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There are a couple answers I can think of at the moment. One is that eukaryotes have membrane bound organelles. This allows eukaryotes to produce more of that organelle in order to adapt to the cells needs. For instance, a muscle cell will have many more mitochondria than a epithelial cell. Eukaryotes are also much bigger than prokaryotes, leaving room for this specialization. The final way is DNA organization. The circular DNA of bacteria can encode for a limited number proteins. Plasmids can expand this a little, but it still pretty tiny compared to the capacity of eukaryotic chromosomes.

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