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Alkali extraction and acid precipitation methods were adopted to isolate protein from quinoa and album seeds of variety Chenopodium. Different pH dispersions (3–11) of isolated proteins were prepared and effects of pH and holding time on protein characteristics were evaluated. The pH-10 of extraction medium was found suitable for protein extraction on the basis of yield, purity, solubility and colour having isoelectric pH of 4.5. Yield and purity of protein isolates (PI) of quinoa and album varied from 8.12 to 12.22%; 74.19 to 85.07% and 7.71 to 10.98%; 77.16 to 86.12%, respectively. Overall, pH and time had significant effect on functional properties of PI of both seeds. Quinoa PI had higher emulsifying activity, emulsion stability, water binding capacity and dispersibility, whereas, foaming capacity and stability were higher for album PI. Nutritional indices were 64.20 and 64.58 for quinoa and album PI, respectively …