FII - Lecture Slides 83 - 99

Question 1

What type of interactions does enzyme binding use?

Answer 1

Non-Covalent interactions (same as protein folding)

Question 2

What are some non-covalent interactions that enzymes use?

Answer 2

• Hydrophobic patches on the surface of target bind
• Van Der Waals forces (negative and positive charge)
• ## Hydrogen Bonding and Ionic Bonding

Question 3

What is the binding of chymotrypsin?

Answer 3

Chymotrypsin bind to the aromatic amino acids: The, Tyr, Trp

It will bind upwards of the peptide chain

Its side binding pocket is larger and hydrophobic, and the target amino acid will be positioned next to the catalytic unit.

Question 4

What is the characteristics of the Trypsin binding pocket?

Answer 4

Trypsin is able to bind Lysine and Arginine

Its binding picket is narrow and positively charged at the end.

Question 5

What is the characteristic of the elastase binding pocket?

Answer 5

Elastase binds Ala and Glycine the best

Its binding pocket is small and hydrophobic

Question 6

What is the target molecule of an enzyme?

Answer 6

A substrate

Question 7

What must a chemical reaction be in order to occur?

Answer 7

It must be spontaneous, and have a negative delta G (Gibbs free energy)

Question 8

Without a catalyst, what must reactions depend on?

Answer 8

Random Events
- Molecule must collide
- Must be in the correct orientation
- require a threshold energy

Question 9

What is Z?

Answer 9

Z is the collision frequency (proximity effect)

Question 10

What is p?

Answer 10

P is your orientation (the probability factor0

Question 11

What do low Ea or high temp make?

Answer 11

Make the fraction bigger, so the reaction is favoured

Question 12

What will happen if you hold the enzyme and substrate close to one another for long enough?

Answer 12

The reaction will proceed and this is known as the proximity effect (increase Z)

Question 13

What is it called when you align the enzyme and the substrate at the active site?

Answer 13

This is known as the orientation effect (probability factor), which will increase p

Question 14

What are the conditions that an enzyme will speed up reaction rates at?

Answer 14

At pH 7 and normal temperature (body temperature - 37 degrees)

Question 15

Nucleophilic Catalyst

Answer 15

Wants to donate electrons and can speed up a reaction by providing a BETTER ncuelophile.

Question 16

What are some amino acids that have some chains that act as nucleophiles?

Answer 16

Cysteine, Histidine, Asp or Glu

Try or Ser, Lys

Question 17

Electrophilic Catalyst

Answer 17

Wants to gain electrons (electron seeking)

Question 18

What amino acids have side chains that are electrophiles?

Answer 18

There are no real amino acids that have good electrophiles.

Question 19

What is a prosthetic group?

Answer 19

A non amino acid helper molecule, that ind at the catalytic site and initiates reaction by withdrawing electrons from substrate.

Question 20

General Acid Catalysis

Answer 20

amino acid side chain that donates H+ to the reaction

Question 21

General Base Catalysis

Answer 21

Amino Acid Side Chain that removes H+ from the reaction

Question 22

What happens when reaction pass through a transition state?

Answer 22

Key atoms may change shape (trigonal planar to tetrahedral) or stretch

Question 23

What will happen of the enzyme activation site is complementary to the transition state?

Answer 23

It will require less activation energy