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User:Kasha Maslowski/Sandbox 2
From Proteopedia
< User:Kasha Maslowski(Difference between revisions)
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| - | <StructureSection load='' size=' | + | <StructureSection load='' size='600' side='right' caption='Just a little droplet of water' scene='82/822541/Water_droplet/2'> |
==Instructions== | ==Instructions== | ||
| - | + | Wait for the 3D representation of a droplet of water to load to the right. Once it has loaded, practice interacting with the model. The following instruction were written using a Chromebook, but will will most likely work on any device with a track pad. | |
| - | <scene name='82/822541/Water_droplet/2'> | + | *Click and hold the trackpad with one finger while dragging across the trackpad to rotate the 3D model. |
| + | *Trace two fingers at once across the trackpad to zoom in and out. | ||
| + | *Clicking the popup button will open a popup window of the 3D model that you can resize. | ||
| + | |||
| + | When you are ready, click on the unknown molecules below. It may take a moment for the model to load. If at any time you would like to see the water droplet model again | ||
| + | <scene name='82/822541/Water_droplet/2'>click here to reload it.</scene><ref name="angel">Herráez, Angel, and Michael Bruist. “Intermolecular Hydrogen Bonds in Liquid Water and in Ice.” Structure of Water and Ice, biomodel.uah.es/en/water/p1.htm | [http://biomodel.uah.es/en/water/p1.htm]</ref> | ||
==Set of Unknown Molecules== | ==Set of Unknown Molecules== | ||
| + | |||
| + | The models in the table below are a random assortment of different biologically important molecules. Please note that molecules highlighted in yellow have many more repeated units than what is shown in the models. Molecule C as shown has two separate subunits, | ||
{| class="wikitable" | {| class="wikitable" | ||
|- | |- | ||
| - | | <scene name='82/822541/Molecule_a/2'>Molecule A</scene> | + | | style="background-color:#fcff2f;" | <scene name='82/822541/Molecule_a/2'>Molecule A</scene><ref name="porto">Molecular models in this page were created or modified from [[PDB files]] by [[User:Alejandro Porto|Alejandro Porto]] using the tool JSME Molecular Editor [http://biomodel.uah.es/en/DIY/JSME/draw.es.htm]</ref> |
| - | |<scene name='82/822541/Molecule_b/1'>Molecule B</scene> | + | | <scene name='82/822541/Molecule_b/1'>Molecule B</scene><ref name="porto" /> |
| - | |<scene name='82/822541/Molecule_c/ | + | | <scene name='82/822541/Molecule_c/14'>Molecule C</scene> |
| - | | <scene name='82/822541/ | + | | <scene name='82/822541/Molecule_d2/1'>Molecule D</scene> |
|- | |- | ||
| - | | <scene name='82/822541/Molecule_e/1'>Molecule E</scene> | + | | style="background-color:#fcff2f;" | <scene name='82/822541/Molecule_e/1'>Molecule E</scene> |
| <scene name='82/822541/Molecule_f/1'>Molecule F</scene> | | <scene name='82/822541/Molecule_f/1'>Molecule F</scene> | ||
| - | | <scene name='82/822541/Molecule_g/1'>Molecule G</scene> | + | | <scene name='82/822541/Molecule_g/1'>Molecule G</scene><ref name="porto" /> |
| - | | <scene name='82/822541/Molecule_h/1'>Molecule H</scene> | + | | style="background-color:#fcff2f;" | <scene name='82/822541/Molecule_h/1'>Molecule H</scene><ref name="porto" /> |
|- | |- | ||
| <scene name='82/822541/Molecule_i/1'>Molecule I</scene> | | <scene name='82/822541/Molecule_i/1'>Molecule I</scene> | ||
| - | | | + | | style="background-color:#fcff2f;" | <scene name='82/822541/Molecule_j3/2'>Molecule J</scene> |
| - | | Molecule K | + | | <scene name='82/822541/Molecule_k/1'>Molecule K</scene> |
| - | | Molecule L | + | | <scene name='82/822541/Molecule_l/1'>Molecule L</scene> |
|- | |- | ||
| - | | Molecule M | + | | <scene name='82/822541/Molecule_m/2'>Molecule M</scene> |
| - | | Molecule N | + | | style="background-color:#fcff2f;" | <scene name='82/822541/Molecule_n/3'>Molecule N</scene><ref name="biot">From Biotopics website[https://www.biotopics.co.uk/jsmol/glycogen.html]</ref> |
| - | | Molecule O | + | | <scene name='82/822541/Molecule_o/1'>Molecule O</scene><ref name="porto" /> |
| - | | Molecule P | + | | <scene name='82/822541/Molecule_p/1'>Molecule P</scene> |
|} | |} | ||
| - | |||
| - | <scene name='82/822541/Molecule_a/2'>Molecule A</scene> | ||
| - | |||
| - | <scene name='82/822541/Molecule_c/11'>Molecule C</scene> | ||
| - | |||
| - | ::<scene name='60/603296/Gliceraldehido/1'>D-gliceraldehyde</scene> molecular structure | ||
| - | |||
| - | ::<scene name='60/603296/Gliceraldehido/2'>L-gliceraldehyde</scene> molecular structure. | ||
| - | |||
| - | ::<scene name='60/603296/Gliceraldehido/3'>Mirror images from each other</scene>. | ||
| - | |||
| - | ::<scene name='60/603296/Glucosa/1'>D-glucose</scene> | ||
| - | |||
| - | ::<scene name='60/603296/Glucopiranosa/10'>carbon C1 and C5 approach</scene> | ||
| - | |||
| - | ::<scene name='60/603296/Glucopiranosa/13'>Pyranose ring</scene>. | ||
| - | |||
| - | ::<scene name='60/603296/Glucopiranosa/9'>α-D-glucopyranose</scene>. | ||
| - | |||
| - | ::<scene name='60/603296/Fructofuranosa/1'>β-D-fructofuranose</scene>. | ||
| - | |||
| - | ::<scene name='60/603296/Glucosamina/1'>D-glucosamine</scene> | ||
| - | |||
| - | ==Disaccharides== | ||
| - | |||
| - | ::<scene name='60/603296/Glucosidico1/1'>2 glucose molecules approach</scene>. | ||
| - | |||
| - | ::<scene name='60/603296/Glucosidico1/3'> 1 water molecule is losed</scene> | ||
| - | |||
| - | ::<scene name='60/603296/Glucosidico2/2'>a glycosidic bond is formed</scene>. | ||
| - | |||
| - | ::<scene name='60/603296/Maltosa/1'>Maltose</scene> shows a α-glycosidic bond | ||
| - | |||
| - | ::<scene name='60/603296/Celobiosa/1'>Cellobiose</scene> shows a β-glycosidic bond, like <scene name='60/603296/Sacarosa/1'>sucrose</scene>. | ||
| - | |||
| - | ==Polysaccharides== | ||
| - | *'''Starch''' | ||
| - | **'''Amylose''' | ||
| - | ::<scene name='60/603296/Amilosa/3'>Maltose (2 residues of glucose)</scene> | ||
| - | |||
| - | ::We add a <scene name='60/603296/Amilosa/4'>3rd</scene>, <scene name='60/603296/Amilosa/5'>4th</scene>, <scene name='60/603296/Amilosa/6'>5th</scene> and <scene name='60/603296/Amilosa/7'>6th</scene> residues. | ||
| - | |||
| - | ::<scene name='60/603296/Amilosa/8'>Activate rotation</scene> to observe helical structure | ||
| - | ::<scene name='60/603296/Amilosa/9'>Zoom out</scene> and adition of more glucose residues to reach a <scene name='60/603296/Amilosa/10'>30 residues</scene> molecule | ||
| - | ::Look from a <scene name='60/603296/Amilosa/11'>polar view</scene>. | ||
| - | **'''Amylopectin'''.- | ||
| - | ::A fragment of ''amylopectin'' including <scene name='60/603296/Amilopectina/1'>5 glucose residues</scene>. | ||
| - | |||
| - | ::Zoom in to show a <scene name='60/603296/Amilopectina/5'>Branch point</scene> | ||
| - | |||
| - | ::<scene name='60/603296/Amilopectina/10'>4 residues at branch point</scene>. | ||
| - | |||
| - | ::By adding to <scene name='60/603296/Amilopectina/12'>initial structure</scene> 25 glucose residues we get a <scene name='60/603296/Amilopectina2/1'>30 residues amylopectin fragment</scene>. | ||
| - | |||
| - | ::<scene name='60/603296/Amilopectina/13'>Zoom out</scene> to show that branch points are spaced by 24-30 glucose residues. | ||
| - | |||
| - | *<scene name='60/603296/Glucogeno/1'>Glycogen</scene>.- Structure like ''amylopectin'' but with branch points spaced by 8-12 glucsoe residues. | ||
| - | |||
| - | *'''Cellulose'''.- | ||
| - | ::<scene name='60/603296/Celulosa/1'>Cellobiose (2 glucose residues)</scene> | ||
| - | |||
| - | ::<scene name='60/603296/Celulosa/2'>Zoom out</scene> | ||
| - | |||
| - | ::We add a <scene name='60/603296/Celulosa/3'>3rd</scene>, a <scene name='60/603296/Celulosa/4'>4th</scene>, a <scene name='60/603296/Celulosa/5'>5th</scene> and a <scene name='60/603296/Celulosa/6'>6th</scene> glucose residue to show the <scene name='60/603296/Celulosa/7'>helical structure</scene> of ''cellulose'' molecule (more extended that the ''amylose'' one). | ||
| - | |||
| - | ::<scene name='60/603296/Celulosa/8'>Zoom out</scene> and adition of new residues to complete a <scene name='60/603296/Celulosa/9'>30 residuos cellulose fragment</scene>. | ||
| - | |||
| - | ::Look from a <scene name='60/603296/Celulosa/10'>polar view</scene> | ||
| - | |||
| - | *<scene name='60/603296/Quitina/6'>Chitin</scene>.- A polymer of <scene name='60/603296/Quitina/4'>β-N-acetil-D-glucosamina</scene>. | ||
| - | ::A <scene name='60/603296/chitin/2'>3 residues</scene> chitin fragment. | ||
| - | *<scene name='60/603296/Hialuron/2'>Hyaluronic acid</scene>.- ''Heteropolysaccharide'' with alternating residues of <scene name='60/603296/Quitina/4'>β-N-acetil-D-glucosamine</scene> and <scene name='60/603296/Glucuronico/1'>glucuronic acid</scene> | ||
</StructureSection> | </StructureSection> | ||
== References == | == References == | ||
| - | *Molecular models in this page were created or modified from [[PDB files]] by [[User:Alejandro Porto|Alejandro Porto]] using the tool JSME Molecular Editor [http://biomodel.uah.es/en/DIY/JSME/draw.es.htm] | ||
<references/> | <references/> | ||
Current revision
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References
- ↑ Herráez, Angel, and Michael Bruist. “Intermolecular Hydrogen Bonds in Liquid Water and in Ice.” Structure of Water and Ice, biomodel.uah.es/en/water/p1.htm | [1]
- ↑ 2.0 2.1 2.2 2.3 2.4 Molecular models in this page were created or modified from PDB files by Alejandro Porto using the tool JSME Molecular Editor [2]
- ↑ From Biotopics website[3]
