User:Stephen Mills/Peptide tutorial 1: Difference between revisions
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Biochemistry Tutorial #1 - Peptides Pt. 1
Which amino acid is this?
Alpha Carbons
Dipeptides
Backbone Atoms
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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. | |||
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' /> | <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' target='Arg_labels'>Click here to see the N and C groups labelled.</scene> | |||
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== == | == == | ||
<Structure load=' | <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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Scroll down to get the answer | 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/> | |||
= = | = = | ||
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<Structure load=' | <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/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/> | |||
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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' 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. | |||
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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'/> | |||
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<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. | |||
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<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. | |||
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[[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.]] | |||
Latest revision as of 07:31, 21 August 2014
Biochemistry Tutorial #1 - Peptides Pt. 1Biochemistry 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).
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?
|
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
|
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.
|
Name the new amino acid.
Scroll down to get the answer
|
This is Tyrosine (Tyr, Y), an aromatic amino acid
Again, identify the amino and carboxy groups involved in peptide bond formation.
Alpha CarbonsAlpha Carbons
Now here are both structures. Identify the α-carbons on each amino acid.
|
to label the α-carbon on Arginine.
|
to label the α-carbon on Tyrosine.
DipeptidesDipeptides
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?
|
Scroll down for more.
|
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: Arg-Tyr or RY
Identify the atoms involved in the peptide bond between Tyrosine and Arginine
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. 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 AtomsBackbone Atoms
|
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.
This dipeptide has a completely extended conformation.
Rotate the molecule and you should notice how planar the peptide bond is.