb106_1.html Poly(A) Polymerase]</td>
<td>[[2q66]]</td>
</tr><tr>
<td>September 2008</td>
<td>[http://www.pdb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb105_1.html Ribonuclease A]</td>
<td>[[1rta]]</td>
</tr><tr>
<td>August 2008</td>
<td>[http://www.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb104_1.html Selenocysteine Synthase]</td>
<td>[[SelB]]</td>
</tr></table></center>-->

==See Also==
<span style="font-size:125%">Many excellent educational pages with contributions from students, listed at [[Student Projects]].</span>

* [http://www.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html 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.
* [[Proteopedia:News#Adoptions in College and University Classes|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]]