MCM 2-35 Enzyme Mechanisms and Therapeutic Inhibition of Enzymes Flashcards Preview

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Flashcards in MCM 2-35 Enzyme Mechanisms and Therapeutic Inhibition of Enzymes Deck (17)
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what do enzymes do and how?

enzymes lower the activation energy of a reaction by

1. direct stabilization of the transition state
2. creating a new reaction pathway "chemical assistance at active site"


the enzyme can perform direct stabilization of the transition state in two ways

1. preferential binding to the transition state - active site first transition state better than the substrate or product, making it bind with much greater affinity. Important catalytic factor in most enzymes

2. proximity and orientation effects - enzymes immobilize substrates by binding them. shape of active site then orients them properly for reaction to occur optimally


Chemical assistance at the active site (4)

1. acid base catalysis
2. covalent catalysis
3. metal ion catalysis
4. electrostatic catalysis


Chemical assistance at the active site - acid-base catalysis

typical players?

enzyme employs acidic/basic residues at active site to aid enzymatic reaction.
a. general acid - weakly acidic residue on enzyme
b. general base - weakly basic residue on enzyme
c. concerted acid/base catalysis - weakly acidic and basic residues on enzyme

typical amino acids
histidine - amphoteric; can behave as an acid or as a base
aspartate/glutamate - basic at physiological pH


Chemical assistance at the active site - covalent catalysis

enzyme forms transient covalent bond with substrate, forming a new intermediate.

typical amino acids include cys, serin, lys, his

organic/inorganic prosthetic groups can also be involved


Chemical assistance at the active site- metal ion catalysis

enzyme uses metal ions to assist catalysis


Chemical assistance at the active site - electrostatic catalysis

enzyme stabilizes transition state of substrate using charge distribution at active site.

typical amino acids include asp, glut, arg, his, lys = charged


what determines the specificity of substrate binding?

in general, structural features near the active site dictate substrate specificity. ex) the serine proteases chymotrypsin, trypsin, elastase all have distinct active site features

despite differences in active site properties, enzymes of a given class will share common catalysis strategies and catalytic residues (ex. the catalytic triad of serine proteases include serine, histidine, and aspartate)



active sites has large, non-polar pocket which causes it to cleave after large, nonpolar sidechains



active site has negatively charged aspartate in its pocket, leading it to cleave proteins after a basic amino acid



active side has bulky, uncharged amino acids in its pocket, causes it to cleave after small, uncharged sidechains (like glycine)


common feature of serine proteases?

all have catalytic triad of ser, his, and aspartate


describe suicide inhibition


it exploits the idea of substrate specificity to render enzymes inactive. suicide inhibitors resemble the proper substrate of the enzyme but convert to a form that binds irreversibly during steps of enzymes activity.

penicillin. glycopeptide transpeptidase recognizes the peptide bond in beta-lactam ring, binds to it. once the peptide bond is catalyzed, amino portion remains and water can no longer enter the active site. the acyl-enzyme intermediate remains. enzyme is inactivated as the active site is permanently /irreversibly occupied.

cyclic structure prevents cleavage


major enzymes as drug targets for HIV treatment

Reverse transcriptase
HIV-1 protease - cleaves polyprotein synthesized by HIV-1 DNA. proteins essential to HIV function cannot function unless they are liberated (cleaved) from the polyprotein


clinical problems with HIV-1 protease inhibitors

emergence of resistance
pharmacokinetic issues
accessing the reservoirs of virus
cost and availability
side effects/long term toxicity
patient compliance
determining when to initiate treatment


how does resistance emerge?

due to the high error rate of RT coupled with large number of virions produced daily = likely every possible viral sequence will be expressed in a short time

some of these sequences produce enzymes that still perform their function but do not bind the inhibitor tightly (high Ki). leads to selection of viruses that can produce functional enzymes which function in the presence of the antiviral drug


common way to fight drug resistance?

administer drug cocktails, known as ART or HAART

cocktail includes number of enzymes, including multiple kinds of RT inhibitors and protease inhibitors. Makes it far less likely that the given strain of virus will be able to resist treatment

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