L6-12 enzymes

• what is the transition state analogues?


  Molecules that mimic the structure of the transition state in a chemical reaction, are inhibitor molecules
• example of transition state analogue:


  yeast aldolase
• low Km means:


  high affinity with the active site and the molecule
• low Ki means 


  inhibitor is more effective
• Km/Ki tells us:


  how much more strongly the inhibitor binds to the active site than the substrate
• first step in catalysis:


  formation of the enzyme-substrate complex (ES)
• who came up with the induced-fit hypothesis

  Daniel Kochland
• the active site is defined as:

  the region of the enzyme that binds the substrate(s) and any cofactor(s)
• where do catalytic amino acids in the active site come from?

  different locations in the primary amino acid sequence
• the substrate binds to the active site by multiple _

  weak interactions
• there are never any _ bonds between the enzyme and the substrate

  covalent
• what are the differences between active site and catalytic site?

  Active site: where substrate binds and reactions occur. Catalytic site: where catalysis takes place within the active site
• active site is made up of:


  ATP binding site, substrate binding site and the catalytic site
• entropy effect is:


  substrate held next to each other or catalytic groups for increased length of time
• orbital steering is:


  the best orientation of substrate relative to reacting atoms, their molecular orbits and catalytic groups
• induced fit means:


  maximal binding involves changes to conformation of E and S
• induced fit improves specificity
• enzyme specificity is:


  a measure of how fussy an enzyme is to binding to a substrate
• induced fit improves specificity by:

  • open conformation allows substrate binding
  • closed conformation reconstitutes catalytic site
  • so enzyme only active when bound to intended substrate
• what are coenzymes?


  Small organic molecules that assist enzymes in carrying out their catalytic functions, non-protein, bind to catalytic site
• what is a cofactor?

  A cofactor is a non-protein molecule or ion that is required for the proper functioning of an enzyme, inorganic (mostly metals), bind near the active site
• cofactors and coenzymes functions:

  • assist in substrate binding (stabilise and orientate)
  • stabilise catalytic site
  • participate in some reaction mechanisms
• 3 types of reaction mechanisms

  • acid base catalysis
  • covalent catalysis
  • electrostatic catalysis
• enzymes increase reaction rates by:

  • hold substrate together
  • promote formation of transition state
  • contribute reactive groups
• isoenzymes are:


  slightly different forms of an enzyme in the same organism but catalyse the same reaction
• enzyme kinetics is:


  using maths to describe how an enzyme or inhibitor works under different conditions
• Ludwig Wilhelmy discovered:


  initial rate of acid hydrolysis of sucrose is proportional to sucrose concentration at constant acid
• Adrian Brown discovered:


  at low substrate concentration the rate is proportional to substrate, however at high substrate the rate becomes independent
• Michaelis-Menten equation:


  forms shape of rectangular hyperbola

  
• Vmax is the:


  maximum possible rate of the reaction at that particular enzyme concentration
• Vmax is an estimate because:

  have to extrapolate due to infinite [S] required
• Km is the:


  substrate concentration at which the velocity of the reaction is half Vmax
• Km is a constant, Vm is only constant for a given enzyme concentration
• km is independent of:

  amount of enzyme and substrate present
• Vm is dependent on the:

  amount of enzyme
• assumptions of Michaelis-Menten equation:

  • reaction is single substrate reaction
  • single binding site possible
  • no reverse component of k2 step of the reaction
• initial velocity helps:


  overcome issue with reverse catalysis and product inhibition as products is negligible in early stages of reaction
• drug design needs lower Km than substrates so it binds more effectively to enzyme active site
• Vm limitations:


  can't use to compare efficiencies between totally unrelated enzymes with unrelated substrates
• overcoming Vm limitation by using turnover number which is:


  number of substrate molecules broken down per molecule of enzyme per second