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Enzymes
Enzymes are highly efficient, selective biological catalysts which
accelerate the approach of metabolic reactions to equilibrium
without changing that equilibrium. Enzymes provide alternative
pathways with lower activation energies. Without enzymes
metabolic reactions would not take place quickly enough for cells
to live. Most enzymes are globular proteins.
The tertiary structure is important for the enzyme to carry out its
functions. A specific area called the active site of the enzyme
molecule binds other molecules called substrates to produce
required products.
 Enzymes are relatively large molecules and form many contact
points with the substrate. In enzyme catalyzed reactions an
intermediate step forms when the enzyme binds to the substrate
called the enzyme substrate complex, the enzyme holds the
substrate in the required orientation for a reaction to occur, by
placing the substrate next to specific amino acids and co factors.
These binding points results from hydrogen bonds, Van der Waals
interactions and ionic interactions, during these chemical reactions
the enzymes themselves are not consumed in the end, one enzyme
can convert many substrate molecules into product.
Enzymes are specific in the types of reactions they catalyze and the
types of substrate they act on; they have particular shapes which
allow them to be unambiguous with which substrate they bind to.
Fig.I.1 Enzyme Activity




Table: 1.1 Enzyme Specificity

Type of Specificity             Characteristics
Absolute                        Enzymes that act on a particular
                                substrate only
Group                           Enzymes that act either
                                relatively or absolutely on
                                substrates in close relations with
                                a particular functional group
Steriochemical                  Enzymes that act on particular
                                sterioisomers
Linkage                         Enzymes that act on a particular
                                bond regardless of the rest of the
                                molecules structure
In metabolism the enzyme usually does not react alone, sometimes
the enzyme cannot convert the substrate to product by itself; this is
facilitated by molecules called co-factors. These enzymes usually
have a binding site for the substrate and another for the co-factor,
the enzyme only catalyses for these to molecules and no other, the
enzyme does this by binding to the substrate first then the cofactor
preventing catalysis of the co factor with anything else.

Fig.I.2: Enzyme activity with co factor.




Inhibitors are compounds that bind enzymes; they disrupt their
activity by preventing either the formation of the enzyme substrate
complex or its breakdown to enzyme and product. There are two
types of inhibition reversible and irreversible. There are different
types of reversible inhibition:
Fig.I.3: Reversible Inhibition.




  a) Competitive Inhibition

  •    Binds to the active site of the free enzyme only, has same
           shape as substrate.
  •    If the enzyme is allosteric the binding of the inhibitor to
           one site prevents the binding of substrate at another in,
           the inhibitor may not have the same shape as the
           substrate.
  •    Km increases.
  •    Vmax is unchanged.
  •    Both cases prevent the formation of the enzyme substrate
           complex.

  b) Noncompetitive Inhibition
       • Binds to either the active site of the free enzyme or the
         active site of the enzyme substrate complex, preventing
         either the formation of the ES complex or the of the ES
         complex to E+P.
       • the substrate still binds to the enzyme
• The inhibitor alters the enzymes shape in such a way
         that the enzyme becomes inactive. The inhibitor does
         not have the same shape as the substrate.
       • Vmax decreases.
       • Km is unchanged.
       •
  c) Uncompetitive inhibition

  • Binds to the active site of the enzyme substrate complex
    only.
  • does not compete with the substrate
  • Prevents breakdown to enzyme and product. The inhibitor
    does not have the same shape as the substrate.
  • Km and Vmax both decrease.
  • Ratio of Vmax/Km is unchanged.

  d) Mixed Inhibition
       • Binds to free enzyme
       • Binding of either the inhibitor or substrate to the
         enzyme decreases the enzymes affinity to the other.
       • Km may increase or decrease.
       • Vmax always decreases.

Irreversible inhibitors bind to enzymes by covalent bonds.
Fig.I.3: Graphs of factors affecting rate of enzyme catalyzed
reactions.

  a) Effect of increasing substrate concentration




As concentration of substrate increases collision frequency
between substrates and active sites of enzymes increases, in turn
increasing rate. Because the number of enzyme molecules is fixed,
eventually all the enzyme active sites become filled with substrate
and the rate reaches a maximum without any further increase.


  b) Effect of increasing temperature.




Increasing temperature increases the kinetic energy in the system
causing more molecules to have sufficient energy to get over the
energy barrier, increasing collisions between substrate and active
sites, further increase in temperature causes the bonds keeping the
protein together to vibrate, when the enzyme reaches optimum
temperature these bonds vibrate so much that they break. The
enzyme’s tertiary structure denatures and changes the shape of the
active site making the enzyme inactive. This denaturation is
cooperative; as soon as the optimum temperature is surpassed the
entire enzyme breaks down, it does not break down bond by bond.

Table :1.2 Enzyme Classification.

Group number     Class              Function                Examples
1.               Oxidoreductases    catalyze oxidation      Cytochrome
                                    reduction reactions.    oxidase, lactate
                                                            dehydrogenase

2.               Transferases       Transferases            Acetate kinase,
                                    catalyze group          alanine deaminase
                                    transfer reactions-
                                    the transfer of a
                                    functional group
                                    from one molecule
                                    to another.
3.               Hydrolases          In hydrolysis          Lipase, sucrase
                                    reactions, C-O, C-N,
                                    and C-S bonds are
                                    cleaved by addition
                                    of H2O in the form
                                    of OH- and H+ to the
                                    atoms forming the
                                    bond.
4.               Lyases             Lyases cleave C-C,      Oxalate
                                    C-O, C-N, and C-S       decarboxylase,
                                    bonds by means          isocitrate lyase
                                    other than
                                    hydrolysis or
                                    oxidation.
5.               Isomerases         Isomerases just         Glucose-phosphate
                                    rearrange the           isomerase, alanine
                                    existing atoms of a     racemase
                                    molecule, that is,
                                    create isomers of the
                                    starting material.
6.               Ligases                                    Acetyl-CoA
                                                            synthetase, DNA
                                                            ligase
Ligases synthesize
C-C, C-S, C-O, and
C-N bonds in
reactions coupled to
the cleavage of high
energy phosphate
bonds in ATP

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Enzymes

  • 1. Enzymes Enzymes are highly efficient, selective biological catalysts which accelerate the approach of metabolic reactions to equilibrium without changing that equilibrium. Enzymes provide alternative pathways with lower activation energies. Without enzymes metabolic reactions would not take place quickly enough for cells to live. Most enzymes are globular proteins. The tertiary structure is important for the enzyme to carry out its functions. A specific area called the active site of the enzyme molecule binds other molecules called substrates to produce required products. Enzymes are relatively large molecules and form many contact points with the substrate. In enzyme catalyzed reactions an intermediate step forms when the enzyme binds to the substrate called the enzyme substrate complex, the enzyme holds the substrate in the required orientation for a reaction to occur, by placing the substrate next to specific amino acids and co factors. These binding points results from hydrogen bonds, Van der Waals interactions and ionic interactions, during these chemical reactions the enzymes themselves are not consumed in the end, one enzyme can convert many substrate molecules into product. Enzymes are specific in the types of reactions they catalyze and the types of substrate they act on; they have particular shapes which allow them to be unambiguous with which substrate they bind to.
  • 2. Fig.I.1 Enzyme Activity Table: 1.1 Enzyme Specificity Type of Specificity Characteristics Absolute Enzymes that act on a particular substrate only Group Enzymes that act either relatively or absolutely on substrates in close relations with a particular functional group Steriochemical Enzymes that act on particular sterioisomers Linkage Enzymes that act on a particular bond regardless of the rest of the molecules structure
  • 3. In metabolism the enzyme usually does not react alone, sometimes the enzyme cannot convert the substrate to product by itself; this is facilitated by molecules called co-factors. These enzymes usually have a binding site for the substrate and another for the co-factor, the enzyme only catalyses for these to molecules and no other, the enzyme does this by binding to the substrate first then the cofactor preventing catalysis of the co factor with anything else. Fig.I.2: Enzyme activity with co factor. Inhibitors are compounds that bind enzymes; they disrupt their activity by preventing either the formation of the enzyme substrate complex or its breakdown to enzyme and product. There are two types of inhibition reversible and irreversible. There are different types of reversible inhibition:
  • 4. Fig.I.3: Reversible Inhibition. a) Competitive Inhibition • Binds to the active site of the free enzyme only, has same shape as substrate. • If the enzyme is allosteric the binding of the inhibitor to one site prevents the binding of substrate at another in, the inhibitor may not have the same shape as the substrate. • Km increases. • Vmax is unchanged. • Both cases prevent the formation of the enzyme substrate complex. b) Noncompetitive Inhibition • Binds to either the active site of the free enzyme or the active site of the enzyme substrate complex, preventing either the formation of the ES complex or the of the ES complex to E+P. • the substrate still binds to the enzyme
  • 5. • The inhibitor alters the enzymes shape in such a way that the enzyme becomes inactive. The inhibitor does not have the same shape as the substrate. • Vmax decreases. • Km is unchanged. • c) Uncompetitive inhibition • Binds to the active site of the enzyme substrate complex only. • does not compete with the substrate • Prevents breakdown to enzyme and product. The inhibitor does not have the same shape as the substrate. • Km and Vmax both decrease. • Ratio of Vmax/Km is unchanged. d) Mixed Inhibition • Binds to free enzyme • Binding of either the inhibitor or substrate to the enzyme decreases the enzymes affinity to the other. • Km may increase or decrease. • Vmax always decreases. Irreversible inhibitors bind to enzymes by covalent bonds.
  • 6. Fig.I.3: Graphs of factors affecting rate of enzyme catalyzed reactions. a) Effect of increasing substrate concentration As concentration of substrate increases collision frequency between substrates and active sites of enzymes increases, in turn increasing rate. Because the number of enzyme molecules is fixed, eventually all the enzyme active sites become filled with substrate and the rate reaches a maximum without any further increase. b) Effect of increasing temperature. Increasing temperature increases the kinetic energy in the system causing more molecules to have sufficient energy to get over the energy barrier, increasing collisions between substrate and active sites, further increase in temperature causes the bonds keeping the protein together to vibrate, when the enzyme reaches optimum
  • 7. temperature these bonds vibrate so much that they break. The enzyme’s tertiary structure denatures and changes the shape of the active site making the enzyme inactive. This denaturation is cooperative; as soon as the optimum temperature is surpassed the entire enzyme breaks down, it does not break down bond by bond. Table :1.2 Enzyme Classification. Group number Class Function Examples 1. Oxidoreductases catalyze oxidation Cytochrome reduction reactions. oxidase, lactate dehydrogenase 2. Transferases Transferases Acetate kinase, catalyze group alanine deaminase transfer reactions- the transfer of a functional group from one molecule to another. 3. Hydrolases In hydrolysis Lipase, sucrase reactions, C-O, C-N, and C-S bonds are cleaved by addition of H2O in the form of OH- and H+ to the atoms forming the bond. 4. Lyases Lyases cleave C-C, Oxalate C-O, C-N, and C-S decarboxylase, bonds by means isocitrate lyase other than hydrolysis or oxidation. 5. Isomerases Isomerases just Glucose-phosphate rearrange the isomerase, alanine existing atoms of a racemase molecule, that is, create isomers of the starting material. 6. Ligases Acetyl-CoA synthetase, DNA ligase
  • 8. Ligases synthesize C-C, C-S, C-O, and C-N bonds in reactions coupled to the cleavage of high energy phosphate bonds in ATP