FBICH 410 1st Edition Lecture 8Outline of Last Lecture - Secondary Structureo Alpha Helixo Beta Sheeto Beta TurnOutline 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 spaceo Secondary structure concerned mostly w/ backboneo Tertiary structure concerned w/ arrangement in space of all atoms in polpep. Chaino Tertiary structure determine by prosthetic group and side chain (interact w/ other side chains and the backbone) interactionso Prosthetic group is a nonamino acid group required for proper structure and functiono Fairly easy to predict 2 structure no so much for 3rd- Quaternary structureo Typical subunits fold independently and then interacto Subunits interact via weak non-covalent interactionso Some unique proteins have disulfide bonds between subunits (ie. Antibodies)o Open Structures: actin and tubulin- Globular v. fibrousThese 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 axiso Globular- functionally and structurally diverse; their folding is governed by a small number of principles (varied and ample 2nd structure  typ. Both alpha and beta)o Hydrophilic surface, interior hydrophobico 3rd structure defined by close packing of 2nd structureo Modular design to large proteino Can contain alpha helices and beta sheet o The large number of H-bonds in secondary structural elements act to neutralize/stabilizepolarity of peptide backboneo Most hydrophobic residues found in interioro 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 structureo Proteins with same motif tend to fold via similar processeso 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 independento Domains tell functiono Motifs tell structureo Domains have a particular structureo Can be proteolytically cleave and retain structure and function- Protein structure families- number of protein domains found in nature is large but limitedo Newly discovered proteins resemble known proteinso Structure depends on sequence, function depends on structureo The closer the sequence identity the closer the structure and function- Fibrous Proteins- contain polypeptide chains organized approx.. parallel along single axiso Consist of long fibers and large sheetso tend to be mechanically strongo insoluble in H20 and dilute salt solutionso play important role in natureo tend to have only 1 type of 2nd structureo examples: keratin (hair), fibroin (silk), collagen (connective tissue)o always have a atypical structure and unusual sequence high conc. Of 1 or 2 AA and many repeatso 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 observedo Silk fibroin- found in silk fibers Antiparallel sheets are aligned parallel to axis of fibers 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 waalso 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