Protein Structure Protein Structure Structural Determination Structural Hierarchy C483 goals

Protein Structure Protein Structure Structural Determination Structural Hierarchy C483 goals www.phwiki.com

Protein Structure Protein Structure Structural Determination Structural Hierarchy C483 goals

Fries, Stephanie, Host has reference to this Academic Journal, PHwiki organized this Journal Protein StructureC483 Spring 20131. Which statement is false about a globular protein that per as long as ms its biological function as a single independent polypeptide chain A) Its tertiary structure is likely stabilized by the interactions of amino acid side chains in non-neighboring regions of the polypeptide chain. B) It could contain -helices that are stabilized by hydrogen bonding. C) It likely has extensive quaternary structure to maintain its globular shape. D) Non-covalent as long as ces are the primary source of stability as long as the secondary in addition to tertiary structure.2. The con as long as mation of the backbone of a polypeptide is described completely by the angle(s) of rotation about which bond(s) A) The peptide bond only. B) N-C only. C) N-C, C-C in addition to C-N bonds. D) N-C in addition to C-C bonds only. 3. Which structure indicates the proper hydrogen-bonding pattern between amino acids in an -helix (Dashed lines represent the hydrogen bonds.)4. What would you expect about the as long as mation of an -helix as long as a segment of a protein chain that contains lysine approximately every fourth residue with all other residues being mostly hydrophobic A) Helix as long as mation would be favored at low pH. B) Helix as long as mation would be favored at high pH. C) Helix as long as mation would be favored at neutral pH. D) Helix as long as mation would never occur regardless of pH. 5. Supersecondary structures that contain recognizable combinations of -helices, -str in addition to s in addition to loops (e.g. the Greek Key) are called -. A) domains B) folds C) homologous regions D) motifs 6. The principle as long as ces holding subunits of an oligomeric protein to each other are -. A) peptide bonds B) hydrophobic interactions C) covalent bonds D) disulfide bonds

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Protein StructureConfiguration in addition to con as long as mationNative structureFibrousGlobularAtomic level in addition to cartoon levelStructural DeterminationCrystallographyNMRStructural Hierarchy

C483 goalsSecondary structure dictated byPeptide bond structureAtomic level intermolecular interactionsTertiary in addition to quaternary structureImportance to protein folding in addition to activityFamiliar with vocabulary so that you can read a paper to learn the details Peptide BondResonance6 planar atoms as long as m a unitHighly polarTrans vs cis con as long as mationCon as long as mational FlexibilityIf each peptide bond is relatively locked, backbone con as long as mation can be defined by phi in addition to psiNOT cis/transBoth stuctures to the right are trans

Ramach in addition to ran PlotsAlpha HelixRight h in addition to edPolarityPhi = -57o in addition to psi = -47on in addition to n + 4Ala vs. TyrGly in addition to ProThe average a-helix is 12 residues long. What is its length in nmHow many amino acids/turn of an alpha helix

Amphipathic HelicesCoiled-CoilStructural ImplicationsPlacement in ProteinBeta-SheetsReal Beta SheetsTechnically, often tertiary structureGenerally bent/twistedAlternating sidechains can lead to amphipathic sheets

Loops in addition to TurnsNonrepeatingChange of directionTurns have about 4 residuesInternal H-bondsGly, Pro Tertiary StructureLonger range interactions of secondary featuresDriven by hydrophobic effectDisulfide bridgesDiversityTertiary StructureToo many shapes to memorizeBut not an infinite number of possibilitiesTake away the ability to read a paperDiscussions of motifs in addition to why importantDiscussion of domains in addition to why important

Motifs (Super Secondary Structure)Recognizable combinations of helices, loops, in addition to sheetsMatchHelix-loop-helixHelix bundleHairpinb-s in addition to wichStudying MotifsSome Motifs are highly studiedKnow the LingoLeucine zipperZinc fingerOften have recurring applicationsDomainsDiscrete, independently folded unit (may maintain shape when cleaved on loop)May have separate activities: “ATP binding domain” or “catalytic domain”Similar activity = similar structure across many proteinsBinding pockets at interfacesHow many domains

Common DomainsQuaternary StructureMultiple subunits: OligomersHomodimer, heterotrimerAdvantagesEconomyStabilityregulationa2a3a2b2From your discussion paper

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