There are many places in the book where there is a loss of innocence. The three best examples surround the trial and the attempted murder.
First, as Atticus was preparing to defend Tom Robinson, word started to get around that Tom was accused of raping Mayella. Jem and Scout heard this news as well. Just by hearing of this heinous trial, they began to lose the innocence of their youth. At one point Scout asks about rape.
“Well, if everybody in Maycomb knows what kind of folks the Ewells are they’d be glad to hire Helen... what’s rape, Cal?”
“It’s somethin‘ you’ll have to ask Mr. Finch about,” she said. “He can explain it better than I can."
Second, when Jem and Scout realize that Atticus did not win the case, they are stunned. They know from the bottom of their hearts that Tom Robinson is innocent. When the racism of the town hits them, Jem weeps and cries out that things are not fair. Jem knows that something is wrong with the world.
It was Jem’s turn to cry. His face was streaked with angry tears as we made our way through the cheerful crowd. “It ain’t right,” he muttered, all the way to the corner of the square where we found Atticus waiting. Atticus was standing under the street light looking as though nothing had happened: his vest was buttoned, his collar and tie were neatly in place, his watch-chain glistened, he was his impassive self again.
“It ain’t right, Atticus,” said Jem. “No son, it’s not right.”
Finally, when Bob Ewell attacks Jem and Scout, there is another wake up call. Both of them experience evil first hand. Heck Tate confirms this with these words:
He pointed with a long forefinger. A shiny clean line stood out on the dull wire. “Bob Ewell meant business,” Mr. Tate muttered.
“He was out of his mind,” said Atticus.