SFP8+9 - Enzymes Flashcards
The active site is relatively small, how many amino acid residues may it be made up of and how many are directly involved in catalysis?
10-15 amino acid residues, 2-3 may be directly involved
What does the rest of the enzyme do?
Structural role
Enzymes use binding energy of substrate interaction to provide additional catalysis, true or false?
True
What enzyme is an example of only using bidning energy and no catalytic groups?
Tyrosyl tRNA synthetase
What is meant by binding energy?
Free energy released upon the interaction of a complementary enzyme and substrate
What is meant by the binding energy must stabilise the transition state of the reaction?
When the reactant binds to the catalyst, it forms a complex that is more stable than either the reactant or the catalyst alone. This binding energy can be used to stabilize the transition state and lower the activation energy of the reaction, increasing the rate of the reaction.
There is greater stabilisation at the enzyme-transition state complex than at the enzyme-substrate complex
The enzyme-transition state complex stabilises this high-energy intermediate by lowering its energy, making it easier for the reactants to proceed to the product
Upon binding, the substrate is distorted. Transition state makes better contacts than the substrate. Induced fit = structure of the enzyme is complementary to the TS only after binding and the active site closes around substrate to form a new environment for catalysis.
How does the enzyme bind to the substrate?
Large number of relatively weak non-covalent interactions
What type of bond to serine proteases hydrolyse?
Peptide bonds
Which carbon is attacked by serine protease?
Carbonyl
What is an example of a serine protease involved in digestion?
Chymotrypsin
What can be added to this to make it non-function (irreversible change)
Organophosphates
How does this work?
Organophosphate molecule binding covalently to the active site serine residue of the serine protease. The organophosphate forms a covalent bond with the serine hydroxyl group, resulting in the inactivation of the enzyme.
What is the triad of residues in serine proteases
Serine, Histidine, Aspartate
What are the frist two steps in the hydrolysis of a peptide bond by the catlytic triad?
- Substrate Binding: The substrate, typically a peptide or protein, binds to the active site of the serine protease. The active site consists of the catalytic triad residues, which are positioned in close proximity to the peptide bond to be cleaved.
- Activation of Serine: The histidine residue in the catalytic triad acts as a general base, abstracting a proton from the serine residue. This deprotonation of serine increases its nucleophilicity, allowing it to attack the carbonyl carbon of the peptide bond in the substrate.
3rd and 4th steps?
- Nucleophilic Attack: The activated serine residue, now in its nucleophilic form (serine-O⁻), attacks the carbonyl carbon of the peptide bond. This nucleophilic attack leads to the formation of a covalent acyl-enzyme intermediate, with the peptide bond temporarily attached to the serine residue.
- Histidine as General Acid: After the nucleophilic attack, the histidine residue acts as a general acid. It donates a proton to the leaving amino group, resulting in the cleavage of the peptide bond. This step generates a new N-terminus for the cleaved product.
