Enzymology Chapter one

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Enzymology Chapter one

• INTRODUCTION
• 2006/09/18

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Aims of this book

• To give a broad account of enzymology and put
  current knowledge into perspective.
• Follow a progression from the properties of
  isolated enzymes to the behaviour of enzymes in
  increasingly complex systems, leading to the
  cells.

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Historical aspects

• Enzymes are catalysts which speed up the rates of
  reactions without themselves undergoing any
  permanent change.
• In a cell, there are a large number of enzymes to
  catalyze all kinds of metabolic reactions.
• How many enzymes in a cells? It depends on the
  cells, e.g. about 1700 enzymes are present in E.
  coli.
• Enzyme is derived from the Greek meaning in
  yeast and was first used by Kühne in 1878.
• In 1897, Bücher demonstrated that filtrates of
  yeast of enzymes could catalyze fermentation.

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Historical aspects

• In 1894 onward, Fischer proposed lock and key
  hypothesis to explain enzyme specificity.

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Historical aspects

• The first enzyme to be crystallized was urease by
  Sumner in 1926, an enzyme catalyzes the
  hydrolysis of urea to yield carbon dioxide and
  ammonia.
• The development of ultracentrifuge by Svedberg in
  1920s provided very high centrifugal fields for
  sedimentation of macromolecules.
• In 1960 the amino-acid sequence of ribonuclease
  was deduced by Hirs.
• In 1965 the 3-dimensional structure of lysozyme
  was deduced by the technique of X-ray
  crystallography.

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Historical aspects

• In 1958 Koshland proposed the induced fit
  theory to account for the catalytic power and
  specificity shown by enzymes.
• In 1963, Monod and his colleagues postulated
  allosteric model of enzyme control mechanism.
• In last ten years, the application of recombinant
  DNA techniques for the study of enzymes has
  produced some remarkable new insights.
• In 1986 Cech discovered that RNA can also act as
  a catalyst for reactions involving hydrolysis of
  RNA and so called ribozymes.

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Remarkable properties of enzymes as catalysts

• Catalytic power
• Specificity
• Regulation

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Catalytic power
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Specificity

• The range of specificity varies between enzymes.
• Some enzymes have low specificities, e.g. certain
  peptidases, phosphatases and esterases,
  degradation enzymes.
• Many enzymes show absolute or near-absolute
  specificity in which they will only catalyze with
  a single substrate, biosynthetic enzymes.
• Another distinct feature of many enzyme-catalyzed
  reactions is their stereospecificity.

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Regulation

• Enzymes may be regulated by small ions or other
  molecules, or by small changes in their covalent
  structure.
• Another common phenomenon in many biosynthetic
  pathways is the feedback inhibition.

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Cofactors

• Cofactors are the non-protein components which
  are required for enzyme activities.
• One group of cofactors is the metal ions.
• The second major class of cofactors is the
  organic cofactors.
• Tightly bound cofactors are called prosthetic
  group
• Holoenzyme, enzyme containing a cofactor or a
  prosthetic group together.
• Apoenzyme, the cofactor is removed from the
  enzyme protein.

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Nomenclature and classification of enzymes

• General classification
• Isoenzymes
• Multienzyme systems

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General classification

• The trivial names are given to many enzymes which
  consist of the suffix-ase added to the
  substrate acted on, e.g lactate dehydrogenase,
  protein kinase.
• Some trivial names are not helpful, e.g.
  catalase, papain, trypsin, rhodanese, etc.
• The present-day accepted nomenclature of enzymes
  is that recommended by the Enzyme Commission
  which was set up in 1955 by the International
  Union of Biochemistry (now known as the
  International Union of Pure and Applied
  Chemistry).
• Enzymes are named according to certain
  well-defined rules.

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General classification

• The six major types of enzyme-catalyzed reactions
  are
• Oxidation-reduction reactions, catalyzed by
  oxidoreductases.
• Group transfer reactions, catalyzed by
  transferases.
• Hydrolytic reactions, catalyzed by hydrolases.
• Elimination reactions in which a double is
  formed, catalyzed by lyases.
• Isomerization reactions, catalyzed by isomerases.
• Reactions in which two molecules are joined at
  the expense of an energy source (usually ATP),
  catalyzed by ligases.

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General classification

• Enzymes are further classified by being assigned
  an Enzyme Commission (EC) number consisting four
  parts (a, b, c, d).
• The first number (a) indicates the type of
  reaction catalyzed and the numbers are taken from
  1 to 6.
• The second number (b) indicates the subclass,
  which usually specifies the type of substrate or
  the bond cleaved more precisely.
• The third number (c) indicates the sub-subclass,
  allowing an even more precise definition of the
  reaction catalyzed.
• The fourth number (d) indicates the serial number
  of the enzyme in its sub-subclass.

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General classification

• Examples of EC numbers of enzymes
• 1.1.1.1 alcohol dehydrogenase
• 1.1.1.27 lactate dehydrogenase
• 2.7.1.1 hexokinase
• 3.6.1.3 adenosinetriphosphatase
• 4.1.2.13 fructose-bisphophate aldolase
• 5.3.1.1 triosephosphate isomerase
• 6.1.1.5 isoleucine-tRNA ligase
• See Appendix, pp450

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Isoenzymes

• Enzymes existing several forms of enzyme
  catalyzing the same reaction, and the differences
  are in term of their amino-acid sequences within
  a single species.
• One of the example is lactate dehydrogenases in
  heart and muscle.

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Multienzyme systems

• Multienzyme systems are proteins that exhibit
  more than one catalytic activity.

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The contents of this book

• Chapter 1, the introduction.
• Chapter 2 to 6, discussing the behaviour of
  isolated enzymes (2), structural characterization
  (3), kinetics (4), catalytic action (5) and
  control of activity (6).
• Chapter 7 and 8 include the multienzyme systems
  and enzymes in the cells.
• Chapter 9 , on enzyme turnover.
• Chapter 10 and 11, applications of enzymes.