Enzymes

• enzymes are globular proteins that interact with substrate molecules catalysing their reaction so it occurs at a faster rate even at body temperature.
• Anabolic - when a larger product is synthesised from smaller substrates. These are the chemical reactions for growth.

  Catabolic - when a larger substrate is broken into smaller products
• Extracellular enzymes are enzymes that are not found in the cell e.g digestive enzymes.

  Intracellular enzymes are enzymes found within a cell e.g catalase which is needed to convert hydrogen peroxide, a biproduct of metabolism, into water and oxygen.
• properties of enzymes:

  • specific 3D shape determined by its tertiary structure.
  • area on the enzyme surface that is complementary to the shape of a specific substrate is called the active site
  • speeds up a chemical reaction by providing an alternate pathway with a lower activation energy
  • enzyme is left unchanged at the end of the reaction
• specificity of an enzyme refers to its ability to catalyse just one reaction or one type of reaction. Only one particular substrate will fit into the active site of the enzyme molecule.
• Lock and key hypothesis:

  • Enzyme and substrate will randomly collide due to their KE
  • Like how only the right key will fit into a lock, only a specific substrate will fit into the active site of an enzyme.
• Induced fit hypothesis Pt 1 :

  • Enzymes and substrates will randomly collide due to their KE
  • At a successful collision, as the substrate does not perfectly fit into the enzyme's active site, the active site will alter its shape to give a perfect fit with the shape of the substrate.
  • As it alters its shape, R groups in the active site will form temporary bonds with the substrate to form an enzyme - substrate complex
• Induced fit hypothesis P2:

  • In anabolic reactions, the two substrates will be brought close together in such a way that a reaction occurs between them
  • In catabolic reactions, bonds within the single substrate will be put under strain and so weaken, lowering the activation energy so the molecule is broken down without needing more external energy, allowing the bonds that form the products to be made.
• substrate concentration in reaction:

  • At the start of the reaction, the highest concentration of substrates are present in the reaction vessel
  • so the frequency of successful collisions between substrates and the enzyme's active sites due to their KE is more probable
  • therefore more enzyme- substrate complexes are formed
  • so more products will be formed.
  • At the end of the reaction, rate of reaction plateaus since the concentration of substrates in the vessel is now at its lowest.
• substrate concentration general pt1 :

  • as substrate concentration increases, rate of reaction increases
  • as the frequency of successful collisions between substrates and the enzyme's active site due to their kinetic energy becomes more probable
  • therefore the number of enzyme- substrate complexes increases
  • therefore the yield of products increases
• substrate concentration pt2:

  • However, when enzyme concentration becomes limiting, the rate of reaction will plataeu as most of the active sites are occupied
  • so enzymes are already working at their maximum rate
  • so further increase in substrates has no effect as it is no longer the limiting factor
• • As enzyme concentration increases, the rate of reaction increases as there are more active sites available for substrate molecules to bind to
  • so the frequency of successful collisions between the enzyme's active site and substrates due to their KE becomes more probable
  • therefore the number of enzyme-substrate complexes formed increases
  • so more product is formed
  • This will continue as long as substrate concentration is not limiting.
  • At a higher enzyme concentration, the same amount of product will be produced but faster.
• • As temperature increases, rate of reaction increases as enzymes and substrates will have more KE and so will move around more rapidly and randomly
  • therefore the frequency of collisions between enzyme's active site and the substrate becomes more probable
  • therefore the number of enzyme-substrate complexes increases
  • therefore the yield of product formed increases.
• • Past optimum temperature, the internal vibrations in the enzymes gets too high due to the extra KE as a results of excessive temperatures.
  • This puts a strain on the hydrogen bonds holding the enzyme in its tertiary structure, causing them to break
  • Therefore, the change in the enzyme's precise tertiary structure means enzymes become denatured where their Active site looses its specific 3D shape
  • which means it is no longer complementary to the substrate so cannot catalyse the reaction
  • therefore the concentration of enzymes with viable active sites decreases so less .... products formed.
• • If the PH is too low, there are too many H+ ions which interferes with the hydrogen and ionic bonds holding the enzyme in its precise tertiary structure.
  • Therefore, the R groups of the amino acids are less able to interact with each other
  • causing the bonds to break and the enzyme to denature where its active site changes shape and loose its specific 3D shape
  • therefore the concentration of enzymes with viable active sites decreases.
• • If the PH is too high, there is too many OH- ions
  • which interferes with the hydrogen and ionic bonds holding the enzyme in its precise tertiary structure
  • this means the R groups of the amino acids are less able to interact with each other causing the bonds to break
  • and the enzyme to denature where its active site changes shape so looses its specific 3D shape
  • meaning there will be less enzymes with viable active sites.
• inhibitors are substances that reduce the rate of reaction as they bind to either the active or allosteric site on the enzyme :

  • competitive reversible or non - reversible
  • non competitive reversible reversible or non - reversible
• Competitive inhibitors have a similiar shape to the substrate and so is complementary to the shape of the active site, therefore can bind to the active site instead, preventing the substrate molecule binding to the enzyme.

  This reduces the number of available active sites so the number of enzyme - substrate complexes decreases so the yield of products formed decreases.

  • The amount of inhibition depends on the relative concentration of the inhibitors and substrates. Increasing the concentration of substrates reduces the competition between enzyme and substrate molecules.
• Non competitive inhibitors bind to the other site on the enzyme surface - allosteric site.

  This causes a change in the precise shape of the enzyme's tertiary structure, which changes the specific 3D shape of the active site to also change.

  Therefore, the substrate will no longer be complementary to the active site so will not be able to bind to it, regardless of how much substrate molecules are added.
• graph for fixed quantitiy of enzymes and inhibitors

  A) competitive inhibitor

  B) non competitive inhibitor

  
• end product inhibition is an example of negative feedback where the end product of a reaction acts as an inhibitor to the regulatory enzyme (usually the first enzyme in pathway ) that produces it, regulating the rate of reaction in a metabolic pathway.

  • This can prevent too much product being formed and resources being wasted
  • example of non-competitive, reversible inhibition
• coenzymes - organic non-protein molecules such as vitamins

  cofactors - inorganic non-protein molecules such as mineral ions

  • coenzymes - act as carriers, transferring chemical groups from one enzyme to the next in multistep pathway reactions
  • cofactors - can facilitate the reaction by binding to the enzyme's active site to make it complementary to the substrate, allowing the substrate and enzyme to bind together
• prosthetic groups are a type of cofactor that is permanently attached to the enzyme e.g haem plays an essential role in the function of haemoglobin
• precursor activation

  • when a precursor enzyme (inactive enzyme) known as an apoenzyme is activated by the binding of a cofactor to the enzyme as this will cause a change in the protein's tertiary structure so that the active site will change shape and become complementary to the shape of the substrate.
  • This means the enzyme becomes a functional enzyme known as a holoenzyme
• precursor enzymes - many enzymes are in their inactive form

  • so that they do not cause damage to cells and tissues
  • so they are only used when they are needed.
• Chloride ions as a cofactor for amylase

  Zinc ions as a prosthetic group for carbonic anhydrase

  Vitamins as an example of coenzymes.
• Some medicinal drugs are enzyme inhibitors e.g.

  • some antiretroviral drugs e.g reverse transcriptase inhibitors which inhibits the enzyme reverse transcriptase from catalysing the replication of viral DNA so prevents the virus from replicating
  • some antibiotics e.g penicillin which inhibits transpeptidase which catalyses the formation of proteins in bacterial cell walls.

  This is why taking the correct dose of medicinal drugs is important as overdosing can be lethal, especially if the inhibitor is non-reversible.
• metabolic poisons interfere with metabolic reactions causing damage, illness or death. They are often enzyme inhibitors e.g.

  cyanide - an irreversible inhibitor of an enzyme that catalyses respiration reactions causing cells to die.
• Q10 - temperature coefficient - shows how rate change as temperature increases by 10 degrees. Most enzyme controlled reactions have a Q10 value of around 2.