1. Know the mechanism for serine proteases and think about potential amino acid
ID: 93163 • Letter: 1
Question
1. Know the mechanism for serine proteases and think about potential amino acid changes to the active site catalytic triad. a. What might still be functional? b. What might slow the kinetics? c. What will cause the enzyme to be inactive? 2. Know the various Michaelis-Menten plots for inhibited and non- inhibited enzymes. a. Why does binding of an inhibitor cause the kinetic effect seen? b. What is the effect of various concentration changes? c. What makes a good inhibitor? 3. Get comfortable with how experimental evidence can support Cor not support) a particular proposed mechanism. 4. Know the ways enzymes are regulated and the effects of various changes (i.e. allosteric effectors, PTMs, isozymes, etc.) 5. For drug-design, be able to evaluate a potential drug based on the mechanism of the enzyme for its effectiveness.Explanation / Answer
Answer 1:- Serine proteases are class of protease enzymes. Serine proteases nearly comprise of one third of all know proteases. The main characteristic of serine proteases is that they contain "catalytic Ser/His/Asp triad". This triad is a coordinated structure, which forms an active catalytic site. The serine-OH group attacks the carbonyl carbon of a peptide bond. A general base Histinde accept aproton from the hydroxyl group of reactive serine and the negatively charched aspartic acid stabilizes positive charge that forms on the histidine residue.
However, changes in the amino acids of the catalytic triad is possible. Serine can be substitued by threonine, histidine can be replaced with glutamic acid and lysine and the aspartic acid can be substitued by a glutamic acid or histidine. In some cases aspartic acid can be eliminated completely. Functionality changes as the amino acid composition changes. Ser/Glu/Asp, Ser/His/Glu and Ser/His/His are present in serine protease, while Ser/Ser/Lys is present in amidase family.
Different active site arrangements used in serine proteases is because of the possibility that such arrangements allow these enzymes to work in different environment. The Ser/Glu/Asp triad can function at low pH. Also, alternate active site geometries allow the cell to regulate proteases that use specific types of active site geometries without interfering with other configurations.
Answer 2:- Enzyme inhibitors are compounds which reduce the velocity of enzyme catalyzed reactions.
Therea are 2 types of inhibitors viz; reversible and irreversible. Both reversible and irreversible inhibitors very helpful for: i. providing information about shape of active site and types of amino acidside chains ii.working out enzyme mechanisms iii. providing info about control of metabolic pathways and iv. design of drugs.
Competitive Inhibition:- Enzyme can bind either substrate or inhibitor, but not both. Either Inhibitor binds in same site as Substrate, or (more rarely) inhibitor binds to different site, causing conformational change in active site so substrate can't bind.
Competitive inhibitor increases apparent Km but doesn't affect Vmax.
Uncompetitive inhibition:- Uncompetitve Inhibitor binds only to Enzyme-Substrate complex.Binding site for Inhibitor is created only upon Substrate binding to the enzyme.
Km is lower with uncompetitive inhibition than without inhibitor. Vmax is lower by exactly same factor as that of Km.
Non competitive Inhibition:- Enzyme can bind both substrate and inhibitor simultaneously, but ESI complex formed can't make product. Inhibitor must dissociate in order for catalysis to occur.
NonCompetitive inhibitor decreses V max but doesn't affect Km.
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