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Bekenstein received his undergraduate education in the Polytechnic University (now the Polytechnic Institute of New York University) in Brooklyn, New York.
Born in Manhattan and raised in the Bronx, he graduated from City College of New York (undergraduate) and Brooklyn Polytechnic Institute (Master’s and PhD in biochemistry, with a dissertation on cholesterol).
When he completed his service in the military, Brenner attended the Polytechnic Institute of Brooklyn where he earned his Master's degree (1949) and later his doctorate (1954) in chemical engineering studying under the renowned Donald Othmer.