MCM 2-35 Enzyme Mechanisms and Therapeutic Inhibition of Enzymes Flashcards
what do enzymes do and how?
enzymes lower the activation energy of a reaction by
- direct stabilization of the transition state
and/or - creating a new reaction pathway “chemical assistance at active site”
the enzyme can perform direct stabilization of the transition state in two ways
- 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
- 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)
- acid base catalysis
- covalent catalysis
- metal ion catalysis
- 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)
chymotrypsin
active sites has large, non-polar pocket which causes it to cleave after large, nonpolar sidechains
trypsin
active site has negatively charged aspartate in its pocket, leading it to cleave proteins after a basic amino acid
elastase
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
ex?
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
Integrase
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
