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Lecture 2_notes - • tertiary tridimensional structure...

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Lecture 2 (4/1/09) Proteins continued polymer concept: make a complex, large molecule from small repeating subunits structure, ionization of amino acid, R-group (= side chain) Asp, D: -c-coo, Asn, N: -c-conh2(*), Cys, C: c-sh, Phe, F: c-ring peptide bond, formation (amino group of one amino acid reacts with carboxyl group of other), properties structure of proteins primary: the sequence of amino acids that are "joined' together to form the polypeptide. Note the amino-terminal end, and the carboxy-terminal end secondary the type of aminoacid in the chain (primary sequence) determine what secondary structure the polypeptide will form alpha helix: a coiled, spring-like structure stabilized by H bond between C=O and N-H of close chain members. beta pleated sheet: parallel polypeptides form a plate stabilized H bond between C=0 and N-H of adjacent chains random coil: no structure
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Unformatted text preview: • tertiary: tridimensional structure made by runs of secondary structure elements (helices and sheets). Can be stabilized by disulfide bonds (-SH + HS- = -S-S-), and by other, non-covalent bonds (H, ionic, etc) • quaternary: separate, two or more, polypeptides come together and form a complex proteins. Stabilized by H, ionic, hydrophobic, van der Waals, disulfide bonds. • denaturation: certain conditions such as heat, acid or base, urea treatments cause loss of structure. Examples: cooking egg white or meat • proteins are immensely flexible compounds that can assume virtually any role and shape (*) important point about Asn. The -NH2 group of Asn can ionize only in strong acid. So, Asn is effectively a "non-charged" amino acid. By contrast, the -COOH of aspartic acid (Asp) is mostly ionized under normal, pH neutral conditions....
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