Proteins II Proteins interact with other molecules ligand anything bound by a protein binding site area of a protein that interacts with a ligand selective binding is mediated by many non covalent bonds forces The folding of polypeptide chain typically creates a cavity on the folded protein s surface where specific amino acid side chains are brought together Proteins have diverse functions speed up the rate of chemical reactions enzymes provide support in and outside of cells COX 1 keratin function in storage and transport hemoglobin Enzymes are proteins that act as catalysts Enzymatic reactions the substrate s ligand binds to an active site binding site substrate is altered upon binding so that the desired reaction is favored Holds substrates in alignment encourages reaction Re arranges electrons stabilizes intermediates Alters bond angles moves towards transition state Enzyme example Lysozyme Lysozymes cleave polysaccharide chains found in bacterial cell walls S substrate E enzyme ES enzyme substrate complex EP enzyme product complex P product Mechanism of lysozyme action Small molecules covalently attached to proteins increase protein functionality used for functions amino acids cannot perform Fe binds oxygen in hemoglobin metals near active sites make transient bonds with the substrate heme group hemoglobin Regulation of protein function Amount of protein Location of protein Modification of protein activity by modifying the protein s shape feedback inhibition of allosteric proteins positive regulation of allosteric proteins protein phosphorylation other covalent modifications of proteins binding of GTP binding and hydrolysis of ATP Allosteric proteins undergo conformational changes upon ligand binding which alters their activity Feedback inhibition occurs when a product of a pathway inhibits an enzyme that acts earlier in the pathway http highered mcgrawhill com olcweb cgi pluginpop cgi it swf 535 535 sites dl free 0072437316 120070 bio1 0 swf Feedback 20Inhibition 20of 20Bioch emical 20Pathways Enzyme regulation can be positive or negative carbamoyl phosphate aspartate carbamoyl aspartate uridine cytidine UTP and CTP inhibits ATCase ATP activates ATCase Protein phosphorylation can inhibit or stimulate protein function kinase attaches phosphates to serine threonine or tyrosine side groups on a target protein phosphatase removes phosphates from a target protein Example Cell cycle progression is controlled by phosphorylation Other covalent modifications also affect protein activity activation DNA binding Binding GTP activates GTP binding proteins Example The elongation factor EF Tu undergoes a large conformational change after GTP hydrolysis Hydrolysis of bound ATP can provide directionality to a series of conformational changes Example myosin walking along an actin microfilament A combination of different protein modifications and binding partners control protein complex assembly and function Antibodies are useful tools for studying proteins Antibodies recognize specific antigens Antibodies can be used for immunoprecipitation Antibodies can be used for as molecular tags during microscopy
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