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Transcript
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