A prefix is a letter or a group of letters that ………. at the beginning of a word.
1) comes 2) come
I agree with Ahmed_btm that (1) ("comes") is the correct answer here. A relative clause doesn't always modify the noun that comes immediately before it. In this case, the relative modifies the noun phrase "a group of letters," whose head -- "group" -- is singular. Hence the verb should agree with the singular subject.
While answer (2) ("come") is not ungrammatical, since it is possible for the relative clause to modify the plural noun "letters," it gives the wrong meaning. With "come," the sentence would refer to groups like "unprenonre-unretromiscontraultra," whereas we want it to individual prefixes, such as "pre."
I think the relative clause modifies both "a letter" and "a group of letters". The reason that it takes the singular form is also because of the word "or". Am I right?
No, the reason for the singular form does not have anything to do with "or." However, the relative clause does implicitly apply to the first disjunct. The sentence may be regarded as a reduction of the following:
A prefix is a letter that comes at the beginning of a word or a group of letters that comes at the beginning of a word.
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