2.1.4 - enzymes

• Enzymes are proteins that act as biological catalysts for intra and extracellular reactions. they affect metabolism of cells and whole organism
• Enzymes have specific tertiary structure which determines the shape of active site complementary to a specific substrate.
• An enzyme that catalyses intracellular reactions is catalase. It catalyses the decomposition of hydrogen peroxide into water and oxygen.
• Two enzymes that catalyse extracellular reactions are

  amylase - carbohydrate that catalyses digestion of starch

  trypsin - catalyses hydrolysis of peptide bonds
• The induced fit model of enzyme action is when:

  shape of active site is not directly complementary to substrate and is flexible

  conformational change enable ES complexes to form

  this puts strain on substrate bonds, lowering activation energy. Bonds in enzyme product complex are weak so product desorbs
• The lock and key model of enzyme action suggests that active site has a rigid shape determined by tertiary structure so is only complementary to one substrate.

  formation of ES complex lowers activation energy

  bonds in enzyme product complex are weak so product desorbs
• The five factors that affect the rate of enzyme controlled reactions

  enzyme concentration

  substrate concentration

  concentration of inhibitors

  pH

  temperature
• Substrate concentration affects rate of reaction as

  given enzyme concentration is fixed, rate increases proportionally to substrate concentration

  the rate levels off when maximum number of ES complexes form at any time
• In enzymes, the formation of the enzyme substrate complex lowers the activation energy of metabolic reactions.
• Enzymes work at cellular level and at whole organism level
• Activation energy is the energy needed to break any existing bonds so new bonds can form
• Because enzymes lower activation energy:

  chemical reactions can happen quickly at lower temperatures
• Anabolic - energy required to build larger molecules
• Intracellular and extracellular enzymes are both made in the cell but IC enzymes work in that cell whereas EC enzymes are released by exocytosis to work
• A specific intracellular enzyme is catalase which works inside cells breaking down hydrogen peroxide
• A specific extracellular enzyme is amylase which breaks down carbohydrates. Or trypsin which breaks down proteins
• Enzyme + substrate ——> enzyme-substrate complex
• Enzyme substrate complex ——> enzyme + product
• In induced fit model the active site is still complementary and specific to substrate but changes shape slightly to accommodate the substrate
• Induced fit model is seen as more accurate as there is more evidence of this
• Enzyme concentration affects rate of reaction because more enzymes mean there are more frequent collisions and more successful collisions.

  rate increases until it levels off when maximum numore of ES complexes have been formed since the substrate is the limiting factor.
• as temperature increases, rate increases until it reaches its optimum temperature where rate starts to decrease

  because kinetic energy increases so enzymes will undergo more frequent / successful collisioins.

  above optimum temp, ionic and hydrogen bonds break so active site is no longer complementary
• The temperature coefficient is Q10

  which measures the change in rate of reaction per 10 degree temperature increase

  Q10 = R2 / R1 (where R represents rate)
• enzymes have a narrow optimum ph.

  Outside range, H+ / OH- ions interfere with hydrogen and ionic bonds in tertiary structure which leads to the enzyme being denatured.
• Competetive inhibitors work by binding to the active site since they have a similar shape to substrate. This temporarily prevents ES complexes from forming until it releases.
• Increasing substrate concentration decreases the effect of competitive inhibitors
• Non-competitive inhibitors work by binding at allosteric site. This triggers conformational change of active site So substrates can no longer bind.
• Increasing substrate concentration has no impact on non-competitive inhibitors.
• End-product inhibition is when one of the products of a reaction acts as a competitive or non-competitive inhibitor for an enzyme involved in the pathway. This prevents further formation of products.
• Irreversible inhibitors permanently prevent formation of ES complexes.
• Reversible inhibitors may be competitive or non-competitive. they bind to enzyme temporarily (hydrogen or ionic bonds). es complexes can form after the inhibitor is released
• Metabolic poison is a substance that damages cells by interfering with metabolic reactions. Usually an inhibitor
• Examples of metabolic poisons are:

  cyanide (non-competitive)

  malonate (competitive)

  arsenic (competitive)
• Some inhibitors may be medicinal drugs:

  penicillin ( non-competitive inhibitor which prevents formation of peptidoglycan in bacterial cell wall)

  ritonavir ( inhibits HIV protease to prevent assembly of new virions )
• Cofactors are non-protein compounds required for enzyme activity. They can be

  coenzymes

  inorganic cofactors

  prosthetic groups
• Coenzymes are organic cofactors. They do not bind permanently and often transport molecules between enzymes.
• Inorganic cofactors facilitate temporary binding between substrate and enzyme

  Often metal ions

  eg) chloride is the cofactor for amylase
• Prosthetic groups are tightly bound cofactors that act as a permanent part of enzymes binding site

  eg) zinc ions for carbonic anhydrase