There are many body clocks over the body.
The “master clock” is a bundle of 20-30k neuronal cells in the hypothalamus called the suprachiasmatic nucleus which sets processes like core body temperature and melatonin. The most important regulating stimulus for this clock is light.
Keeping the clocks all over the body (muscle tissues, intestine, brain, etc.) in alignment is important and phase shifts are what result in symptoms such as jet lag.
Insulin sensitivity is higher earlier in the day; an example of why considering chronobiology in nutrition may be a worthwhile endeavour.