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BIOL 2020 (13)
K Wheaton (4)
Chapter 4

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York University
BIOL 2020
K Wheaton

Protein 3D structure - AA is the primary structure - 3D structure is the secondary structure - Bonds between R chains are tertiary structures - Multiple complex polypeptide chains are quaternary structure 4.1 Primary Structure: AA are linked by peptide bonds to form polypeptide chains - 3D structure depends on its primary structure - Peptide/amide bond linkage joining amino acids - Formation of a dipeptide is joined by the loss of a water molecule - Peptide bonds are very stable, slow hydrolysis when catalyst absent - Polypeptide chains have polarity because both ends are different alpha amino end is the beginning and alpha carboxyl is the end - Polypeptide has a reg repeating part called the main chain or backbone, variable part is the side chain, backbone is rich in hydrogen bonding potential - Each residue contains a C=O which is a good hydrogen bond acceptor, but the amino group is a good donor or it. - Largest protein is titin (muscle) - Oligopeptides=small numbers of amino acids - Disulfide bonds=oxidation of a pair of cysteine residues (cystine) - The AA sequence work by sanger shows that proteins have precisely defined AA sequences. - Knowing AA sequences helps with: 3D structure, knowing its mechanism, molecular pathology - Peptide bond is planar, and has double bonds so it has resonance therefore constrains it against rotation, peptide bonds are uncharged - Trans=2 alpha carbons are on opposite sides - Cis=2 alpha carbons are on teh same side - Almost all proteins are in trans. - The freedom of rotation about 2 bonds of each amino acid allows proteins to fold in many different ways - Torsion angles: angle of rotation between alpha carbon and N is phi, and angle of rotation between 2 carbons is psi - Ramachandran diagram: 2D plot of possible angles - Steric exclusion: 2 atoms cannot be in the same place at the same time, restricts # of polypeptide conformations and is this powerful for organization. 4.2 secondary structure: polypeptide chains can fold into regular structures  Polypeptide chains can fold into alpha helix and beta pleated sheets , turns and loops  Bonds form near one another in linear sequence or primary structure  Alpha helix is stabilized by hydrogen bonds between NH and CO groups os the main chain, every 4 residues  All the main chain CO and NH groups are hydrogen bonded. Each residue related to the next by a “rise” or translation  Rotation of 100 degrees so it forms 3.6 amino acid residues per turn  Pitch=length of one complete turn along the helix.  Righthanded helices are more energetically favourable , fewer clashes, so most are found in this form.  Proline is a helix breaker  25% of all water soluble proteins are alpha helice
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