Serine Proteases Flashcards
What do proteases do and how are proteins able to exist in acell
Have would you speed up the addition elimination reaction to break a peptide bond
How would you improve the proteolysis of a protein
What makes a good nucleophile and leaving group
Give 3 examples of serine proteases, where they’re found and their function
(They cleave peptide bonds)
What is the catalytic triad
Name and draw the residues in the catalytic triad, and what is the function of the triad
Draw the mechanism for the action of a serine protease
How can ser-195 be identified in a serine protease
How was his-57 identified
What is the role of an oxyanion hole in a serine protease
The oxyanion hole is a structural feature within the active site of serine proteases that stabilizes the negatively charged oxygen atom of the tetrahedral intermediate. This intermediate is formed when the serine residue of the enzyme attacks the carbonyl carbon of the peptide bond, resulting in the cleavage of the bond and the formation of a new covalent bond between the serine residue and the carbonyl oxygen of the substrate.
The stabilization of the oxyanion intermediate is critical for the catalytic efficiency of serine proteases because it helps to lower the activation energy barrier for the reaction. Without the oxyanion hole, the tetrahedral intermediate would be highly unstable due to the negative charge on the oxygen atom. The oxyanion hole achieves stabilization by providing hydrogen bonding interactions with the oxygen atom of the tetrahedral intermediate, thereby reducing its reactivity and facilitating the completion of the catalytic cycle.
How is the specificity of proteases defined
How is the specificity of serine proteases determined
The specificity of proteases is often defined in terms of the amino acid residues found in the substrate-binding sites of the enzyme, particularly the S1 and P1 pockets.
S1 Pocket: This refers to the substrate-binding site in the active site of the protease where the amino acid residue at the scissile bond of the substrate binds. The amino acid residue in the substrate that interacts with the S1 pocket is known as the P1 residue. The specificity of a protease at the S1 pocket is determined by the size, shape, and chemical properties of this pocket. Different proteases have different preferences for the amino acid residues that can fit into their S1 pocket. For example, some proteases may preferentially cleave peptide bonds after small amino acids, while others may prefer bulky or charged residues.
P1 Pocket: This refers to the complementary region on the substrate where the amino acid residue that interacts with the S1 pocket is located. The amino acid residue at the scissile bond is referred to as the P1 residue. The specificity of a protease at the P1 pocket is determined by the amino acid residue present at this position in the substrate. Proteases may have preferences for specific amino acid residues at the P1 position, depending on the interactions that occur between the P1 residue and the protease’s active site.
What is divergent evolution
What is convergent evolution
Distantly related organisms independently evolve simmer traits to adapt similar necessities
What is the general rate of chymotrypsin activity
What is the explanation for the burst phase of chymotrypsin activity
How do cysteine proteases work
How do aspartyl proteases work
How do metallo proteases work
What is hydrolysis of the peptide bond favoured by
How are serine proteases synthesised and haw is trypsinogen activated
How is chymotrypsinogen activated
