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lecture08 - LECTURE 8 11 September 2009(P J Hollenbeck BIOL...

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-1- LECTURE 8. 11 September 2009 (P. J. Hollenbeck) BIOL 231 PROTEIN STRUCTURE Read: Chap 4: 119-140; Panels 2-5 (pp. 72-73) & 4-2 (pp. 128-29); DVD from your text, study animations: 4.1 (Alpha helix); 4.2 (Beta sheet); 4.3 (Using PDB files); 4.4 (Viewing proteins); 4.5 (Coiled-coil); 4.6 (Oligomeric proteins) Problem assignment: 24, 25; Exam I’04, #1; Exam I’05, #1, #2; ECB Q4-11 <be sure to download the set of additional figures that accompany this lecture> I. Amino acids and the peptide bond (A) Peptide bond – an amide linkage (1) As we have discussed, the building blocks for proteins are amino acids. These are amphoteric molecules – they can act as both acids and bases. There are 20 different amino acids commonly found in proteins, but they share a general structure. (2) To build a protein, amino acids are connected in an unbranched chain via the amide linkages that we have already discussed. The PEPTIDE BOND between the carboxyl carbon of one amino acid and the amino nitrogen of the next is usually drawn as a single bond, but in fact it has double bond character – in particular, it DOES NOT rotate. (3) Because they lose their free amino and carboxyl groups in the polymerization, we refer to the subunits contained in a polypeptide as amino acid “residues.” (4) Direction: proteins are always synthesized by the addition a new amino acid to the free carboxyl group at the end of the growing chain, never to the amino group at the other end. Thus we describe a protein as having an amino- or N-terminus, and a carboxyl- or C-terminus . This will be a major topic in our future study of the mechanism of protein synthesis. (5) The “backbone” of a protein is the continuous chain of covalently-bonded atoms, from N to á carbon to C to N of the next residue to á carbon, and so on. As we will see below, this backbone takes on very different higher order structures, depending in part on the R groups of the amino acid residues.
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-2- (B) R groups (or “side chains”) of amino acids (1) The R groups of the 20 common amino acids distinguish them from each other. They can be non-polar (hydrophobic), uncharged polar , or charged polar (which includes the acidic and basic R-groups). There are also three amino acids (see below) that have unusual properties that affect protein structure, and it is worth considering them separately. R groups in all categories vary considerably in size and shape. (2) The R groups of the amino acid residues give each region of a polypeptide its chemical character. Hydrophobic R groups will tend to be buried together in the center of the protein, polar or charged R groups will tend to be on the outside of the protein, in contact with the aqueous surroundings, and so on. Thus, R groups can
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