Lecture 8: How do enzymes catalyse reactions

Question 1

What is covalent catalysis?

Answer 1

The formation of a reactive, short lived intermediate, which is covalently attached to the enzyme

Question 2

What type of amino acids are likely to be involved in acid-base catalysis?

Answer 2

Amino acids likely involved in acid-base catalysis include:

Aspartic acid (Asp): Acts as a proton donor or acceptor.

Glutamic acid (Glu): Functions similarly, aiding in proton transfer.

Histidine (His): Often involved due to its ability to gain or lose a proton at physiological pH.

Arginine (Arg): less common but can still participate in catalytic activities

These amino acids help stabilize transition states and facilitate reactions by donating or accepting protons.

Question 3

What is expected to bind tightest to an enzyme: the substrate, product or transition state?

Answer 3

The transition state is expected to bind the tightest to an enzyme. Enzymes are designed to stabilize the transition state of a reaction, reducing the activation energy and increasing the reaction rate. This tight binding to the transition state is key to the enzyme’s catalytic efficiency.

Question 4

Which of the three forms the best basis for drug design: Substrate, transition state or product?

Answer 4

The transition state forms the best basis for drug design. Drugs that mimic the transition state (transition state analogues) can bind more tightly to the enzyme, effectively inhibiting its activity by blocking the enzyme’s active site, making them highly effective as enzyme inhibitors.

Question 5

How is the progression of a reaction through the transition state affected by the presence of an enzyme?

Answer 5

The presence of an enzyme lowers the activation energy required to reach the transition state, making it easier for the reaction to progress.

After the transition state, the reaction proceeds to form the products. The transition state is the highest energy point in the reaction pathway. Once the transition state is overcome, the reaction continues downhill in energy, leading to the formation of stable products.

Question 6

What are the two models used to describe enzyme-substrate binding?

Answer 6

Lock-and-Key model - Shape of the substrate and the conformation of the active site are complementary

Induced-fit model - the enzyme undergoes a conformational change upon binding substrate. Active site takes shape only after the enzyme binds the substrate

Question 7

What types of bonds might we find between an enzyme and substrate?

Answer 7

Types of enzyme-substrate bond:

Ionic bonds (a.k.a. salt bridges):
* Make use of charged side chains (Asp, Glu, Arg, Lys).

Hydrogen bonds:
* Side chain or backbone O and N atoms can often act as hydrogen 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

Question 8

How is ΔG°‡ lowered?

Answer 8

1. Ground state destabilisation.
2. Transition state stabilisation.
3. Alternate reaction pathway with a different (lower-energy) transition state.

(1) and (2) can be achieved the same way: by having an active site that has shape/ charge complementarity to the Transition State, not the substrate.

Question 9

Name five catalytic mechanisms in which enzymes are involved:

Answer 9

1. Preferential binding of transition state - The transition state is expected to bind the tightest to an enzyme. Enzymes are designed to stabilize the transition state of a reaction, reducing the activation energy and increasing the reaction rate. This tight binding to the transition state is key to the enzyme’s catalytic efficiency.
2. Proximity and orientation effects - They bring substrates close together and align them correctly, reducing activation energy and increasing reaction efficiency. This precise arrangement enhances the chances of successful reactions.
3. Acid-base catalysis - involves the transfer of H+ (histidine is a good example as it can donate or receive a proton thus operates well in high or low pH conditions)
4. Metal ion catalysis:
   - These metals provide substrate orientation (specific coordination geometries)
   - ability to act as Lewis acids (accepting e-) to polarise H2O or other functional groups
   - sites for electron transfer (RedOx)
5. Covalent catalysis - Covalent catalysis involves the formation of a covalent intermediate between the enzyme and the substrate. This transient covalent bond facilitates the reaction by stabilizing the transition state and lowering the activation energy.

Question 10

What role does Mg2+ play in Hexokinase activity?

Answer 10

Mg2+ ion balances negative charge of transition state, stabilising the transition state.

This helps hexokinase control glycolysis when phosphorylating glucose.

Question 11

What are 2 features of the enzyme active site which are important for determining the specificity of the reaction?

Answer 11

1. It has amino acid side chains projecting into it
2. It binds substrates via multiple weak interactions - weak bonds can only be formed when relevant atoms are precisely positioned

Question 12

What allows the enzyme to distinguish between identical groups on the substrate?

Answer 12

The asymmetric shape of the active site

Question 13

What are the three stages in covalent catalysis?

Answer 13

1. Nucleophilic reaction between the enzyme and the substrate
2. Electrophilic withdrawal of electrons from the substrate
3. Elimination reaction

Question 14

Describe the induced fit between glucose and hexokinase:

Answer 14

Hexokinase undergoes an induced fit conformational change when glucose binds, preventing the hydrolysis of ATP.

Hexokinase has two conformational states:
1. The open state, prior to glucose binding. ATP is bound to the large lobe of the enzyme, far away from the glucose binding site.
2. The closed state once glucose binds to the hexokinase active site. This change closes the two lobes around the glucose substrate.