Down 1-0 in the three-Test series, England elected to bat first in the crucial match and Chopra led from the front for them with a determined century.
The skipper combined with Billy Godleman to put on 121 for the first wicket before Godleman was bowled by Shahbaz Nadeem for 40.
Nadeem was the pick of Indian bowlers yesterday, taking three wickets in 30 overs, which included 12 maidens. The left armer conceded only 55 runs in his spell.
Meanwhile, Godleman's dismissal brought in Rory Hamilton-Brown, who added 12 before being run out.
It went horribly wrong for the hosts after that as Michael O'Shea followed Rory back to the pavilion, lbw for nought off a Nadeem delivery. Adam Lyth (1) did not last long either and became a victim of Nadeem, as the hosts slumped to 165 for four.
Wickets fell all around him but Chopra continued with his patient innings, which included 20 fours. But he also departed at 123 bowled by Abu Necheem Ahmed, leaving the hosts on a precarious 199 for five.
However, the Indians, who appeared to have gained an upperhand at this stage, were pushed to the back foot as Adil Rashid and Mark Nelson stopped the rot by putting on 60 runs for the sixth wicket which took England's total beyond 250.
Nelson was unfortunate to depart hit wicket for 31 but Rashid remained firm and reached his half-century (59 not out) before stumps were drawn for the day.
Brief Scores on Day one: Eng U-19: 279 for six (Varun Chopra 123, Adil Rashid 59 not out, Shahbaz Nadeem 3/55)