lecture5 - Protein a complex polymer consisting of Protein...

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Protein Structure Protein Structure Protein: Protein: a complex polymer consisting of a complex polymer consisting of combinations of the 20 amino acids linked by combinations of the 20 amino acids linked by peptide bonds peptide bonds 1° structure: 1° structure: the linear sequence of amino acids in a polypeptide chain, determines a protein’s properties read from the N-terminal end to the C-terminal end N-term L-G-T-V-R-D-H C-term is NOT the same as N-term V-H-D-L-G-R-T C-term
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Protein structure cont. Protein structure cont. 2° structure: 2° structure: the ordered 3-dimensional arrangements (conformations) in localized regions of a polypeptide chain refers only to interactions of the peptide backbone, although these are impacted by side chains results from hydrogen bonding between the amide N-H and carbonyl groups of peptide backbone examples include α -helix and β -pleated sheet
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α α -helix -helix coil of the helix is clockwise one polypeptide per helix there are 3.6 amino acids per turn repeat distance is 5.4 Å (0.54 nm) each peptide bond is planar (rigid) C=O of each peptide bond is hydrogen bonded to the N-H of the fourth amino acid away C=O----H-N hydrogen bonds are PARALLEL to the helical axis all R groups point outward from the helix
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α α -helix cont. -helix cont. Several factors can disrupt an α -helix proline creates a bend because of the restricted rotation due to its cyclic structure its α -amino group has no free N-H for hydrogen bonding Incorporated into side chain strong electrostatic repulsion caused by the proximity of several side chains of like charge, e.g., Lys and Arg (both positive) or Glu and Asp (both negative) steric repulsion caused by the proximity of bulky side chains, e.g., Val, Ile, Thr
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β β -pleated sheet -pleated sheet polypeptide chains lie adjacent to one another; may be parallel or anti- parallel may be between different parts of same chain or different polypeptide chains R groups alternate, first above and then below plane C=O---H-N hydrogen bonds are between adjacent chains and PERPENDICULAR to the direction of the sheet
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β β -pleated sheets cont. -pleated sheets cont. β -pleated sheets can be between 2 or more polypeptide strands
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α α -helices & -helices & β β -pleated sheets -pleated sheets Supersecondary structures: Supersecondary structures: contribute to tertiary structure, the combination of α - and/or
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lecture5 - Protein a complex polymer consisting of Protein...

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