Lecture 8 - How do enzymes catalyse reactions?

Question 1

Where does enzyme-substrate binding occur

Answer 1

The active site

Question 2

What does the active site do?

Answer 2

1. has amino acid side chains projecting into it
2. binds the substrate via several weak interactions
3. determines the specificity of the reaction

Question 3

What is considered optimal binding?

Answer 3

Not too tightly bound

Question 4

What are the types of enzyme-substrate bonds?

Answer 4

1. Ionic bonds
2. Hydrogen bonds
3. van der waals interactions
4. Covalent bonds (rare)

Question 5

What do ionic bonds do?

Answer 5

Make use of charged side chains, e.g salt bridges.

Question 6

What are hydrogen bonds?

Answer 6

Side chain or backbone O and N atoms can often act as hydrogen bond donors and acceptors.

Question 7

What are van der waals interactions?

Answer 7

Between any protein and substate atoms in close proximity, (weakest of the interactions)

Question 8

What are covalent bonds?

Answer 8

Sharing of electrons pairs between atoms, relatively rare, much stronger than other bonds.

Question 9

What do enzymes show?

Answer 9

Geometric and stereospecificity (lock and key or induced fit with active site)

Question 10

What is the lock and key model?

Answer 10

The shape of the substrate and the conformation of the active site are complementary to one another

Question 11

What is the induced-fit model?

Answer 11

The enzyme undergoes a conformational change upon binding to substrate. Shape of active site becomes complementary.

Question 12

Are enzymes dynamic or static?

Answer 12

Dynamic

Question 13

How is ΔG lowered?

Answer 13

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

Question 14

How can ground state destabilisation and transition state stabilisation occur?

Answer 14

By having an active site that has shape/charge complementarity to the transition state, not the substrate

Question 15

What are the 5 types of enzyme catalytic mechanisms?

Answer 15

1. Preferential Binding of the Transition State
2. Proximity and Orientation Effect
3. Acid-Base Catalysis
4. Metal Ion Catalysis
5. Covalent Catalysis

Question 16

How does preferential binding of the transition state work?

Answer 16

Lowers activation energy by binding tightly to transition state

Question 17

How do proximity and orientation effects work?

Answer 17

Enzymes bring substrate molecules into close proximity and orient them in the correct spatial arrangement, reducing energy use.

Question 18

For two molecules to react they need to be?

Answer 18

Close together and in the right orientation

Question 19

What does acid-base catalysis involve?

Answer 19

H+ transfer

Question 20

What does metal ion catalysis provide?

Answer 20

Substrate orientation, Ability to act as lewis acids (electron acceptors), Sites for electron transfer.

Question 21

What does Covalent catalysis involve?

Answer 21

Nucleophilic attack of Enzyme-X. Formation of a reactive, short-lived intermediate, which is covalently attached to the enzyme.

Question 22

What do enzyme-substrate interaction rely on?

Answer 22

multiple, weak interactions and often induced fit.