Below is the catalytic mechanism of Trypsin, a protease often used in biochemistry to cut proteins into fragments for analysis. Please identify the method(s) of catalysis used in each step of Trypsin's mechanism. Provide a one-sentence rationale for your identification.
Trypsin, Chymotrypsin, and Elastase are homologous proteases; they perform the same function using conserved active site residues. Despite their similar enzyme mechanisms, they each have a different set of substrates. Trypsin cleaves peptide bonds between Lys or Arg; Chymotrypsin cleaves peptides bond between large, bulky amino acids; Elastase cleaved peptide bonds between small, uncharged amino acids. In a 2-3 sentences, hypothesize why these three enzymes only act of certain substrates despite performing essentially the same function and by the same mechanism.