Murthy was born in the small village of Mathur situated in the Shimoga District of Karnataka State.
After his Pre-University education at Shimoga, Murthy joined the Central College in Bangalore as an honours student of physics.
Following this, he joined the Indian Institute of Technology, Madras (the present Chennai) to study masters course in physics.
After spending 4 years, which gave the Murthy the experience and confidence to initiate his own studies in structural biology, he returned to the Indian Institute of Science, Bangalore.
During the initial year, he was associated with the Department of Physics following which he joined the Molecular Biophysics Unit of the same Institute, where he has remained since.
At that time, there were no experimental facilities for carrying out macromolecular structural work at the Indian Institute of Science, or anywhere else in the country.
His unique teaching methodology combined with his passion for the science he was doing was infectious and has inspired a generation of scientists.