BIOC 460, Spring 2008LEC 10, Enzymes - Introduction 1Lecture 10Enzymes: IntroductionReading: Berg, Tymoczko & Stryer, 6th ed., Chapter 8, pp. 205-217 (These pages in textbook are very important -- concepts ofthermodynamics are fundamental to all of biochemistry.)Thermodynamics practice problems (same as for Lecture 2):http://www.biochem.arizona.edu/classes/bioc460/spring/460web/lectures/ThermoPracticeProblems_08.pdf(also linked in lecture notes directory)Enzymes introduction sample problems:http://www.biochem.arizona.edu/classes/bioc460/spring/460web/lectures/LEC10_EnzIntrod/EnzIntrodSampleProblems.pdf(also linked in lecture notes directory)Key Concepts• Enzymes are biological catalysts, very powerful and very specific.– Enzymes increase rates of (bio)chemical reactions but have noeffect on Keq (and no effect on overall ΔG) of the reaction.• Some enzymes need cofactors (inorganic ions or organic/metalloorganiccoenzymes, derived from vitamins) for their catalytic activities.– Different cofactors are useful for different kinds of chemical reactions,including transfers of specific kinds of groups or transfers ofelectrons.• Kinetics: the study of reaction rates. Rates depend on rate constants.– Rate constants depend inversely and exponentially on Arrheniusactivation energy, ΔG‡, the difference in free energy between freeenergy of transition state and free energy of reactant(s).– Rate constants are increased by catalysts (enzymes), becauseenzymes decrease ΔG‡.– Enzymes lower ΔG‡ by affecting either ΔH‡ or ΔS‡ (or both).– One way enzymes reduce ΔG‡ is by tight binding (noncovalent) of thetransition state.– Enzymes generally change the pathways by which reactions occur.– Rate enhancement (factor by which enzyme increases the rate ofa reaction) is determined by Δ ΔG‡, the decrease in ΔG‡ broughtabout by enzyme compared with uncatalyzed reaction's ΔG‡.Learning Objectives(See also posted Thermo and Enzymes-Introduction sample problems.)• Terminology: rate enhancement, cofactor, coenzyme, apoenzyme,holoenzyme, prosthetic group, catalyst, activation energy, transitionstate. (Review: equilibrium constant, mass action ratio for a reaction,biochemical standard conditions, standard free energy change, actualfree energy change).• Describe the general properties of enzymes as catalysts that areespecially important for their roles as biological catalysts.• Explain the effect of a catalyst on the rate of a reaction, and on theequilibrium constant of a reaction.• Define "standard free energy change" and give the symbol for thatparameter.• Write the mathematical expression relating ΔG°' to Keq', and be able tointerconvert ΔG°' and Keq'.• Calculate the actual free energy change (ΔG'), given the startingconcentrations of appropriate chemical species and either ΔG°' or Keq'.• Describe the relation between ΔG' and the rate of a reaction; using ΔG',predict reaction direction.Learning Objectives, continued• Express the velocity of a simple reaction in terms of the rate constantand the concentration of the reactant.• Express the equilibrium constant of a reaction in terms of the equilibriummass action ratio.• Express the equilibrium constant of a reaction in terms of the rateconstants for the forward and reverse directions. (Note that equilibriumconstants are symbolized with upper case K and rate constants withlower case k.)• If an enzyme increases the rate constant for the forward reaction by afactor of 108, by what factor does it increase the rate constant for theback reaction? What is the rate enhancement brought about by thecatalyst for that reaction?• Draw the free energy diagram of a hypothetical reaction and show how acatalyst may increase the rate of the reaction, pointing out on thediagram ΔG for the overall reaction, ΔG‡uncat, and ΔG‡cat.• Indicate (and name) the quantity on a free energy diagram (HINT: it's aspecific kind of ΔG) that determines the magnitude of the rate constantfor the reaction at a given temperature. You don't have to memorize theequation relating this quantity to k.• What reaction parameter (kinetic parameter) do enzymes affect in orderto increase the rate?Enzymes: Introduction• Enzymes are proteins.– (ribozymes: catalytic RNA molecules)• biological catalysts– not chemically altered in reaction– do not change equilibrium constant (Keq) for reaction– increase rate of reaction by providing a pathway of loweractivation energy to get from reactants to products– operate under physiological conditions (moderate temps., aroundneutral pH, low conc. in aqueous environment)– work by forming complexes with their substrates (binding), thusproviding unique microenvironment for reaction to proceed, theactive site– VERY HIGH SPECIFICITY for both reaction catalyzed and substrate used– VERY HIGH CATALYTIC EFFICIENCY– ACTIVITIES of some enzymes REGULATEDCATALYTIC POWER OF ENZYMES• RATE ENHANCEMENT = catalyzed rate constant/uncatalyzed rateconstant = factor by which catalyst increases rate of reaction• Examples:Berg et al., Table 8-1BIOC 460, Spring 2008LEC 10, Enzymes - Introduction 2SPECIFICITY OF ENZYMES• Enzymes very specific– for substrate acted upon– for reaction catalyzed• Example: Proteases are a whole class of enzymes that all catalyzehydrolysis of peptide bonds:Substrate Specificity -- proteases as an example• Substrate specificity (e.g., of proteases) due to precise interaction ofenzyme with substrate– result of 3-D structure of enzyme active site where substrate hasto bind and be properly oriented for catalysis to occurBerg et al., Fig. 8-1(A) Trypsin catalyzes hydrolysis of peptide bonds on carboxyl side of Lys and Arg residues (digestive function in small intestine, cleaves just about any protein it encounters after (eventually) every Lys and Arg)(B) Thrombin (involved in blood clotting cascade) catalyzes hydrolysis of peptide bonds between Arg and Gly residues in specific sequences in specific protein substrates (activated only where blood needs to clot, works only on very specific target protein) Enzyme Specificity, continued• substrate specificity of proteases --another example, chymotrypsin:– cleaves on carboxyl side of aromatic and hydrophobic amino acidresidues– evolutionarily related to trypsin– Genes for trypsin and chymotrypsin are homologous.• Ancestral
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