These sheets rods and loops arrange themselves in a

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Unformatted text preview: produce a “beta sheet”. Beta pleated sheet These rods and cylinders are referred to as regions of secondary structure. The likelihood of folding up into one or the other of these is determined by the sequence of R groups (geegaws h anging off the backbone). Biochemists can predict, based on a protein’s sequence, which parts of the protein will form which sorts of secondary structures. These sheets, rods, and loops arrange themselves in a given posi5on in space that determines the structure of the ac5ve site. This ter5ary structure is very hard to predict from the protein’s sequence. The R groups determine tertiary structure CHARGED + POLAR Space-filling model What do greasy R groups have to do with anything? Greasy R groups are termed “hydrophobic” because they tend to interact with other greasy things (other greasy R groups, membranes) and exclude water and charged or polar R groups. Hydrophobic R groups oden congregate at the center of proteins, leaving polar and charged groups on the outside. Oxidized AFFECT 2o To S-S “Ribbon” model GREASY FAT BALLS This “hydrophobic effect” is caused largely by the exclusion of fa[y substances by water, to maximize H bonding between water molecules. CHARGED - of various sizes and shapes Ter5ary (and q uaternary) structure is stabilized by a variety of weak interac5ons between R groups Considering how many millions of possible structures could be “folded” from a single protein, it’s pre[y amazing that proteins fold up right pre[y much every 5me they’re made. New proteins must have some help doing this because… Most unfolded (= denatured) proteins never fold up correctly again. Puzzle of the “protein folding rules” Folded “native” protein If the world’s greatest experts were given the sequence of amino acids in an unknown protein….. Could they tell you the 3D structure of the protein, or its function? Not really -- they could sa...
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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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