I guess that comes from some form of euphonic contraction, that took over to the point it´s not correct anymore not to do it, similarly to what happens in French and Italian with the definite article: la+vowel becomes l´, or in English with a/an.
Is there any kind of pattern to know which words drop their vowel, or is it something we have to learn along with the words? I notice all your examples are 2-syllable words, and the last vowel is i/ı/ü/u.
You have to learn those words, however there are some indications that gives us a clue about this kind of vowel dropping ;
* Some organ names with two syllables, when they take suffix starting with a vowel, their middle [second] sound drops.
burun ---> burun + um ----> burnum
boyun ---> boyun + u ----> boynu
ağız ---> ağız + ımız ----> ağzımız
alın ---> alın + ın -----> alnın
karın ---> karın + ım ----> karnım
beyin ---> beyin + i ----> beyni
* When some two syllable words having wide vowels [a,e ,o ,ö] in their first syllable and narrow vowels [ı ,i, u ,ü ] in their second syllable , take suffix starting with a vowel, the middle sound drops.
alın ---> alın + ı ----> alnı
resim ----> resim + im ---> resmim
bağır ---> bağır + ım ---> bağrım
gönül ----> gönül + üm ---> gönlüm
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