Proteins IIProteins 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) COX-1 •provide support in and outside of cells keratin •function in storage and transport hemoglobinEnzymes 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 stateEnzyme example: Lysozyme Lysozymes cleave polysaccharide chains found in bacterial cell walls. S = substrate E = enzyme ES = enzyme substrate complex EP = enzyme product complex P = productMechanism of lysozyme actionSmall 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 ATPAllosteric 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.mcgraw-hill.com/olcweb/cgi/pluginpop.cgi?it=swf::535::535::/sites/dl/free/0072437316/120070/bio10.swf::Feedback%20Inhibition%20of%20Biochemical%20PathwaysEnzyme regulation can be positive or negative. carbamoyl phosphate + aspartate → →→ → carbamoyl aspartate → → uridine, cytidine UTP and CTP = inhibits ATCase ATP = activates ATCaseProtein 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 proteinExample: Cell cycle progression is controlled by phosphorylation.Other covalent modifications also affect protein activity. DNA binding activationBinding 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 microfilamentA 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
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