View source for User:Robert Dutnall/Chem331 Tutorial1a

== Biochemistry Tutorial #1 - Peptides (Part 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).

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?==

<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.



''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' />








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'>Click here to see the N and C groups labelled.</scene> 




















== ==
<Structure load='Arginine.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
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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' />

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/Sandbox_2_Peptide_tutorial/Tyrosinelabels/1'>Click here to have the N and C groups labeled.</scene>

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==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' />

<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Argininealpha/2'>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' />

<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Tyrosinealpha/2'>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' />









<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/Peptide_tutorial_1/Argtyraalabels/2'>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' />


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>

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



<scene name='User:Stephen_Mills/Peptide_tutorial_1/Argtyramide/3'>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.
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==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.




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









[[User:Robert Dutnall/Chem331_Tutorial1b|Click here to go on to the next part of this tutorial.]]