Proteases Flashcards
Protease (peptidase_
group of enzymes that catalyze the break down (hydrolysis) of peptide bonds of proteins or peptides with the participation of a water molecule
limited proteolysis
-breaking specific peptide bonds
unlimited proteolysis
-breakdown complete peptide to amino acids
True or false: proteases only occur in the lab setting
False: occur naturally in all organisms
-digestion and blood clotting
-some viruses (HIV) use proteases in their reproductive cycle
Covalent catalysis
-catalyze amide hydrolysis INDIRECTLY
-serine proteases
-Threonine Proteases
-Cysteine proteases
General acid-base cataylis
-catalyze amide hydrolysis DIRECTLY
-Aspartic acid proteases
-Metalloproteases
-Glutamic acid proteases
Endopeptidase
-cleave in the middle of a peptide
Exopeptidase
-cleave the terminal amino acid of the substrate
Zymogen
-pro enzyme
-inactive enzyme precursor
-requires a biochemical change revealing active site
Trypsin
-cleaves peptide amide bond where the carboxyl side (towards N terminus) or the amino acid
-P1-0 Lys or Arg
-S1= negatively charged, Asp and 2 Gly
Chymotrypsin
cleaves peptide amide bonds where the carboxyl side(toward N terminus) of the amino acid
-P1=Tyr, Trp, Phe
-S1=deep hydrophobic pocket
Elastase
P1=Ala/Val
S1= smaller than chymotrypsin site
Mechanism of serine proteases
1)oxyanion hole
2) tetrahedral intermediate
3) acylenzyme
4) tetrahedral intermediate
Purpose of oxyanion hole
1) anchor the substrate
2) stabilize the transition state
role of ASP in serine protease
the carboxylate in ASP increases the basicity of the imidazole moiety in His
role of His in serine protease
the imidazole in HIS increases the nucleophilicity of the Ser OH
role of Ser in serine protease
the OH serves as a nucleophile to react with the amide carbonyl group
Serpin
-acronymic name given to a family pf serine protease inhibitors that share a complex tertiary structure
PMSF
-irreversible serine protease inhibitor
-inhibits many serine proteases and cysteine proteases
Mechanism of Cysteine Protease
-nucleophilic attack
-tetrahedral intermediate
-formation of acyl-enzyme: amine product
-nucleophilic attack by water
-2nd tetrahedral intermediate
-breakdown
role of His in cyteine protease
the imidazole in His increases the nucleophilicity of the Cys-SH
role of Cys in cysteine protease
the SH serves as a nucleophile to react with the amide carbonyl group
Threonine proteases
-only enzymes that utilize a threonine residue as a catalytic nucleophile for amide hydrolysis are the proteasomes
trypsin like Threonine proteases
P1=Arg/Lys
