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

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Identify each amino acid in this dipeptide.

What is the short-hand notation for this dipeptide?

Click here to show the labels on each amino acid.

<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.

Click here to label each terminus.

<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.

Click here to have them highlighted.

<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.

Click here to have those atoms change color.

<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.

<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.

'''Write down this distance and submit it to your instructor.'''

==Oligopeptides==

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.

For this part, you may need to resize and move the molecule around. To remind you:

To Rotate: left drag

To Zoom: scroll button or shift + left drag

To Translate: ctrl + right drag (On a Mac, this doesn't work in FireFox, but does work in Safari).

'''Identify where Y and R are located in this oligopeptide.'''

<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.

Also notice how the bulky side-chains point away from the backbone of the peptide.

'''Identify where C and D are located in this peptide.'''

Click here to have C and D colored purple.</scene>

Notice how Cysteine's thiol (SH) group points outward from the 5mer backbone at an angle that would allow for the stable formation of the disulfide bond.

'''Identify the remaining amino acid in this peptide.'''

'''Write down the short-hand notation for this pentapeptide, in the correct order from the N-terminus to the C-terminus and submit this to your instructor.'''

==Last Part!!==

Now a test peptide.

'''Identify the sequence of this peptide and submit the answer to your instructor.'''

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

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'''

'''Congratulations! You have just finished the first Biochemistry Tutorial'''

[[User:Stephen_Mills/Biochemistry_Tutorials|Click here to go back to the main Tutorial page.]]

@@ Line 4: / Line 4: @@
 Identify each amino acid in this dipeptide.
-<Structure load='CysAsp3.pdb' size='300' frame='true' align='left' caption='Insert caption here' scene='Insert optional scene name here' />
+<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?
-Click here to show the labels on each amino acid.
+<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.
-Click here to label each terminus.
+<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.
-Click here to have them highlighted.
+<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.
-Click here to have those atoms change color.
+<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.
+<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.
+'''Write down this distance and submit it to your instructor.'''
+<br/><br/><br/><br/><br/><br/><br/><br/><br/><br/>
+==Oligopeptides==
+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' name='penta'/>
+For this part, you may need to resize and move the molecule around. To remind you:<br/>
+To Rotate: left drag<br/>
+To Zoom: scroll button or shift + left drag<br/>
+To Translate: ctrl + right drag (On a Mac, this doesn't work in FireFox, but does work in Safari).<br/>
+'''Identify where Y and R are located in this oligopeptide.'''
+<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.
+Also notice how the bulky side-chains point away from the backbone of the peptide.
+'''Identify where C and D are located in this peptide.'''
+<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>
+Notice how Cysteine's thiol (SH) group points outward from the 5mer backbone at an angle that would allow for the stable formation of the disulfide bond.<br/>
+'''Identify the remaining amino acid in this peptide.'''<br/>
+'''Write down the short-hand notation for this pentapeptide, in the correct order from the N-terminus to the C-terminus and submit this to your instructor.'''
+<br/><br/><br/><br/><br/><br/><br/><br/>
+==Last Part!!==
+Now a test peptide.
+<Structure load='WHENISPIEDAY3.pdb' size='600' frame='true' align='left' caption='' scene='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Test_peptide/1' />
+'''Identify the sequence of this peptide and submit the answer to your instructor.'''<br/>
+You will probably need to move the molecule around and rotate it to see the whole structure.
+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'''
+<br/><br/><br/><br/>
+'''Congratulations! You have just finished the first Biochemistry Tutorial'''
+[[User:Stephen_Mills/Biochemistry_Tutorials|Click here to go back to the main Tutorial page.]]