Enzyme Catalysis Flashcards
How are enzymes thought to stabilize transition states?
Enzymes prefer to bind transition states over substrates and thus reduce activation energy. They bind intermediates with higher affinity than reactants.
How do K(S) and K(T) compare?
K(S) is the constant for the reaction between enzyme and substrate to yield the enzyme-substrate complex.
K(T) is the constant for the reaction between enzyme and transition state to yield the enzyme-transition state complex.
K(T)
By which step is reaction rate determined?
The rate of the step with the highest activation energy determines reaction rate.
What are the four mechanisms of catalysis?
Proximity and strain effects
Electrostatic effects
Acid-base catalysis
Covalent catalysis
What are proximity and strain effects?
The substrate fits the catalytic site with optimal orientation, then the enzyme changes conformation to give a strained enzyme-substrate complex.
What are electrostatic effects?
Binding/active site excludes H20, which lowers the dielectric constant [remember, dielectric constant is a measure of the capacity of a solution to reduce electrostatic attraction between charged molecules/ions]. This strengthens the electrostatic interaction between enzyme and substrate.
What is acid-base catalysis? What is an example of this type of reaction? How does it work?
An example is hydrolysis of esters to yield carboxylic acid and alcohol. Esters are stable at neutral pH, but can be hydrolyzed at high or low pH.
No enzyme is involved here–only water and an acid/base.
Functional groups on amino acid sidechains can also act as general acids, bases, or both–depending on pH.
E.g. Histidine
How does covalent catalysis work?
A nucleophilic side chain forms unstable covalent bonds with a substrate–e.g. during polypeptide digestion by serine proteases.
Which amino acids can perform catalysis?
Only those with polar or charged side chains.
How do serine proteases work?
They form an ester by attacking an amide with the serine OH group. Then the ester is separated into serine and a carboxylic acid via hydrolysis.
What is the role of alkali and alkaline earth metals in organisms?
They are loosely bound and usually play a structural role. Examples are Na, K, Mg, Ca.
What is the role of transition metals in organisms?
They are tightly bound, involved in catalysis, and are electrophiles (Lewis acids/electron acceptors). Examples are Zn, Fe, Cu.
What does carbonic anhydrase do? How does it work?
Carbonic anhydrase converts CO2 to carbonic acid. The structure of the active site is as follows:
One zinc ion bound to three histidines and the oxygen of one water molecule.
The mechanism is as follows:
1) Water is deprotonated to yield an OH group on zinc.
2) CO2 arrives on the scene.
3) The OH group attacks the CO2 carbon, and the electrons from one of the CO2 C-O double bonds are pushed up onto the oxygen atom.
4) An H2O molecule attacks the zinc and HCO3- is released.
What are coenzymes? What are the three main types?
Coenzymes are organic molecules that are loosely bound to enzymes, and are mostly vitamin derivatives.
The main types are:
1) Electron/hydrogen transfer [remember, hydrogen transfer is really a proxy for electron transfer]–e.g. NAD+, NADP+, FAD+, FMN, CoQ, BH4
2) Group transfer–e.g. TPP, CoA, pyroxidal phosphate, TH4, SAM
3) High energy transfer potential–UDP-glucose, CDP
What is triose phosphate isomerase? How does it work?
Triose phosphate isomerase converts dihydroxyacetone phosphate (DHAP) to glyceraldehyde-3-phosphate (G3P) via an enediol intermediate.
[Remember: An enediol is an alkene with hydroxyl groups attached to the carbons at either end of the double bond.]
The mechanism is an acid-base catalysis carried out be Glu and His in the active site of TPI:
1) The carboxyl group of Glu abstracts H+ from C1 of DHAP.
2) His donates an H+ to the C2 yielding the enediol intermediate.
3) His abstracts H+ from the C1 hydroxyl group
4) C2 abstracts H+ from the protonated Glu, yielding G3P.
