My take on Sheldon Cooper’s childhood comes from many hours of watching the show, reading about his life, and my own history with conservative fundamentalism, which I find kinda funny.
The East of Texas. The Gulf Coast. Hot heat, dry winds, and revival tents. Not the place you’d expect someone with an IQ of 187 to grow up. Sheldon didn’t expect it either. Neither did his mother. In the world where Sheldon was born, church was the utmost important. And part of church was knowing what you’d been told was true was actually true – without question.
Sheldon’s hell of a childhood began very early on. His mother put him into the Christian school in his town. A “good little school,” as she called it. It was good – if you were white, pretty dumb, and willing to believe whatever you were told. From the very beginning, he hated it. He’d go to the library whenever he could get his mom to drive him there and check out books on science. His mom sat back in the stacks, reading through different translations of the Bible, so she never noticed what he was reading. Not that she read any other languages, but she liked to read what the English translations SAID were in the other language translations. When it was time to go home, he’d just throw a Young People’s Guide To the Bible on top of the other books he was getting, and she’d never notice. That way, Sheldon was able to learn about science, even at home.
He was done with the whole school thing by the age of 10, basically because the school she’d put him in wasn’t anywhere he could actually thrive. It was one of those uber conservative Christian schools where Sheldon and his classmates watched videos of humans and dinosaurs co-existing, and practiced “rapture drills” in which they talked about what to do when those four horsemen came on-up-and-at-em out of the sky. Sheldon knew he was done with the place when he was attempting to finish up the 6th grade as a six year old. The boy next to him startled at the sound of a freight train two blocks down and grasped the side of his desk. “Its the rapture, its the rapture!” the kid cried out. Sheldon was six. Just six years old. But he knew it was ridiculous.
Sheldon also knew he was in trouble when he told his mom about the same instance later on, over a dinner of mashed potatoes and fried chicken. Which Sheldon ALSO hated. His mother put down her fork and said, very sternly, “Sheldon, don’t you DARE make fun of those who believe. Otherwise one of these times it won’t be a train but the actual rapture, and you’ll be left behind.”
She continued his hell of a religious education in the summers, totting him from one small town to another for her religious revivals. Which really weren’t so bad, when he was young, because Sheldon got to run around half crazy with the other kids. As long as he kept his brains to himself, that was. Because those other kids weren’t anything like him.
At least his mom was smart enough to let him go to college when he turned 11. By that time, she was so frustrated with his refusal to believe what he was told that she figured once he got college out of the way, maybe he could settle down and do something with his life – like become a preacher – put that good smart brain to use memorizing the gospel. Deep down she knew he probably wouldn’t, 

but she figured it was worth a try. She at least wanted him to take a few classes on Creationism, so that he could get his facts straight, but alas the school he went to simply didn’t offer them. So he didn’t. Got his PhD when he was 16, and never looked back.
Once he was far enough away, his relationship with his mom actually got a little stronger. Mostly because when he was gone, she could pretend that he was going to church as he should. He promised her he’d go to church once a year, and she promised him she’d pray for him. So it goes, with these folks.