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Moreover, alterations in the composition and secondary structure of proteins were also observed in accompany with a decrease in the Amide I/Amide II ratio and an increase of the loose β-sheet structure protein. LEV caused an elevated level of lipid peroxidation, while SMX induced a more obvious protein aggregation. The findings from this study showed that FTIR could reveal the toxic mechanism of these two antibiotics to algae at the biochemical level by linking alterations in biomolecules to biochemical dynamics and function. Bisphenol