There are many body clocks over the body.
The “master clock” is a bundle of twenty-to-thirty-thousand neuronal cells in the hypothalamus. This “suprachiasmatic nucleus” sets processes like core body temperature and melatonin. The most consequential regulating stimulus for this clock is light.
Keeping the clocks all over the body (muscle tissues, intestine, brain, etc.) in alignment impacts how well we function. Phase shifts in which they become misaligned 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.