FII - Lecture Slides 83 - 99 Flashcards
What type of interactions does enzyme binding use?
Non-Covalent interactions (same as protein folding)
What are some non-covalent interactions that enzymes use?
- Hydrophobic patches on the surface of target bind
- Van Der Waals forces (negative and positive charge)
- ## Hydrogen Bonding and Ionic Bonding
What is the binding of chymotrypsin?
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.
What is the characteristics of the Trypsin binding pocket?
Trypsin is able to bind Lysine and Arginine
Its binding picket is narrow and positively charged at the end.
What is the characteristic of the elastase binding pocket?
Elastase binds Ala and Glycine the best
Its binding pocket is small and hydrophobic
What is the target molecule of an enzyme?
A substrate
What must a chemical reaction be in order to occur?
It must be spontaneous, and have a negative delta G (Gibbs free energy)
Without a catalyst, what must reactions depend on?
Random Events
- Molecule must collide
- Must be in the correct orientation
- require a threshold energy
What is Z?
Z is the collision frequency (proximity effect)
What is p?
P is your orientation (the probability factor0
What do low Ea or high temp make?
Make the fraction bigger, so the reaction is favoured
What will happen if you hold the enzyme and substrate close to one another for long enough?
The reaction will proceed and this is known as the proximity effect (increase Z)
What is it called when you align the enzyme and the substrate at the active site?
This is known as the orientation effect (probability factor), which will increase p
What are the conditions that an enzyme will speed up reaction rates at?
At pH 7 and normal temperature (body temperature - 37 degrees)
Nucleophilic Catalyst
Wants to donate electrons and can speed up a reaction by providing a BETTER ncuelophile.
What are some amino acids that have some chains that act as nucleophiles?
Cysteine, Histidine, Asp or Glu
Try or Ser, Lys
Electrophilic Catalyst
Wants to gain electrons (electron seeking)
What amino acids have side chains that are electrophiles?
There are no real amino acids that have good electrophiles.
What is a prosthetic group?
A non amino acid helper molecule, that ind at the catalytic site and initiates reaction by withdrawing electrons from substrate.
General Acid Catalysis
amino acid side chain that donates H+ to the reaction
General Base Catalysis
Amino Acid Side Chain that removes H+ from the reaction
What happens when reaction pass through a transition state?
Key atoms may change shape (trigonal planar to tetrahedral) or stretch
What will happen of the enzyme activation site is complementary to the transition state?
It will require less activation energy
