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Chapter 6

CHAPTER 6.doc

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Department
Chemistry
Course
CHY 204
Professor
Mario Estable
Semester
Fall

Description
CHAPTER 6: ENZYMES -Enzymes are catalyctic, have a high degree of specificity for substrates, accelerate velocity of rxn & function in aw solns along very mild conditions of temp & pH. 6.1 Intro to Enzymes -with the exception of a small group of catalyctic RNA/ribozymes, all enzymes are pro. Typically large w/ MW ranging from 12,000 to 1 million (12,000 / 110 =109 AA; 1 million / 110 = 9000 AA). Some enzymes only req aa residues for activity but other req additional components such as cofactors—either one of more inorganic elements (Fe2+, Mg2+, Mn2+ & Zn2+) or coenzymes which are complex of organic/metalo-organic molecules. Coenzymes act as transient carriers of specific func groups (5’-deozyadenosylcobalamin/coenzyme B12 transfers H atoms & akyl group; precursor is vit B12) mostly derived from vitamins & organic nutrients req in small amts in diet. Some enzymes both req a coenzyme & another metal ions for activity; a coenzyme/metal ion that is tightly bound to the enzyme pro is called prosthetic group. A holoenzyme is a complete, catalytically active enzyme together w/ bound coenzyme &/ metal ions; the pro part of it is called apoenzyme or apopro. Some enzymes are modified by phosphorylation, glycosylation, etc & many of these processes are involved in regulation of enzyme activity. Zn2+ is a cofactor for alcohol dehydrogenase. -Enzymes are classified by the reactions they catalyze: Nomenclature involves adding –ase to name of substrate or phrase describing activity, unrelated common names & EC (enzyme commission). Most enzymes catalyze the transfer of e-s, atoms & func groups thus are classified, give code #s & assigned names according to the type of transfer rxn, group donor & group acceptor. The 4 digit # enzyme commission: 1) designates class, 2) subclass, 3) specifics about rxn, 4) more specifics. Eg. ATP + glucose  ADP + D-glucose-6-phosphate -Formal name is glucose 6 transferase. E.C.#2.7.1.1.: 2 designates class name (transferases), 7 designates subclass (phosphotransferase), 1 designates specifics (OH acceptor), 1 designates more specifics (P group acceptor D-glucose). Common name is hexokinase. 6.2 How enzymes work -Enzyme catalyzed rxns occur w/in confines of a pocket on enzyme called active site. The substrate is the molecule bound in the active site & acted upon by the enzyme. Enzyme st substrate complex was 1 proposed by Charles Adolphe Wurtz. -Enzymes inc rxn rates: E + S ESEP E + P –Transient transition state (E,S,P: enzyme, substrate, product). Any rxn such as SP can be described by a reaction coordinate diagram where free energy of system is plotted against progress of rxn. ΔG is free energy change, ΔG° is std free energy change which is temp of 298K, partial pressure of each gas 1 atm (101.3kPa), [ ] of each solute 1M, ΔG’^0 is biochemical ΔG° at pH 7, ΔG is activation energy & ΔGb is binding energy. The ground state is the starting pt for either forward/reverse rxn. Enzymes do not affect equilibrium, only the rates of rxn; the equilibrium b/w SP reflects the diff in free energies in their ground state (free energy of P at ground state is lower than that of S thus ΔG’^0 is negative & equilibria favours P. Enyzmes affect rates of rxns by dec activation energy which is the diff b/w ground state & transition state (not a chemical species but a fleeting molec moment in which events, eg. Bond breakage, bond formation & charge development have proceeded to the precise pt at which decay to either substrate/product is equally likely). The role of enzymes is to accelerate interconversion of S&P w/o getting used up & w/o affecting equilibria but rxn reaches equilibria faster when appropriate enzyme is present b/c rate of rxn is inc. -Eg. C12H22O11 + 12 O2  12 CO2 + 11 H2O: Has a --ΔG’^0, doesn’t occur w/o enzymes to catalyze rxn by dec the a.e. Reaction intermediates is any species on the rxn pathway that has finite chemical lifetime; these intermediates occupy valleys in the diagram thus the interconversion of 2 sequential rxn intermediates is a rxn step. The rate limiting step is the step w/ the highest a.e., ie. The highest energy pt in the diagram for introconversion of S & P, important in rxns that occur in several steps. -Reaction rates & Equilibria have precise thermodynamic defns: K’eq = [P][S] ΔG’^0 = --RT In K’eq; R is gas constant 8.315J/mol K, T is absolute T at 298 K (25°C). Pint is that K’eq is directly related to overall std free energy change for the rxn, ie, a large --ΔG’^0 reflects a favourable rxn equilibrium but doesn’t mean rxn proceeds rapidly. Rate of any rxn is determined by the [reactant] & rate constant, k (s^-1). For S ,V is the velocity of rxn (V= k[S]) which is a 1 order rxn. -A few principles explain the catalyctic power & specificity of enzymes: 1) Transient covalent interactions w/ enzyme func groups provide alternative lower a.e. pathways. 2) Noncovalent interactions w/ enzyme provide energy for reducing a.e. What sets apart enzymes from most catalysts is the formation of ES complex which mediated by hydrogen bonds, hydrophobic & ionic interactions + release of small amt of free energy that stabilizes interaction, called binding energy or ΔGb (ie. A major source of free energy used by enzymes to lower the a.e. of rxns). 2 principles that provide explanation for how enzymes use noncovalent binding energy: 1) Much of catalyctic power of enzyme is ultimately derived from the free energy released in forming many weak bonds & interactions b/w enzyme-substrate & this binding energy contributes to specificity & catalysis. 2) Weak interactions are optimized in the rxn trasition state; enzyme active sites are complementary not to the substrates but their transition states as they are converted to products during rxn. -Weak interactions b/w enzyme & substrate are optimized in transition state: enzyme specificity studied by Emile Fischer propose induce fit idea. Eg. An imaginary enzyme (stickase) designed to catalyze breakage of metal stick: a) before the stick is broken, it must first be bent (transition state). In both stickase ex, magnetic interactions take the place of weak bonding interactions b/w enzyme-substrate; b) a stickase w/ magnet-lined pocket complementary in structure to the stick (the substrate) stabilizes the substrate thus bending is impeded by the magnetic attraction b/w stick & stickase; c) an enzyme w/ a pocket complementary to the rxn transition state helps to destabilize the stick, contributing to the catalysis of rxn. The binding energy of magnetic interactions compensates for the inc in free energy req to bend the stick. The rxn diagrams show the complimentarity to substrate & not transition state; ΔGm reflects diff b/w transition state energies & un/catalyzed rxns which is contributed by magnetic interactions b/w stick & stickase; when the enzyme is complementary to the substrate, the ES complex is more stable & has less free energy in ground state than substrate alone resulting in an inc in a.e. The req for multiple weak interactions to drive catalysis is one reason why enzymes are so large. -ΔGb contributes to rxn specificity & catalysis: ΔGb lowers a.e., neg & contributes to specificity of rxn—the ability to discriminate b/w a substrate & competing molec. If an enzyme active site has func groups arranged optimally to produce various weak interactions w/ a particular substrate in the transition state, the enzyme won’t be able to interact to the same degree w/ any other molec, eg. If substrate has OH group that interacts w/ Glu on the enzyme, a molec lacking a OH group at that posn will be a poorer substrate for the enzyme. In general, specificity is derived from the formation of many weak interactions b/w enzyme & its specific substrate. -Factors that contribute to a.e. incl: (ΔGb thus results from sum of weak interactions w/ substrate & the transition state) 1) entropy reduction constrains relative motions of reactants/substrates which makes it more likely substrate binds to enzyme. Binding energy holds the substrates in proper orientation to react b/c productive collisions in soln is rare. Substrates align w/ enzymes involving induced fit. Ie. Constraining the motion of 2 reactants inc rxn rate. 2) Formation of weak bo
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