These gee gaws interact with specic substrates but

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Unformatted text preview: y some general things and make some guesses, but X-ray crystallographers still have job security The bottom line generalities-A 3-D structure is held together by many weak interactions. Allows spontaneous folding of a 1D (linear) polymer into a stable 3D conformation. (it gets progressively more stable as it folds) - Greasy R-groups predominate i nside -- the core of the sphere Charged/polar R-groups are outside -- make surface features to do the catalysis Most proteins have multiple subunits -- binding specificity due to specific surface interactions + SPONTANEOUS FOLDING generates a solid with PATTERNS of “gee-gaws” ON THE SURFACE. These Gee-Gaws interact with specific substrates. + But before we go on, don’t forget… proteins do a LOT of things besides catalysis… •Act as motors •Acts as carriers or pores •Define cell shape (form the cytoskeleton) •Regulate many processes •Determine cell ­cell interac5ons Adjuncts to protein catalysts (aka prosthe;c groups, cofactors) (note similari5es to mineral catalysts) 1. 2. What are the “weak interac5ons” that determine how a protein folds up? A. B. C. D. E. Metals  ­ ­ Zinc, Magnesium, Iron, Manganese Metal ­binding cofactors ­ ­ heme, chlorophyll Like the protein part of the enzyme, cofactors come out of the reac5on unscathed. They are catalysts, not substrates. Pep5de bonds Ionic bonds Hydrophobic interac5ons Hydrogen bonds B, C, and D are correct “Coenzymes” ­ are really substrates (they get used up) and include our old friends NAD, FAD, and ATP Three types of protein iron-sulfur clusters (here’s one- a 4Fe-4S cluster) cysteine Another iron-carrying enzyme -cytochrome b- carries a heme cofactor cysteine E˚’ Ferredoxin (Fe+++ -> Fe++) = -0.43 E˚’ Cytochrome bmito (Fe+++ -> Fe++) = 0.02 E˚’ (Fe+++ -> Fe++) = 0.77 cysteine The protein and its cofactor drastically modify the reduc...
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This note was uploaded on 05/17/2013 for the course BIS 100 taught by Professor Charles during the Winter '11 term at UC Davis.

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