Properties of Enzymes and Catalysis Flashcards
How to name enzymes?
First describes the substrate
Second is the enzyme group that describes the reaction
What are some features of enzymes?
High reaction rate - 10^6 to 10^12 times greater than uncatalysed
Works under mild conditions - neutral pH, temp below 100 & atmospheric pressure
Specificity - with respect to substrates (due to stereochemistry)
Can be regulated - allosteric control (bind somewhere other than active site), covalent modification & amount synthesised
What are the enzyme groups?
Oxidoreductases Transferases Hydrolases Lyases Isomerases Ligases
These groups are 1-6 and that is the enzyme classification
What is an oxidoreductase?
Redox reaction
What is a transferase?
Transfer of functional groups
What is a hydrolase?
Hydrolysis reactions
What are lyases?
Group elimination to form double bonds
What are ligases?
Bond formation coupled with ATP hydrolysis
What are isomerases?
Isomerisation
What is the active site? Types of complementarity?
An indentation or cleft on the surface of an enzyme that performs the catalysis
Geometric complementarity - the cleft is complementary in shape to the substrate
Electronic complementarity - amino acids in the cleft are arranged specifically to attract the substrate
What are the proposed enzyme mechanisms?
Lock and key - enzyme and substrate are perfectly complementary
Induced fit - when the substrate binds the active site alters it shape to fit perfectly
Selected fit - the enzyme explores different structures and is most stable in the structure at the time of the substrate binding
What forced are involved in induced fit?
Van der waals
Electrostatic attraction
Hydrogen bonding
Hydrophobic interactions
Why are enzymes stereospecific?
They tend to be chiral due to the proteins consisting of L-amino acids
Therefore form asymmetric active sites
Therefore some enzymes are only specific for one compound
What do some enzymes require? Why?
Cofactors (the enzymes “chemical teeth”)
Enzymes aren’t suitable alone for redox reactions and group transfer reactions
Types of cofactors?
Metal ions
Eg Cu 2+, Fe 3+ or Zn 2+
Coenzymes:
Cosubstrates - transiently bound (loosely)
Eg NAD, NADP
Prosthetic group - permanently bound to the protein via covalent bonds
Coenzymes must be regenerated- to complete the catalytic cycle, it must return to original state
What are the states of an enzyme?
Apoenzyme - inactive enzyme
Holoenzyme - active enzyme
Apoenzyme + cofactor ⇌ holoenzyme
What is the transition state? Enzymes effect?
The point of highest free energy in a reaction
The enzyme doesn’t alter the ΔG but can decrease the ΔG++ (the difference in Gibbs free energy between the transition state and the reactants)
This allows the reaction to approach equilibrium faster than without a catalyst
So they reduce the free energy of the transition state and therefore stabilise the transition state
What is the reaction coordinate?
Reactants proceeding along the path of minimum free energy
So a plot called a transition state diagram is the free energy v the reaction coordinate
What can be produced in a multistep reaction?
The step with the highest transition state free energy acts as a ‘bottleneck’ and is called the rate determining step
What are the types of catalytic mechnanisms enzymes employ?
Acid-base catalysis Covalent catalysis Metal ion catalysis Proximity and orientation effects Preferential binding of the transition state complex
What is acid catalysis?
A process where a proton is transferred from an acid which lowers the free energy of a reaction’s transition state
What is base catalysis?
A proton is abstracted by a base in order to increase the rate
Give an example of acid-base catalysis?
Bovine pancreatic RNase A
It is secreted by the pancreas into the small intestine where it hydrolyses RNA to its component nucelotides
It has a His12 residue to act as a base and a His119 residue to act as an acid to first promote nucleophilic attack and bond cleavage
After this they swap roles and now promote hydrolysis
Which amino acids are useful as acid/bases and why?
Asp, Glu, His, Cys, Tyr, and Lys
They have pK’s in/near the physiological pH range, allowing them to act as a acid/and or base