Catalytic Mechanism of Enzyme Reaction

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					Catalytic Mechanism of Enzyme Reaction

Remarkable properties of Enzymes as catalysts
  1. Catalytic power
  2. Specificity
  3. Regulation

Ad1. Catalytic Power
  - enzymes increase the rate of reaction by as
    much as 1012 –fold

  - not many examples  to compare between the
    rates of an enzyme-catalyzed reaction and the
    reaction occurring under similar conditions
    (temperature, pH etc) but in the absence of
    enzyme  as it is too low to be measured

  - Comparison between enzymatic and non-
    enzymatic catalysts  also difficult. As
    enzymatic catalysts occur :
       o Much higher rates
       o Lower temperature
    It is well illustrated by the process of nitrogen
    fixation (N2  ammonia)  catalyzes by
    nitrogenase complex (300 K ,pH neutral)
    Industrial synthesis of ammonia from nitrogen
    and hydrogen  temp 700-900 K, pressure 100-
    900 atm, with iron catalyst

Ad2. Specificity
  - enzyme  highly specific both in :
      o nature of substrate
      o the reaction they catalyze
  - the range of specificity varies between enzymes
      o low specificity  the specificity base on
        bond specificity
        ex. Peptidase, phoshatase, esterase 
        utilize a wide range of substrates which
        contain the required chemical bond
        mostly for degradative enzymes but not
        biosynthetic enzymes.
      o intermediate specificity  group specificity
        ex. Hexokinase  catalyse the
        phosphorylation of a variety of sugars
        provided they are aldohexose
      o absolute / near absolute specificity.  only
        catalyse a reaction with a single substrate at
        an appreciable rate

Ad3. Regulation
  - The catalytic activity  regulated by small ions
    or other molecules
  - Ex.
      The breakdown of glycogen in skeletal muscle
      Carbohydrate reserved  degraded to generate
      ATP  required for muscle contraction
      The muscle contraction is triggered by release
      of Ca2+ from the sarcoplasmic reticulum 
      also ensure the continuation of ATP
      Feedback inhibition phenomena  common in
      many biosynthetic pathway
      Ex. Biosynthetic pathway leading to the
      synthesis of pyrimidine nucleotide  the end
      product UTP and CTP  block the first
       they are able to to limit the flow of
      metabolites into the pathway and regulate
      their own biosynthesis
 A catalyst works simply by lowering the energy
  barrier of a reaction, ΔGº±
 Catalysts provide an alternative way
 the catalyst increases the fraction of molecules
  that have enough energy to attain the transition
  state, thus making the reaction go faster in both
 The position of the equilibrium (the amount of
  product versus reactant) is unchanged by a
 Catalysts lower the energy barrier in two ways:

        o The catalyst binds a substrate in an
          intermediate conformation that resembles
          the transition state, but has a lower
          energy.  lead to multiple intermediate
          states that bypass the transition state. An
          intermediate state is a metastable state of
          a molecule.
        o In a non-catalyzed reaction the entropy
          may be highly negative due to the highly
          specific orientation required in order for a
          reaction to occur. Catalysts can lower the
          negative entropy by binding reacting
          molecules only in the proper mutual
          orientation, thus increasing their reactivity

        E + S ↔ ES ↔ EP ↔ E + P

Collision Theory

Molecular velocity determines the binding of enzyme
and substrate, thereby determine ES formation and
Enzyme catalytic velocity
Transient ES complex undergo INTRA-Molecular
straining  decreasing initial energy requirement for
catalytic reaction to produce reaction product

The highest point of the energy profile is
designated the transition state of the reaction

In all cases,  the catalyst does not cause a shift in
the equilibrium between reactant (s) and product (s)
 only increases the rate at which that equilibrium
is attained.

Various factors leading to the rate enhancements 
      a. proximity and orientation effects
      b. acid-base catalyst
      c. covalent catalyst
      d. strain or distortion
      e. changes in environment

ad.a proximity and orientation effects

commonly  an enzyme could increase the rate of
reaction involving more than one substrate by 

    binding the substrates at adjacent sites and
  therefore cringing them into close proximity with
                      each other

so reaction occur more readily

Orientation with respect to each other  influence
the rate of reaction
    Enzymes  make sure that the reactants are in
the correct orientation as they approach each other

In this examples the restrictions placed on rotation
of single bonds by bridge structure  ensures that
the preferred orientation of the reacting groups
closely resembles that of the transition state of the

Less rotational entropy (degrees of freedom) occurs
as the reaction proceed towards the transition state

The smaller negative entropy of activation  lead to
an increase in the rate of reaction

Adb. Acid-Base catalyst

Many reactions of the type catalyzed by enzymes are
known to be catalyzed by acids and/or base

Since enzymes contain a number of amino acid side
chains which are capable of acting as proton donors
or acceptors  acid-base catalysis  important
Adc. Covalent catalysis (intermediate formation)

Reactions can be speeded up by the formation of

Many of the examples of covalent catalysis in
enzyme-catalyzed reactions involve attack by a
nucleophilic side chain at electron-deficient centre in
the substrate  nucleophilic catalysis

Ad.d Strain or distortion

A substrate may be distorted on binding to the
appropriate enzyme  speed up the reaction if the
distortion lowered the free energy of activation by
making the geometry and electronic structure of the
substrate more closely resemble the transition state

Strain also give a stabilization of the transition
state of the reaction
Enzymes  make favorable contact with the
transition state of the substrate

Ad5. changes in environment

The rates of many organic reactions are highly
sensitive to the nature of of the solvents in which
they occur


   The induced fit model of enzyme action is a
    modification of the lock-and-key model originally
    proposed by Emil Fischer in 1894
   The lock-and-key model proposes that an
    Enzyme/substrate pair is like a lock and key.
    Though it explains the specificity of enzyme
    /substrate pairs, it does little to explain
    catalysis, because a lock does not change a key
    the way an enzyme changes a substrate.
   In 1958, Daniel Koshland proposed the induced
    fit model to explain enzymatic catalysis 
    proposed that distortion of the enzyme and the
    substrate is an important event in catalysis.

Enzymes do more than simply bind and position
substrates, however. Enzymes

   1. Bind substrate(s);

   2. Lower the energy of the transition state; and

   3. Directly promote the catalytic event  occur as
      a result of specific amino acid side chains that
      physically interact with the substrate and end
      up promoting the reaction.

When the catalytic process is complete, the enzyme
must be able to release the product or products and
return to its original state for another round of

Triose Phosphate Isomerase Catalysis

Triose phosphate isomerase catalyzes the following

   Glyceraldehyde-3-Phosphate (G3P) <=> cis-
    enediol intermediate <=> Dihydroxyacetone
    Phosphate (DHAP)

The active enzyme is a dimer of two identical
The active site (the place on the enzyme where
catalysis occurs) can accommodate either G3P or
At the active site, a glutamate residue (Glu 165) and
a histidine (His 95) are essential for function of the
enzyme. The reaction steps :

    E + G3P <=> E-G3P (Binding of G3P)

   E-G3P <=> E-ed (Conversion to enediol)

   E-ed <=> E-DHAP (Conversion to DHAP)

   E-DHAP <=> E + DHAP (Release of DHAP)
Like other enzymes, triose phosphate isomerase
lowers the energy barriers of the transition

Both triose phosphate isomerase and serine
proteases have a histidine and an acidic residue
in their active site. Histidine is very common in
active sites, because it readily accepts or donates
protons at physiological pH.
Multisubstrate Reactions

   Most biochemical reactions involve two or more
    substrates, often resulting in multiple products.
   An example is proteolysis, which involves two
    substrates (the polypeptide and water) and two
    products (the two fragments of the cleaved
    polypeptide chain).
   When an enzyme binds two or more substrates
    and releases multiple products, the order of
    the steps becomes an important feature of the
    enzyme mechanism. Several classes of
    mechanisms include the following:

      o Random substrate binding
      o Ordered substrate binding
      o The "ping-pong" mechanism

Ad. Random substrate binding
    In this mechanism, either substrate can be
    bound first, though in many cases one substrate
    will be favored for initial binding, and its
    binding may promote the binding of the other.
Ad. Ordered substrate binding
    This mechanism occurs when one substrate
    must bind before a second one can bind
     often observed in oxidations of substrates by
    the coenzyme nicotinamide adenine dinucleotide

Ad. The ping-pong mechanism
    This occurs when a catalytic sequence of events
   occurs, such as one substrate is bound, one
   product is released, a second substrate is bound,
   and a second product is released.