Lecture 10 - how do enzymes catalyze reactions

Question 1

where does enzyme substrate binding occur

Answer 1

at the active site

Question 2

what projects into the active site

Answer 2

amino acid side chains

Question 3

how does the substrate bind to the active site

Answer 3

via several weak interactions

Question 4

what is optimal binding

Answer 4

• many, weak interactions ensure specificity and reversibility
• not too tight

Question 5

what are the 4 types of enzyme bonds

Answer 5

ionic bonds = make use of charged side chains (Asp, Glu, Arg, Lys)

hydrogen bonds = side chain or backbone O and N 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 6

what kind of shape is the active site

Answer 6

asymmetric

Question 7

what are the 4 catalytic mechanisms

Answer 7

1. preferential binding of the transition state
2. proximity and orientation effects
3. acid-base catalyst
4. metal ion catalysis

Question 8

what is proximity and orientation effects

Answer 8

for two molecules to react they need to be close together and in the correct orientation

Question 9

what does acid base catalyst involve

Answer 9

proton transfer (H+)

Question 10

what is covalent catalysis

Answer 10

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