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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.
You can rotate the amino acid by holding down the right mouse button and dragging.






''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.


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


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=  =
=  =
<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='Arginine.pdb' size='300' frame='true' align='left' caption=' ' scene='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Tyrosine/1' />
<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='Arginine.pdb' size='300' frame='true' align='left' caption=' ' scene='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Tyrosine/1' />
<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/Sandbox_2_Peptide_tutorial/Tyrosinelabels/1'>Click here to have the N and C groups labeled.</scene>
<scene name='User:Stephen_Mills/Peptide_tutorial_1/Tyrosinelabels/1' target='Tyr_labels'>Click here to have the N and C groups labeled.</scene>


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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 to label the α-carbon on Arginine.</scene>
<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' target='Tyr_alpha'>Click here</scene> to label the α-carbon on Tyrosine.


<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Tyrosinealpha/2'>Click here to label the α-carbon on Tyrosine.</scene>
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==Dipeptides==
==Dipeptides==
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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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Click <scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Argtyrtermini/1'>here</scene> to label the N and C termini.
<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Argtyrtermini/1' target='ArgTyr'>Click here to label the N and C termini.</scene>






Click <scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Argtyraalabels/1'>here</scene> to label the two amino acids.
<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/Sandbox_2_Peptide_tutorial/Argtyr/1' />
<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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The short way to name this dipeptide is: <big>'''Arg-Tyr'''</big> or <big>'''RY'''</big>
The short way to name this dipeptide is: <big>'''Arg-Tyr'''</big> or <big>'''RY'''</big>
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Identify the atoms involved in the peptide bond between Tyrosine and Arginine




Identify the atoms involved in the peptide bond between Tyrosine and Arginine


Click <scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Argtyramide/1'>here</scene> to change the color of those atoms to white.
<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_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.
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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. Click <scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Argtyrtransamide/1'>here</scene> to show this trans bond. The exception are peptide bonds involving proline (when P is on the C-terminal side of the bond) - these can be trans or cis.
==Backbone Atoms==


<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' target='ArgTyrBackbone'>Click here to turn off the side chains.</scene>


This dipeptide has a completely extended conformation.








Rotate the molecule and you should notice how planar the peptide bond is.




==Backbone Atoms==


<Structure load='ArgTyr.pdb' size='500' frame='true' align='left' caption='' scene='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Argtyr/1' />




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>


This dipeptide has a completely extended conformation.






[[User:Stephen Mills/Peptide tutorial_2|Click here to go on to the next part of this tutorial.]]


Rotate the molecule and you should notice how planar the peptide bond is.
[[User:Stephen_Mills/Biochemistry_Tutorials|Click here to go back to the main Tutorial page.]]
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