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Amino acid displays a free amino group in the peptide

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Dear OTA,
I have 2 multiple questions as attached. I have done those but have some doubts. The questions are in red and my answer is in black.

Need to get explanation why the option B in #61 is wrong (heavy references) and why option A in #53 is wrong (also references)
Basically I need to know why only 1 option is good for each question.

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Solution Preview

For the first question, the correct answer is alanine.

Gln doesn't have a free amino group. It has an amide group.
Arg doesn't have a free amino group either. It has a very complex functional group.
Ser has no NH2 group at all. The only NH2 group it has will be bound up in the peptide ...

Solution Summary

The expert examines amino acid displaying a free amino group in the peptide. An explanation of these options are determined.

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Amino Acid Problems

(See attached file for full problem description)

9. An organism of unknown origin produces a potent inhibitor of nerve conduction which you wish to sequence. Amino acid analysis shows the peptide's composition to be 5 Ala, 1 Lys, 1 Phe. Reaction of the intact peptide with phenylisothiocyanate (Edman's reagent) followed by treatment with trifluoroacetic acid liberates a phenylthiohydantoin (PTH)-derivative of alanine. Trypsin cleavage of the intact peptide gives a tripeptide and a tetrapeptide, with compositions 3 Ala, 1 Phe and 1 Lys, 2 Ala. Reaction of the intact peptide with chymotrypsin yields a hexapeptide plus free alanine. What is the inhibitor's sequence? (Justify your answer by explaining how each treatment would produce the observed products.)

10. A solution which contains a mixture of three tripeptides -- 1) Tyr-Lys-Thr, 2) Asp-Met-Ala, and 3) Asp-Cys-Arg -- is spotted in the middle of three strips of filter paper. Each strip is then subjected to paper electrophoresis at a different pH: 2.0, 6.0, and 13.0. Sketch the patterns of separation you would expect for these tripeptides at each of these pHs, indicating their positions relative to one another and to the anode (i.e., + electrode), spot of application (i.e., origin), and cathode (i.e., - electrode). See Table 4.1 in the Garrett and Grisham text for pKas. Hint: the separation is based on the net charge carried by the peptides.

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