The glottal stop is a consonant of Arabic, but the script Arabic inherited from Nabataean Aramaic had no letter for it. The earliest Arabic writing left it unmarked, and that gap is one of the reasons the script needed the reforms of its first two centuries. The solution eventually adopted was to borrow a sign rather than add a letter. A small hook, hamza, described in the grammatical tradition as derived from the head of the letter ayn, is written above or below an existing letter that acts as its seat.
Alif is the commonest of those seats. At the beginning of a word the glottal stop is always carried on an alif, which is why so many Arabic words appear on the page to begin with the same upright stroke while sounding quite different. In the middle and at the end of a word the seat is chosen according to the surrounding vowels, so that one consonant may sit on an alif, on a waw, on an undotted ya, or on nothing at all. Learners meet this as a set of rules to be memorised. Scribes met it as a live question, and manuscripts of the same text differ in the choices they make.
A further complication is that alif also writes the long vowel a, and in some spellings it is silent and purely orthographic, such as the alif written after a plural verb ending. An alif on the page may therefore be a vowel, a consonant seat, or a mark that is not pronounced at all. Reading Arabic aloud depends on knowing the word and not only on decoding the letters, which is one reason the recited tradition and the written one developed alongside each other rather than one out of the other.