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: | For this part, you may need to resize and move the molecule around. To remind you:<br/> | ||
To Rotate: left drag | To Rotate: left drag<br/> | ||
To Zoom: scroll button or shift + left drag | 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). | 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.''' | '''Identify where Y and R are located in this oligopeptide.''' | ||
<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Pentapeptide_yr/ | <scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Pentapeptide_yr/2'>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/ | <scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Pentapeptide_cd/2'> | ||
Click here to have C and D colored purple.</scene> | 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. | 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.''' | '''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.''' | '''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/> | <br/><br/><br/><br/><br/><br/><br/><br/> | ||
==Last Part!!== | |||
Now a test peptide. | |||
'''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 it down, 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''' | |||
