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Questions and Answers
What amino acid residues are primarily involved as nucleophiles in aspartic proteases?
What amino acid residues are primarily involved as nucleophiles in aspartic proteases?
Which characteristic distinguishes aspartic proteases from serine proteases?
Which characteristic distinguishes aspartic proteases from serine proteases?
What is the significance of the pH-dependence in the mechanism of aspartic proteases?
What is the significance of the pH-dependence in the mechanism of aspartic proteases?
What is the role of protease inhibitors in the treatment of HIV?
What is the role of protease inhibitors in the treatment of HIV?
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In the context of HIV-1 protease, which structural feature contributes to its function?
In the context of HIV-1 protease, which structural feature contributes to its function?
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What class of enzymes do trypsin, chymotrypsin, and elastase belong to?
What class of enzymes do trypsin, chymotrypsin, and elastase belong to?
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Which amino acid side chains are preferentially cleaved by trypsin?
Which amino acid side chains are preferentially cleaved by trypsin?
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What does the substrate-binding pocket of elastase primarily accommodate?
What does the substrate-binding pocket of elastase primarily accommodate?
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Which enzyme is specifically mentioned as not being a protease but is mechanistically similar?
Which enzyme is specifically mentioned as not being a protease but is mechanistically similar?
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What structural feature is common to the serine proteases like trypsin, chymotrypsin, and elastase?
What structural feature is common to the serine proteases like trypsin, chymotrypsin, and elastase?
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What distinguishes the specificity of chymotrypsin from trypsin?
What distinguishes the specificity of chymotrypsin from trypsin?
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Which protease participates in the blood clotting cascade?
Which protease participates in the blood clotting cascade?
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How does the catalytic site of serine proteases function in the context of substrate interaction?
How does the catalytic site of serine proteases function in the context of substrate interaction?
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What is the primary function of Asp102 in the chymotrypsin mechanism?
What is the primary function of Asp102 in the chymotrypsin mechanism?
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Which component stabilizes the tetrahedral oxyanion intermediate in chymotrypsin?
Which component stabilizes the tetrahedral oxyanion intermediate in chymotrypsin?
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What type of catalysis is suggested by the presence of a covalent bond in the chymotrypsin mechanism?
What type of catalysis is suggested by the presence of a covalent bond in the chymotrypsin mechanism?
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Which step in the chymotrypsin mechanism is characterized as a 'burst kinetics' phenomenon?
Which step in the chymotrypsin mechanism is characterized as a 'burst kinetics' phenomenon?
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What is indicated by the term 'oxyanion hole' in the chymotrypsin mechanism?
What is indicated by the term 'oxyanion hole' in the chymotrypsin mechanism?
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Which residues are typically involved in the catalytic triad in hydrolases and transferases?
Which residues are typically involved in the catalytic triad in hydrolases and transferases?
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In chymotrypsin kinetics, what does the observation of burst kinetics suggest about the reaction steps?
In chymotrypsin kinetics, what does the observation of burst kinetics suggest about the reaction steps?
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What does His57 primarily function as in the chymotrypsin mechanism?
What does His57 primarily function as in the chymotrypsin mechanism?
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Study Notes
Serine Proteases
- Trypsin, chymotrypsin, elastase, thrombin, subtilisin, plasmin, and tissue plasminogen activator are all serine proteases.
- They are secreted as proenzymes or zymogens.
- Serine proteases cleave polypeptide chains.
- They have similar sequences, structures, and mechanisms.
- Acetylcholinesterase also has a similar mechanism to serine proteases, but is not a protease.
Trypsin, Chymotrypsin and Elastase
- Trypsin cleaves after Arg or Lys (basic amino acids) except when either is followed by Pro.
- Chymotrypsin cleaves after Phe or Tyr (aromatic amino acids).
- Elastase cleaves after small, neutral amino acid residues.
Structure
- Chymotrypsin (and other serine proteases) contains a catalytic triad, which is composed of Asp, His, and Ser.
Substrate Binding Pocket
- The nature of the pocket determines the specificity of the enzyme.
- Trypsin has a negatively charged substrate-binding pocket for basic residues.
- Chymotrypsin has a hydrophobic pocket to bind aromatic residues.
- Elastase has a bulky substrate-binding pocket with Thr and Val residues to accommodate small amino acids.
Chymotrypsin Kinetics
- Chymotrypsin kinetics exhibit burst kinetics- this suggests a fast initial step and a slow second step.
- Burst kinetics are assayed using an artificial substrate that releases a product that absorbs at 400 nm.
Serine Protease Mechanism
- Serine proteases use a combination of covalent and general acid-base catalysis.
- The catalytic triad works as follows:
- Asp orients and stabilizes His.
- His acts as a general acid and base.
- Ser195 forms a covalent bond with the peptide to be cleaved, changing the trigonal carbon to tetrahedral.
- The tetrahedral oxyanion intermediate is stabilized by Gly193 and Ser195.
- The oxyanion hole is composed of two amide groups.
Catalytic Triads
- Found in several hydrolases and transferase enzymes.
- Involve divergent and convergent evolution
- Residues are far away in the primary structure.
- Catalytic triads are composed of:
- Acid that orients and stabilizes the base (Asp, Glu, His)
- Base that polarizes the nucleophile (His, rarely Lys)
- Nucleophile that attacks the substrate (Ser, Cys, sometimes Thr)
Aspartic Proteases
- Aspartic proteases have a different structure and mechanism than serine proteases.
- They contain two Asp residues in the active site.
- They cleave peptide bonds between two hydrophobic amino acids.
- They do not involve covalent catalysis.
pH Dependence of Aspartic Proteases
- Aspartic proteases are active at acidic pH.
- The mechanism requires that one Asp is protonated and the other is deprotonated when the substrate binds.
- The LBHB allows 'hydrogen tunneling'.
HIV-1 Protease
- A novel aspartic protease, HIV-1 protease, cleaves polyprotein products of the HIV genome.
- It is also a remarkably good imitation of mammalian aspartic proteases.
- HIV-1 protease is a homodimer, which makes it more genetically economical for the virus.
- It has a two-fold symmetric active site with different 'flaps'.
Protease Inhibitors for AIDS Patients
- Protease inhibitors are a common treatment for AIDS.
- They block the active site of HIV-1 protease so new viral particles cannot be created.
- Structure-based drug design has been used to create several inhibitors that work in a dish.
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Description
Explore the fascinating world of serine proteases, including trypsin, chymotrypsin, and elastase. This quiz delves into their structures, mechanisms, and specificity in cleaving polypeptide chains. Test your knowledge on these essential enzymes and their catalytic functions.
