Enzymes 2 - Harmer Flashcards
What controls the rate of the reaction?
the energy barrier between the starting point and the transition state
enzymes work by lowering this E barrier, increasing the % of molecules that have the E to access the TS
What is critical to function
protein structure
How do enzymes lower the TS? (7)
by stabilising the transition state
- near attack conformations
- covalent catalysis
- acid base catalysis
- low barrier H bonds
- metal ion catalysis
- induced fit
- hydrophobic binding pockets
Covalent catalysis
e.g. digestive enzymes
contain active sites with catalytic residues that form temporary covalent bonds with the substrate
can donate protons to the substrate
Near attack catalysis
contain active sites that create micro environments to bring substrate(s) molecules in close proximity and correct orientation (to allow collision)
Acid base catalysis
contain active sites that contain residues such as histidine that can participate in H+ transfer.
acid base catalysis (H+ transfer) can create either
- a strong nucleophile
- stabilise a charge
- stabilise electrostatic interactions of transition states
e.g. triose phosphate isomerase
Metal ion catalysis
metal atoms such as zinc, magnesium and iron can lose and gain electrons easily (and so gain and lose charge)
positive charges on metal ions allows them to:
- stabilise/shield charges and transient and intermediate structures
- assist in forming a strong nucleophile: often activating water allowing the formation of reactive OH- ions
- charge can bind the substrate in the active site
- can form strong bonds where disulfide bonds cannot be used (e.g. strongly reducing environments)
e.g. matrilysin
Induced fit catalysis
the folding of a protein allows enzymes to stabilise the TS indirectly
the enzyme folds leaving some unfavourable element, when the substrate binds the enzyme conformation is altered so it is more stable - this reduces the E of the TS
can be a strained conformation or a repulsion of charges
e.g. human udp galactose 4 epimerase
