13 - Cofactors

• How do Catalysts effect the position and direction of equilibrium?

  They do not effect the position or direction, however, they vastly increase the rate of catalysis, allowing the reactions necessary for life to take place
• How do enzymes enhance the rate of reaction?

  By lowering the activation energy (numerous weak interactions between E&S are optimised)
• What did J.B.S Haldane suggest the mechanism of enzymes was in 1930?

  He suggested multiple weak bonding interactions between an enzyme and its substrate might be used to catalyse reactions
• What model did Daniel Koshland suggest in 1959?


  The induced fit model
• Why does the induced fit model not work?

  The enzyme doesn't distort towards the transition state
• What is an example of an enzyme that requires no chemical groups other than amino acids residues to catalyse its reaction?

  Lysosome enzymes
• What is the name given to NON-PROTEIN components that an enzyme may need for its activity?

  Cofactors
• What are organic Cofactors generally known as?

  Co-enzymes
• What name might be given to an cofactor that is tightly associated with its enzyme?

  Prosthetic group
• What is an example of an enzyme with a prosthetic group?

  The flavin group in Succinate dehydrogenase/mitochondrial respiratory chain complex II
• What name might be given to a Co-enzyme which is loosely associated with its enzyme?

  A co-substrate
• Give an example of a co-substrate

  NAD/NADP
• Describe the metal Cation co-factors

  Metal ions (Na+, Mg2+), may be important in folding. The multiple oxidation states of some ions (Fe, Cu) may be important to their function
• For enzymes with a prosthetic group, what name is given to then in the absence of a co-factor/co-enzyme?

  Apoenzyme (Inactive)
• What name is given to the enzyme in the presence of the bound cofactor?

  Holoenyzme (Active)
• What vitamin is NAD+/NADP derived from?

  Vitamin B3/Niacin
• What vitamin is FMN/FAD derived from?

  Vitamin B2/Riboflavin
• What vitamin is Coenzyme A derived from?

  Vitamin B5/Panthothenate
• What vitamin is Pyridoxal Phosphate derived from?

  Vitamin B6/Pyridoxine
• What does NAD and NADP stand for?

  - Nicotinamide adenine dinucleotide

  - Nicotinamide adenine dinucleotide phosphate
• Describe the function of NAD and NADP

  - Undergo reversible reduction of their Nicotinamide ring, accepts a hydride ion H- (equivalent of 1 proton and 2 electrons)

  -Nicotinamide ring is derived from niacin, so these Co factors are sometimes referred to as pyridine nucleotides
• What does NAD+ primarily function in?

  The reversible oxidation of aldehydes and alcohols
• Give a physiologically relevant example of this:

  - NAD+ acts as a cofactor in the oxidation of alcohol to acetaldehyde by alcohol dehydrogenase (toxic)

  - NAD+ acts as a cofactor in the oxidation of acetaldehyde to acetic acid by aldehyde dehydrogenase (non-toxic)
• What does the reduction of NAD+ do to the benzinoid ring of the Nicotinamide?

  It reduces the benzenoid ring to a quinoid form
• How is this useful for assays?

  The reduction of this ring produces a new absorption maxima at 340nm in UV absorption spectroscopy
• What is the typical intracellular NAD/NADH concentration?

  10^-5M
• When the NAD/NADH ratio is high, what is favoured?

  The transfer of the hydride from the substrate > Catabolism
• What is the typical intracellular concentration of NADP/NADPH?

  10^-6M
• When the NADPH/NADP ratio is high, what is favoured?

  The transfer of hydride to the substrate > Anabolism
• How might high potential e- be required in bio synthetic pathways?


  May be required as precursors and pathway intermediates are generally more oxidised, and products are generally more reduced
• What is the most common electron donor in bio synthetic pathways?

  NADPH, used predominantly for reductive biosynthesis
• What does the phosphate provide?

  A tag of 'specificity
• What is a major source of NADPH in cells?

  The Penrose phosphate pathway, an offshoot of Glucose-6-Phosphate
• How does NAD+ function primarily?

  In the oxidation of alcohols and aldehydes
• What is a general rule for enzymes?

  They are very specific for either NAD or NADP
• What is a rare example of an enzyme that uses either?

  Transdeanimation by glutamate dehydrogenase uses NADH or NADPH as a co-enzyme
• How might enzymes be even more specific?

  Certain enzymes only use certain hydrogens on the Nicotinamide ring (A or B), due to the way the hydrogen might bind to the active site
• What is specificity determined by?


  The interactions with amino acid side chains within the co-enzyme binding pocket
• What types of interactions could these be?

  Hydrophobic interactions, electrostatic interactions and hydrogen bonds
• What is an example of this?

  Lactase dehydrogenase, where pyruvate and an NAD cofactor are oriented very specifically, bound to an Arginine 171 and Histidine 195