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Unformatted text preview: UNM Biochemis ry Educa ion Depar men of Biochemis ry & Molecular Biology BIOC 423 Int oducto y Biochemist y Protein Structure OBJECTIVES • Describe the structure of the peptide bond, showing geometry, charge distribution and H-bonding groups. • Draw the peptide backbone of a 5-residue portion of a protein. • Compare and contrast primary, secondary, tertiary and quaternary protein structures: what are the bonds or interactions involved in each? • Understand the forces that stabilize and destabilize the secondary structure of proteins; what are the effects (constraints) of amino acid sequence on an alpha helical structure; On a beta structure and the beta turn? • What is the basic structure of and collagen? How does the primary structures lead to higher-level structures? • Understand the forces that stabilize the tertiary structure of proteins. Be able to draw partial structures illustrating these interactions. • Know the fundamental rules governing structural patterns of soluble proteins. OUTLINE Peptide bonds Chemistry Structure Polypeptide orientation Number of possible polypeptides Overview of protein structure Primary Structure - AA sequence plus disulfide bonds Secondary Structure- local spatial arrangement of the polypeptide backbone Tertiary Structure- 3-D structure of entire polypeptide Quaternary Structure- spatial arrangement of subunits; applies only to proteins constructed of more than one polypeptide. Primary structure Peptide bonds, interactions Secondary structure Important bonds, interactions Alpha helix: structure Beta-structures: beta sheets, beta turns Fibrous proteins For fibrous proteins secondary structure is the dominant motif. Collagen: structure Protein Tertiary Structure Important bonds, interactions Protein Quaternary Structure Important bonds, interactions? Primary structure leads to all other levels of architecture Anfinsen Experiment Denaturation, Renaturation Denaturation: extremes of pH; detergents; denaturing agents, alcohols; mercaptoethanol LECTURE Peptide bonds Peptide bonds are formed by a condensation reaction between the alpha carboxyl group of one AA and the alpha amino group of another. Water is eliminated in this reaction. In the example below Ala and Gln are condensed to yield the dipeptide Ala- Gln. You should note that the resulting dipeptide also contains an amino and carboxyl group allowing a similar condensation type of reaction to continue adding amino acids to each end of the molecule producing a linear polypeptide chain. For orientation, we refer to the two different ends of the polypeptide chain as the amino terminal and the carboxyl terminal ends. This reaction can continue to produce extremely large polypeptides called proteins . You should note that at each residue in the polypeptide chain there is the option of including any one of the 20 amino acids. This allows an incredible heterogeneity. For a dipeptide (2 amino acids) there is 20 X 20 = 400 different sequences of amino acids. For a tripeptide (3 amino acids) there is 20 x 20 x 20 = 8000 sequences of amino acids....
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This note was uploaded on 04/05/2008 for the course BIOCHEM 423 taught by Professor Osgood during the Spring '08 term at New Mexico.
- Spring '08
- molecular biology