lecture 10 - enzyme catalysis Flashcards
Where does enzyme-substrate binding occur?
The active site
What is the structure of an active site?
Has several amino acid side chains projecting into it that create binding specificity
How does the active site bind substrate?
Via several weak interactions with amino acid residues
What is the equation for the reaction of substrate and enzyme?
E + S ⇌ ES ⇌ EX‡ → EP
Why are Enzyme-substrate bonds weak but numerous?
To ensure specificity and reversibility
What is molecular complementarity in terms of enzymes?
When enzyme and substrate have complementary atoms/functional groups that bind precisely to one another in the active site
What are the 4 types of enzyme-substrate bonds?
Ionic bonds, hydrogen bonds, van der Waal’s interactions, covalent bonds
What are ionic enzyme-substrate bonds?
Attractions between charged (protonated/deprotonated) amino acid side chains
What are hydrogen enzyme-substrate bonds?
H-bonds between side chain or backbone O and N atoms of amino acids
What are enzyme-substrate van der Waals interactions?
Interactions between any protein and substrate atoms in close proximity
What is the weakest type of chemical bond?
van der Waals/dispersion forces
What are covalent enzyme-substrate bonds?
A rare type of strong bond between atoms of the substrate and protein atoms
How are active sites stereospecific?
If the active sites are asymmetric, they can distinguish between stereoisomers (D or L)
What are the 2 types of enzyme-substrate binding model?
Lock & Key and Induced Fit
What is the principle of the lock & key model?
The shape of the substrate and the conformation of the active site are complementary to each other, so no shape change is needed.
What is the principle of the Induced Fit Model?
Enzymes must undergo conformational changes upon binding to the substrate, in order for the active site to have a shape complementary to the substrate
Are enzymes dynamic or static in terms of shape?
Dynamic
What are the 3 ways that enzymes lower activation energy?
Ground state destabilisation, Transition state stabilisation, Alternate reaction pathway with a different transition state
How do enzymes lower activation energy via ground state destabilisation?
By having an active site that has shape/charge complementarity to the transition state, rather than the substrate
How do enzymes lower activation energy via transition state stabilisation?
By having an active site that has shape/charge complementarity to the transition state, rather than the substrate.
What are the 5 key catalytic mechanisms?
Preferential binding of the transition state, proximity & orientation effects, acid-base catalysis, metal ion catalysis and covalent catalysis
What are transition state analogues?
Chemicals that resemble the transition states of substrates but are more stable, so can bind to the relevant enzymes, inhibiting natural substrate reactions
What are the proximity and orientation mechanisms of enzymes?
Enzymes can hold substrates in the correct position (close together and in correct orientation) to readily react
What is acid-base catalysis in terms of enzymes?
When amino acids in the active site are involved in proton transfer (loss at low pH and gain at high pH) to facilitate the reaction
What amino acid is commonly involved in a acid-base catalysis, and why?
Histidine, because its pKa is close to physiological pH and therefore can accept or donate protons depending on the environment of the active site
What are the 3 key functions of metal ions in catalysis?
Substrate orientation, act as Lewis Acid, site of electrons transfer
What is the substrate orientation functions of metal ions in catalysis?
Able to orientate substrate within the active site due to specific coordination geometries
What is the Lewis Acid function of metal ions in catalysis?
Ability to act as Lewis acids/electron pair acceptors to polarise H2O or other functional groups
What is the electron transfer function of metal ions in catalysis?
Allow for electron transfer reactions such as redox reactions, which can be used to balance the negative charge of transition states, bringing down the activation energy
What is covalent catalysis in terms of enzymes?
Involves the formation of a reactive, short-lived intermediate, e.g. nucleophilic side chain, which is covalently attached to the enzyme
