User:Stephen Mills/Peptide tutorial 1: Difference between revisions
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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/Peptide_tutorial_1/Argtyraalabels/2'>Click here to label the two amino acids.</scene> | <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/Peptide_tutorial_1/Argtyraalabels/2' /> | <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/Peptide_tutorial_1/Argtyramide/3'>Click here to change the color of those atoms to purple.</scene> | <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'>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. | 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/><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. | ||
