Lec09 Questions.docx

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Biological Sciences
Shelley A.Brunt

Lec09 Slide 3 a. what are mechanisms by which amino acids catalyze reactions? i. chemical modes 1. acid base 2. covalent Slide 6 i. formation of free radicals are highly caustic to cellular function 1. extra reactive -- react with anything 2. damage cells Slide 8 1. graph 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 Slide 11 a. enzyme is potentiating the reaction by bringing reactions in close proximity i. what does potentiating mean? 1. potential to go forward Slide 14 1. polar amino acid residues on enzyme (or coenzymes on occasion) undergo chemical change during enzymatic catalysis a. why? i. acid base catalysis? ii. also due to covalent catalysis b. what did she emphasize about this point? Slide 15 i. do we need to know the principal functions of each amino acid? 1. yes a. review the principal functions b. difference between lysine and arginine i. one is different in terms of pI Slide 20 1. general acid base catalysis vs specific acid base catalysis a. specific i. catalysis by H+ or OH- b. general 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 Slide 21 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 Slide 24 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 significantly? 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 Slide 27 1. know when its active and inactive and why Slide 30 2. Know the steps 3. know what happens 4. visualize it and understand the steps 5. point form 6. mechanism 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 Slide 34 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? S
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