Slide 1Slide 2Slide 3Slide 4Slide 5Slide 6Slide 7Slide 8Slide 9Slide 10Slide 11Slide 12Slide 13Slide 14Slide 15Slide 16Slide 17Slide 18Slide 19Slide 20Slide 21Slide 22Slide 23Slide 24UNIT III:AMINO ACIDS, PROTEINS, & ENZYMESLecture 3: EnzymesHow do proteins carry out their biological functions?By interacting with other molecules (sometimes other proteins) - mostly weak interactions, such as H-bonds, ionic bonds, & hydrophobic interactions - VERY specificSome examples:O2 binding to hemoglobin and myoglobinEnzymes (biological catalysts) binding to their “substrates”Receptors binding to signaling molecules (e.g ., hormones, NT)Structural protein interactions - muscle contraction (actin-myosin) - cytokinesis (tubulin & cell division)Antigen-antibody binding – immune responseWhat are enzymes? What’s the big deal about them?Enzymes are highly specific biochemical catalysts - usually proteins - but “ribozymes” too – RNA catalysts (Biochem 108)They speed up biochemical Rx immenselyThey do NOT alter the equilibrium of the RxThey are necessary: - so Rx can occur quickly & efficiently @ temperatures and pH ranges compatible with life- to allow control of chemical Rx in cells rate enhancements (cat/uncat) up to 1.1 x 1021ODC uncatalyzed Rx half-complete in 78 million years enzyme Rx in 0.018 seconds!How well do they work??Uncatalyzed vs enzyme RxHorvat & Wolfenden, PNAS, 2005How do enzymes (biochemical catalysts) work?Yes!!For a reaction to occur, molecules must collide with each other with enough energy (energy of activation) to break and/or make bonds - frequency of collisions depends on their concentration - groups that are going to react must be in correct orientation Enzymes increase Rx rates by: - binding the reactants (increasing “local concentration”) - holding reactants in correct orientation - providing chemical/physical environment favorable to RxEnzymeEnzyme-substratecomplex [E-S]No RxNo RxNo RxNo RxSubstrates“Active”siteSubstratebindingsitesEnzyme Enzyme + substrate[E-S]Binding of enzymes to their substrates is highly specificThe substrate must be complementary inin shape, size, & chemical properties to the “active site” of the enzyme for it tobe able to bind, and it mush have the correct functional groups to react.Enzyme-substrate binding is analogous tothe exact fit of a “lock and key.”But remember that proteins are “plastic” - subtle changes in shape are often partof enzyme catalysisProgress of reaction (S P)Energy levelof reactantsEnergy levelof product(s)E + PE + S-GActivation energy for nonenzymatic(uncatalyzed) reactionActivation energy for enzymatic(catalyzed) reactionNet free energy change[E-S]complexG (free energy)How do enzymes (biochemical catalysts) work?All chemical reactions require input of energy to break and/ormake bonds. The energy required to initiate this process is the energy of activation. Enzymes decrease the energy of activation required for a reaction to take place (just like other catalysts)Formation of the enzyme-substrate complex, [E-S], makes the Rx energeticallymuch more feasible; thisresults in an increase in therate of the Rx.A single enzyme molecule catalyzes the same Rx many times(very, very quickly too!)Enzymes are NOT permanently changed in the Rx they catalyze - they are neither consumed nor destroyedOnce an enzyme has released its product, it is ready to bind more substrate and begin a new cycle of catalysisEnzyme+substratesEnzyme + productEnzyme-productcomplexActivated[E-S]complexTurnover can be VERY rapid(103/sec)Round and round it goes!+ H2OGlucose + fructose sucrose + H2OMany enzymes require cofactors (metal ions) or coenzymes (small organic molecules) for activityCofactors – metal ions such as zinc (Zn++),magnesium (Mg++), manganese (Mn++), iron(Fe++), copper (Cu++), & cobalt (Co++).They must be bound to the enzyme tomaintain the correct structure of theactive site Enzyme + substrateNo [E-S]No RxFunctional enzyme(w/ cofactor) [E-S] formsRxoccursXSome enzymes require coenzymes - small organicmolecules - for activity. Coenzymes are bound atthe active site, and actually participate in the Rx. Coenzymes are derived from vitamins.Eat healthy &/ortake your pills!Most commonly used enzyme names have the suffix “ase” attached to: - the substrate for the Rx (e.g., glucokinase, sucrase, protease, lipase) or to - a description of the action performed (e.g., glucose oxidase, triose phosphate isomerase, lactate dehydrogenase, phosphofructokinase).But sometimes, old common names have been around so long that(almost) everyone uses them instead. For example: Pepsin – a stomach protease Trypsin – a protease in the small intestine Debranching enzyme – glycogen degradationHow do you recognize an enzyme from its name?Most enzyme reactions fall within five general categories:1. oxidation-reduction reactions: Oxidoreductases catalyze reactions in whichelectrons are transferred from one compound to another (energy metabolism). 2. formation vs cleavage of C-C and other bonds: Formation of new bonds is often catalyzed by ligases, enzymes that require energy input in the form ofATP. The most common mechanism of bond cleavage involves hydrolysis (see below), but there are others as well. 3. internal rearrangements on molecules: Isomerases catalyze intramolecular rearrangements, resulting in a different isomer.4. group transfers among molecules: Transferases catalyze the transfer of functional groups between molecules. Transaminases, which transfer amino groups, and kinases, which transfer phosphate groups, are two good examples. Metabolic intermediates are often activated by phosphorylation; this allows them to easily undergo subsequent reactions.5. condensation vs hydrolysis reactions: These reactions involve joining molecules together, often to form polymers, with elimination of a water molecule. Hydrolysis reactions break these bonds by addition of water, giving back the original monomeric units. There are thousands of specific enzyme Rx in the cellFactors that influence enzyme activityA number of external factors can influence enzyme activity: - temperature - pH - substrate concentration(s) - binding of regulatory molecules a) inhibitors b) activatorsFactors that influence enzyme activity: TemperatureOptimal temperature for enzymes inmammals is close to body temperatureSome enzymes of “extremophiles” can function at