Enzymes – Part I

Biochemistry I

Lecture 1                                                        2009 (J.S.)









                        2   Enzymes function under mild reaction conditions:

–  at atmospheric pressure,

–  at low temperature

             (most of the enzymes are denatured above 50 °C),

–  in limited range of pH values

             (denaturation of enzymes in extremely acidic as                           well as
alkaline solutions),

–  in dilute solutions (at very low enzyme concentrations).

3   Enzymes are highly specific catalysts





Chiral substrates are bound to the stereospecific enzymes at three sites:



                                4  Enzymes are regulated catalysts

                                        Enzyme nomenclature



Major class 1      Oxidoreductases

catalyze oxidation-reduction of substrates.

Subclasses and frequent recommended names:

   – dehydrogenases catalyze transfers of two hydrogen atoms,

   – oxygenases catalyze incorporation of one or two atoms of

         oxygen into the substrate (monooxygenases, dioxygenases),

   – oxidases catalyze transfers of electrons between substrates

         (e.g. cytochrome c oxidase, ferroxidase),

   – peroxidases catalyze breakdown of peroxides.

Major class 2    Transferases

catalyze transfers of an atomic group from one to another substrate.

Subclasses and frequent recommended names:

   – aminotransferases, methyltransferases, glucosyltransferases,

   – phosphomutases catalysing transfers of the groups PO[3]^2– within

        certain molecules,

   – kinases phosphorylating substrates by the transfer of the

        phosphoryl group PO[3]^2– from ATP (e.g. hexokinases,

        proteinkinases, pyruvate kinase).

Major class  3      Hydrolases

Major class 4       Lyases

Major class 5     Isomerases

catalyze intramolecular rearrangements of atoms.

Frequent names:

  – epimerases,

  – racemases,

  – (some types of) mutases.

Major class 6     Ligases

catalyze formation of high-energy bonds C–C, C–O, C–N in the reaction coupled with hydrolysis of
another high-energy compound (usually molecule ATP).

Frequent recommended names

     – carboxylases

     – synthetases (e.g. glutamine synthetase; don't change for                           synthases
in class 4!)

Classification numbers of enzymes

EC (abbr. Enzyme Commission)

     major class number

      . subclass number

            . sub-subclass number

                  . the enzyme's arbitrarily assigned serial

                                                               number in its subsubclass

Example:

Recommended name:  Alanine aminotransferase    (ALT)

Code number:                 EC 2.6.1.2

     - Major class            2     Transferases

     - Subclass                 6       - transferring nitrogenous groups

     - Sub-subclass           1           - transferring amino groups

     - Enzyme's number      2               Alanine aminotransferase

Systematic name:      L-Alanine:2-oxoglutarate aminotransferase

                                     The structure of enzymes

    Not speaking of ribozymes, enzymes are proteins mostly of globular type. Some of them exhibit
simple or complicated quaternary structures (oligomeric enzymes and multienzyme complexes).















NAD^+ is the coenzyme of dehydrogenases
It acts as an oxidant that takes off  two atoms of hydrogen from the substrate.
One atom plus one electron (hydride anion H^–) is added to the para-position of the pyridinium
ring, the remaining H^+ binds to the enzyme.





FAD  -  flavin adenine dinucleotide and

FMN   - flavin mononucleotide

act as oxidants in certain types catalyzed by dehydrogenases.



Molybdopterin

Tetrahydrobiopterin (BH[4])

acts as the coenzyme – a reductant – in certain hydroxylations

catalyzed by monooxygenases.

It supplies two atoms of hydrogen and is oxidized to the

quinoid form of dihydropterin:





is a substituted 1,4-benzoquinone that acts as the electron acceptor

for flavoprotein dehydrogenases in the respiratory chain.

It has a side chain containing a variable number of (in animals usually 10)

isoprenoid units. Because of its high hydrophobicity, it is entirely dissolved in

the inner mitochondrial membrane.

                                            Cytochromes