enzymes

• Enzyme


  A substance - usually a protein - that acts as a catalyst for a biological reaction
• Enzymes don't affect the equilibrium constant of a reaction and can't bring about a chemical change that is otherwise unfavorable

  
• Enzyme action


  Acts only to lower the activation energy for a reaction, thereby making the reaction take place more rapidly

  
• Enzymes will catalyze only a single reaction of a single compound, called the enzyme's substrate
• Enzymes


  • Amylase
  • Papain
• Recommended enzyme name


  Short name with "-ase" suffix attached to the substrate or description of the action
• Systematic enzyme name


  More complete name divided into six major classes: Oxidoreductases, Transferases, Hydrolases, Lyases, Isomerases, Ligases

  
• Active site


  • Enzyme molecules contain a special pocket or cleft that contains amino acid side chains that participate in substrate binding and catalysis
  • The substrate binds the enzyme, forming an enzyme-substrate (ES) complex
  • ES is converted to an enzyme-product (EP) complex that subsequently dissociates to enzyme and product
• Catalytic efficiency


  • Enzymes are highly efficient, proceeding 103-108 times faster than uncatalyzed reactions
  • The number of molecules of substrate converted to product per enzyme molecule per second is called the turnover number, or kcat and typically is 102-104s-1
• Enzyme specificity


  • Enzymes are highly specific, interacting with one or few substrates and catalyzing only one type of chemical reaction
• Holoenzyme


  The active enzyme with its nonprotein component
• Apoenzyme


  An enzyme without its nonprotein moiety and is inactive
• Cofactor

  A metal ion such as Zn2+ or Fe2+
• Coenzyme


  A small organic molecule
• Cosubstrate


  A coenzyme that only transiently associates with the enzyme
• Prosthetic group


  A coenzyme that is permanently associated with the enzyme and returned to its original form
• Enzyme regulation


  • Enzyme activity can be regulated, that is, increased or decreased, so that the rate of product formation responds to cellular need
• Enzyme localization


  • Many enzymes are localized in specific organelles within the cell to isolate the reaction substrate or product from other competing reactions and provide a favorable environment for the reaction

  
• Free energy of activation


  The energy difference between that of the reactants and a high-energy intermediate that occurs during the formation of product

  
• Enzyme catalysis


  1. Transition-state stabilization

  2. Other mechanisms like general acid-base catalysis and covalent ES complex formation

  
• Reaction velocity (v)


  The number of substrate molecules converted to product per unit time
• Michaelis-Menten equation


  Relates the initial velocity of an enzyme catalyzed reaction to substrate concentration (S)

  
• Michaelis-Menten constant (Km)


  Provides a basis for evaluating the affinity of enzyme for a substrate, the greater the Km the less affinity of enzyme for substrate

  
• Enzyme concentration (E)


  The rate of an enzyme catalyzed reaction is directly proportional to enzyme concentration

  
• Temperature and pH


  As temperature and pH increases, thermal denaturation decreases the effective enzyme concentration and decreases the reaction rate

  
• Competitive inhibition


  Inhibitors have a close resemblance to the substrate and competes with the substrate for the active site of the enzyme, reducing the amount of substrate converted into product per unit time

  
• Competitive inhibition


  • Substrate: Succinic acid, Inhibitor: Malonate
• Competitive inhibition


  Inhibitor can bind to the enzyme but not the substrate-enzyme complex. Increases Km but does not change Vmax.

  
• Michaelis-Menten plot with competitive inhibition


  • Vmax remains the same, but Km increases.
• Lineweaver-Burk plot with competitive inhibition


  • Lines intersect on the y-axis, indicating no change in Vmax but an increase in Km.
• Competitive inhibition examples


  • Substrate: Succinic acid; Inhibitor: Malonate
  • Substrate: PABA; Inhibitor: Sulfa drugs
• Non-competitive inhibition


  Inhibitor can bind to both the enzyme and the enzyme-substrate complex. Does not change Km but decreases Vmax.

  
• Michaelis-Menten plot with non-competitive inhibition


  • Vmax decreases, Km does not change.
• Lineweaver-Burk plot with non-competitive inhibition


  • Lines intersect on the x-axis, indicating a decrease in Vmax but no change in Km.
• Uncompetitive inhibition


  Inhibitor can only bind to the enzyme-substrate complex, not the free enzyme. Decreases both Km and Vmax.

  
• Uncompetitive inhibition example


  • Substrate: Coenzyme A; Inhibitor: Pi or inorganic phosphate; Enzyme: succinyl Coenzyme A synthetase
• Other types of inhibition

  • Substrate inhibition
  • Kcat inhibition
  • Feedback inhibition
• Allosteric enzymes have multiple binding sites, and the binding of one substrate can induce structural or electronic changes that alter the affinities of the vacant sites.
• Allosteric enzymes yield a sigmoidal velocity curve, which provides a more sensitive control of reaction rate at moderate specific velocities by varying substrate concentration.

  
• Cofactors


  Required by enzymes to carry out their catalytic functions. Help bind the substrate to the active site.