( ( The ( contaminated ( metal ions ) ) ) ( ( are ( bonded ( into ( the ( protein biologically ) ) ) ) ) . ) )
(ROOT (S (NP (DT The) (ADJP (VBN contaminated)) (NN metal) (NNS ions)) (VP (VBP are) (VP (VBG bonded) (PP (IN into) (NP (DT the) (NN protein) (NN biologically))))) (. .)))
The contaminated metal ions are bonded into the protein biologically.
(ROOT (S (NP (JJ Metallic) (NNS bonds)) (VP (VBP hold) (PRT (RP together)) (NP (NP (JJ positive) (NN metal) (NNS ions)) (CC and) (NP (PRP$ their) (JJ valence) (NNS electrons)))) (. .)))