enzymes

• enzymes


  biological catalysts that increase the rate of a chemical reaction but is not used up as a result of that reaction

  • an enzyme is a catalyst that catalyses a biochemical reaction and are generally made from proteins
  • most biochemical reactions result in a change in free energy
• carbonic anhydrase

  HCO3− + H+   ↔ CO2 + H2O 
• carbonic anhydrase 


  • uncatalysed= slower kinetics
  • catalysed= 10^7 reactions per second
• exergonic and endergonic reactions

  • when a chemical reaction takes place energy is either taken in or released. this depends on the relative strengths of the bonds being formed
  • exergonic= energy is released to the surroundings. the bonds being formed are stronger than the bonds being broken. catabolic reactions
  • endergonic reactions: energy is absorbed from the surroundings. the bonds being formed are weaker than the bonds being broken> anabolic reactions

  
• What does the change in Gibbs free energy (delta G) determine for a reaction?

  It determines if a reaction goes forward
• What is Gibbs free energy used to calculate?

  Maximum reversible work at constant temperature and pressure
• What does a negative Gibbs free energy indicate?

  Reaction is spontaneous
• What does a Gibbs free energy of zero indicate?

  Reaction is at equilibrium
• What does a positive Gibbs free energy indicate?

  Reaction runs in reverse - not spontaneous
• What is the significance of Gibbs free energy in chemical processes?

  • Indicates spontaneity of a reaction
  • Calculates energy available for work
  • Helps predict reaction direction
• How does Gibbs free energy relate to chemical reactions?

  It tells if a process is spontaneous or non-spontaneous
• If a reaction has a Gibbs free energy of $-5 \text{ kJ/mol}$, what can be inferred?


  The reaction is spontaneous
• If a reaction has a Gibbs free energy of $3 \text{ kJ/mol}$, what does this imply?


  The reaction runs in reverse - not spontaneous
• How can Gibbs free energy be used to predict the direction of a reaction?

  By assessing its sign: negative, zero, or positive
• enzyme catalysis


  • rate reaction depends on activation energy and Gibbs free energy
  • Gibbs free energy ^0 represents amount of energy per one mole of reactants
  • activation energy= energy required to raise the average energy of 1 cold reactants to transition state energy
  • enzymes provide alternative pathway with lower activation energy
  • as activation energy decreases, reaction rate increases
• substrate, enzyme and active site

  1. Substrate enters active site of enzyme 
  2. Enzyme/ substrate complex forms 
  3. Substrate is converted to products 
  4. Products leave the active site of the enzyme 
• transitional state stabilisation theory

  • Used to describe enzyme- substrate interactions 

  An enzyme stabalises the transition state of a reaction 

  1. In a random mixture of reactants, chance collisions are needed in order for the transition state to form 
  2. By binding the reactants, the enzyme lowers the entropy of the system, by increasing the rate of conversion of reactants to products 
• TS  is not a chemical species with any significant stability and should not be confused with a reaction intermediate (such as ES or EP). 

  It is simply a fleeting molecular moment in which events such as bond breakage, bond formation, and charge development have proceeded to the precise point at which decay to either substrate or product is equally likely.

  At AL or equivalent you were probably taught that the active site of the E is complementary to the S.

  More correctly, the active site of the E binds most tightly to the TS. 
• • An enzyme increases reaction rate by stabalising the transition states (ts) this occurs by subtle interactions between the residues or groups within the enzyme active site and the atoms of the substrate 
  • The greater the degree of ts stablisation, the faster the reaction will proceed relative to the uncatalysed reaction 
  • In ts, bonds are half made and half broken so it is an unstable state, and it is at the ts that the energy of the system is at its maximum 
  • So catalysts stabalise the reactants in the ts allowing old bonds to break and new ones to form
• simple substitution

  
• What is the chemical basis of enzyme catalysis?

  Enzyme stabilizes the transition state
• How does an enzyme help in stabilizing the transition state?

  By orienting substrates in the active site
• What role do functional groups play in enzyme catalysis?

  They participate in chemical catalysis events
• What are the main chemical catalysis events in enzyme activity?

  • Covalent bond formation between enzyme and substrate
  • Acid or base catalysis by functional groups
  • Introduction of strain into substrate
• What is one method of catalysis involving enzyme functional groups?

  Covalent bond formation with substrate
• How do functional groups on the enzyme assist in acid or base catalysis?

  By donating or accepting H+ to/from substrate
• What effect does introducing strain into the substrate have?

  It makes the substrate more easily converted to product
• What types of distortions are introduced into the substrate during enzyme catalysis?

  Bond angle and bond length distortions
• How do enzymes lower the FE of the TS?

  A catalyst has no influence on the FE values of the S and P, hence does not change ΔG.

  Instead a catalyst reduces ΔG‡, usually by stabilising the intermediate structure formed at TS. 

  A catalyst therefore decreases size of the energy barrier that has to be crossed in order to convert the S to P.

  Because the energy barrier is easier to cross the rate of reaction increases
• How does an enzyme stabilize the transition state (TS) of a reaction?

  By reducing entropy.
• What does entropy measure in thermodynamics?

  The disorder of a system.
• How does entropy contribute to the free energy (FE) value?

  By affecting the ΔG‡ value.
• What happens to entropy when an enzyme reduces the transition state (TS)?

  It reduces the entropy of the TS.
• What is the initial system at the start of the reaction described?

  A-R + B.
• How many molecules of A-R and B are mentioned in the cell?

  100 molecules of A-R and 100 of B.
• What is the behavior of A-R and B in the absence of an enzyme?

  They diffuse randomly due to chance collisions.
• Why are chance encounters between A-R and B infrequent?

  Due to the high entropy of the system.
• How does an enzyme increase the reaction rate?

  By binding A-R and B in correct positioning.
• What if the reaction is endergonic?

  These reactions require an input of energy to reach completion. Many E obtain this energy by coupling the endergonic reaction with a second reaction that generates energy. This is called energy coupling. Often the second reaction is hydrolysis of the nucleotide ATP, which gives ADP and inorganic phosphate. The FE released by this exergonic reaction is used by the E to drive the coupled endergonic reaction.
• What effect does the enzyme have on the transition state (TS)?

  It introduces order into the system.