I don't understand how D could be the answer. Is it really supported well in the passage?
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Support for the answer is via the final sentence of paragraph 1, which states there is a small number of E1 proteins, a large family of E2 proteins, and 3 families of E3 proteins. The three families of E3 proteins allows for greater variety of E3 enzymes, allowing the identification of more protein/protein binding sites than a 'small number' or a 'single family' as with E1 and E2 enzyme types.
Your answer choice of B is incorrect because hydrolysis of peptide bonds is facilitated by enzyme catalysis alluded to by the mention of recruitment of proteosomes in the second sentence of the second paragraph, which as a general rule is utilized because many biological reactions are non-spontaneous or inherently slow spontaneous reactions (peptide bond hydrolysis especially so, which is good since otherwise proteins would be spontaneously breaking down in aqueous cellular environments all the time).
As for other answer choices, there is no mention of an ATP-dependent mechanism in the passage for ubiquitination (no support for A) and it is explicitly stated in sentence one of paragraph two that multiple ubiquitin molecules are added to a protein (choice C is wrong).
Hope this helps!