The Neurochemistry of Sleep


Your daily and nightly cycles of waking and sleeping are controlled by your circadian rhythm.

  1. 1.1 What is your circadian rhythm?

    Your circadian rhythm is a neurochemical mechanism which coordinates a multitude of physiological, metabolic and hormonal cycles which ebb and flow throughout your body and brain across each ~24 hour period.

  2. 1.2 How does your body keep its circadian rhythm?

    In your brain there is a collection of “pacemaker” cells which collectively make up your Suprachiasmatic nucleus (SCN). The SCN is part of your hypothalamus, a region which forms an interface between your body and brain. The SCN is your brain’s “master clock” which has an intrinsic timekeeping mechanism. Removing your SCN instantly prevents your body from operating in any kind of circadian fashion.

    How does the ‘clock’ work?
    Your brain keeps time through a specific pattern of chemical synthesis and gene expression operating on a miniature scale within each timekeeping cell in the SCN. The operation of telling the time involves a oscillating feedback loop: Two “activating” proteins CLOCK and BMAL1 are present at the start of the day but their production is steadily inhibited as a consequence of the generation two key repressor proteins - CRY and PER - as the day progresses. Levels of CRY and PER are therefore high during the night but then initiate chemical processes which cause their own levels to dissipate through the night. This withdraws their inhibition of CLOCK and BMAL1 which can then increase in readiness for the onset of the following day.

    Are there clocks in other parts of the brain and body?
    Cells in other regions of the brain and body also operate as remote clocks and perform similar pattern of chemical protein synthesis to support the body-wide process of coordinating the physiological, hormonal and metabolic process which underpin behaviours such as sleeping and eating.

    How does the SCN tell other regions of the brain and body what time it is?
    This oscillating pattern of chemical synthesis alters the frequency at which the SCN sends out waves of electrical messages - faster (6-10 Hz) during the day, and slower (<1 Hz) during the night. These waves of neural activity, emitted from all the timekeeping cells of the SCN in a synchronized fashion, indicate to other regions of the brain what time it is and create a neural rhythm, against which all other metabolic processes can be synchronized.

    How does this part of the brain tell the other parts of our brain to wake up or sleep?
    The SCN sends out messages to various other regions of the brain. For example it sends signals to the preoptic area, an important sleep centre in the brain; the dorsomedial nucleus of the hypothalamus which regulates wakefulness via the modulation of hypocretin/orexin; as well as regions (e.g. the paraventricular hypothalamic nucleus) which oversee the release of sleep-wake modulating chemicals such as melatonin and cortisol.

  3. 1.3 GABA - What are the different mechanisms for signalling or modulating our circadian rhythm?
    • 1.3.1 - GABA

      GABA is an inhibitory neurotransmitter which has widespread effects on your circadian rhythm both from within GABAergic cells, and also when it is co-expressed - piggybacking - in cells which release other neurotransmitters (e.g. dopamine). GABA is one of the major neurotransmitters operating within the SCN and helps to synchronize the signals being sent out from SCN cells to other cells in the brain. GABA also plays a key role in adjusting the signalling output of the SCN to compensate for the lengthening and shortening of daylight periods as the seasons change throughout the year.

    • 1.3.2 Serotonin / 5-hydroxyindoleacetate

      Serotonin, originating from a region of the brain called the raphe nucleus, is known to modulate the way the SCN responds to light signals from the retina. Alternations in this serotonergic pathway to the SCN is thought to be one of the causes of Seasonal Affective Disorder (SAD). Serotonin is also a precursor to melatonin (via N-acetyl-serotonin), a hormone released into the body from the brain’s pineal gland which helps regulate sleep and wakefulness (and can be used as a supplement to help counteract the effects of jet lag).

    • 1.3.3 Glutamate

      As the main excitatory neurotransmitter in the brain, glutamate plays an important role in regulating your circadian rhythm. It is an important player in the process of keeping time, and disturbances in glutamate levels in the SCN result in “time shifts”, where your circadian clock, and its associated homeostatic processes, become misaligned from their typical ~24 hour cycle.

    • 1.3.4 Dopamine / DOPAC

      The neurotransmitter dopamine, working within your retina, acts to modulate your circadian rhythms by helping to initiate the signals which tell the SCN that it is light outside. Dopamine also helps regulates, and is regulated by, the circadian cycles operating within other regions of the brain such as the olfactory bulb, striatum, midbrain and hypothalamus. The effect of dopamine on the circadian clock is especially obvious in individuals with Parkinson’s disease, who have a dysfunctional dopamine system, and who have disturbances to their biological timekeeping mechanism.

  4. 1.4 What can disrupt our circadian rhythms?
    1. 1.4.1 Light Exposure

      Light-sensitive cells within your retina, which contain the chemical melanopsin, send messages to your SCN to tell it when it is light outside. Although the absence of light and dark cues doesn’t stop your circadian rhythms working completely, their presence helps to keep the clock “entrained” to natural, and artificial, rhythms of illumination. Light stimulation is also one way of “resetting” your circadian clock after it is disrupted.

    2. 1.4.2 Inconsistent Sleep/Wake Patterns

      Modern life increasingly demands that people don’t always keep to a stable pattern of sleeping and waking. The choice to work in an ever-changing shift pattern, to travel across time-zones or even to stay up later at the weekend compared to a weekday, can all cause major disruptions to your circadian rhythms.

    3. Disruption of your circadian rhythm due to lifestyle, or medical reasons, leads to a desynchronization between your master clock and the remote clocks present in your body’s periphery. For example, as our circadian rhythm is not only involved in regulating our sleep wake cycle, but also in regulating our eating habits, disrupting your circadian rhythm can cause you to gain weight as you end up eating at the “wrong time”. It also has wide ranging effects on the development and progression of depression, neurological disorders, obesity, diabetes, cardiovascular disease, and gastrointestinal disorders.


Sleep and waking result from a dynamic interplay - a tug of war - between regions which are involved in keeping your brain awake, and regions which are involved in keeping your brain in a state of sleep. Sleep happens when your sleep promoting regions are active - when they are “winning”.

  1. 2.1 Why do we get sleepy? Fall asleep?

    When you are awake, the electrochemical activity which generates your thoughts, feelings and decisions generates a series of chemical byproducts. Over the waking day, the level of these chemicals - or sleep promoting factors as they are called - increases. This build up generates a sleep propensity - a need for sleep - which, when it reaches a threshold level, helps blocks the activity in other regions of your brain which are making sure that you stay awake. They also contributes to the activation of sleep promoting regions to set in motion the night-time regime of sleeping.

  2. 2.2 What does your body and brain do as it starts falling asleep?

    You circadian rhythm regulates your sleep-wake cycle via your Suprachiasmatic Nucleus - your brain’s master clock. Your preoptic region receives signals, (albeit indirectly) from your suprachiasmatic nucleus as well as direct signals from light-sensitive regions of your retina, providing information about whether it is dark or light in your external world. This helps to coordinate the process of falling asleep with other physiological processes regulated by your body clock.

    Which part of your brain is activated by your circadian rhythm?
    One the the main regions in the brain which causes you to fall asleep - your sleep centre - is called the preoptic area. This is located within your hypothalamus and is especially active when you are about to fall asleep and also during the night whilst you are sleeping. Your preoptic area works by sending out inhibitory signals to areas of your brain involved in keeping it awake (e.g. your ascending reticular activating system - see below), blocking their wake-promoting neural messages and initiating the process of falling asleep.

    How does the preoptic area cause you to fall asleep?
    The cells in your preoptic area which are “sleep inducing” use chemicals such as the neurotransmitter GABA and the neuropeptide galanin as their chemical messengers. These inhibitory chemicals are released at “synapses” which form the contact-interface between the preoptic cells and cells within your opposing wake-promoting areas. This acts to “switch off” those wake regions, preventing them from sending their messages up into the brain and causing you to fall into a state of sleep.

  3. 2.3 What are the key sleep promoting factors / mechanisms for activating the sleep part of your brain?

    Many different sleep promoting factors have been identified. These includes chemicals such as adenosine, nitric oxide, prostaglandin D2, and a variety of cytokines (cells made by your immune system). Out of these, it is adenosine which is considered to be one of the most important.

    1. 2.3.1 GABA

      GABA is the main inhibitory neurotransmitter involved in switching off state of wakefulness. Although it does not so much act as chemical marker for the end of the day, it is critically involved in coordinating the actual process of falling asleep via its action within preoptic cells which inhibit the activity of wake-promoting brain regions.

    2. 2.3.2 Adenosine

      Adenosine is a byproduct of metabolic and electrical activity both within your neurons - the cells which carry the electrical impulses around the brain - and within their supporting glial cells. This means that the level of adenosine in particular regions of your brain is an indication of the amount of time you have spent awake that day. The higher the level of adenosine, the more hours you have been awake and the closer you are to needing sleep.

      Adenosine promotes sleep by influencing various sleep-wake pathways in the brain. One of it’s main routes of action is by directly inhibiting regions which are tasked with keeping the brain awake, in particular specialized cells in the hypothalamus which contain the chemical orexin/hypocretin, as well as cholinergic cells (containing the neurotransmitter acetylcholine) in the brain stem - see more below. In addition, adenosine is also able to send excitatory messages to the preoptic region, which in turn inhibits wake-promoting regions.

      Adenosine receptors (the protein structures via which adenosine mediates its effect) are antagonized (blocked) by caffeine and theophylline (found in cocoa beans). This can act to delay the impact of adenosine as a sleep promoting factor.

    3. 2.3.3 Nitric Oxide

      Nitric oxide is actually a small gaseous molecule which is synthesized by enzymes in the brain. It promotes promotes sleep through a variety of mechanisms but one of the main ones is by promoting the release of adenosine and therefore initiating the kind of sleep-promoting effects described above.

    4. 2.3.4 Melatonin

      Melatonin is produced by a particular gland located at the base of your brain called your pineal gland. It is mainly released during the night under the regulation of your Suprachiasmatic Nucleus. Melatonin release is also sensitive to light signals from the retina and works to entrain your internal sleep-wake cycle to an external clock. This is one of the reasons why melatonin supplements are commonly used to treat circadian disturbances, such as those caused by jet lag.

  4. 2.4 What might keep us from falling asleep, physically and neurochemically?
    1. 2.4.1 Excitatory Neurotransmitters & Hormones (Norepinephrine, Epinephrine, Cortisol)

      During the day, you are faced with various physical, social, emotional or mental challenges which cause your brain and body to release a series of chemicals which prepare you for action. Neurotransmitters such as norepinephrine (and it’s related hormone epinephrine) help to put your brain in a state of high alert and up-regulate activity in wake-promoting regions to ensure that they stay awake and alert. In addition, the hormone cortisol which is released from your brain-to-body HPA (hypothalamic-pituitary-adrenal) axis in a time of high-stress - as well as morning waking - can act to ensure you remain in a state of wakefulness (but not always in a good way!).

    2. 2.4.2 Orexin / Hypocretin

      Cells containing Orexin/hypocretin, a wake promoting factor (see below) are especially busy when you are standing up, walking around, or generally being out and about. This is one of the mechanisms through which your brain makes sure that you don’t just spontaneously fall asleep at an inopportune moment, even if you are very tired. This is most strikingly observed in narcoleptic individuals who have a orexin/hypocretin deficiency and find themselves spontaneously falling asleep at a moment's notice.

  5. 2.5 How do you make sure you stay asleep?

    When a typical nighttime sleep period lasts ~7-8 hours long, getting to sleep is only the very start. Over the next few hours, your brain has to keep you in this state. This is where the mutual relationship between your brain’s sleep and wake region is critical. Because by inhibiting your brain’s “wake” regions, the preoptic area doesn’t just “switch them off”, doing so also removes the very inhibitory signals originating from these regions which were themselves keeping the preoptic area shut down. This reciprocal cycle of inhibition is what helps to create a stable sleep state during the night.


The patterns of brain activity associated with sleeping are usually measured using a technique called electroencephalography (EEG) which involves placing recording electrodes on the scalp and then measuring, and amplifying, their electrical output. Sleep is divided into two main phases - non-rapid eye movement sleep (NREM) and rapid eye movement (REM) sleep. During the night you cycle repeatedly between NREM and REM sleep at regular intervals.

  1. 3.1 What is NREM Sleep?

    NREM sleep is the type of sleep which is associated with slow rolling eye movements. There are several sub-stages of NREM sleep but one of the most important stages is usually considered to be deep sleep, or slow wave sleep (stage 3-4) where the brain waves are oscillating at a low (~1-4Hz) frequency. This is thought to be the one of the main stages of sleep where all the events and activities of the waking day are consolidated into your memory to ensure that they can be properly remembered at a later date. The stages of NREM sleep also contain their own characteristic patterns of neural activity, for example, K-complexes and sleep spindles.

    What are K-Complexes and sleep spindles?
    K-Complexes are a brief, and particularly large, downward and upward spikes in electrical activity found in the later stages of NREM sleep. Their function has still proved elusive to scientists but may represent a pre-warning for a momentary awakening, or, alternatively, a pre-signal for transitioning into deeper, slow wave sleep, supporting the maintenance of an ongoing sleep state.

    Sleep spindles manifest themselves often within stage 2 NREM sleep as short “bursts” of electrical activity typically lasting ~0.5 to 3 seconds. They are thought to originate from the thalamus, a critical relay centre in the brain between your sensory-processing areas and other regions of the brain. In this way, spindles act to ensure that sensory stimuli - in other words sounds, touch sensations or smells which might be in your surrounding environment - don’t disturb your sleep. They have also been shown to be important in memory consolidation during sleep.

  2. 3.2 What are the neurochemical mechanisms associated with NREM sleep?
    1. 3.2.1. GABA:
      Sleep is associated with activation of the preoptic area which predominantly uses the neurotransmitter GABA and the neuropeptide galanin as it’s chemical messengers. NREM sleep is therefore predominantly associated with these two neurochemicals.
    2. 3.2.2. Serotonin:
      During NREM sleep, one of the actions of serotonin is to inhibit acetylcholine signals which predominantly support REM sleep. In this sense, serotonin helps to regulate the onset of REM sleep during the night.
  3. 3.3 What is REM Sleep?

    Traditionally REM sleep has been associated with dreaming, although some forms of dreaming do also take place in NREM sleep. REM sleep is exemplified, not only by rapid eye movements but also by a form of movement paralysis - something that you can sometimes consciously experience if woken suddenly from a dream.

    What is the brain doing during REM sleep?
    During REM sleep, some of the brain systems which are more typically associated with being an awake state of mind become active. One particular region of your brain stem - the Pons - is particularly important in generating REM sleep and contains so called “REM-on” cells.

    Why can’t you move during REM sleep?
    REM is also associated with movement paralysis. This is also caused by acetylcholine signals from your pons being send down your spine. These signals are inhibitory and they act to on cells which control your muscle movements. In doing so they make sure that you don’t act out, in the real world, the actions and events taking place in your dreams.

  4. 3.4 What are the neurochemical mechanisms associated with REM sleep?
    1. 3.4.1. Acetylcholine
      – The main neurochemical which is released from these “REM-on” cells in the pons is the neurotransmitter acetylcholine. Activation of these acetylcholine cells creates a particular oscillating pattern of electrical activity - so called PGO waves - abbreviated from Ponto-Geniculo-Occipital. These waves pass from your pons through to areas of your brain which are involved in visual processing (you occipital cortex) and help to create the vivid imaginary world which plays out inside your dreams.


  1. 4.1 How does your body know to wake up

    Within, and surrounding, your brainstem, which phylogenetically speaking is one of the oldest parts of your brain, there is a set of regions (called nuclei) which collectively form your “ascending reticular activating system”, or ARAS for short. This forms a significant chunk of your brain’s “wake system”. The ARAS send signals directly into your cortex and also to your thalamus - a central gating hub which controls which signals can gain access into your cortex.

    How does the reticular activating system wake us up?
    During sleep, your ARAS system is being inhibited by sleep promoting regions in the brain, predominantly your preoptic area. Waking occurs when this inhibition is weakened, which allows the ARAS to start “firing” again. This causes it to send out inhibitory signals back to your preoptic area to “switch it off”. Activation of the various chemical nuclei within the ARAS also initiates a widespread network of brain signals which arouse your body and brain into a state of wakefulness.

    What causes the ARAS to “wake up”?
    There are a variety of “wake-promoting” chemicals which act to coordinate the process of waking up. These include Orexin/Hypocretin - a neuropeptide that was given two names because it was discovered at the same time by two independent research groups - as well as corticotrophin-releasing factor and adrenocorticotrophic hormone. These two latter chemicals form part of a physiological axis within your body (called the hypothalamo-pituitary adrenal axis, HPA) which is more commonly associated with your stress response, but also plays an important role in waking, and gearing you up for the day ahead.

  2. 4.2 How does your brain keep awake during the day?

    When the ARAS is active, it not only keeps you awake, it also inhibits your brain’s “sleep promoting” regions, such as the preoptic area. Neurons sent out from the ARAS and other wake promoting regions, carry neurochemicals such as norepinephrine, acetylcholine, serotonin and histamine. These have an inhibitory effect on the preoptic area, stopping you from falling asleep during the day.

  3. What are the neurochemicals involved in waking you up and keeping you awake?

    Within each the different nuclei of the ARAS, as well as nearby wake-promoting brain structures, there are collections of cells which release a variety of neurochemicals. These include acetylcholine (from the laterodorsal tegmental nucleus, pedunculopontine nucleus) serotonin (from the raphe nucleus), norepinephrine (from the locus coeruleus), histamine (from the tuberomammillary nucleus), as well as dopamine which is released from the Ventral tegmental area.

    1. 4.3.1 Orexin / Hypocretin

      Orexin/Hypocretin, is found in cells within a particular subregion of the hypothalamus. Orexin/Hypocretin works by switching on the various neurochemical nuclei in the ARAS, effectively “waking them up”. This includes nuclei which release neurochemicals such as serotonin, norepinephrine, histamine, acetylcholine as well as dopamine (from the ventral tegmental area) which together form large-scale neuronal networks which extend throughout the brain to support your daily waking behaviours.

    2. 4.3.2 Acetylcholine

      In addition to its role in REM sleep, the neurotransmitter Acetylcholine (ACh) also plays an important role in the process of waking you up and keeping you awake, as activation of ACh cells generates “fast brain waves” which are a hallmark of being in an awake state (as opposed to the slower waves associated with NREM/deep sleep) and which help to support multiple functions including attention, memory, sensory processing.

    3. 4.3.3 Norepinephrine

      Norepinephrine is one of your brain’s “ready for action” chemical. In that way it increases your brain’s level of arousal and helps contribute to your state of wakefulness throughout the day.

    4. 4.3.4 Serotonin

      Serotonin is an important chemical in supporting the process of waking you up and some wake-promoting serotonin cells are themselves sensitive to light. The role of serotonin in wakefulness can be seen in people who take selective serotonin reuptake inhibitors (SSRIs) - which act to elongate the duration of serotonin action in their synapses - and who have problems sleeping. Activation of serotonin cells also leads to the activation of other wake-promoting cells to reinforce the process of staying awake throughout the day. Serotonin is also involved in regulating your body temperature and is involved in the mechanisms by which being cold wakes you up.

    5. 4.3.5 Histamine

      Histamine, released from a subregion of the hypothalamus called the tuberomammillary nucleus is critically involved in regulating wakefulness and in sustaining a state of brain arousal during the day, something that has been known since the discovery of the sedative effect of antihistamine drugs. This is in part due to the fact that histamine-containing-cells work together with cells containing as ACh and Orexin/hypocretin which together have widespread wake-promoting effects in the brain.

    6. 4.3.6 Dopamine

      Although not specifically part of the reticular activating system, dopamine, released from various midbrain nuclei such as the ventral tegmental area, also plays an important role in waking up and keeping you awake during the day. In particular, its role in wakefulness is thought to be linked to the way that dopamine motivates you to take action and seek out rewards, something that necessitates being an wakeful and active state of mind.