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Unformatted text preview: -1-LECTURE 8. 11 September 2009 (P. J. Hollenbeck)BIOL 231PROTEIN STRUCTURERead: 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 I04, #1; Exam I05, #1, #2; ECBQ4-11<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 areamphotericmolecules they can act as both acids and bases. There are 20 differentamino 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 theamide linkages that we have already discussed. The PEPTIDE BOND between thecarboxyl carbon of one amino acid and the amino nitrogen of the next is usually drawnas a single bond, but in fact it has double bond character in particular, it DOES NOTrotate. (3) Because they lose their free amino and carboxyl groups in the polymerization, we refer to thesubunits contained in a polypeptide as amino acidresidues.(4) Direction: proteins are always synthesized bythe addition a new amino acid to the free carboxylgroup at the end of the growing chain, never to theamino group at the other end. Thus we describe aprotein as having an amino- or N-terminus, and acarboxyl- or C-terminus . This will be a major topicin our future study of the mechanism of proteinsynthesis.(5) The backbone of a protein is the continuouschain of covalently-bonded atoms, from N to carbon to C to N of the next residue to carbon,and so on. As we will see below, this backbonetakes on very different higher order structures,depending in part on the R groups of the amino acidresidues.-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 (whichincludes 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 consideringthem 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 itschemical character. Hydrophobic R groups will tend to be buried together in thecenter of the protein, polar or charged R groups will tend to be on the outside of theprotein, in contact with the aqueous surroundings, and so on. Thus, R groups cancontribute to overall protein shape and folding through their properties and...
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- Fall '08