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
What is covalent cataylsis?
Covalent catalysis accelerates reaction rates through the transient formation of a catalyst–substrate covalent bond
Usually requires a nucleophile on the catalyst and an electrophile on the substrate
Describe a general outline of covalent cataylsis?
- The nucleophilic reaction between the catalyst and the substrate to form a covalent bond.
- The withdrawal of electrons from the reaction center by the now electrophilic catalyst.
- The elimination of the catalyst, a reaction that is essentially the reverse of stage 1
What is an nucleophile and an electrophile?
Nucleophile - negatively charged or contain unshared pair of electrons to form covalent bonds with electron-deficient centres (closely related to basicity)
Electrophile - positively charged and can contain an unfilled valence electron shell
What makes a good covalent catalyst?
It can’t form a very stable covalent bond and it is harder to decompose
Therefore it needs contradictory properties of high nucleophilicity and ability to form a good leaving group
e.g. groups with high polarizability
Examples of good covalent catalysts?
Unprotonated amino group of lysine Imidazole group of histidine Thiol group of cysteine Carboxyl group of aspartic acid Hydroxyl group of serine
What is metal ion catalysis?
Using metal ions as cofactors called - metalloenzymes
They are tightly bound cofactors
Mainly transition state elements - they are directly involved
Na+, K+ and Ca2+ - used to stabilise the structure and hold its shape together
Mg2+ and Zn2+ - can stabilise and/or take part in the reaction directly
How are metal ions used in catalytic processes?
- By binding to substrates to orient them properly for reaction.
- By mediating redox reactions through reversible changes in the metal ion’s oxidation state
- By electrostatically stabilizing or shielding negative charges
- They can bind water molecules and make them more acidic
Example of metal ion catalysis?
Carbonic anhydrase and Zn2+ catalysing:
CO2 + H2O HCO3- + H+
Zn2+ binds to water polarizing and making it more acidic and allowing it to give up a proton more easily
His64 then assists in base catalysis
How does proximity and orientation effects help catalysis?
The enzyme provides a surface to increase local concentration
Binding to the substrate brings the molecules closer together and they can then react
It stabilises the binding in the correct orientation
The enzymes freeze and rotational/translational movement
What is another element to proximity and orientation effects?
Electrostatic catalysis is where charged groups can help stabilise the transition state
The expulsion of water enhances this
The charge distribution around the active sites of enzymes may also guide polar substrates toward their binding site
Describe the effects of enzymes preferentially binding to the transition state?
An enzyme may bind the transition state of the reaction it catalyzes with greater affinity than its substrates or products
Enzymes that preferentially bind the transition state structure increase its concentration and therefore proportionally increase the reaction rate
What can transition states act as?
Transition state analogs (similar structures) are enzyme inhibitors
How can the transition state be achieved?
If there is stress/stain on surrounding groups it can push other groups together, distorting the bond angles making the molecule look like the transition state
What has the understanding of transition states lead to?
The basis for drug design due to understanding specific enzyme reaction mechanisms
