どの歯が痛むのですか。

which; what (way)

tooth

indicates sentence subject (occasionally object); indicates possessive (esp. in literary expressions); but; however; still; and

to hurt; to feel a pain; to be injured; to be spoiled (e.g. food)

indicates possessive; nominalizes verbs and adjectives; substitutes for "ga" in subordinate phrases; (at sentence-end, falling tone) indicates a confident conclusion; (at sentence-end) indicates emotional emphasis; (at sentence-end, rising tone) indicates question

be; is

indicates a question (sometimes rhetorical); or; whether or not; some- (e.g. something, someone); indicates doubt, uncertainty, etc.; emphatic prefix; suffix forming adjectives or adverbs; in that way