Although such variation could be the result of things like when the word was borrowed into the language, this variation is probably due to the prosodic structure of the words; we get different vowel sounds because of the way that stress influences vowel quality in English.
In English, unstressed vowels are generally reduced. Take the word record for example.
- The noun form takes first syllable stress: [ˈrɛ kɚd]. If you aren’t familiar with IPA, note in particular the [ɛ] vowel and the [ɚ] r-colored schwa vowel. Schwa (and sometimes [ɪ]) is what often shows up in reduced, unstressed vowels in English. Since stress is on the first syllable, we get the r-colored schwa in the second syllable.
- The verb form takes second syllable stress: [rə ˈkoɹd]. Note that the now-unstressed [ɛ] was reduced to [ə], schwa, while the [ɚ] now retains the full [o] sound (with an [ɹ] “r” after it).
Now for bicycle and unicycle:
- bicycle [ˈbaɪ sɪ kəl] has primary stress on the first syllable. The “cy” syllable is unstressed, and so it is pronounced as a mere [sɪ] (or even [sə] by some). Note that tricycle has the same stress pattern, and has the same vowel.
- unicycle [ˈju nɪ ˌsaɪ kəl], being a longer word, has multiple stressed syllables. Primary stress, again, falls on syllable #1, but the important thing is that secondary stress falls on syllable #3, the “cy” syllable. This means that “cy” is pronounced as a full [saɪ] instead of a reduced [sɪ]. Note that motorcycle has the same stress pattern and, again, same vowel.
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