What Is the Biological Clock in Sleep?

Circadian Rhythm Determines Timing of Sleep and Wakefulness

A woman notes the passage of time.

If someone casually remarks about their "biological clock," what exactly do they mean? Learn about the uses of the phrase biological clock in reproductive health and sleep. Discover where the body's biological clock resides, how it regulates circadian patterns like sleep and wakefulness, and how disorders result when the timing of the clock becomes misaligned with the natural patterns of light and darkness.

What Is the Biological Clock?

First, it is important to recognize that the term biological clock is used in reference to two very different concepts. Many people, especially women, use the phrase to describe the waning years of optimal reproductive health. As an example, if a woman's biological clock is ticking, it means that she is becoming older and her ability to conceive and carry a healthy child to term may be in decline. It can describe a simple desire to have a child and, when ticking, be perceived as an impetus for procreation. In general, reproductive health is viewed as declining in the 30s and certainly suboptimal by age 40, but advances in reproductive medicine have extended this time frame to some extent. Due to the ability of men to father children late into adulthood, they may not face the same time pressure.

This is not how the term is used within the context of sleep medicine, however.

Instead, the biological clock refers to the body's ability to time innate processes to the external environment, most notably the timing of light and darkness, temperature, and resource accessibility. Sleep is believed to be optimally controlled by two processes: homeostatic sleep drive and the circadian alerting signal.

Sleep drive, or sleep debt, refers to the fact that the longer you stay awake, the sleepier you will become. This has to do with the build up of sleep-inducing chemicals, including adenosine, within the brain. Sleep is, at least in part, a process of removing these chemicals from the brain's tissues. The alerting signal is a contrary system to sleep drive that promotes wakefulness in a very regular fashion.

Therefore, the biological clock is the mechanism found within living organisms that coordinates the timing of physiological functions and behaviors to the natural day-night cycle. These processes include sleep and wakefulness, as well as control body temperature and hormone release. We are starting to learn more about where the clock exists and how it is controlled.

Where Is the Biological Clock?

The master clock is an area called the suprachiasmatic nucleus, a small region of the brain found within the anterior hypothalamus. It exerts hormonal control to peripheral clocks that have been described in many cell types, including everything from heart to liver to fat tissues.

Coordination of these rhythms is believed to allow optimal use of resources, access to food, and protection from predators across species.

Even though a master clock exists, if it becomes damaged or lost, each cell is able to maintain its own rhythm. In fact, when placed in isolation, these cells are able to follow a circadian - or near 24-hour - pattern all by themselves. Therefore, the precise timing machinery is present in virtually every cell of the body and exquisitely written into the cell's genetic code.

Broken Clocks: The Occurrence of Circadian Disorders

In many ways, the various circadian rhythm disorders may occur due to biologic clocks that have lost their synchrony to the natural environment. This may be due to numerous factors, including genetics, blindness, lifestyle or habits, and degenerative diseases like Alzheimer's disease. Many of these conditions result in difficulties with insomnia and poorly timed sleepiness.

One of the most powerful influences of the body's biological clock is light exposure. Importantly, morning light can be a profound reset of our natural tendency to shift the timing of our sleep later. As a result, it encourages morning wakefulness and aids our ability to fall asleep at the start of the sleep period. Though longer periods of morning light exposure may be necessary in some, even brief 15-minute intervals outside upon awakening may be adequate to reinforce the natural timing of sleep and wakefulness.

If you believe that you may have symptoms suggestive of a circadian rhythm disorder, speak with a sleep specialist. A few weeks of evaluation with a sleep log or actigraphy may identify the nature of the problem, including dysfunction of your biological clock, and lead to the treatment needed to sleep well at night and function optimally during the day.


Kryger, MH et al. "Principles and Practice of Sleep Medicine." ExpertConsult, 5th edition, 2011.

Moore-Ede, MC et al. “A physiological system measuring time, “ in The Clocks That Time Us. Cambridge, Massachusetts, Harvard University Press, 1984, p. 3.

Peters, BR. “Irregular Bedtimes and Awakenings.” Evaluation of Sleep ComplaintsSleep Med Clinic. 9(2014)481-489.

Ramsey, KM and Bass, J. “Animal models for disorders of chronobiology: cell and tissue,” in Principles and Practices of Sleep Medicine. Edited by Kryger MH, Roth T, Dement WC. St. Louis, Missouri, Elsevier Saunders, 2011, pp. 463-467.

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