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Because acquired immunity does not develop until after

invasion by a foreign organism or toxin, it is clear that the body must have some mechanism for recognizing this
invasion. Each toxin or each type of organism almost

always contains one or more specific chemical compounds in its makeup that are different from all other compounds. In general, these are proteins or large poly-saccharides, and it is they that initiate the acquired immunity. These substances are called antigens(antibody generations).

-- guyton and hall textbook of medical physiology

As an non-native English speaker, the bold words from above paragraph did border me a lot.

(1)Typically, is always followed with me/it/he/she, but in this case, it's totally different.

(2)What dose this they in bold refer to?
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sdasd tontIn general, these are proteins or large poly-saccharides, and it is they that initiate the acquired immunity.
In the above, "they" refers to "proteins or large poly-saccharides."

For an explanation of that cleft structure, have a look at the explanation in the link below.
http://dictionary.cambridge.org/grammar/british-grammar/cleft-sentences-it-was-in-june-we-got-mar...