More info please
The answer depends on a lot of things.
What are the specs on these systems? If these systems are Pentiums, I would say that high CPU utilization would be expected under the circumstances you stated. But if they're relatively new Intel Core 2 or AMD Opteron, then that would be a different story.
Also, how big is the database, and what kinds of transactions are being performed? Are these queries updates or inserts, or are there more selects? How complex are the queries? How big is the database? Also, is this database replicated to each of the individual systems or do they reside on one system? If that's the case, the access latency could be a problem.
As for your specific question, I wouldn't think MySQL settings would necessarily affect the amount of CPU Apache takes except for any operations specifically related to MySQL. The 'persistent connections' setting in MySQL is actually designed to improve performance by reducing the need to make new connections every time a web site makes an access to the database. You could try turning off the setting and see if it makes a difference.
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