Enzymes and Kinetics Flashcards
What is a general way to describe how enzymes work?
The substrate binds to the active site, forms the enzyme-substrate complex, then the product leaves
What is the active site?
A pocket in the surface of the enzyme formed from precise 3D arrangements of the amino acids and/or prosthetic groups
What does the thermodynamics tell us about a reaction?
If the reaction is energetically favourable, which side is favoured by the equilibrium, what is the final distribution of products and reactants
What does the kinetics tell us about a reaction?
How fast the reaction will get to that final distribution
If deltaG < 0:
a) endergonic or exergonic?
b) products or reactants favoured?
a) exergonic
b) products
If deltaG > 0:
a) endergonic or exergonic?
b) products or reactants favoured?
a) endergonic
b) reactants
Do enzymes change the thermodynamics or the kinetics?
Only the kinetics
What is the transition state?
The high energy state at the peak of the activation barrier. It has an equal chance of becoming the product or substrate
How do enzymes speed up the reaction rate?
They lower the activation energy and interact with the reactants so that they reach the transition state easier
Do enzymes change the final distribution of products and reactants?
No, that is governed by deltaG, which enzymes do not change
What are 4 ways enzymes lower the activation energy?
- Desolvation
- Participating in the reaction
- Proximity and orientation effects
- Selective stabilization of the transition state
What is desolvation? Why does this help speed up the reaction?
Removing the reactants from water. It helps cause an induced fit between binding partners and forms the functional active site. Water can also interfere with reactions
What are proximity and orientation effects? Why does this help speed up the reaction?
The enzyme holds the two substrates together in the right orientation. The reaction goes faster than if they were floating around and hoping to bump into each other in the right orientation
How does an enzyme participate in the reaction?
Can provide functional groups, act as a nucleophile, acid-base assistance, redox reactions, then get regenerated later
What is selective stabilization of the transition state? Why does this help speed up the reaction?
The active site forms additional favourable interactions with the transition state. This makes the transition state favourable to form and lowers its energy
What are cofactors?
Non amino acid groups that provide additional chemical functionality. Includes metal ions and coenzymes
What is the mechanism of enzymes?
Break up a large reaction into several smaller ones that still have a lower activation energy overall
What is the function of lysozymes?
Cleaves peptidoglycan so bacteria can’t withstand osmotic pressure
What are the two important amino acids for the catalytic function of lysozyme?
Glu35 and Asp52
What is different about Glu35 in lysozyme?
It is surrounded by hydrophobic amino acids. It is unfavourable for it to be in the A- form, so it stays in HA and has a much higher pKa
What is the optimal pH for lysozyme?
5
What is the mechanism by which lysozyme breaks down peptidoglycan?
- Asp52 acts as a nucleophile and attacks the glycosidic bond
- Forms a covalent bond with the peptidoglycan
- Glu35 protonates it and half of the product is released
- SN2 attack from water
- Glu35 deprotonates the water
- Breaks covalent bond with Asp52
- Second half of the product is released and regenerates the enzyme
Why is enzyme kinetics useful?
Can tell us the reaction mechanism, how it changes with different enzymes and substrates, the functioning of inhibitors
What shape is the Michaelis-Menten graph?
Hyperbolic
