HC2

• All reactions involving proton transfer are acid/base catalyzed.
• pKa is highly dependent on the micro environment of the enzyme
• Bifunctional catalysis is possible because of the specific orientation and location of amino acid residues in the active site.
• A perfect catalyst is a catalyst where the rate of the reaction is limited by how fast a molecule can be difused into the active site.
• Catalyse is an example of an enzyme that approaches kinetic perfection, this is when the reaction rate is only controlled by diffusion limitation.
• kcat/km is close to 10^9, then it is most likely kinetic perfect
• Enzymes are only as fast as they need to be. If it is faster is can disrupt the metabolism
• The Michaelis-Menten model is a kinetic model that describes one-substrate reactions in terms of the rate-determining step
• There are five assumptions with the Michaelis-Menten model:

  1. Enzyme binds only a single substrate
  2. Only one kinetically significant step between [ES] and [P]
  3. Production formation is irreversible
  4. The quasi steady-state approximation is made ([ES] rapidly reaches constant value)
  5. Total amount of enzyme remains constant ([ES] + [E] = [E0])
• The quasi steady state approximation is a small but constant concentration of the enzyme-substrate complex. So the rate of formation of ES = the rate of breakdown of ES.
• Enzymes bind the transition state well, not the substrate
• Km roughly indicates the binding strength, a lower Km indicates stronger binding
• Turnover frequency (s-1), the rate is not limited by binding, but only by the catalytic turnover
• turnover number says something about the stability
• At high [S] it is the first order reaction kinetics. At low substrate concentration there is an empty active site, and the rate of reaction is a bimolecular reaction between free E and free S
• kcat/km is known as the catalytic efficiency
• Kcat/KM reflects both affinity and catalytic ability, allowing comparison between substrates and enzymes, this can also never be faster than the diffusion rate
• There are two types of inhibition: competitive and non-competitive. Competitive binds at the active site, non-competitive binds elsewhere but still deactivates the enzyme.
• Competitive inhibition has the same vmax, non-competitive inhibition has a different vmax.
• enzyme catalysis uses two common mechanisms: acid/base catalysis and covalent/nucleophilic catalysis
• Enzymes must (mostly) operate at physological pH in the range 5-9
• pka drops lower by having an adjacant positive charge.
• You can have a protonated carboxylic acid by a hydrophobic apolar environment so the oxygen can not stabilize and the species becomes less stable and the equilibrium shifts to the left.
• The specific orientation and location of amino acid residues in the active site allows bifunctional catalysis. This is where there is Protonation of one part of a substrate and at the same time deprotonate antoher part of the molecule.
• Lewis acids can activate substrates for acid/base catalysis
• Covalent catalysis is rare in solution, but quite typical for enzymes. The catalytic cycle goes through a covalently bound intermediate
• Covalent catalysis is effective because:

  1. It allows orientation of the nucleophile (high effective concentrration)
  2. The nucleophile is largely desolvated in the actve site (water is excluded): activation
• Serine proteases are peptidases and cleave amide bonds in polypeptides
• Three residues (the catalytic triad) work in concert to facilitate the reaction, to create a potent nucleophile
• An alcohol is less acidic than a phenol and thus the pka must be higher
• The lower the pka, the stronger the acid
• Oxyanion hole, the hydrogen bonds stabilize the tetrahedral intermediate, this is the transition state, so it also stabilizes the transition state. There is a build up of charge in the tetrahedral intermediate, if it is stabilized the peak of the transition state will also be lower
• convergent evolution is where the same active site is formed from different protein folds/two evolutionary origins
• Strain energy in enzyme catalysis, the enzyme twists the molecule in a higher energy conformation toward the transition state, this is made up un a more hydrogen bonds in a different part of the enzyme
• Strain energy: if a substrate is bound in a strained conformation (by rotating or changing) that is closer to the transition state than the ground state conformation, then the activation energy will be lower
• What is ES'?

  A)

  A) Stained conformation

  
• Selectivity of an enzyme: the ability of the enzyme to select a certain substrate or functional group out of many
• Specificity of an enzyme: a property of the reaction, i.e. the production of a single regio- or stereo isomer of the product
• What is pictured below?

  A

  A) Stereoselectivity

  B) Stereospecificity

  
• Asymmetric induction is the chiral product from achiral substrates.