enzymes

• the active site is the part of an enzyme where substrate molecules bind to form an enzyme-substrate complex
• metabolites - molecules produced in metabolic reactions that are not used in the synthesis of new molecules
• enzymes

  • globular proteins
  • active site determined by tertiary structure
• turnover rate- the number of reactions that an enzyme can molecule can catalyse per second
• intracellular enzymes - enzymes that work inside cells

  eg catalyse - protects cell from damage by breaking down hydrogen peroxide into water and oxygen, involved in phagocytosis
• extracellular enzymes - work outside cells catalysing hydrolysis reactions to break down macromolecules

  eg - amylase: produced in salivary glands to digest starch into maltose

  eg - trypsin: produced in pancreas to break peptide bonds
• how enzymes work

  the role of enzymes is to speed up metabolic reactions

  enzymes make substrates into products - can be catabolic reactions (where substrates are broken down) or anabolic reactions (where substrates are joined)
• lactase - breakdown of lactose into glucose and galactose
• catalase - breakdown of hydrogen peroxide into water and oxygen
• rubisco - binding of carbon dioxide to rubp in the stroma
• atp-ase - breakdown of atp to produce adp and pi
• glycogen synthease - enzyme that catalyses the conversion of glucose into glycogen
• activation energy

  • energy stored in bonds between atoms
  • bonds must be broken to bind new atoms
  • activation energy is the extra energy required to begin a chemical reaction
  • enzymes decrease activation energy by providing an active site where reactions can occur more easily
• anabolic reactions - if two molecules need to be joined, attaching to the enzyme holds them close together in the correct orientation, reducing repulsion between the molecules so they can bind more easily
• catabolic reactions - fitting into the active site puts a strain upon bonds in the substrate, this means the molecule breaks up more easily
• lock and key - enzyme and substrate must be complementary to each other
• induced fit - the active site changes shape slightly to fit the substrate upon collision
• factors affecting rate of reaction

  • temperature - as temp increase the kinetic energy increases, more frequent collisions, enzymes denature at high temps
  • pH - as pH increases enzyme activity increases, enzymes denature at both extremes
  • substrate concentration - more frequent collisions at beginning, more substrate complexes
  • enzyme concentration - initial increase, substrate concentration is limiting factor
• kinetic energy and collusion theory

  • molecules move randomly because of kinetic energy and collisions happen and random. As a fluid is heated, the kinetic energy of molecules increases and collisions occur more frequently. These collisions occur with greater force.
  • enzyme substrate complexes form
• optimum temperature - the temperature that gives the maximum rate of reaction.

  increase the temp too high and the molecules in the protein will vibrate too much and the bonds in the tertiary structure will break
• denaturation - when the tertiary structure of the enzyme if changed

  • vibrations can break hydrogen and ionic bonds
• rate of reaction and temperature coefficient

  ror = 1/time taken to reach end point (s-1)

  • the temperature coefficient refers to the increase in the rate of a process when the temp is increased by 10
  • in most ror is doubled for every 10
• q 10 formula
• pH - measure of the proton concentration, the higher the H+ conc the lower the pH value

  • H+ ions affect the ionic and hydrogen bonds in ternary structure of protein because of their positive charge
  • the induced fit theory states that an important part of enzyme function is that the active site relies on charged area on the R groups of amino acids
  • H+ ions are attracted to negatively charged groups and cluster around them
• how cells modify enzyme concentration

  enzyme avaliability depends on the rate of synthesis of the enzyme and its rate of degradation, which are controlled by the cell

  • enzyme synthesis - genes can be switched on/off
  • enzyme degradation - proteins broken down into amino acids. Useful for eliminating abnormal proteins and regulating metabolism
• initial reaction rate - the maximum possible rate for an enzyme under conditions of the experiment

  • limiting factors cause plateaus
• measuring rate of enzyme controlled reaction

  • measure how much product appears over a period of time
  • measure how much substrate disappears over a period of time
• cofactors - non-protein molecules that are required for enzyme activity
• inorganic cofactors - ions

  • not permanently bound
  • help enzyme and substrate bind
  • don't participate in reaction therefore not used up
  • ion can affect charge distribution
  • eg chloride ions and amylase
• organic cofactors - coenzymes

  • non-protein molecules bind temporarily to active site
  • can be carriers moving chemical groups
  • eg NAD and FAD
• prosthetic groups - coenzymes that are permanent parts of an enzyme

  • carbonic anhydrase contains zinc as a prosthetic group
  • carbonic anhydrase converts c02 into carbonic acid
• enzyme inhibitors - any substance that slows down the rate of reaction by affecting the enzyme

  • can be reversible or irreversible and can affect active site or allosteric site
• inhibitors can be reversible or irreversible, depending on the bonds

  • covalent bonds - inhibitor cannot be removed therefore irreversible
  • hydrogen bonds - inhibitor can be removed therefore reversible
• competitive inhibition - molecules with a similar shape to the enzyme active site, block the active site from binding with the substrate

  • the level of inhibition is dependent on the relative concentration of inhibitor and substrate
• non competitive inhibition - bind to the allosteric site, changing the active site of the enzyme

  • increasing concentration of substrate won't affect
• end product inhibition - the end product bins to an earlier enzyme in the sequence (reversible non competitive) changing the active site and reducing ror, causing less product to be made