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Lecture4 - Lecture 4 Background Reading Berg et al Garrett...

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Lecture 4 9/30/11 Background Reading: Berg, et al.: pages 33 – 36 Garrett and Grisham: pages 96 - 100 Segel, Page 94 Outline: Peptide bond formation. Peptides. Complementarity. Neuropeptides. Determining the amino acid composition of a peptide. Amino acid sequence determination. Amino-terminal amino acid determination. Carboxyl-terminal amino acid determination.
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Peptide bond formation Amino acids are linked together in a peptide linkage that links the α - COOH group of one amino acid and the α - amino group of another amino acid. The peptide bond is an amide linkage and the carboxyl and amino groups that make up this linkage can no longer ionize. Small polymers formed by this linkage are called peptides and can range in size from a small dipeptide to about 40 - 60 amino acids. Above that size they are called proteins.
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By convention peptides and proteins are always designated beginning with the amino acid that has a free amino terminal end. The peptide shown on the previous page would be called glycylalanine or GA. Consider a peptide made of four amino acids as follows:
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MDLY
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Peptides Polymers of amino acids. O C CH 3 H 3 N + C H COO - H N C H H COO - CH 3 H 3 N + C H COO - H H 3 N + C H Alanine Glycine + H 2 O + Alanylglycine AG The carboxyl and amino groups involved in the peptide linkage cannot ionize. This dipeptide has only two pka’s: pKa 1 = 3.16 pKa 2 = 8.24 pKa 1 pKa 2 Only the α -amino group of the alanine and the COOH group of glycine are capable of ionizing.
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Peptides can vary: 1) in kind of amino acid 2) amount of each amino acid 3) arrangement of amino acids - Sequence For the dipeptide containing alanine and glycine have only two possibilities in sequence: AG and GA Tripeptide – composed of three amino acids. If each of these amino acids is different from one another, have 6 possible sequences (3 factorial, 3!).
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