BIOLOGICAL CLOCKS

[BSHC]

BIOLOGICAL CLOCKS

Cells know the time

Cells are the fundamentals of life. All life’s processes happen in and by cells. One of the most amazing characteristics of cells is the fact that they know what time it is.

The fact that we humans possess a ‘biological clock’ is well known. During the night our body works differently from the daytime: we need sleep, at a certain moment it is nearly impossible to stay awake. Accidents happen very often in late night or early morning, a time at which a human being should be sleeping (Chernobyl, Exxon Valdez, etc).

That fever is at its highest during the late afternoon is well known, but especially since more and more people make journeys, often in short time over a long distance, many of us experience their clocks in the shape of ‘jetlag’, which occurs because the different clocks of our body react differently. It can last a week before they work again in tune. We have a lot of different clocks in our body, possibly even one in every cell.

The problems people experience with jetlag have stimulated the development of chronobiology. Also in connection with space travel much research is being done in this field: how will the body manage when it does not experience the earthly day-night-rhythm for years?

The graphic of our daily body temperature shows the co-operation of homeostasis and clock: at every time of the day the clock decides the perfect temperature, the real temperature is near that value, fluctuating because of feedback processes as part of the homeostatic system.

Homeostasis is a system that makes the organism - up to a certain level - independent of its environment. (Homeostasis is: the possibility every living system has to keep its inner system balanced, like our body keeps its temperature constant, independently of the outside temperature). Of course each living system must at the same time adapt to its environment. Many processes happen adapted to day or night, or to the seasons. This is not strange. Life has evolved on earth and has from the beginning been submitted to day and night. Often organisms are so adapted to day and night that they have a system that causes the adaptation already before night falls or morning begins. Biological clocks take care that things happen at the right time. Homeostasis is nowadays seen as one of the fundamental aspects of life, having a biological clock may be as fundamental.

The best way for an organism to keep its homeostasis is to prepare itself in time before a change occurs (i.e. wake up in time before the moment you can start collecting food (for a bird), spread your leaves just before it gets light and photosynthesis can start (for a plant), etc) This can save your life: the eyes of fishes need about 20 minutes to adapt to light (or darkness). If they only start adapting to light after it gets light, the animal can miss a prey, or a predator and become a prey it self. That this system is already very old was proved in research on the horse-shoe-crab (Limulus) a species that already walks the bottom of the ocean for 350 million years.

Limulus (horse-shoe-crab)

The sensitivity of the eyes of this animal changes twice a day: during the night the receptors of its eyes are 1 000 000 times as sensitive as during the day. In continuous darkness or continuous light in the lab this changing continues normally.

Chronobiology

Chronobiology studies the biological rhythms:

    - ultradian rhythms, shorter than a day - with a length, from thousandths of a second (like the pulses in neurons) or seconds (like the heartbeat) to the rhythm of about 90 minutes in our sleeping cycle (from REM-sleep to deep sleep)

   - circadian rhythms, which last about one day, like the sleep-waking rhythm, the body temperature, but also our sensitivity to pain or alcohol, reaction time, levels of hormones in the blood etc.

   - infradian rhythms, longer than a day. The most well known is de female cycle (often linked with the moon cycle, but there is no indication that this link is real (other mammals have rhythms of 3 weeks, or 9 days etc, only by accident humans have 28 days), Infradian are also year rhythms like bird migration. Also rhythms of a few days exist. Not only man, but also several animals (insects, but also some fungi!) have rhythms of some days. Humans have a rhythm of 5 - 9 days, which also occurs in complete isolation. Our week is not just a heritage of the Jewish culture, it has a biological basis. The immune system has a clear weekly rhythm.

Actogram.

Sensors in the floor of his cage measure the activity of a lab animal. After 22 days the lighting was made continuous. The animal still has a regular activity and resting rhythm, but based on his biological clock which does not work exactly in 24 hours: a circadian rhythm.

Circadian rhythms

Many patterns of change in plants and animals happen every day, always after about 24 hours. This circadian rhythm is the best known and probably most general rhythm in living creatures. It lasts about one day (‘circa dies’). In normal circumstances this clock is set every day by light, darkness, or - as in our species - by social signals.

By now about hundred processes in our body are known to have their own clock and circadian rhythm.

Ultradian rhythms

The cycle of the moon has a clear influence on processes on earth, but probably less than many people like to believe. Animals living in the sea organise their reproduction during full or new moon. This is a practical solution to make sure that eggs and sperm appear at the same time. But they possibly react more on the tides than on the moonlight itself. Some night active animals have a clear moon rhythm, but this has to do with the fact that they only walk around when it is really dark, in the full moon they are not safe. This automatically leads to a moon cycle.

The question if humans ever had a moon cycle can not be answered. That the female cycle has the same length is, is a coincidence. There is no connection with a special phase of the moon. The story that baby’s are born during full moon is proven nonsense, anyway in our western society. If this was ever the case in more primitive societies has never been investigated as far as I know.

Cycades

We do not know if yearly rhythms like bird migration and reproduction processes of most animals are also based on the same 24-hour-clock. Probably something like a ‘year clock’ exists. Many animals have to know when it is time to be active again at the end of winter without any signal from outside: bats wintering deep in caves know when it is spring. Migrating birds breeding far north of the polar circle have to leave their breeding grounds already early in summer long before it is getting colder, or they will fall victim of the sudden cold. Birds wintering in the tropics must know when to start flying north.

Cycads must in any case have a system to measure time: their larvae live underground (sucking root juices); they all appear all at the same time 13 or 17 years (depending on the species) after the eggs were laid. Within a few weeks they mate, produce eggs and die. One can imagine that they can know the season from the changing composition of the root juices, but how they count the years nobody knows.

One scientist kept ground squirrels in the lab in continuous circumstances (some had continuous light, others continuous darkness and the third group 12 hours light, 12 hours darkness the year round.) All animals kept their hibernation patterns Their circa-annual rhythm lasted about 11 months. When ground squirrels in natural circumstances wake up from hibernation they immediately set their circadian clocks. Thea can leave their holes at the right time. Their eyes must be extremely sensitive for differences in light intensity. They immediately know the time of the day.

Plant clocks

We all know plants that blossom in spring, or only in autumn, and other species blossoming the year round as long as is is no too cold. (daisy). Many plants seem to ‘know’ what the season is. Circadian rhythms also occur in plants.

Mimosa leaves of De Mairan and Darwin

Darwin described in his book The Power of Movement in Plants (1880) how the leave of Mimosa fold in the evening and open in the morning. In 1720 the Frenchman De Mairan wrote about this already. De Mairan told also how this movement continued in continuous darkness, and that all leaves of a plant move at the same time. He proved already the existence of a biological clocks in these plants. He also showed that this rhythm continued in constant temperature, and that the rhythm was not exactly 24 hours, but a little different for every individual plant.

In 1729 De Mairan in Paris discovered that the flowers of the ‘Heliotrope’ (this name means something like ‘sun turner’, like the sunflower this plant turn its flowers to the sun) which opens its flowers in the morning and closes them in the evening, does this also in continuous darkness. De Mairan discovered the biological clock, but did not use this term.

Many plants need a signal for forming their flowers; we call them ‘long day’ or ‘short day’ plants: early spring flowers and autumn flowers need an short day, summer flowers need a long day. In reality the length of the night is decisive: when short-day-plants receive a light signal in the night no flowers appear. Chrysanthemums blossoming in late summer form their flowers during the time of long days and short nights.

Nowadays we can buy them the year round because producers can manipulate the light in the greenhouse. These plants must have a clock with which they compare the length of the night.

Flower clock

Also for these plants it is true that they must prepare in time: if they must have flowers in autumn the must start forming the buds in summer, if they would start only in autumn they would be too late. The same is true for opening the flower or producing a smell at a certain time of the day: this must be ready at the time the needed insects are active. Als de bestuiving door nachtvlinders moet gebeuren, moeten de bloemen klaar zijn als de schemering invalt.

Linnaeus knew the rhythms of many flowers so well that he was able to construct a flower clock. Many species open and close at fixed times. By planting these in the right order in a circle according to their opening or closing time you can make a clock that shows the exact time.

Biological clocks in humans

Even before we knew what the biological clock really is, it was known that some people were ‘morning-‘ or ‘evening-people’. This runs in families. Evening-people probably have a longer period in their circadian rhythm, so that they are not yet sleepy in the evening, when it is time to go to sleep. Their inner rhythm can last 25 hours or even more. People have been staying in caves or in the far north during the polar summer in constant darkness or constant light without contact with the outside world. They would fall asleep and wake up at regular times, but not every 24 hours, usually a bit later every day. zodat ze ’s avonds, als het bedtijd is, nog lang geen slaap hebben. Hun eigen inwendige ritme gaat uit van van 25 of meer uur. Men heeft mensen in grotten of tijdens de poolzomer langdurig zonder klok of contact met de buitenwereld laten leven in constante duisternis of constant licht. Dan bleek dat ze op regelmatige tijden sliepen en wakker werden, maar dat hun eigen ritme geen 24 uur duurde, maar meestal iets meer.

A newborn baby does not yet have a circadian rhythm. This develops after some months spontaneously.

Up to the end of the 19th century most people lived in the natural rhythm of day and night. They did have candles or oil lamps, but you can not do too much by that sort of light. After the invention of the light bulb people started sleeping much less. During the middle of the 19th century adults slept nine to ten hours per night, now only seven on average - some people think this is the cause of many problems of our time. In the far north you can still see that people sleep much less in summer - children playing outside until very late. During the polar night they sleep very much, some people not leaving their beds at all. Winter depressions are very common there.

In our modern society the natural rhythm of day and night has practically disappeared. In de USA shops are open 24 hours and many people work in shifts. In Europe we are following this development.

Can we ignore our natural rhythms without consequenses?

The fact that elderly people often sleep less, wake up more often, or sometimes have trouble falling asleep can partly be explained by the fact that their biological clock is no longer functioning well, but it can also be explained by their way of living: often they hardly come outside anymore, so that the melatonin stays in their blood all the time, which makes them a little sleepy and slow the whole day. A light therapy - or just going outside much more - often helps a lot.

The feminine cycle

It is clear that the menstrual cycle influences many processes in the female body, for instance susceptibility for infections.

The female cycle has often been used to show that women are not fit for certain jobs, because women would be less responsible during certain phases of their cycle. It has been shown that the sense of smell is most sensitive during ovulation while spatial insight is lowest at the same time. But the real differences are very small. Men have been proven also to have a monthly cycle, for instance in some of the hormones, growing of the beard, seize of the prostate etc. (By the way, men have a strong daily cycle in their testosterone which influences their alertness and other things, so - what about their responsibility?).

"Zeitgeber"

The organism has its own clock (and even more than one) as we have seen, but this does not run exactly 24 hours. We use light to make our clock correct, but we can also use things like eating times etc as ‘zeitgeber’ (=”time giver” the German word is used here usually) . This makes it also possible to change. If the system would be too strict we would not be able to stay awake late sometimes or to get up extra early. Already adapting to different day length during the seasons asks for some flexibility.

The rhythms of the organs in our body show some differences: the adrenals have a day of less than 24 hours and the liver one of more than 24 hours. Without daily zeitgeber the organs would no longer work synchronous, and we would for instance get hungry when still asleep. When people in an experiment experience a shift of day and night some rhythms will adapt quite quickly and others much slower. Only after 8 days everything is working synchronous again.

Guessing what time it is

Sometimes the afternoon seems to last and sometimes it is over before you know. This is not just suggestion; this is caused by our metabolism.

When somebody is feverish an hour seems to be endless. A feverish person counts seconds too fast. With every degree higher fever our sense of time is 10% faster. When somebody has a temperature of 40⁰ C 30 seconds are experienced as a full minute.

Because our body temperature rises during the day afternoons seem to last longer than mornings.

Therefore one can say that a mouse lives faster because their metabolism is faster. It usually lives only one and a half year. A young mouse’s day could be compared with a human month or so. The well known idea that a year of a dog or a cat can be compared with 7 years of human life is not quite right, because we stay abnormally long children: our youth - say until 20 years of age - should be compared with the first year of a cat or dog.

Eating times

Our metabolism is not a simple calculation of the calories we eat and the calories we burn to know how much we grow or loose.

It makes a difference at which time we eat our meals. An experimental group got during one week daily 2000 calories; half of them was eating everything as breakfast and the other half of the group ate everything as supper. The next week the other way round. When they were eating only in the morning they lost half a kilo in that week, when they were eating in the evening they gained half a kilo.

In the morning we need carbohydrates, which can easily be turned into energy, in the evening part of our food is used for reserve; we need more proteins then for the reparation processes that happen mainly during the night. Growing also happens during the night. This is because hormones have a daily cycle too: cortisol and norepinefrin have their climax in the morning and serotonin in the evening. Growth hormone is only delivered to the blood during the night .

Until recently it was thought that regular eating times is a typical human behaviour, a result of our culture, while animals eat when the body needs food, for instance when the blood sugar is low . Not so. Golden hamsters eat both during the day and the night in many short episodes. If they do not get food during 12 hours per day they loose weight and will starve: they are not able to eat more during the other 12 hours. Animals have fixed eating times too. If a rat gets no food during 14, 25 or 42 hours, it will eat extra after the 25 hours interval but not after 14 or even after 42 hours, because this falls at a moment they are not used to eat. They eat normally once a day.

Doctors should listen to the rhythm of an illness

We should better stay in bed in the morning for that is a dangerous time: most heart attacks happen in the morning shortly after getting up.

Many diseases show a clear rhythm (rheumatism, migraine, asthma etc). Also the result of therapy can be very different depending on the cycle: when a woman with breast cancer is operated during the second half of her cycle, the chance to get it back is 25%, when the surgery is done during the first half it is 37%. But it is still rarely so that the planning of the treatment is made according to this knowledge.

The effectiveness of drugs can depend on the time of day they are taken. Both the effect and the side effects can be very different depending on the moment of taking them. Slowly some insight in these rhythms is growing, but doctors find it often difficult to take in consideration.

Where can our biological clock be found?

The word ‘biological clock’ was being used long before the actual clock was found. It is a miniscule piece of the brain (20 000 cells in all) just above the chiasma opticum (the place where the optic nerves are crossing). The suprachiasmatic nucleus (SCN) is no bigger than a quarter of a cubic millimetre. Because it is so close to the optic nerve it can get information directly from the eyes.

In newborn babies this part of the brain is not yet ready; this explains why they do not have a clear daily rhythm yet. In old people brain cells die, also in this part, this explains why their rhythm often deteriorates. Especially when people are demented this can give problems.

The place of the suprachiasmatic nucleus

Studies on the brains of people who died in hospitals (so that their brains could be frozen very soon after death) have shown that the SCN looks different during the night from what is looks like in the daytime and in autumn it is different from what it looks like in spring. Vasopressin is a protein that is best known because it works as a hormone influencing blood pressure (hence the name), it is also a neurotransmitter. It does not fall apart immediately after death. The presence of this substance can easily be demonstrated in the brain. It turns out to show much variation: the number of cell producing vasopressin is fifty percent higher during the day than during the night, and in autumn there are two and a half to three times more than in spring. In young people this variation is much bigger than in people older than fifty.

These fluctuations coincide with other fluctuations, like the amount of sleeping hours per 24 hours - this is most in autumn and least in May/June. Testosterone is lowest in spring and rising toward autumn and low in the morning and high in the end of the afternoon (in young men, in older men it is more equal).

The biological clock turns out not only to regulate sleeping and waking but also the functions connected with reproduction. For animals this is logical, their reproduction is seasonal, it is important that the young ones can find enough food at the moment they have to start finding their own food. The moment of birth does not need to happen at a time of abundance, but the moment of weaning has. Polar bears are born during the worst of seasons, the beginning of the polar winter, but when the young bears leave their den it is spring and when they start looking for their own food it is high summer.

The cells of the SCN have each their own rhythm: when they are grown on a medium they continue to show that rhythm. (There even exist cells from other tissues that still show their 24-hours rhythm after being grown outside the body during 30 years!) The SCN gets its information from the eye, not from the rods and cones with which we see but from special cells in the ganglion layer. These specialised cells have discovered only very recently.

Diagram of the basic cell types of the retina

R=rods (upper left B must be R), C=cones, H=horizontal cells, A= amacrine cells, G=ganglion cells. MG=melanopsin ganglion cell, these cells act as ‘brightness detectors’ they regulate a range of different physiological and behavioural responses to light including circadian rhythms (Foster & Hankins 2002)

If a blind organism is blind because of damage in the visual cortex of the brain, while the eyes are in tact, he will have a normal circadian rhythm, but when the eyes are absent or the optic nerve is not working there will only be the inner rhythm without reacting to the Zeitgeber - if it is a mammal. In mammals circa 1% of the light sensitive cells in the retina are the ganglion cells that give only information to the SCN. Birds and reptiles have light sensitive cells within the brain (in the pineal gland).

Blind people can use social factors as Zeitgeber and thereby set their biological clock.

Besides the central clock in the brain we have a series of other ‘clocks’ in our body. About one hundred processes in the body have been counted having their own clock system.

Melatonin

Seasonal influences probably are caused by actions of the pineal gland, producing melatonin. In reptiles and birds the pineal is the so-called ‘third eye’, directly influenced by light. In mammals it is influenced through the eyes. When it gets dark the gland starts the production of melatonin, when it gets light again it stops. During longer nights more melatonin is produced.

Probably melatonin influences the biological clock and this again influences the hypothalamus and through this the pituitary. The hormones produced here in turn influence metabolism and the sexual organs. The more melatonin the less activity in the SCN and the weaker the activity of the sexual organs. This explains why Inuit women have hardly any ovulations and menstrual cycle in winter (this is the reason why some people try to use melatonin as contraception pill). The question if humans have seasonal changes is difficult to answer. Our modern life style, holidays in summer etc make such possible differences quite invisible.

Melatonin became very famous when it was discovered that it can be used against jetlag. In some countries it is freely available to be used against jetlag or as a healthy sleeping pill. To use it as a contraceptive would demand such high doses that one would immediately fall asleep - which works of course contraceptive too.

Probably it is not a very good idea to fight jetlag with melatonin. Because many organs in our body have their own rhythm it could damage the balance of the many systems. Better use natural sunlight to adapt to the new day and night rhythm.

The circadian clock affects the daily rhythms of many psycholocial processes.

This diagram depicts the circadian patterns of someone who rises early in the morning, eats lunch about noon and sleeps at night. Although circadian rhythms tend to be synchronized with cycles of light and dark other factors such as ambient temperature, meal times, stress and exercise can influence the timing as well.

It is possible to influence the biological clock directly, bur indirect methods are better: people working in nightshift sleep better when they work in the night under very strong lamps. Also Alzheimer patients who have lost the function of their biological clock for a big part will get their sleep and wake rhythm at least partly back if they are subjected to very strong light. They will also be less restless thanks to this light therapy.

When people are subjected to other day-and-night-rhythms than the earthly 24 hours, they do not react well. People staying in space more than three months start sleeping badly, feel tired etc. On Mars the day is a little longer than on Earth, and the light is more yellowish. Our photoreceptors are mainly sensitive for the blue part of the spectrum. Chronobiologists think that long stays on Mars could be disastrous. A good argument to stop planning trips to Mars?

The SCN is different in men and women - in women it is longer, in men more rounded. This means that it can have more connections in the brain of women (we do not know if this has a function).

The biological clock has something to do with sexual preference too: male rats with a high testosterone prefer females at the end of the night but male partners in the first part of the night. These animals had 50% more cells producing vasopressin than usual, and given more or less melatonin their behaviour changed.

The Dutch neurologist Swaab discovered in 1989 that homosexual men have a very big SCN. According to Swaab homosexual men do not have ‘feminine brains’, but they are really different, they are in a way a ‘third gender’.

The oldest clocks

Up to 1986 nobody believed that bacteria could have a biological clock. They have very short lifespan (half an hour to several hours, in any case shorter than a day). But we can not compare the lifespan of a bacterium (or other unicellular organism that reproduces by dividing itself) with the lifespan of a multicellular organism reproducing sexually or asexually. A cell dividing itself does not die but continues living in its daughter cells. When scientists found that cyanobacteria have photosynthesis during the daytime and nitrogen fixation during the night they realised that these organisms must have a clock too.

Cyanobacteria (also called blue green algae) belong to the oldest life forms. They have a biological clock and must do so already for three billion years. These organisms produce oxygen using their chlorophyll, but they are also able to fix nitrogen, because they have the enzyme nitrogenase . All living beings need chemically fixed nitrogen (for their proteins etc) but other life forms do not have this enzyme so they depend on bacteria for this. The problem is that this enzyme is destroyed by oxygen. Bacteria have solved this problem by having photosynthesis during the day and nitrogen fixation during the night. (Some other types have both processes simultaneous but in different compartments of the cell).

Cyanobacteria prepare their photosynthesis apparatus in time before it gets light - if this is not ready when the sun rises sunlight can damage the cell because free radicals will appear with light, they can break down certain chemicals. If the sunshine is less than needed the photosynthesis apparatus is turned off.

They have a distinct timetable for their activities; also cell divisions happen at regular times. In the laboratory they keep this time table also in continuous dark or light.

Cyanobacteria are not only scientifically interesting they are also economically important, for instance in the wet rice culture: if there are enough of them in the water they produce the nitrates needed by the rice plants, so no fertiliser need to be applied.

The fact that their cell divisions must happen at specific times has to do with UV light. This is so dangerous that DNA in a human skin after 4 hours on a summer beach shows 10 faults in the DNA of every skin cell. This explains that sunlight can cause skin cancer, even if most of these faults will be repaired in the cells. Unicellular organisms prevent this damage by dividing at specific times.

Up to half a billion years ago the ozone layer was not yet thick enough to absorb most of the UV light. During the process of copying the DNA before cell division the sensitivity for UV is greatest. Lynn Rothschild (USA) showed that the cyanobacteria in the ‘microbial mats’ (as they are found near hot springs and in the shallow waters of some coasts, and that are formed by the same life forms as the oldest cyanobacteria) start making new DNA in the morning as soon as it gets light (using energy from photosynthesis), but stop the process during the hours that the sun is high. Photosynthesis proceeds in the mean time. These cells must have a clock mechanism that guarantees that the process of cell division, of which DNA production is a part, happens at the best time of the day. Unicellular organisms of other types have their cell division during the night. If unicellular organisms, even the most primitive forms have already a biological clock, it is not strange that multicellular organisms have it too - and that probably every cell in our body has one.

The biological clock originally evolved to protect the DNA from damage. Cyanobacteria are not able to swim to deeper water to protect themselves. There are algae that do swim down, but they also need a clock. Especially these organisms need a clock. If they would only stop the process when the radiation is already strong, the damage has happened already.

Bacteria with a jetlag?

The fact that bacteria possess a biological clock makes the research easier. It is quite easy to cause mutations in bacteria.

This makes it possible to find out how the system works. Several mutants have been found with a different circadian rhythm: some with 16 hours, others even 60 hours. This shows there exists a genetic basis for the clock. Today several genes are known to be responsible for the clock.

One of the studies used a nice technique: the gene for luciferase (the enzyme causing light in some organisms) was built in in the genome of the bacteria under study. This made it possible to see with the naked eye if the clock was working: the bacteria would give light at certain times of the day. This also proved that the whole metabolism and not only photosynthesis is regulated by the cell clock.

One more interesting aspect of this study is that bacteria must be able to ‘see’, to know light and darkness, so that they can adapt to the real day and night. In these organisms a compound cinnamon acid, was found, this is related to retinal, the compound in our eyes reacting on light.

The difference between human and bacterium is much smaller than people like tot think! Also in other studies it was found that most genes in higher organisms can be found in bacteria.

The actual ‘clock’

A clock can be defined as a system that shows a regular and predictable effect. The motion of the earth around its axis and the route of the earth around the sun are clocks in this definition. We know mechanical clocks (the pendulum clock) and atomic clocks based on the regular oscillation of certain atoms. Mechanical clocks are not possible in living systems, atomic clock not probable. All life’s processes happen on the scale of molecules, mostly enzymes. Biological clocks are no exception.

Already for a long time mutants with different circadian rhythms have been known, proving that there exists a genetic basis.

Much work has been done on the fruit fly Drosophila, which is popular with geneticists. This animal has a clear day-and-night rhythm. Mutants of the fly have been found with different lengths of their cycle. The flies leave their pupa always at the beginning of the day, but this also can be changed by such a mutation.

In one study the gene of luciferase was added tot the clock-gene, after which the animals were periodically giving light with all of their body. This shows that all cells possess the clock mechanism.

The molecular clock found in the fly is for the most part identical with that of the mouse (and other mammals, so also with ours). This means that the system must be at least 700 million years old (older than the common ancestor). In plants and fungi other genes are responsible for the clock, but the system is the same. This means that the biological clock must have evolved more than once. Het principe is altijd als volgt:

The principle is always like this: a protein is produced following the scheme: Gene >> mRNA >> protein (this is the mechanism to construct proteins in all cells) The protein in this case has two characteristics: it is degraded after a certain amount of time (but always the same amount of time!) and it suppresses the expression‎ of its own gene (this can be done by one protein or in combination with a second protein).If for instance the protein is degraded after 24 hours, the gene can always during some time every 24 hour produce the protein (until the moment there is enough of the protein again) . This can be the signal to start or stop certain processes in the cell

The biological clock of the fruitfly.

The actual model of the biological clock, molecular clock of the fruit fly: a protein complex consisting of CLOCK and CYCLE connects with DNA causing the production of the proteins PER and TIM. A ‘kinase’ (an enzyme) in the cell breaks down PER, but after some time there is enough TIM to build the PER/TIM complex before the PER is broken down. The protein complex PER/TIM turns the CLOCK/CYCLE complex off. After a certain time the PER/TIM complexes are broken down, after which the cycle can start again. The time needed to break down the PER/TIM complex decides the length of the cycle. Biological clocks in other types of organisms (like fungi, plants, bacteria) use the same principle using slightly different proteins.

This makes understandable that some mutants give a longer or shorter period: a protein that degrades slower or faster can be the result of a small change in the gene. If light has influence on the building or breaking down of the protein the clock can be adjusted by light. In continuous light or darkness the system will run in its own rhythm.

Probably there are more proteins that have to cooperate to make the system run.

There are still many questions about the exact working of the clock: how many proteins are really involved? How does the feedback system work exactly? How can the compound leave or enter the nucleus of the cell? Which processes are subjected to the clock?

40 years of hard work were needed to get some insight in the system. For a long time nobody believed that a clock based on proteins was possible because one of the fundamental characteristics of reactions of proteins is the fact that the speed of their reactions changes with the temperature. Cold blooded animals and plants have perfectly working clocks too, which means that the system is not depending on the temperature. Today we think we understand the system, but nobody can explain how it can be independent of temperature.

The day and night rhythm of a unicellular organism producing light  (like Noctiluca causing the lighting of the sea during warm summer nights). Only during the night this creature produces clear light, not during the day. This also happens in continuous circumstances. The graphics shows that also other activities of this organism show a circadian rhythm.

The evolution and the clock

The bacteria living around the ‘black smokers’ in the deep ocean have not yet been studied for their clock. Some scientist think life has started there. If that is the case, and if these bacteria have been there ever since, they will not possess a biological clock. If it turns out that they have one, this would prove that they are descendants of life forms that once were living on the surface in day light.

Organelles in cells - like mitochondria and chloroplasts - descend from bacteria living inside other cells (endosymbiosis) that lost their independence and evolved to merely parts of cells. This can be proved because they kept part of their own DNA. Some people think that also other parts of cells have evolved in this way. But it cannot be proved because they have no longer any DNA.

The evolution of the cellular clocks could have happened in two ways:

1. The mechanism is very fundamental and old and entered ‘modern ’ cells by endosymbiosis in the same way as mitochondria
2. The mechanism is so simple that it evolved several times during evolution.

It is also possible that both things happened. Plants and fungi have different genes but as far as we now know the mechanism is the same.

Life time

Since Darwin we know that evolution is an essential feature of living things. Since some decades it is more and more clear that homeostasis is one more essential feature of life. Ook bij organismen die in eeuwige duisternis leven (zoals grottenvissen) blijkt nog altijd een levensritme, dus werkende biologische klokken, aanwezig te zijn.

If we could take a look inside a living cell, we would see a continuous re-organising of molecules, continuous birthing and degrading of molecules that react to each other in a certain regular pattern - as long as the cell is alive. One can compare it with riding a bicycle: it is possible as long as one keeps moving. A cell is alive as long as the processes keep going and the homeostasis maintained. Standing still means death of the cell. A cell must be prepared for changes in the outside world to be able to keep its homeostasis. For this a clock is needed. Even organisms living in eternal darkness (like the blind fishes living in caves) still have their daily rhythm; this means they own working clocks. It is quite possible that the possession of a working biological clock is one more essential feature of living creatures.

The riddle of the temperature independence begs for some speculation. Some thinkers speculate that in our brain more is going on than just molecules and electrical currents, they think that consciousness must be explained by quantum processes. Could also the biological clock have a quantum basis? For the time being we do not have possibilities to find out.

Loes Pihlajamaa-Glimmerveen

2005

Literature:

R. Foster & L. Kreitzman, RHYTHMS OF LIFE The Biological clocks that Control the Daily Lives of Every Living Thing (Profile Books, 2004).

C. Orlock, INNER TIME (Birch Lane Press, 1993).

J.D. Palmer: THE LIVING CLOCK, The Orchestrator of Biological Rhythms (Oxford University Press, 2002)