1SdSttProteins: 3D-StructureChapter 6(9 / 17/ 2009)SecondaryStructure–The peptide group–Alpha helices and beta sheets–Nomenclature of protein secondary structureTertiaryStructureThree Dimensional Protein StructuresConformation: Spatial arrangement of atoms that depend on bonds and bond rotations.Proteins can change conformation, however, most proteins have a stable “native” conformation.The native protein is folded through weak interactions:a) Hydrophobic interactionsb) Hydrogen-bondsc) Ionic interactionsd) Van der Waals attractionsThere are four levels of protein structure1. Primary structure1°= Amino acid sequence, the linear order of AA’s.Remember from the N-terminus to the C-terminusAbove all else this dictates the structure and function of the protein.2. Secondary structure2°= Local spatial alignment of amino acids without regard to side chains.Usually repeated structures Examples: α-helix, β-sheets, random coil, or β-turns3. Tertiary Structure3°= the 3-dimensional structure of an entire peptide.Great in detail but vague to generalize. Can reveal the detailed chemical mechanisms of an enzyme.4. Quaternary Structure4°two or more peptide chains associated with a protein.Spatial arrangements of subunits.Example of each level of protein structureProtein Structure Terminology
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