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Unformatted text preview: -1-LECTURE 8. 10 September 2010 (P. J. Hollenbeck)BIOL 231PROTEIN STRUCTURERead: Chap 4: 119-140; Panels 2-5 (pp. 72-73) & 4-2 (pp. 128-29); DVD: study animations: 4.2 (Alpha helix); 4.4 (Beta sheet); 4.1 (Viewing proteins); 4.3 (Coiled-coil); 4.6 (Oligomeric proteins)Problem assignment: 24, 25; Exam I07, #3; 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 it has double bond character it DOES NOT rotate. (3) Because they lose their free amino and carboxyl groups in the polymerization, werefer to the subunits contained in a polypeptide as amino acid residues.(4) Direction: proteins are alwayssynthesized by the addition a new aminoacid to the free carboxyl group at the end ofthe growing chain, never to the amino groupat the other end. Thus we describe a proteinas having an amino- or N-terminus, and acarboxyl- or C-terminus . This will be amajor topic in our future study of themechanism of protein synthesis.(5) The backbone of a protein is thecontinuous chain of covalently-bondedatoms, from N to carbon to C to N of thenext residue to carbon, and so on. As wewill see below, this backbone takes on verydifferent higher order structures, dependingin part on the R groups of the amino acidresidues.-2-(B) R groups (or side chains) of amino acids (1) The 20 common amino acids are distinguished from each other by their R groups. These 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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