lec 5 - BL/CH 401 Lecture #5 Protein Covalent Structure...

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BL/CH 401 Lecture #5 Protein Covalent Structure (Protein Primary Structure) I. Peptide Bonds, Peptides and Proteins Proteins are sometimes called Polypeptides, since they contain many Peptide Bonds {*Figure 1*} The peptide bond is an amide bond {*Figure 2*} Water is lost in forming an amide bond. Structural Character of Amide Groups: Understanding the chemical character of the amide is very important, since the peptide bond of proteins is an amide bond.
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Amides have a partial double bond character and also a partial charge character because of the resonance forms shown in the above graphic. Another way to look at the partial charge and double bond of an amide is shown above. Since the free electrons of the Nitrogen atom are tied up in forming the partial double bond, the Nitrogen can not accept a proton (H+). This Nitrogen also has a partial positive charge, which tends to repel the proton (H+) and prevents it from binding to the nitrogen. Comparison of an amino acid, a dipeptide and a tripeptide: {*Figure 3*}
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Amino Acid = Gly; dipeptide = Gly-Ala; tripeptide = Gly-Ala-Ser Peptides = Mini-Proteins {*Figure 4*} A pentapeptide -- GlyAlaSerPheGln 1st amino acid is always written on the left and called the Amino terminal, since it is always the only amino acid of the peptide with a free alpha-amino group. Last amino acid is always written on the right and called the Carboxyl terminus, since it is always the only amino acid of the peptide with a free alpha-carboxylic acid group. Full structure of a Protein {*Figure 5*} Amino acid sequence of a Protein. II. Amino Acid Composition Amino Acid analysis yields a protein's Amino Acid Composition, in other words the amounts of each amino acid in the protein. All proteins have unique amino acid compositions. Amino acid compositions of a few proteins (see list proteins below table) Values for Amino Acids are in Number of Residues per Molecule of Protein
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Amino Acid \ Protein A B C D E F G H I Nonpolar Ala (A) 12 6 9 1 3 27 15 12 27 Val (V) 13 3 7 1 4 13 18 6 14 Leu (L) 15 6 8 2 6 18 18 8 38 Ile (I) 9 8 4 0 1 0 0 6 12 Pro (P) 11 4 4 0 1 7 7 2 2 Met (M) 1 3 0 1 0 2 1 2 2 Phe (F) 10 3 2 2 3 7 8 3 4 Trp (W) 2 1 1 1 0 1 2 6 0 Polar, Uncharged Gly (G) 13 13 6 1 4 7 13 12 14 Ser (S) 28 2 7 4 3 11 5
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This note was uploaded on 09/02/2009 for the course BIO BL 401 taught by Professor Wilbur during the Spring '07 term at Michigan Technological University.

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lec 5 - BL/CH 401 Lecture #5 Protein Covalent Structure...

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