1 Enzymes

• Enzymes increase the rate at which a chemical reaction proceeds
• Carbonic anhydrase: HCO3- + H+ = CO2 + H2O
• Without carbonic anhydrase the reaction rate is 0.1 molecules per s (s-1). With carbonic anhydrase the reaction rate is 1,000,000 s-1. This is (107) times faster.
• Enzymes do not change the positions of chemical equilibria (they increase both forward and reverse rates)
• Enzymes do not undergo net change when they participate in reactions as catalysts
• Enzymes are proteins (but some make use of chemical groups other than amino acids)
• Some RNA molecules operate as enzymes (ribozymes)
• Catalytic power can be demonstrated by the ‘turnover number’ or ‘catalytic constant’ kcat
• kcat = number of molecules of ‘substrate’ that one enzyme molecule can convert in 1 second
• carbonic anhydrase, kcat = 1,000,000 s-1
• Acetylcholinesterase (AChE) kcat = 6,500 s-1
• DNA polymerase 1 kcat = 15 s-1
• Lysozyme kcat = 0.5 s-1
• Enzyme catalytic properties are very sensitive to conditions. For example acetylcholinesterase has a kcat of 6,500 but only under homo sapien conditions of pH8, 27 °C and acetyl thiocholine
• BRENDA - a database of enzymes
• The reactants in an enzyme-catalysed reaction are known as substrates; converted to products
• Small molecules not part of the enzyme but which are required for activity are known as cofactors
• Some cofactors are metal ions others are organic molecules, co-enzymes or prosthetic groups:-Vitamins (B1, C)

  –Non-vitamins (co-enzyme  Q10/ubiquinone,nucleotides), etc

  –Heme group and related porphyrins (e.g. cobalamin, B12)
• An enzyme lacking an essential cofactor or coenzyme is known as an apoenzyme; the complete machinery is known as the holoenzyme
• (EC 1) oxidoreductases - perform oxidation/reduction reactions
• (EC 2) transferases - transfer a group
• (EC 3) hydrolases - water cleaves a bond
• (EC4) lyases - non-hydrolytic cleavage, addition or removal of groups
• (EC 5) isomerases - intramolecular rearrangement
• (EC 6) ligases - join two molecules
• 6 enzyme classifications:

  (EC 1) oxidoreductases

  (EC 2) transferases

  (EC 3) hydrolases

  (EC 4) lyases

  (EC 5) isomerases

  (EC 6) ligases
• An example of (EC 1) oxidoreductase is lactate dehydrogenase

  Pyruvate + NADH     =   Lactate + NAD+
• An example of (EC 2) transferase is hexokinase

  Hexose-CH2OH + MgATP2−     =     Hexose-CH2O-PO32− + MgADP− + H+
• An example of (EC 3) hydrolase is glucose-6-phosphatase

    A–B + H2O      =      A–OH + B–H

    G-6-P + H2O     =    Glucose + Phosphoric acid
• An example of (EC 4) lyase is carbonic anhydrase

  HCO3- + H+     =        H2CO3.       =      CO2 + H2O
• An example of (EC 5) isomerase is triose-phosphate isomerase

    Dihydroxyacetone phosphate   =   D-glyceraldehyde 3-phosphate
• An example of (EC 6) ligase is amino-acyl tRNA synthetases

    amino acid + tRNA + ATP     =      aminoacyl-tRNA + AMP + PPi
• Enzymes are capable of superb discrimination between similar molecules (specificity)

  e.g. DL isomers, positional isomers, chain length etc
• Specificity implies that enzymes recognize and bind substrates in an enzyme:substrate (ES) complex

  –most enzymes are highly specific
• Some enzymes are aspecific such as papain or savinase which are used in washing powder to break down any protein on clothes when washing.
• Trypsin hydrolyses peptide bonds at the C-terminal side of lysine or arginine
• Chymotrypsin hydrolyses peptide bonds at the C-terminal side of phenylalanine, tyrosine or tryptophan
• Thrombin hydrolyses the arginine-glycine bond
• mammalian proteases such as Trypsin, Chymotrypsin and Thrombin are EC3
• All proteases are hydrolases so EC3 as water is involved in bond cleavage