User:Stephen Mills/Peptide tutorial 1 - Revision history

Stephen Mills: /* Backbone Atoms */

2014-08-21T04:31:01Z

Backbone Atoms

← Older revision		Revision as of 04:31, 21 August 2014
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	==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.

Stephen Mills: /* Dipeptides */

2014-08-21T04:29:41Z

Dipeptides

← Older revision		Revision as of 04:29, 21 August 2014
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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/>

Stephen Mills: /* Alpha Carbons */

2014-08-21T04:25:00Z

Alpha Carbons

← Older revision		Revision as of 04:25, 21 August 2014
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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/>

Stephen Mills at 04:22, 21 August 2014

2014-08-21T04:22:32Z

← Older revision		Revision as of 04:22, 21 August 2014
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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>

	<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/>

Stephen Mills: Undo revision 1974084 by Stephen Mills (Talk)

2014-08-21T03:54:35Z

Undo revision 1974084 by Stephen Mills (Talk)

← Older revision		Revision as of 03:54, 21 August 2014
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	<scene name='User:Stephen_Mills/~~Peptide_tutorial_1~~/Argininelabels/1'>Click here to see the N and C groups labelled.</scene>		<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Argininelabels/1'>Click here to see the N and C groups labelled.</scene>

Stephen Mills: Undo revision 1974085 by Stephen Mills (Talk)

2014-08-21T03:54:06Z

Undo revision 1974085 by Stephen Mills (Talk)

← Older revision		Revision as of 03:54, 21 August 2014
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	==Which amino acid is this?==		==Which amino acid is this?==

	<Structure load='Arginine.pdb' size='300' frame='true' align='left' caption='' scene='User:Stephen_Mills/~~Peptide_tutorial_1~~/Arginine/3' />		<Structure load='Arginine.pdb' size='300' frame='true' align='left' caption='' scene='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Arginine/3' />

	Scroll down when you know what it is.		Scroll down when you know what it is.

Stephen Mills: Undo revision 1974086 by Stephen Mills (Talk)

2014-08-21T03:53:47Z

Undo revision 1974086 by Stephen Mills (Talk)

← Older revision		Revision as of 03:53, 21 August 2014
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	<Structure load='Arginine.pdb' size='300' frame='true' align='left' caption='' scene='User:Stephen_Mills/Peptide_tutorial_1/Arginine/3' />		<Structure load='Arginine.pdb' size='300' frame='true' align='left' caption='' scene='User:Stephen_Mills/Peptide_tutorial_1/Arginine/3' />

	~~<scene name='45/458451/Argininelabel/1'>Click here~~ when ~~you think~~ you know what it is.~~</scene>~~		Scroll down when you know what it is.

Stephen Mills: Undo revision 1974087 by Stephen Mills (Talk)

2014-08-21T03:53:18Z

Undo revision 1974087 by Stephen Mills (Talk)

← Older revision		Revision as of 03:53, 21 August 2014
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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='45/458451/Argininelabel/1' />~~

Stephen Mills at 03:49, 21 August 2014

2014-08-21T03:49:09Z

← Older revision		Revision as of 03:49, 21 August 2014
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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='45/458451/Argininelabel/1' />

Stephen Mills at 03:43, 21 August 2014

2014-08-21T03:43:56Z

← Older revision		Revision as of 03:43, 21 August 2014
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	<Structure load='Arginine.pdb' size='300' frame='true' align='left' caption='' scene='User:Stephen_Mills/Peptide_tutorial_1/Arginine/3' />		<Structure load='Arginine.pdb' size='300' frame='true' align='left' caption='' scene='User:Stephen_Mills/Peptide_tutorial_1/Arginine/3' />

	~~Scroll down~~ when you know what it is.		<scene name='45/458451/Argininelabel/1'>Click here when you think you know what it is.</scene>