Why does my main desktop computer whine at night?

Our desktop computer was intermittently making strange whining sounds in the early mornings. I thought it might be some type of virus data mining our computer for personal or financial information.  I think it turned out to be a problem between Windows Vista and the update software of our HP desktop PC.  When I manually allowed the update to go through the whining ceased.  I wonder how long this has been happening without my knowing it because we had to have the power supply on this computer replaced after it failed.  Maybe this problem put a strain on the power supply somehow.