Download Chapter Twenty-Seven: Amino Acids

CHAPTER TWENTY-SEVEN: AMINO ACIDS
1. Structure (28.1A)
2. Acid/Base properties (28.1B)
a. Zwitterions
b. pKa’s
c. Isoelectric Point definition
3. Twenty -amino acids (Fig 28.2)
4. Synthesis of Amino Acids (28.2)
a. SN2 reaction of ammonia with -haloacid
b. Diethyl acetamidomalonate alkylation, hydrolysis and decarboxylation
5. Peptides (28.5AB)
6. The peptide bond
7. Primary structure
8. Sequencing (28.6)
a. Cleavage
o With aqueous acid at every peptide bond
o With cyanogen bromide BrCN at methionine C terminus
o With chymotripsin at phe, tyr, trp
o With Tripsin at lys, arg
o Using Edman Degradation (28.6B) at N-terminus with S=C=N-Ph
o DNFB to identify N-terminus
b. Separation and Identification of aa fragments
o Gel electrophoresis (high charge density elutes first)
o Ion-exchange chromatography (potential applied at variable pH)
c. By Mass Spectrometry
9. Peptide Synthesis (28.7) (aa1-aa2)
a. Traditional solution synthesis
o Protect N-terminus of aa1
o Common N protecting groups: carbamate esters
o Protect C-terminus of aa2
o Common carboxylate protecting groups: esters
o Join together (with DCC as activator)
b. Merrifield Solid Phase synthesis (28.8)
o Protect N-terminus
o Bond carboxylate of aa2 to solid support (via SN2 with Benzyl
chloride branches)
o Remove N-protection w dilute base
o Rinse solid support
o Add second N-protected amino acid via C-terminus
LEARNING OUTCOMES:
 Identify amino acids.
 Identify the structure of a specific amino acid at a given pH
 Understand the role of protecting groups in Organic synthesis
 Propose a series of reactions to produce a given polypeptide.
 Understand the bonding and non-bonding forces responsible for protein structure.
 Propose a sequence of steps to sequence a polypeptide.
 Given evidence on the results of a polypeptide sequencing experiment, deduce the
primary structure.
 Draw the mechanism for Edman degradation of a peptide using curved arrow
formalism.
 Propose an appropriate laboratory method(s) for the separation and identification of a
protein.
SAMPLE EXAM PROBLEMS:
1. Draw the fragments that would form if the following polypeptide were treated with
chymotripsin:
Phe-Val-Asn-Gln-Tyr-His-Leu-Gly-Ser-His-Leu-Val-Glu-Ala
2. Draw the structure of the amino acid cysteine at pH 8.
3. A heptapeptide containes the amino acids arginine, glycine, isoleucine,
phenylalanine, proline (two residues) and valine.
Treatment of the heptapeptide with trypsin gives arginine and a hepeptide.
Some of the fragments that were obtained by partial hydrolyses of the heptapeptide
are Pro-Phe-Ile, Arg-Gly-Pro, Pro-Phe-Ile-Val and Pro-Pro.
Assign a structure to the heptapeptide.
4. Draw the organic products A, B and C missing from the following reaction sequence.
Include stereochemistry where appropriate:
COOH 2C
O
H
NH3+
Cl
A
NaOH
SOCl2
NH3
B
C