m3 - Protein Structure and Function Readings: Ch. 3...

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Readings: Ch. 3 (pp59-68) Protein Structure and Function
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3-dimensional shape From sequence to function
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The R-groups extend from the polypeptide backbone Adapted from Deb Pires • Each amino acid is linked by a covalent peptide bond. • The repeated amide nitrogen atom (N), central carbon (C α ), and carbonyl carbon atom (C) form the backbone of a protein molecule from which the various side chains project.
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The polypeptide backbone has directionality • As a consequence of the peptide linkage, the backbone exhibits directionality because all the amino groups (NH 3 ) are located on the same side of the C α -atom. • The sequence of a protein is conventionally written with its N- terminus on the left and the C-terminus on the right.
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Three characteristics are important about the backbone 1. R groups extend away from the backbone 2. It has directionality 3. The backbone is flexible and provides many sites for H-bonding. Adapted from Deb Pires Identify the sites of H-bond formation on the polypeptide backbone. The polypeptide backbone: A plethora of sites for H-bond formation
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The Relationship between Form and Function • Protein structure can be described at several levels of organization, each emphasizing a different aspect and each dependent on different types of interactions. • Four levels of protein structure are used to describe how a protein is constructed.
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Adapted from Deb Pires The 4 levels of Protein Structure
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Primary Structure
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1 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 105 110 115 120 125 129 Amino acid Primary Structure • The primary structure of a protein is the specific linear sequence of amino acids that constitute the polypeptide chain. • There are 20 n possible polypeptides that can be formed, where n is the number of amino acids present in the chain. aa#1 20 aa#2 20 aa#3 20 aa#4 20 = 160,000 • The arrangement of amino acids makes each protein different.
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Changes in the primary structure may lead to disease (a) Normal red blood cell Normal hemoglobin 1 2 3 4 5 6 7. . . 146 (b) Sickled red blood cell Sickle-cell hemoglobin 2 3 1 4 5 6 7. . . 146 • The substitution of one amino acid for another in hemoglobin causes sickle-cell disease. • A slight change in the primary structure of a protein affects its ability to function. Amino acid sequence 3-Dimensional Shape or Abolish Function • The primary structure helps to determine all other levels of structure
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Did you know that each RBC contains about 300 million Hb molecules? Primary Structure is what starts it all
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Conformation : the 3-dimensional arrangement of the atoms in a molecule (Refers to the spatial organization of proteins). Proteins exist as 3-Dimensional Structures
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The Primary Structure will Determine how a Protein will Fold Adapted from Deb Pires • Secondary and tertiary structure describe the “folding of a protein.” Secondary structure is determined by local backbone interactions Tertiary structure is determined by interactions between the side chains Proteins fold in a manner to achieve the lowest energy state
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• Proteins fold into a conformation with the lowest energy state Adapted from Deb Pires Protein Folding
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Secondary Structure
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This note was uploaded on 03/05/2008 for the course LIFESCI 3 taught by Professor Staff during the Fall '06 term at UCLA.