Although both trypsin and pepsin are proteolytic enzymes secreted by the digestive system in order to digest proteins, they differ in many aspects.

• Origin: Pepsin is the chief digestive enzyme in stomach, which is produced by the gastric gland in stomach and is a component of gastric juice, while trypsin in produced by the pancreas and is a component of pancreatic juice.
• Activation: The inactive form of pepsin, pepsinogen, is activated by HCl of the gastric juice, whilst the inactive form of trypsin, trypsinogen, is activated by an enzyme called enterokinase.
• Catalysis mechanism: Pepsin is an aspartic protease which uses a catalytic aspartate in its active site, while trypsin is a serine protease employing the serine residue in active site.
• Optimal pH: The optimum pH for pepsin activity is 1.8, while trypsin works best in alkaline pH (pH 7.5-8).
• Types: Pepsin has four different types, i.e. pepsin A, B, C and D, while trypsin has two types, ?- and ?-trypsin.
• Specificity: Pepsin hydrolyzes peptide bonds between large hydrophobic amino acid residues, whereas trypsin hydrolyzes peptide bonds at the C-terminal side of lysine or arginine.
• Function: Pepsin acts on proteins and converts them into peptones, while trypsin converts peptones into polypeptides.