How do Enzymes Catalyse Reactions? Flashcards
What are the features of an active site?
- Have amino acid side chains pointing into it
- Binds substrates through multiple weak interactions
- Enzyme active site determines the specificity of the reaction
Why are weak bonds advantageous?
Many, weak interactions ensure specificity and reversibility.
- several bonds are required for substrate binding
- weak bonds can only generally form if the substrate is precisely positioned
- it is easy to break weak bonds
Molecular complementarity between enzyme and substrate is critical
What are the types of enzyme-substrate bond?
Ionic bonds (also called salt bridges)
- makes use of charged side chains
Hydrogen bonds:
- side chains or backbone O and N atoms can often act as H bond donors and acceptors
Van der Waals interactions:
- between any protein and substrate atoms in close proximity; weakest of the interactions
Covalent bonds:
- relatively rare; much stronger than the other bonds
What are the two models for substrate binding?
Lock and key, and induced fit.
Glucose and hexokinase show induced fit, where the domains come together and the side chains slightly rotate to form the correctly shaped active site
How is delta G (Gibbs energy) lowered?
- Ground state destabilisation
- Transition state stabilisation
- Provide an alternative reaction pathway with a different, lower energy transition state
(1 and 2 are TS optimal binding)
1 and 2 can be achieved the same way: by having an active site that has shape/charge complementary to the transition state, not the substrate.
What are the catalytic mechanisms?
- Preferential binding of the transition state
- Proximity and orientation effects
- Acid-base catalysis
- Metal ion catalysis
- Covalent catalysis
Describe preferential binding of the transition state
Prediction: an enzyme should bind the transition state more tightly than it binds the substrate
Problem: transition states are transient and cannot be isolated - so need to design and synthesise an analogue (the analogue fits better in the active site
Describe proximity and orientation effects
for two molecules to react they need to be close together and in the right orientation
Describe acid-base catalysis
involves transfer of protons from acids or bases.
histidine is particularly suitable for these types of reactions because its pKa is close to physiological pH, so depending on the environment His can donate or accept a proton
Describe metal ion catalysis
At least a this of known enzymes require metal ions for catalytic activity. These metals provide:
- substrate orientations (because of their specific coordination geometries)
- their ability to act as lewis acids (electron acceptors) to polarise water or other functional groups
- sites for election transfer (so redox reactions)
eg. hexokinase uses Mg2+ as a cofactor because it balances the charge of the transition state and aligns everything perfectly in the active site
Descrive covalent catalysis
involves the formation of a reactive, short-lived intermediate, which is covalently attached to the enzyme.
Describe how enzymes show geometric and stereospecificity
Provided the shape of the active site is asymmetric, the enzyme can distinguish between identical groups on the substrate.
Describe transition state analogues as drugs
When designing drugs you target the transition state because that’s what the enzyme is designed to act on.
- enzymes are often targets for drugs and other beneficial agents
- transition state analogues often make ideal enzyme inhibitors
- enalapril and aliskiren lower blood pressure
- statins lower serum cholesterol
- protease inhibitors are AIDS drugs
- juvenile hormone esterase is a pesticide target
- tamiflu is an inhibitor of influenza neuraminidase
