Website is getting very high load due to "UPDATE cache SET data..."
Given your server already has APC installed, you do not need to keep cache in database at all. And probably shouldn't.

Install APC module (for older Drupal versions see Cacherouter or Cache Backport) to move your cache from MySQL to RAM. Without it, APC only caches opcode, not Drupal's cache data. Also, APC Status or APC Admin module helps with monitoring.

It might be wise to exclude form cache from APC and keep it in database, but that's material for another question.

For APC optimization, see this question.