Mechanisms and structures

Question 1

How can intermediates be stabilised?

Answer 1

-by oxyanion holes (active site pocket made up of backbone amides and +ve aa residues that stabilise -ve O:-)
-metal ions

Question 2

What are the roles of metal ions in catalysis?

Answer 2

-stabilise intermediates
-position substrates/nucleophiles/etc (eg. position molecule so that it can be activated into nucleophile by surrounding residues)
-act as acid (ie. accepts e-)

Question 3

Which amino acid residues are catalytically involved in the electron flow of an enzyme reaction?

Answer 3

polar amino acids
eg. Cys, Ser, Thr, Tys, His, Asp, Arg, Asp, Glu, etc etc

Question 4

What do non-catalytic amino acids do in enzyme reactions?

Answer 4

-interact with hydrophobic regions of substrate (via stacking and van der waals)
-increase pKa of environment (can’t stabilise -ve ions so more basic)