Learn Farsi: گربه غمگین است چون خیس است.

چون works just like "because" in English! It connects two complete ideas. Here, it links گربه غمگین است (the cat is sad) and خیس است (it is wet). You do not have to change the word order of the second part at all.

Where is the word for "it" in the second half of the sentence?

Farsi often drops pronouns (like "he", "she", or "it") when it is already obvious who or what we are talking about. Since we just mentioned the cat, we do not need to add a word for "it" before خیس است (is wet).

Could I start the whole sentence with چون?

Yes! Just like in English, you can flip the order and put the "because" part first. For example, you could say چون گربه خیس است، غمگین است (Because the cat is wet, it is sad).

Why does the verb است (is) appear at the very end of both parts of the sentence?

In Farsi, the verb almost always goes at the very end of its phrase or clause. So instead of saying "The cat is sad" (Subject + Verb + Adjective) like in English, Farsi puts the verb last: "Cat sad is" (Subject + Adjective + Verb).