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.#220.127.116.11.: 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
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
substrate complex was 1 proposed by Charles Adolphe Wurtz.
-Enzymes inc rxn rates: E + S ESEP E + P –Transient transition state (E,S,P:
enzyme, substrate, product). Any rxn such as SP 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 SP 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
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