User:Stephen Mills/Peptide tutorial 2
Peptide 2:
Let's look at another dipeptide.
Identify each amino acid in this dipeptide.
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What is the short-hand notation for this dipeptide?
Click here to show the labels on each amino acid.
Identify which amino acid is at the N-terminus and which is at the C-terminus.
Click here to label each terminus.
Identify the α carbons of each amino acid.
Click here to have them highlighted.
Identify the atoms involved in the peptide bond in this dipeptide.
Click here to have those atoms change color.
Now, measure the distance between the α carbons. Click here to get a good starting configuration.
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.
