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Biochem Test 2 Notes - Biochemistry Test 2 Notes-Fall 2009...

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Biochemistry Test 2 Notes-Fall 2009 1) Tertiary Structures: ! Similar to secondary structures since they build tert stuctures. " Arrangement of all atoms of a single poplypeptide in 3D space. i. Single polypeptide Monomer: 1 subunit Multimer: multi subunits = 4 2) Types of proteins: ! Fibrous Proteins i. Insoluble in H20 ii. Function in structure iii. Cell scaffolding iv. Cell morphology v. Cell integrity, connective tissue " Globular proteins: (main focus) i. Soluble in H20 ii. Function in ligand binding iii. Protein-protein interactions (usually 1 globular and 1 membrane) iv. Transport v. Metabolic processing (catalysis) # Membrane-bound proteins: i. Function in ligand binding ii. Protein-protein interactions iii. Across-membrane transport iv. Metablic processing (catalysis) v. Cell-to-cell communication $ Put together by…. i. Long interrupted stretches of secondary structures (long alpha helices) ii. Simple sequences (repeated over and over again) 3) Central features of tertiary structures: ! Almost all globular proteins have large portions of defined secondary structures " Mostly all alpha helices and b-pleated # Compact structure stabilized by polar and nonpolar interactions i. Packing density: 0.7-0.75 This is almost as tightly packed as you can get ii. Very little available space-optimum packing $ Core dominated by non-polar (hydrophobic) side-chains i. Contains highly defined secondary structures ii. Most alpha-helices and beta-pleated found in core. iii. Very little turns/loops, irregular, or disorder found. Example Leucine: Fig 1 a. Polar groups buried with polar side chains b. Polar groups need polar interactions c. Both of these are best accomplished with a-helices and b- pleated
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Core Vs. Surface -Hydrophobic (non-polar) side chains Hydrophilic (polar) side chains (globular proteins have shell of H2O -Defined secondary structures dominate rare to find other types -also contains alpha-helices and B-pleated, but they are amphipathic. (polar on 1 side and non- polar on the other side. -Loops/turns, irregular, disorder are found and function here 4) Alpha-helices in larger context: ! Coiled-coil-common motifs for paired alpha-helices i. Heptad repeat-orientation for R-groups in repeated every 7 amino acids. a-helix must be tighter than usual. 3.5 amino aicds per turn ! causes twisting (usually 3.6 a.a’s per turn) ii. Figure 2 iii. Non-polar side chains: a "! a’ hydrophobic interaction d "! d’ hydrophobic interaction iv. Ionic residue: g " ! e’ hydrophilic e " ! hydrophilic a. ex: leucine zipper b. note- coiled-coil structures are found in several transcription factors and other DNA-binding proteins. 5) Hierarchy of tertiary structure: motif ! Association of contiguous secondary elements. " Example: i. Coiled-coil ii. Helix-turn-helix (DNA binding protein) Ex: DNA binding 3-helix bundle (Lac repressor) iii. B-meander: (each strand goes into next-up, down, up, down) Many together form B-propeller Ex: B-propeller (neuramindase) iv. Greek Key (2 formed together B-sandwich) Ex: B-sandwich ( ! -crstallin) Lens protein (stays stabilized or decays !
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