biochem summer midterm lesson 2

• Enzymes


  Biologic catalysts that accelerate chemical reactions

  
• Enzymes


  • They hasten chemical reactions by lowering activation energy
  • They are not consumed during the reactions
  • They do not undergo a chemical change after the reactions

  
• Activation energy


  The energy needed to start a chemical reaction
• Chemical reaction


  1. Reactant (large stone) rolls up hill

  2. Reactant breaks into products (stone rolls down and breaks into pieces)

  3. Activation energy is the energy needed to roll the stone up the hill
• All chemical reactions in biological systems have an energy barrier which prevents reactions from proceeding in a spontaneous manner
• Activation energy


  The input of energy required to break the energy barrier or to start the reaction
• Enzymes


  They lower the activation energy for the reaction to proceed, thus speeding up the chemical reaction

  
• Enzymes


  • Their presence does not affect the nature and properties of the products
  • They are highly specific in their action and their substrate
  • They are sensitive to pH, temperature and substrate concentration

  
• Levels of protein structure

  • Primary - covalent bonds between amino acids
  • Secondary - H-bonds within the polypeptide chain
  • Tertiary - interactions between side chains
  • Quaternary - interactions between polypeptide chains

  
• Denaturation


  Breaking of weak linkages or bonds within a protein molecule that are responsible for the highly ordered structure of the protein in its natural state, resulting in a looser, more random structure

  
• Enzyme commission nomenclature (E.C.)

  1st digit = class, 2nd digit = subclass, 3rd digit = sub-class, 4th digit = serial number

  
• Enzyme classes based on the reactions they catalyze

  • Oxidoreductase
  • Transferase
  • Hydrolase
  • Lyase
  • Isomerase
  • Ligase

  
• Substrate


  Substance acted upon by the enzyme

  
• Products


  The resulting chemicals after the enzyme-catalyzed reactions
• Active site


  Region of an enzyme where substrate molecules bind and undergo a chemical reaction

  
• Allosteric site


  Any site other than the active site of the enzyme

  
• Binding site


  The portion that selects the substrate and binds to it
• Catalytic site


  Site that performs the catalytic action of the enzyme

  
• Apoenzyme


  Protein part of an enzyme
• Holoenzyme


  The non-protein part (cofactor) together with the protein part (apoenzyme) forms a holoenzyme

  
• Cofactors


  Non-protein molecules or metallic ions attached to the enzyme that enhance its function; without these, enzymes remain in the inactive "apoenzyme" form

  
• Types of cofactors


  • Inorganic cofactors (metal atoms)
  • Organic cofactors (prosthetic groups - more tightly bound, coenzymes - bind more loosely)
• Enzyme kinetics


  1. Enzyme interacts with substrate to form enzyme-substrate complex (ES)

  2. Reaction followed by decomposition of ES to regenerate free enzyme (E) and new product (P)

  
• Michaelis-Menten kinetics


  Graphical representation of the relationship between rate of reaction and substrate concentration, resulting in a hyperbolic curve

  
• Michaelis-Menten kinetics


  • At low substrate concentration, rate of reaction increases steeply with increasing substrate
  • At high substrate concentration, rate of reaction reaches maximum velocity (Vmax) as all enzyme active sites are saturated
  • Km is the substrate concentration at which the reaction rate is 1/2 of Vmax

  
• Km


  An inverse measure of the affinity of the enzyme for its substrate

  
• The higher the Km, the lower the affinity of the substrate to the enzyme; the lower the Km, the higher the affinity of the substrate to the enzyme

  
• Factors affecting enzymatic reactions

  • Substrate concentration
  • Enzyme concentration
  • pH
  • Temperature
  • Cofactors
  • Presence of inhibitors

  
• Competitive inhibitors


  Resemble the substrate and bind to the active site of the enzyme, preventing substrate binding; their effect can be reversed by increasing substrate concentration

  
• Noncompetitive inhibitors


  Bind to the enzyme away from the active site, altering the shape and reducing the effectiveness of the active site; their effect cannot be reversed by increasing substrate concentration

  
• Uncompetitive inhibitors


  Bind only to the enzyme-substrate complex, reducing the effectiveness of the active site; their effect cannot be reversed by increasing substrate concentration

  
• Fischer's lock and key model


  Assumes the active site of the enzyme and the substrate are exactly shaped to fit each other

  
• Koshland's induced fit model

  The enzyme structure is flexible and reshapes to become complementary to the substrate upon binding

  
• The induced fit model suggests that enzymes can act on substrates that do not perfectly fit the active site, as the enzyme structure changes to accommodate the substrate