BIOCHEM

• Enzymes are not consumed during the reaction but merely help the reaction occur more rapidly
• Enzymes are named based on the function of the enzyme, type of reaction catalyzed, and the substrate identity
• Models of Enzyme Action

  1. Enzyme Active Site: Small part of an enzyme's structure involved in catalysis

  2. Enzyme-Substrate Complex: Intermediate reaction species formed when a substrate binds to the active site

  3. Lock-and-Key Model: Active site in the enzyme has a fixed, rigid geometrical conformation

  4. Induced-Fit Model: Enzyme's active site is not rigid and static, allowing for changes to accommodate a substrate
• Most enzymes are globular proteins
• Enzyme Specificity


  Extent to which an enzyme's activity is restricted to a specific substrate
• Enzymes are compounds, usually proteins, that act as catalysts for biochemical reactions
• 3 Important Aspects in the Naming Process of Enzymes

  • Suffix: Most enzymes end in the suffix "ase"
  • Type of reaction catalyzed by an enzyme is often used as a prefix
  • Identity of substrate and type of reaction catalyzed
• Enzyme Structure

  • Simple Enzyme: Composed only of protein
  • Conjugated Enzyme: Has a non-protein part in addition to a protein part
  • Apoenzyme: Protein of the conjugated enzyme
  • Cofactor: Non-protein part of the conjugated enzyme
  • Holoenzyme: Biochemically active conjugated enzyme produced from an apoenzyme and a cofactor
  • Coenzyme: Serves as a cofactor in a conjugated enzyme
• Classification of Enzymes

  • Oxidoreductase: Catalyzes an oxidation-reduction reaction
  • Transferase: Catalyzes the transfer of a functional group from one molecule to another
  • Hydrolase: Catalyzes the hydrolysis reaction
  • Lyase: Catalyzes the addition or removal of a group without hydrolysis or oxidation
  • Isomerase: Catalyzes the isomerisation of a substrate
  • Ligase: Catalyzes the bonding together of two molecules
• Enzymes cause cellular reactions to occur millions of times faster
• Enzyme Flexibility


  • Allows for changes in the shape or geometry of the active site of an enzyme to accommodate a substrate
  • Result of the enzyme’s flexibility; it adapts the incoming substrate
• Stereochemical Specificity


  Act on a particular isomer
• Turnover Number


  Number of substrate molecules transformed per minute by one molecule of enzyme under optimum conditions of temperature, pH, and saturation
• Types of Enzyme Specificity

  • Absolute Specificity
  • Group Specificity
  • Linkage Specificity
  • Stereochemical Specificity
• Linkage Specificity


  • Act on a particular type of bond, irrespective of the rest of the molecular structure
  • Example: Phosphatases hydrolyze phosphate – ester bonds in all types of phosphate esters
• Reversible Competitive Inhibition


  • Competitive Enzyme Inhibitor - Molecule that competes with the substrate for occupancy of the enzyme's active site
  • Remains unchanged as it binds to the enzyme's active site
  • Reversible process because it is maintained by weak interactions
  • Can be reduced by increasing the concentration of the substrate
• Temperature

  • Measure of kinetic energy of molecules
  • Higher temperatures mean molecules are moving faster and colliding more frequently
  • Optimum temperature is the temperature at which an enzyme exhibits maximum activity
• Substrate Concentration

  Increased concentration of substrate will affect enzyme activity
• Extremozymes


  • A microbial enzyme active at conditions that would inactivate human enzymes as well as enzymes present in other types of higher organisms
  • Extremophile - Microorganisms that thrive in extreme environments
  • Examples: Acidophiles, Alkaliphiles, Hyperthermophiles, Halophiles, Cryophiles
• Enzyme Inhibition


  Substance that slows or stops the normal catalytic function of an enzyme by binding to it
• pH

  • The charge on acidic and basic amino acids located at the active site depends on pH
  • Small pH changes can result in enzyme denaturation and subsequent loss of catalytic activity
  • Biochemical buffers help maintain the optimum pH for an enzyme
  • Optimum pH is the pH at which an enzyme exhibits maximum activity
• Absolute Specificity


  • Catalyze only one reaction
  • Most restrictive of all specificities
  • Example: Catalase – enzyme with absolute specificity
• Reversible Non-Competitive Inhibition


  Non-competitive Enzyme Inhibitor - Molecule that decreases enzyme activity
• Types of Enzyme Inhibition

  • Reversible Competitive Inhibition
  • Reversible Non-Competitive Inhibition
  • Irreversible Inhibition
• Optimum pH for enzymes

  • Pepsin - Active in the stomach, functions best at pH 2.0
  • Trypsin - Operates in the small intestines, functions best at pH 8.0
• Group Specificity


  • Act only on molecules that have a specific functional group, such as hydroxyl, amino, or phosphate groups
  • Example: Carboxylpeptidase is group specific
• Factors that Affect Enzyme Activity

  1. Temperature

  2. pH

  3. Substrate Concentration

  4. Enzyme Concentration
• Enzyme Specificity


  Extent to which an enzyme’s activity is restricted to a specific substrate, a specific group of substrate, a specific type of chemical bond, or a specific type of chemical reaction
• Enzyme Concentration


  • Kept in a low number because enzymes are not consumed in the reaction
  • The greater the enzyme concentration, the greater the reaction rate
• Positive Regulator


  • Increase enzyme activity; The shape of the active site is changed such that it can more readily accept substrate
• Non-competitive Enzyme Inhibitor


  Molecule that decreases enzyme activity by binding to a site on an enzyme other than the active site
• Proteolytic Enzymes


  • Catalyze the breaking of peptide bonds that maintain the primary structure of protein; Generated in an inactive form and converted to active form when they are needed
• Allosteric Enzyme


  • Have Quaternary Structure; Have 2 kinds of binding sites (for substrates and for regulators); Active and regulatory binding sites are distinct from each other in both location and shape; Binding of a molecule at the regulatory site causes changes in the overall three-dimensional structure of the enzyme, including structural changes at the active site
• Enzyme-substrate interaction


  1. It binds to the enzyme's active site

  2. Reversible process because it is maintained by weak interactions

  3. Can be reduced by increasing the concentration of the substrate
• Enzyme with two or more Protein Chains and 2 Kinds of Binding Sites

  • Regulators
• Negative Regulator


  • Decrease enzyme activity; Changes to the active site are such that substrate is less readily accepted
• Irreversible Enzyme Inhibitor


  Molecule that inactivates enzyme by forming a strong covalent bond to an amino acid side-chain group at the enzyme's active site
• Feedback Control


  A process in which activation or inhibition of the first reaction in a reaction sequence is controlled by a product of the reaction sequence; Negative Feedback
• Enzyme Inhibition

  1. Reversible Non-Competitive Inhibition

  2. Irreversible Inhibition
• Covalent Modification of Enzyme


  Process in which enzyme activity is altered by covalently modifying the structure of the enzyme through attachment of a chemical group or removal of a chemical group from a particular amino acid within the enzyme structure; Phosphorylation; Dephosphorylation