The operation that Charlie receives does not actually involve donating any brain cells from the mouse Algernon. In fact, the nature of the operation is purposefully left vague.
Keep in mind that the original story was written in 1958, at a time when medical science was significantly less advanced than it is now. Like many science fiction stories, the "science" is often left up to the imagination. All we know as readers is that Algernon's intelligence has increased dramatically as a result of the surgery, and we are asked to accept that fact on its face without any sort of explanation.
Fortunately, the story itself is so compelling that it really doesn't matter if we know exactly how the operation increases intelligence. The real focus, as in any good piece of literature, is on character development. When Charlie's intelligence increases, he does not become correspondingly happier. In fact, he struggles with the newfound knowledge that the world is a much more cynical and unkind place than he knew before, when he did not have the intelligence to see peoples' real motives and the effects of their actions.
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