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The Klingon Dictionary doesn’t provide any specific guidance for how one would insert {nuq} and {‘Iv} into copular sentences.  Although these are pronouns in most Western languages, they are not identified or treated as such in the Klingon Dictionary (e.g., the entries in the actual dictionary itself list them as question words and not pronouns, the question section says to treat these words “as nouns,” etc.).  Thus, my gut instinct would tell me that those words could not function as a copula a la the personal pronouns per sections 5.1 and 6.3.  Instead, you should insert the words directly into the copular construction just as if they were a noun, per the instructions in section 6.4.

I’m not sure if Dr. Okrand or the grammarians here have addressed this particular point in the past, but I noticed that the dialogue in Star Trek VI seems to support this idea, but with a twist.  When the listening post demands the Enterprise identify herself, it sounds like the actor is attempting to say, {Dujvetlh oH nuq, rin.}  Assuming I heard correctly, I would translate that as “What is that ship, over.”  So my questions are:

(1) Did I hear that correctly?  I don’t think the actor had very good pronunciation, and I’m doubting myself that I’m correctly interpreting what he’s trying to say. 

(2) I would expect that the question word would be marked with the topic suffix, as would be typical for such constructions.  Did the actor just inadvertently leave it off, or do question words just not take the topic marker in such constructions.  Thus, would “Who are you?” be {SoH ‘Iv} or {SoH ‘Iv’e’}?

Dr. Okrand once said, on an msn newsgroup:
“Question words (in this case, nuq “what?”) function the same way pronouns do in questions with “to be” in the English translations. Thus, the question yIH nuq? “What is a tribble?” is exactly parallel the statement yIH ‘oH “It is a tribble” (where yIH is “tribble” and ‘oH is “it”). The answer to the question yIH nuq? (“What is a tribble?”) would presumably be a definition or description of a tribble.”

Though he says “question words”, I believe he may have only been referring to the question words that replace nouns directly, i.e. {‘Iv} and {nuq}. Thus, your first instinct was correct that they can be used in a copula similarly to how a pronoun can be. Thus the question, “Who is the captain?” can be {HoD ‘Iv?}. I believe that we have never seen {-‘e’} applied to a question word, so I would shy away from constructions like *SoH ‘Iv’e’?* or *HoD ghaH ‘Iv’e’?* since we just don’t know that it is acceptable. In a question like {SoH ‘Iv}, I believe we could just assume that {SoH} is being used as an object and stick with {SoH ‘Iv} being “Who are you?” and {‘Iv SoH} being “You are whom?”. However, being that it is a copular construction, I have no problems actually translating both as “Who are you?” Similarly, you could ask, {‘Iv ghaH HoD’e’?} for “The captain is whom?”, but I would still probably actually put it in English as, “Who is the captain?”

Since {nuq} and {‘Iv} replace the nouns which are the answers to the question, there’s no reason {-‘e’} can’t be applied to a question word. {Sojvetlh ‘oH nuq’e’} is in Power Klingon. {DevwI’ ghaH ‘Iv’e’} is in the shooting script for Into Darkness, but the line was overdubbed.

{HoD ghaH ‘Iv’e’} is a perfectly good question. Its answer is, e.g., {HoD ghaH Qanqor’e’}, since {‘Iv} replaced {Qanqor}.

The problem with *{SoH ‘Iv’e’} is that {‘Iv} hasn’t replaced anything. I can’t answer, *{SoH De’vID’e’}. It’s not a grammatical sentence, aside from the fact that when you ask a “you” question, you expect an “I” answer, so simply substituting the answer for {‘Iv} won’t work here.