Lec09 Slide 3
a. what are mechanisms by which amino acids catalyze reactions?
i. chemical modes
1. acid base
i. formation of free radicals are highly caustic to cellular function
1. extra reactive -- react with anything
2. damage cells
a. x axis
i. course of reaction
ii. reaction coordinate
iii. progress of bond breaking proceeds to the right
b. y axis
i. free energy
c. do not need to know how to draw enzyme catalysis diagrams
a. enzyme is potentiating the reaction by bringing reactions in close proximity
i. what does potentiating mean?
1. potential to go forward
1. polar amino acid residues on enzyme (or coenzymes on occasion) undergo chemical change
during enzymatic catalysis
i. acid base catalysis?
ii. also due to covalent catalysis
b. what did she emphasize about this point?
i. do we need to know the principal functions of each amino acid?
a. review the principal functions
b. difference between lysine and arginine i. one is different in terms of pI
1. general acid base catalysis vs specific acid base catalysis
i. catalysis by H+ or OH-
i. any negative vs positive groups (not specifically H+ / OH-)
c. the active site of the enzymes are providing the biological solution of acid or bases
i. missed what she emphasized about this point
1. region where acid base takes place
i. B can also take part in cleavage of other bonds involving water
2. forming OH by removal of proton
3. not really certain about this point
1. how to you titrate the side chains?
a. slowly adding pH to determine the points when cysteine and
histidine become protonated
i. also respectively activated and inactivated
ii. why is it perturbed?
1. what does this mean?
a. how does the microenvironment
contribute to the perturbed pKa? why is
the thiolate pKa changed so
ii. what did she say about hyperbolic and sigmoidal curves?
1. what is active and what is not?
a. bell shaped involves two ionizable groups
b. sigmoidal involves on ion ionizable groups
1. know when its active and inactive and why
2. Know the steps
3. know what happens 4. visualize it and understand the steps
5. point form
a. step 1
i. DHAP binds to enzyme
ii. carbonyl of DHAP forms h bond with his
iii. carboxylate of glutamate is ionized (negative) takes proton away from C1
b. step 2
i. DHAP deprotonates histidine
ii. change in the double bond from C=O to C=C
iii. formation of stronger h bond
c. step 3
i. deprotonated his takes a proton from OH group of C1
d. step 4
i. glu-165 donates proton to C2 (double bond with h)
e. step 5
i. final product released
i. binding site channel is lined with hydrophilic residues
1. why not hydrophobic?
a. because the free oxygen radical is negatively charged, the
binding site needs to be hydrophilic
2. Missed what she said about positive charges
3. What emphasis?