User:Stephen Mills/Peptide tutorial 1: Difference between revisions
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Scroll down when you know what it is. | Scroll down when you know what it is. | ||
''Note: in these tutorials, the images are 3D interactive images. You can manipulate them as you wish to get a better view of the molecules.'' | |||
You can rotate the amino acid by holding down the right mouse button and dragging. | You can rotate the amino acid by holding down the right mouse button and dragging. | ||
Other things you can do: | |||
::To rotate: left drag | |||
::To Zoom: scroll button or shift + left drag | |||
::To Translate: ctrl + right drag | |||
::Right click to bring up an options menu | |||
<br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/> | |||
= = | = = | ||
<Structure load='Arginine.pdb' size='300' frame='true' align='left' caption='' scene='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Arginine/3' /> | <Structure load='Arginine.pdb' size='300' frame='true' align='left' caption='' scene='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Arginine/3' name='Arg_labels'/> | ||
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<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Argininelabels/1'>Click here to see the N and C groups labelled.</scene> | <scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Argininelabels/1' target='Arg_labels'>Click here to see the N and C groups labelled.</scene> | ||
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== == | == == | ||
<Structure load=' | <Structure load='Tyrosine.pdb' size='300' frame='true' align='left' caption=' ' scene='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Tyrosine/1' /> | ||
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<Structure load=' | <Structure load='Tyrosine.pdb' size='300' frame='true' align='left' caption=' ' scene='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Tyrosine/1' name='Tyr_labels'/> | ||
This is Tyrosine (Tyr, Y), an aromatic amino acid | This is Tyrosine (Tyr, Y), an aromatic amino acid | ||
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Again, identify the amino and carboxy groups involved in peptide bond formation. | Again, identify the amino and carboxy groups involved in peptide bond formation. | ||
<scene name='User:Stephen_Mills/ | <scene name='User:Stephen_Mills/Peptide_tutorial_1/Tyrosinelabels/1' target='Tyr_labels'>Click here to have the N and C groups labeled.</scene> | ||
<br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/> | <br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/> | ||
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<Structure load='Arginine.pdb' size='300' frame='true' align='left' caption='Arginine' scene='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Arginine/3' /> | <Structure load='Arginine.pdb' size='300' frame='true' align='left' caption='Arginine' scene='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Arginine/3' name='Arg_alpha'/> | ||
<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Argininealpha/2'>Click here</scene> to label the α-carbon on Arginine. | <scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Argininealpha/2' target='Arg_alpha'>Click here</scene> to label the α-carbon on Arginine. | ||
<Structure load='Tyrosine.pdb' size='300' frame='true' align='right' caption='Tyrosine' scene='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Tyrosine/1' /> | <Structure load='Tyrosine.pdb' size='300' frame='true' align='right' caption='Tyrosine' scene='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Tyrosine/1' name='Tyr_alpha'/> | ||
<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Tyrosinealpha/2'>Click here</scene> to label the α-carbon on Tyrosine. | <scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Tyrosinealpha/2' target='Tyr_alpha'>Click here</scene> to label the α-carbon on Tyrosine. | ||
<br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/> | <br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/> | ||
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Which amino acid is at the N terminus? Which is at the C terminus? | Which amino acid is at the N terminus? Which is at the C terminus? | ||
<Structure load='ArgTyr.pdb' size='500' frame='true' align='left' caption='' scene='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Argtyr/1' /> | <Structure load='ArgTyr.pdb' size='500' frame='true' align='left' caption='' scene='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Argtyr/1' name='ArgTyr'/> | ||
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<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Argtyrtermini/1'>Click here to label the N and C termini.</scene> | <scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Argtyrtermini/1' target='ArgTyr'>Click here to label the N and C termini.</scene> | ||
<scene name='User:Stephen_Mills/ | <scene name='User:Stephen_Mills/Peptide_tutorial_1/Argtyraalabels/2' target='ArgTyr'>Click here to label the two amino acids.</scene> | ||
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<Structure load='ArgTyr.pdb' size='500' frame='true' align='left' caption='' scene='User:Stephen_Mills/ | <Structure load='ArgTyr.pdb' size='500' frame='true' align='left' caption='' scene='User:Stephen_Mills/Peptide_tutorial_1/Argtyraalabels/2' name='ArgTyrAmide'/> | ||
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<scene name='User:Stephen_Mills/ | <scene name='User:Stephen_Mills/Peptide_tutorial_1/Argtyramide/3' target='ArgTyrAmide'>Click here to change the color of those atoms to purple.</scene> | ||
Peptide bonds almost always assume the trans conformation: that in which successive alpha carbon atoms are on opposite sides of the peptide (C-N) bond joining them. <scene name='User:Stephen_Mills/ | Peptide bonds almost always assume the trans conformation: that in which successive alpha carbon atoms are on opposite sides of the peptide (C-N) bond joining them. <scene name='User:Stephen_Mills/Peptide_tutorial_1/Argtyrtransamide/3' target='ArgTyrAmide'>Click here to show this trans bond.</scene> The exception are peptide bonds involving proline (when P is on the C-terminal side of the bond) - these can be trans or cis. | ||
<br/><br/><br/><br/><br/><br/> | <br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/> | ||
==Backbone Atoms== | ==Backbone Atoms== | ||
<Structure load='ArgTyr.pdb' size='500' frame='true' align='left' caption='' scene='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Argtyr/1' /> | <Structure load='ArgTyr.pdb' size='500' frame='true' align='left' caption='' scene='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Argtyr/1' name='ArgTyrBackbone'/> | ||
If the R groups (side chains) of the amino acids are no longer displayed, then you will be looking at the backbone of the dipeptide. <scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Argtyrbackbone/1'>Click here to turn off the side chains.</scene> | If the R groups (side chains) of the amino acids are no longer displayed, then you will be looking at the backbone of the dipeptide. <scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Argtyrbackbone/1' target='ArgTyrBackbone'>Click here to turn off the side chains.</scene> | ||
This dipeptide has a completely extended conformation. | This dipeptide has a completely extended conformation. | ||
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Click here to go on to the next part of this tutorial. | [[User:Stephen Mills/Peptide tutorial_2|Click here to go on to the next part of this tutorial.]] | ||
[[User:Stephen_Mills/Biochemistry_Tutorials|Click here to go back to the main Tutorial page.]] | |||