Lecture 4 Flashcards
Catalysis is achieved by one of two mechanisms. What are those 2 mechanisms and which enzymes are in each of these 2 categories?
1) Enhance the reactivity of water to make it a better nucleophile (acid/base catalysis). Aspartyl and Zinc proteases work in this way.
2) Use an alternate initial nucleophile to make a more reactive electrophile in the substrate (nucleophilic catalsysis). Serine/Threonine and Cysteine proteases work in this way.
What are the 2 key characteristics of the threonine protease active site?
1) The catalytic threonine is at the N-terminus of the protein
2) The n-terminal amino group will function as the base in this reaction to facilitate deprotonation of the Thr hydroxyl group
What type of intermediate is formed in the threonine protease mechanism?
Acyl enzyme intermediate
When/where does water attack the peptide during the threonine protease mechanism?
Water attacks the acyl enzyme intermediate (more reactive than the amide)
Briefly explain how the proteasome works.
A damaged or dysfunctional protein is targeted for destruction by being ubiquitinylated with poly-ubiquitin. This directs the ubiquitinylated protein to the proteasome for degradation. Inside the proteasome channel are active sites that function as threonine proteases.
What would a threonine protease inhibitor possess?
A site(s) that is a good electrophile (LUMO) because threonine proteases function through nucleophilic catalysis so these electrophilic sites may intercept the nucleophilic side chain
What would an aspartyl protease inhibitor possess?
Inhibitors often possess groups that mimic the transition state (sp3 tetrahedral groups that contain alcohol groups) or inhibitors bind to the residues that stabilize the tetrahedral geometry
Are amidases specific? Where are they localized in the body?
No - they will hydrolyze amide bonds non specifically
They are localized in the liver
Esterases:
1) Where are they located in the body?
2) How are they useful in the formation of pro-drugs?
1) The liver and blood plasma
2) They can mask reactive functional groups to prolong the effect and increase absorption of drugs
It is energetically unfavorable to form a peptide bond (Thermodynamic barrier i.e. energy of product = peptide bond formation is larger than the energy of the reactants = free amino acids). How does nature get around this issue?
It uses ATP to drive peptide bond formation.
Phosphates linked to good leaving groups are sites of _____ ______.
Nucleophilic attack
When phosphates are attacked, how are they displaced?
Through an SN2 like mechanism
Explain how the electron/electron repulsion that is present in ATP provides kinetic stability despite the thermodynamic favorability of breaking the phosphoanhydride bond.
The phosphates in ATP have two adjacent oxygens which both carry a negative charge. This means there is a lot of electron density surrounding the phosphates and so it is unfavorable for the electrons of a nucleophile to interact with those electrons in order to attack the phosphate. Thus, these e-/e- repulsions shield the phosphate from nucleophilic attack. It is thermodynamically favorable to break the P-O-P bonds in ATP (meaning that doing so releases energy), but this is shielded from happening by the e-/e- repulsions.
What does Mg2+ coordination do?
Mg2+ acts as a lewis acid drawing e- density away from the negatively charged oxygens attached to the phosphate. Doing so makes the phosphate more open to nucleophilic attack since the electron density surrounding the phosphate is shielded by the presence of Mg2+.
What kind of geometry does Boron have? What hybridization? What is unique about Boron?
Boron is planar, sp2, and has an empty p-orbital which is an excellent LUMO
