Enzyme action

• Transition state analogue

  Molecules similar in structure to the transition state but with higher affinity for the enzyme act as enzyme inhibitors
• Induced-fit hypothesis

  1. Substrate binds weakly to the enzyme using non-covalent bonds

  2. This triggers a conformational change of the enzyme and substrate, forming the transition state

  3. Products are released, triggering another conformational change of the enzyme back to its original shape
• Active site

  Where the substrates and cofactors bind
• When the primary structure of the enzyme folds

  The catalytic amino acids are brought into close proximity
• Bonds formed between substrate and enzyme

  Ionic and Hydrogen bonds
• What binds the substrate

  The amino acid residues in the active site
• How the substrate-binding site ensures specificity

  By recognising specific amino acid sequences in the target protein
• How the active site facilitates reactions

  1. Entropy effect

  2. Orbital steering

  3. Induced fit
• Entropy effect

  Substrates are held next to each other or the catalytic groups to increase the chances of a collision with the amino acids in the active site
• Orbital steering

  The substrate is orientated relative to the catalytic groups to increase the chances of a collision with the amino acids in the active site
• How induced fit facilitates reactions

  1. The bonds in the substrate are weakened, releasing energy. This decreases the energy required to produce the weak transition state

  2. It also improves the specificity of the enzyme
• How induced fit improves specificity

  When the enzyme is unbound, the active site is opened. Once the target protein binds, the closed conformation reconstitutes the catalytic site
• Apoenzyme

  An enzyme without the cofactor and coenzyme
• Holoenzyme

  An enzyme with the cofactor and coenzyme bound
• Coenzymes

  Non-protein organic substances. They can bind reversibly or irreversibly
• Irreversibly bound cofactor

  Prosthetic group
• Where coenzymes bind

  Catalytic site
• Where cofactors bind

  Near or in the active site
• Cofactors

  Inorganic substances, mainly metal ions
• Roles of cofactors and coenzymes

  To increase the range of reactions that an enzyme can catalyse
• Role of coenzymes


  To act as a donor to a single substrate or transfer groups between substrates
• Roles of cofactors

  • Formation of co-ordinating bonds with the substrate in order to facilitate binding, stabilisation and orientation
  • Stabilise the catalytic site's conformation
  • Participate in acid-base catalysis and Redox reactions
• How cofactors participate in acid-base or redox reactions

  They are positively charged and so can act as electrophiles by accepting electrons
• Main reaction mechanisms of enzymes

  • General Acid-base catalysis
  • Covalent catalysis
  • Electrostatic catalysis
• General acid-base catalysis

  The acidic and basic groups of the amino acid residues in the active site of the enzyme facilitate the transfer of protons to or from the substrate
• Catalytic residues in acid-base catalysis

  • Aspartate
  • Histidine
  • Serine
• Acid-base catalysis

  1. Substrate binds

  2. Histidine acts as a base by accepting protons from serine

  3. Serine acts as a nucleophile by attacking Delta +ve carbon in the carbonyl group

  4. This forms a tetrahedral intermediate

  5. Histidine acts as an acid by donating a proton to the intermediate

  6. The intermediate collapses as the peptide bond is broken

  7. Acyl enzyme intermediate is formed between serine and the substrate
• Covalent catalysis

  The formation of a covalent link between the substrate and catalytic residues
• Main catalytic residues in covalent catalysis

  • Serine
  • Histidine
  • Lysine
  • Cysteine
• What mechanism usually a precursor for covalent catalysis

  acid-base catalysis
• Covalent catalysis

  1. Acid-base mechanism

  2. Amino acid residues act as nucleophiles and form a covalent bond with the substrate

  3. Acyl enzyme intermediate is broken by hydrolysis

  4. Product is released
• Electrostatic catalysis

  The formation of an ionic bond between the enzyme and substrate in order to stabilise the transition state
• What is involved in electrostatic catalysis

  • Acid or basic residues
  • Metal cofactors
• Residues involved in electrostatic catalysis

  • Lysine
  • Glutamic acid
  • Arginine
  • Aspartic acid
• Enzyme with a zinc cofactor

  Zinc metalloproteinase