User:Stephen Mills/Peptide tutorial 1: Difference between revisions
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== Biochemistry Tutorial #1 - Peptides == | == Biochemistry Tutorial #1 - Peptides Pt. 1== | ||
The alpha amino acids polymerize, or bond, through the elimination of a water molecule. Polymers composed of two amino acid residues are known as dipeptides. Longer polymers are called oligopeptides (up to around 20 amino acids) or polypeptides (> 20 amino acids). Proteins can contain any number of amino acids linked together but each has a unique length (number of amino acids) and sequence (the identity and order of amino acids in the polymer). | The alpha amino acids polymerize, or bond, through the elimination of a water molecule. Polymers composed of two amino acid residues are known as dipeptides. Longer polymers are called oligopeptides (up to around 20 amino acids) or polypeptides (> 20 amino acids). Proteins can contain any number of amino acids linked together but each has a unique length (number of amino acids) and sequence (the identity and order of amino acids in the polymer). | ||
In this excercise, you will identify amino acids, the amino and carboxy groups involved in the peptide bond, look at peptide bonds and oligopeptide structure and finally also examine disulfide bonds. | In this excercise, you will identify amino acids, the amino and carboxy groups involved in the peptide bond, look at peptide bonds and oligopeptide structure and finally also examine disulfide bonds. | ||
==Which amino acid is this?== | ==Which amino acid is this?== | ||
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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' name='Arg_labels'/> | |||
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This is Arginine (Arg, R) and amino acid with a positively charged side chain. | |||
Identify the α-amino and α-carboxy groups involved in peptide bond formation. | |||
<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='Tyrosine.pdb' size='300' frame='true' align='left' caption=' ' scene='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Tyrosine/1' /> | |||
<big>'''Name the new amino acid.'''</big> | |||
Scroll down to get the answer | |||
<br/> | |||
<br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/> | |||
<br/><br/><br/><br/><br/><br/><br/> | |||
= = | = = | ||
<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 | |||
Again, identify the amino and carboxy groups involved in peptide bond formation. | |||
<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/> | |||
==Alpha Carbons== | |||
Now here are both structures. | |||
Identify the α-carbons on each amino acid. | |||
<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' 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' 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. | |||
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==Dipeptides== | |||
Identify the main chain groups and side chains of this dipeptide. | |||
Distinguish which end is the amino terminus and which amino acid is at the carboxyl 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' name='ArgTyr'/> | |||
<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' target='ArgTyr'>Click here to label the two amino acids.</scene> | |||
Scroll down for more. | |||
<Structure load='ArgTyr.pdb' size='500' frame='true' align='left' caption='' scene='User:Stephen_Mills/Peptide_tutorial_1/Argtyraalabels/2' name='ArgTyrAmide'/> | |||
Notice that the Arginine is on the amino terminal end and the Tyrosine is on the carboxy terminal end. | |||
The short way to name this dipeptide is: <big>'''Arg-Tyr'''</big> or <big>'''RY'''</big> | |||
<br/><br/><br/> | |||
Identify the atoms involved in the peptide bond between Tyrosine and Arginine | |||
<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. | |||
<br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/> | |||
==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. | |||
[[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.]] | |||