Enzyme mechanism Flashcards
if 2S and 2P
A+B C+D
M-M kinetic - different set up
measure 4 different Km
change [S] and measure Rate
each keep S - saturated level and change other conc
e.g. Km for A - saturated [B] and gradual increase of [A]
multiple S/P reaction
sequential method
ping pong method
sequential method
E+A+B -> EAB -> ECD -> E+C+D
binding might be ordered (bind first and other bind next) or random
ping pong method
A+B never meet and E at same time
E+A -> EA -> E.C -> Eā -> EB -> ED -> E+D
Eā - modified
activation energy
change in energy to small multiple step using E
E+S -> ES -> ET -> EP -> E+P
binding energy partially offsets Ae
E strategies
general
specific chemical
general E strategies
position of R
distortion of R
stabilisation of ET
provision enclosed chemical environment
general - position of R
position R correctly for interaction - bind to each other - one angle
general - distortion of R
less stable therefore undergo reactivity
change in environment - favour reaction
general - stabilisation of ET
affinity -> ET>S>P
bind and orders of magnitude more strongly than S
general - provision
enclosed chemical environment
e.g. pH differ from outside
specific chemical
3 catalysis: covalent, acid/base and metal ion
combo of non-covalent binding effect and covalent chemical interaction
covalent catalysis
a.s.r react with S
modify bond and change energy disruption
a.s.r
active site residue
acid/base catalysis
a.s.r accept/donate H+
basic and acidic a.a
Cys, Ser, Tyr
metal ion catalysis
various type
chemical strategies - proteolysis
hydrolyse peptide bond by boiling in 6M HCl for 24hrs
serine protease
Gene duplication and divergence
same reaction but different S
example serine protease
trypsin
chymotrypsin
elastase (all found in digestive juice)
thrombin (blood clotting)
specificity by pocket
region in enzyme - gives specificity
e.g. chymotrypsin, trypsin, elastase
main polypeptide line up and cut at same relative position
specificity by pocket - chymotrypsin
empty space for large a.a
specificity by pocket - trypsin
-ve bind strongly to +ve charge S
specificity by pocket - elastase
bulky HP side chain = narrow space - small side chain
chymotrypsin
catalytic triad (D/H/S) - positioned - Ser-His-Asp
mechanism - chymotrypsin (1)
Nu- attach on polypeptide carbonyl-acid/base catalysis -> alkoxide ion form bond with C on S chain
mechanism - chymotrypsin (2)
covalent intermediate -> S covalent attach to E = tetrahedral intermediate = destabilisation of S - oxyanion hole
mechanism - chymotrypsin (3)
cleave and lose C-terminal fragment -> leaves as peptide bond broken
mechanism - chymotrypsin (4)
Nu- attach on polypeptide carbonyl by H2O - H removed by His = OH- Nu- - acid/base catalysis
mechanism - chymotrypsin (5)
covalent intermediate - regenerate carbonyl at N term is = tetrahedral = set retrieve H from N of His and covalent bond with Ser - 0
mechanism - chymotrypsin (6)
cleave and loss of N-terminal fragment - OG position
oxyanion hole
always present inactive site
shown 0 can move in when single bonded
planar to tetrahedral -> 0 form H with NH of gly109 and Ser195
example oxyanion hole
cysteine protease - H lost at Cys = sulphur Nu-
metalloprotease - Nu- attach Zinc
DIDF
react with Ser195
TPCK
react with His57
