CHEM 160 - LE 2

• Enzymes


  Biological catalysts
• Enzyme catalyzed reaction


  • Proceeds rapidly under mild conditions
  • Lowers the activation energy for a reaction
• Enzymes


  • Usually highly specific for the reactions they catalyze
  • Determine the patterns of chemical transformation
  • Mediate the transformation of one energy to another
• Glycolysis


  Catalysis takes place at the active site
• Nearly all enzymes are proteins
• Enzymes


  • Has the capacity to bind specifically a very wide range of molecules
• Ribozymes


  Enzymes that are RNA in nature
• Enzymes

  • Highly specific both in the reactions that they catalyze and in their choice of reactants called substrates
  • Usually catalyzes a single chemical reaction or a set of closely related reactions

  
• Cofactors


  • Nonprotein helpers
  • Bind to the active site and function in catalysis
  • Inorganic molecules
  • Usually involved in redox reactions
  • Small ions

  
• Coenzymes


  • Organic molecule that acts as cofactor
  • Usually are carriers
  • Bigger compared to cofactors
• Apoenzymes


  Enzyme without its cofactors
• Holoenzymes


  Complete, catalytically active enzyme

  
• Substrate concentration


  • Point of saturation - maximum

  
• pH


  • Can affect 3d structure of enzymes (because most are proteins)
  • Optimal pH - 7.4
• Temperature


  • As temperature increases, the rate of reaction increases
• Active Sites of Enzymes


  • Region that binds the substrates and cofactors
  • Also contains the residues (catalytic groups) that directly participate in the making and breaking of bonds
  • Not all amino acids involved in the protein are in the catalytic groups
  • Amino acids direct the catalytic residues to interact with each other or hold them together
• Characteristics of Active Site


  • 3d cleft formed by groups that come from different parts of amino acid sequence
  • Takes up a relatively small part of the total volume
  • Extra amino acids serve as scaffold to create 3d active site
  • Constitute the regulatory sites of interaction with proteins, or channels to bring substrate to the active site
  • Cleft or crevices
  • Has a nonpolar character that enhances the binding of substrate as well as catalysis
  • Substrates are bound to enzyme by multiple weak interactions
  • Specificity of binding depends on the precisely defined arrangement of atoms in an active site

  
• Lock and key model


  Fisher - For every lock (enzyme) there is a key (substrate)
• Induced fit model


  Daniel E. Koshland Jr.
• Classification of Enzymes


  • Oxidoreductases
  • Transferases
  • Hydrolases
  • Lyases
  • Isomerases
  • Ligases

  
• Oxidoreductases


  Catalyse oxidation or reduction reactions, where electrons are transferred from one molecule (the reductant) to another molecule (the oxidant)
• Redox Reaction


  • Transfer of electron
  • Ethanol lost H (undergo oxidation)
  • NAD+ gained H (undergo reduction)
• Transferases


  • Catalyse the movement of a functional group from one molecule to another
  • Very diverse; can include phosphate, methyl, and glycosyl groups
  • Kinase - when phosphate are transferred
• Hydrolases


  Hydrolysis of a substrate or breaking of a chemical bond with the use of water
• Lyases


  Breaking of various chemical bonds (C-C, C-O, C-N, and C-S), by means of other than hydrolysis and oxidation often forming/breaking new double bond or a new ring structure
• Isomerases


  Transfer of groups within molecules to form isomeric forms
• Ligases


  • Responsible for the catalysis of ligation; joining of two substrates
  • Usually chemical potential energy is required, so the reaction is coupled to the hydrolysis of a diphosphate bond in a nucleotide triphosphate such as ATP
  • DNA ligase (joins okazaki fragments)
• Enzymes


  Biological catalysts

  
• Enzyme catalyzed reaction


  • Proceeds rapidly under mild conditions
  • Lowers the activation energy for a reaction

  
• Enzymes


  • Usually highly specific for the reactions they catalyze
  • Determine the patterns of chemical transformation
  • Mediate the transformation of one energy to another

  
• Enzyme catalysis

  Catalysis takes place at the active site

  
• Nearly all enzymes are proteins
• Enzymes

  • Have the capacity to bind specifically a very wide range of molecules
• Ribozymes


  Enzymes that are RNA in nature
• Enzymes

  • Highly specific both in the reactions that they catalyze and in their choice of reactants called substrates
  • Usually catalyzes a single chemical reaction or a set of closely related reactions

  
• Cofactors

  Nonprotein helpers that bind to the active site and function in catalysis

  
• Coenzymes


  Organic molecules that act as cofactors, usually are carriers and bigger compared to cofactors
• Apoenzymes


  Enzymes without their cofactors
• Holoenzymes


  Complete, catalytically active enzymes

  
• Substrate concentration


  • Point of saturation - maximum