Enzymes, Part 1 Flashcards
- major classes of enzymes - biochemical properties of enzymes
enzymes
- 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
oxidoreductases
- 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
transferase
- transfer carbon, nitrogen or phosphate containing groups
- ex: serine – serine hydroxymethyl transferase – glycine
hydrolases
- 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
lyases
- 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
isomerases
- 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
ligases
- 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
polymerases
- catalyze polymerization reactions such as synthesis of DNA and RNA
proteases
- break down proteins by hydrolyzing bonds btwn amino acids
kinases
- catalyze the addition of phosphate groups to molecules
ATPases
- hydrolyze ATP (Na, K ATPase)
synthases
- synthesize molecules in anabolic reactions by condensing 2 smaller molecules together (ATP synthase)
phosphatase
- catalyze hydrolytic removal of a phosphate group from a molecule
synthetase vs synthase
synthetase requires ATP, synthase does not require ATP
phophatase vs phosphorylase
phosphatase uses water to remove phosphoryl group, phosphorylase uses Pi to break a bond and generate a phosphorylated product
dehydrogenase
- NAD+/FAD is an electron acceptor in a redox reaction
oxidase vs oxygenase
oxidase: O2 is the acceptor and oxygen atoms are not incorporated into substrate
oxygenase: one or both oxygen atoms are incorporated
active sites
- 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)
cofactors
- metal ions such as Cu2+ and Fe2+
holoenzyme
active enzyme E + CF (enzyme + cofactor)
apoenzyme
inactive enzyme E - CF (enzyme - cofactor)
coenzyme
- nonprotein small organic molecule
- many are derived from vitamins
cosubstrates
- transiently associated
prosthetic groups
- permanently bound
regulation
- enzyme activity can be regulated (increased or decreased) so that the rate of product responds to cellular needs
location in cell
- many enzymes are located in specific organelles in cell (compartmentalization) -> some reactions are isolated from others (avoiding competition for substrate or enabling more favorable conditions)
stabilizing the transition state
- an enzyme can greatly increase the concentration of the reactive intermediate that can be converted to product accelerating the reaction
