Enzymes, Part 1

• act as mediators for all reactions in biological systems • are substrate-specific protein catalysts • they increase the rate of reactions without being changed or used up during process • selectively channel reactants (called substrates) into energetically favorable pathways • 3D structures of proteins generates sites for other molecules allowing reversible binding of them

• catalyze reactions in which one molecule is oxidized while the other is reduced, transfer of electrons H+ (oxidases, reductases, dehydrogenases) • ex: lactate – lactate dehydrogenase – pyruvate

• transfer carbon, nitrogen or phosphate containing groups - ex: serine – serine hydroxymethyl transferase – glycine

• enzymes that catalyze a hydrolytic cleavage reaction (=t transfer or functional groups to water) (nucleases and proteases) • catalyze cleavage of bonds by addition of water • ex: urea – urease – carbone dioxide and ammonia

• catalyze the cleavage of C-C, C-S, and C-N bonds, addition of groups to double bonds or formation of double bonds by removal of groups • ex: pyruvate – pyruvate decarboxylase – acetaldehyde + carbon dioxide

• catalyze the rearrangement of bonds within a single molecule, transfer or groups within molecules to yield isomeric forms • catalyze racemization of optical or geometric isomers • ex: methylmalonyl CoA – methylmalonyl CoA mutase – succinyl CoA

• join together (ligate) two molecules in an energy-dependent process (DNA ligase joins 2 DNA molecules), formation of C-C, C-S, C-O and C-N bonds by condensation actions coupled to cleavage of ATP or similar cofactor • catalyze formation of bonds btwn carbon and O,S,N coupled to hydrolysis of high-energy phosphates • ex: pyruvate – pyruvate carboxylase – oxaloacetate

• catalyze polymerization reactions such as synthesis of DNA and RNA

• break down proteins by hydrolyzing bonds btwn amino acids

• catalyze the addition of phosphate groups to molecules

• hydrolyze ATP (Na, K ATPase)

• synthesize molecules in anabolic reactions by condensing 2 smaller molecules together (ATP synthase)

• catalyze hydrolytic removal of a phosphate group from a molecule

synthetase requires ATP, synthase does not require ATP

phosphatase uses water to remove phosphoryl group, phosphorylase uses Pi to break a bond and generate a phosphorylated product

• NAD+/FAD is an electron acceptor in a redox reaction

oxidase: O2 is the acceptor and oxygen atoms are not incorporated into substrate oxygenase: one or both oxygen atoms are incorporated

• special pocket on enzymes that have high specificity • contains AA side chains that participate in substrate binding and catalysis • this binding causes a conformational change in the enzyme that allows catalysis (EP)

• metal ions such as Cu2+ and Fe2+

active enzyme E + CF (enzyme + cofactor)

inactive enzyme E - CF (enzyme - cofactor)

• nonprotein small organic molecule - many are derived from vitamins

• transiently associated

• permanently bound