The basic model of a biological clock consists of 3 parts – a central oscillator that generates the rhythm, inputs that detect Zeitgebers and entrain the oscillator, and outputs that translate the rhythm from the oscillator into overt rhythms.  

Although this basic model is rather an oversimplification, as inputs can be outputs as well (e.g. photoreceptors), and outputs can feedback on the oscillator, altering its pace, it is a good starting point for examining the molecular clockwork of the clock.

The Oscillator 

The oscillator generates the rhythm of the biological clock. There are two levels of regulation – negative feedback and post-transcriptional control.

Negative feedback

Negative feedback is when the protein product of a gene acts the gene itself to down regulate its expression. This creates an oscillating pattern of gene expression. Negative feedback occurs at least once in every biological clock.

In some cases, the inhibition is direct, with the protein product of a gene inhibiting its transcription. In other cases, the inhibition is indirect. The protein product of a gene does not directly inhibit the gene. Instead it inhibits another protein that is responsible for triggering the transcription of its gene. 

A generalised negative feedback loop. The inhibition of the gene is either direct (a), with the protein directly inhibiting its own transcription, or indirect (b) with the gene product inhibiting a positive element that causes the transcription of the gene.

In both cases, the inhibition causes rhythmic transcription of the gene, and rhythmic levels of the protein. The gene will be transcribed, causing an increase in the amount of mRNA and protein up to a certain level. At this point the protein inhibits the transcription of the gene. This reduces the amount of mRNA and protein being produced. When the levels of protein are reduced sufficiently, the inhibition of the gene is lifted and transcription starts again.

The following chapters illustrate feedback loops in four different organisms:





Post-transcriptional control

Although the feedback loops in themselves are enough to generate a rhythmic signal, they cannot account for how a clock spans 24 hours. Post-transcriptional control of the genes allows the clock to cycle with a 24 hour period, maintain the cycling of the clock components from transcription to output and provides a buffer to abrupt changes that might disrupt the clock. 

Post transcriptional control also provides a way for the clock to be reset by Zeitgebers. 

There are 4 post-transcriptional mechanisms at work in the biological clock:

Control of RNA - In some clocks cycling occurs at the mRNA levels rather than the transcription level. This has been shown particularly in Drosophila. There may also be alternate splicing of mRNA according to environmental conditions such as cold or light.

Translational control - In every clock there is a delay between the peak levels of the mRNA of one gene and the corresponding protein to allow levels of mRNA to accumulate before the gene is repressed by negative feedback.

Nuclear translocation - In every known clock, a key step is the translocation of a protein from the cytoplasm into the nucleus. In every case the protein is part of the negative arm of the clock.

Protein degradation - Although the cycling of many clock proteins is due to rhythmic expression, hand in hand with this is the rapid degradation of proteins. All cycling proteins in any biological clock have a short half-life, to prevent them from accumulating until equilibrium is reached. In most cases the degradation is by the ubiquitin-proteosome pathway, and the proteins are targeted for destruction by progressive phosphorylation.


One of the key properties of a circadian rhythm is its ability to be reset by external environmental cues (Zeitgebers). To do this the environmental cues must be detected by detectors that must then translate them into alterations in the activity of genes or proteins in the central oscillator, either directly or via intermediate. 

Although there are many different Zeitgebers (see the “clock” section), the predominant one is nearly always light. Light alters the phase of the oscillator by acting on the negative elements of the feedback loop. This affects the phase of these elements and thus in turn affects the phase of the oscillator. This is achieved either by light degrading a clock component whose levels decline during the day (overcoming the clock mechanisms that stabilises that protein), or indices a component with levels that increase during the night (overcoming clock mediated repression. In all clocks, the clock itself controls one or more of the constituents of the resetting pathway. This means that a clock is more susceptible to resetting at certain times of the day than others (e.g. dusk and dawn). This property is known as gating of the light input. 

The following chapter illustrate the light input pathways in four different organisms:






Most outputs are generated using the cis- and trans- acting elements to create cyclic transcription of output genes. The products of these in turn act on other genes and systems to form rhythmic cellular and physiological processes. 

Although the systems regulated by the biological clock vary from species to species, there are some systems common to all of organisms. For example systems that help prevent genomic damage by UV light from the sun, or genes that produce enzymes or hormones that help regulate energy metabolism (Harmer et al. 2001), or mediate coordination of carbon, nitrogen and sulphur pathways (Harmer et al 2000). Many of these clock regulated genes also feedback on the oscillator, helping to synchronise the clocks in different cells. 

The following chapter illustrates some of the output pathways in 4 different organisms: