Enzymology Leimkühler

Question 1

Catalyst: Definition

Answer 1

A Catalyst is a compound that takes part in a reaction by increasing the rate of the reaction without being consumed and without changing the chemical equilibrium of the reaction. The reaction is accelerated by a reduction of the activation energy.

Question 2

Gibbs free energy in thermodynamics

Answer 2

1. A reaction will occur without the input of energy, or spontaneously, only if ΔG is negative. Such reactions are called exergonic reactions.
2. If a reaction is at equilibrium, there is no net change in the amount of reactant or product. At equilibrium, ΔG =0.
3. A reaction will not occur spontaneously if the ΔG is positive. These reactions are called endergonic reactions.
4. The ΔG of a reaction depends only on the free energy difference between reactants and products and is independent of how the reaction occurs.
5. The ΔG of a reaction provides no information about the rate of the reaction

Question 3

Enzymes: forming transition state

Answer 3

binding of substrate and enzyme is importante for catalysis
Binding energy is the free energy released upon interaction of the enzyme and substrate.
Binding energy is greatest when the enzyme interacts with the transition state, thus facilitating the formation of the transition state.

Question 4

Catalytic reactions

Answer 4

Common catalytic strategies include:

1. General acid-base catalysis: A molecule other than water donates or accepts a proton.
2. Electrostatic catalysis: stabilization of a charge by a charge from an amino acid at the active site
3. Metal ion catalysis: Metal ions function in a number of ways, including serving as an electrophilic catalyst.
4. Catalysis by approximation: The enzyme brings two substrates together in an orientation that facilitates catalysis.
5. Covalent catalysis: The active site contains a nucleophile that is briefly covalently modified.

Question 5

Acid-base catalysis

Answer 5

amino acid chains can act as acid basis catalysis
acid-base reactions are governed by side chains pka’s
catalysis is often sensitive to pH changes
pH rate profiles can distinguish between acid-base catalysis and lead to the identificantion parcitipating catalytic residues (mutagenesis)

Question 6

Electrostatic catalysis

Answer 6

when a charged transition state can not be stabilized by acid-base catalysis ( like ionization), charge can be neutrolized by opposite charged group from the catalysis (active side of the enzyme)
AA chains that practise electro static catalysis: Asp, Glu, Lys, His, Arg
active side of an enzyme: serveral electro static interactions (also known as ion pairs or salt bridges)
they can collectivly attack susbstrate in active side pocket (= Ground state destabilisation) and stabilize the transition state contribution to reduction in activation barrier (Orthotidine monophosphate decarboxylase and ground state destabilisation

Question 7

Metal ion catalysis

Answer 7

•13 different Metall-Ions were identified with roles in biologic reactions:
Mg, Zn, Fe, Mn, Ca, Co, Mo, W, Cu, Na, K, Ni, V