User:Stephen Mills/Peptide tutorial 2: Difference between revisions
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<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' /> | ||
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/1'>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/1'> | |||
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.''' | |||
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