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User:Stephen Mills/Peptide tutorial 2: Difference between revisions

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Identify each amino acid in this dipeptide.
Identify each amino acid in this dipeptide.
<Structure load='CysAsp3.pdb' size='400' frame='true' align='left' caption='Second Dipeptide' scene='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Cysaspstart/1' />
<Structure load='CysAsp3.pdb' size='400' frame='true' align='left' caption='Second Dipeptide' scene='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Cysaspstart/1' name='CysAsp'/>


What is the short-hand notation for this dipeptide?
What is the short-hand notation for this dipeptide?


<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Cysasplabels/2'>Click here to show the labels on each amino acid.</scene>
<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Cysasplabels/2' target='CysAsp'>Click here to show the labels on each amino acid.</scene>


Identify which amino acid is at the N-terminus and which is at the C-terminus.
Identify which amino acid is at the N-terminus and which is at the C-terminus.


<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Cysasptermini/1'>Click here to label each terminus.</scene>
<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Cysasptermini/1' target='CysAsp'>Click here to label each terminus.</scene>


Identify the α carbons of each amino acid.
Identify the α carbons of each amino acid.


<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Cysaspalphas/1'>Click here to have them highlighted.</scene>
<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Cysaspalphas/1' target='CysAsp'>Click here to have them highlighted.</scene>


Identify the atoms involved in the peptide bond in this dipeptide.
Identify the atoms involved in the peptide bond in this dipeptide.


<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Cysaspamide/1'>Click here to have those atoms change color.</scene>
<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Cysaspamide/1' target='CysAsp'>Click here to have those atoms change color.</scene>


Now, measure the distance between the α carbons.
Now, measure the distance between the α carbons.
<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Cysaspmeasure/1'>Click here to get a good starting configuration.</scene>
<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Cysaspmeasure/1' target='CysAsp'>Click here to get a good starting configuration.</scene>


To measure a distance, Double click on the first atom, then double click on the second atom. You may need to rotate the molecule a bit to see the distance well. Try it now.
To measure a distance, Double click on the first atom, then double click on the second atom. You may need to rotate the molecule a bit to see the distance well. Try it now.
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Now you are ready to work with oligopeptides, or polymers composed of 3-20 amino acid residues. These polymers are linear; that is, each amino acid is linked to it's neighbor in a head-to-tail fashion rather than forming branched chains. You will be observing a 5mer in this tutorial.
Now you are ready to work with oligopeptides, or polymers composed of 3-20 amino acid residues. These polymers are linear; that is, each amino acid is linked to it's neighbor in a head-to-tail fashion rather than forming branched chains. You will be observing a 5mer in this tutorial.


<Structure load='GDCRY.pdb' size='500' frame='true' align='left' caption='' scene='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Pentapeptide_start/1' />
<Structure load='GDCRY.pdb' size='500' frame='true' align='left' caption='' scene='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Pentapeptide_start/1' name='penta'/>


For this part, you may need to resize and move the molecule around. To remind you:<br/>
For this part, you may need to resize and move the molecule around. To remind you:<br/>
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'''Identify where Y and R are located in this oligopeptide.'''
'''Identify where Y and R are located in this oligopeptide.'''


<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Pentapeptide_yr/2'>Click here to have Y and R colored purple.</scene>
<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Pentapeptide_yr/2' target='penta'>Click here to have Y and R colored purple.</scene>


Notice that the NH of Y is bonded to the carbonyl of R.
Notice that the NH of Y is bonded to the carbonyl of R.
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'''Identify where C and D are located in this peptide.'''
'''Identify where C and D are located in this peptide.'''
<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Pentapeptide_cd/2'>
<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Pentapeptide_cd/2' target='penta'>
Click here to have C and D colored purple.</scene>
Click here to have C and D colored purple.</scene>


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You will probably need to move the molecule around and rotate it to see the whole structure.
You will probably need to move the molecule around and rotate it to see the whole structure.


When you write it down, it will spell out a question.
When you write down the sequence in the one letter codes, it will spell out a question.


'''Submit the sequence of the peptide '''''and''''' the answer to the question'''
'''Submit the sequence of the peptide '''''and''''' the answer to the question'''
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'''Congratulations! You have just finished the first Biochemistry Tutorial'''
'''Congratulations! You have just finished the first Biochemistry Tutorial'''
[[User:Stephen_Mills/Biochemistry_Tutorials|Click here to go back to the main Tutorial page.]]
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