Learn Farsi: لاک‌پشتی که خرچنگ با آن قدم می‌زند، پیر نیست. - The turtle that the crab is walking with is not old.

This is a "resumptive pronoun," which is exactly what this lesson is teaching! In English, we can end a relative clause with a preposition ("the turtle that the crab is walking with"). In Farsi, you cannot leave a preposition hanging. You must follow it with a pronoun that points back to the main noun. So, Farsi literally says: "The turtle that the crab is walking with it..."

Why does لاک‌پشت (turtle) end with an ی if the translation says "the turtle" and not "a turtle"?

This is the restrictive ی. In Farsi, when you are about to specify exactly which noun you are talking about using a که (that) clause, you usually add an ی to the end of the noun. Even though it looks like the indefinite article for "a", in this specific grammar structure it acts more like "the specific [turtle] that...".

Could I use با او instead of با آن since the turtle is an animal?

Yes, you could! Grammatically, آن (it/that) is the standard choice for non-human nouns like animals. However, in stories, fables, or casual speech where animals are personified (doing human things, like going for a walk together), Iranians frequently use او (he/she). Both are perfectly fine in this context.

What is the literal meaning of the verb قدم می‌زند?

The compound verb is قدم زدن. The noun قدم means "step" or "footstep," and the verb means "to hit" or "to strike." So literally, it means "striking steps," which is the standard Farsi expression for "to walk" or "to stroll."