F BICH 410 1st Edition Lecture 8 Outline of Last Lecture Secondary Structure o Alpha Helix o Beta Sheet o Beta Turn Outline of Current Lecture Alpha helices won t have Gly or Pro Secondary structure propensities based on statistical distribution of amino acids AA in alpha helix beta sheet and turn or loop using known structures Novel seq are scanned and assessed for likelihood of being beta alpha Globular and Fibrous Tertiary structure folding of polypeptide chain in 3D space o Secondary structure concerned mostly w backbone o Tertiary structure concerned w arrangement in space of all atoms in polpep Chain o Tertiary structure determine by prosthetic group and side chain interact w other side chains and the backbone interactions o Prosthetic group is a nonamino acid group required for proper structure and function o Fairly easy to predict 2 structure no so much for 3 rd Quaternary structure o Typical subunits fold independently and then interact o Subunits interact via weak non covalent interactions o Some unique proteins have disulfide bonds between subunits ie Antibodies o Open Structures actin and tubulin Globular v fibrous These notes represent a detailed interpretation of the professor s lecture GradeBuddy is best used as a supplement to your own notes not as a substitute o Globular proteins which are more or less spherical shape majority of proteins o Fibrous contain polypeptide chains organized approx parallel along a single axis o Globular functionally and structurally diverse their folding is governed by a small number of principles varied and ample 2 nd structure typ Both alpha and beta o Hydrophilic surface interior hydrophobic o 3rd structure defined by close packing of 2 nd structure o Modular design to large protein o Can contain alpha helices and beta sheet o The large number of H bonds in secondary structural elements act to neutralize stabilize polarity of peptide backbone o Most hydrophobic residues found in interior o Many polar charged face outside those that are interior participate in Hbond or ionic intramolecular interactions o Polar noncharged can be found throughout Amphipathic amphiphilic helix and beta Interior of protein is more analogous to an organic solvent this the pKas of ionizable side chains are slightly changed Motif smallest repeating unit aka supersecondary structure o Proteins with same motif tend to fold via similar processes o B meander Green Key Alpha Alpha beta alpha beta Domains proteins of 250 residues are less typical to have a compact globular structure Very large polypeptide chains tend to fold in 2 or more clusters known as domains modules Domains are contained in a single polypeptide chain Subunits are in separate polypeptide chain Small segments usually connect neighboring domains Domains can be structurally and functionally independent o Domains tell function o Motifs tell structure o Domains have a particular structure o Can be proteolytically cleave and retain structure and function Protein structure families number of protein domains found in nature is large but limited o Newly discovered proteins resemble known proteins o Structure depends on sequence function depends on structure o The closer the sequence identity the closer the structure and function Fibrous Proteins contain polypeptide chains organized approx parallel along single axis o Consist of long fibers and large sheets o tend to be mechanically strong o insoluble in H20 and dilute salt solutions o play important role in nature o tend to have only 1 type of 2nd structure o examples keratin hair fibroin silk collagen connective tissue o always have a atypical structure and unusual sequence o o high conc Of 1 or 2 AA and many repeats alpha keratin found in hari fingernails ect basic unit is a dimer of alpha helix with high Cys count alpha helix rod 300 residues primary strucutre of helical rods consist of 7 residues repeats abcdefg with a and d always non polar large hydrophobic patches alpha keratin high ordered structure soiled coil association via hydrophobic patch disulfide bond hold proto filament and fibril together curly hair crosslinking of polypep structure permanent involves reducing and oxidizing disulfide bonds set or wetting and drying rearranges the H bond between helices and fibers Pitch decreases approx 5 1A which is what Astbury observed Silk fibroin found in silk fibers Antiparallel sheets are aligned parallel to axis of fibers o Beta sheet stack to form microcrystalline arrays Alternate sequence Gly X Gly X with X being Ala or Ser Beta sheet held together b backbone hydrogen bonds but the stack of beta sheet associates via van der waals Collagen basic unit is tropocollagen 3 left handed helical chains interwoven to produce a right handed superhelical twist Collagen 1 3 AA are Gly Pro and HydroPro are 1 3 of AA acids as well Many nontypical AA incorporated in structure