Phenomena of Nature: Cells-Chemical Organisation – Dr. Sayed Abdul Wadud


“And the things of various colours that He has created for you in the earth, in them is a Sign for those who keep the working of the Divine laws before them”.


As stated earlier, the first living bodies on earth were single cells. These gradually evolved into animals and plants that we see now. The world today thus consists of unicellular as well as multicellular organisms, the basic unit being a cell. Every cell differs from the other in certain respects. Moreover the chemical constituents of a cell are changing every moment. New materials enter a cell. Reactions within a cell change the incoming materials into new compounds, some of which are redistributed within the cell substance, others including the waste products leave the cell. These changes are continuous. But inspite of all the differences between cells and changes within cells, there are certain basic features which are common to all of them. Functions of a cell are based on the properties of its chemical constituents.


95 per cent of the weight of a cell consists of four elements; oxygen 62 per cent, carbon 20 per cent, hydrogen 10 per cent and nitrogen 3 per cent. The rest 5 per cent of the weight of a cell consists of thirty other elements, including calcium, iron, sodium, potassium, magnesium, iodine, phosphorus, chlorine and sulphur as the main ingredients. In addition trace elements are present in particular types of cells. All the elements described above are present in the oceans. The cells having originated in the oceans, their contents and composition are a reflection of the oceanic water.

Minerals. All minerals present in a cell are present in the form of solution, except calcium salts which are present in the form of crystals around individual bone forming cells. Another element namely silicon is also present in crystal form in the outer cells of certain grasses.

Organic Components. As noted already, these are Carbohydrates (which include sugars and polysaccharides) fats, proteins, nitrogen-bases drivatives which include adenoL’iie phosphates and nucleic acids. Like minerals, some of the organic substances form hard parts, for example wood, horn and chitin (the external covering of insects).

Carbohydrates. These, as we know, consist of carbon, hydrogen and oxygen. A carbohydrate with five carbons (C5H10O5) is called pentose. Common example is ribose. That with six carbons (C6H12O6) is called Hexose. Common examples are glucose, fructose and galactose. Sugars such as Pentose or Hexose are called monosaccharides as each represents a single sugar unit. Two monosaccharides joined together form a Disaccharide, a double sugar. Example is cane-sugar which is a combination of glucose and fructose. Two or more disaccharide molecules combine to make a polysaccharide. Examples are cellulose, glycogen etc.

Fats. As seen already, fats are formed by combination of one glycerine molecule and three fatty acid molecules. Like coal or petrol in an engine, fats serve as fuel in cells. They also form boundary membrances of cells where they contribute to controlling the movements of materials into and out of cells*

Proteins. Are polymers of Amino acids. A protein may contain any type, any number and any sequence ofamino-acids. Proteins may be categorised as Fibrous and Globular. Fibrous Proteins are relatively insoluble in water and provide the building materials for the structural framework of cells. Fats, carbohydrates and other materials get secondarily deposited in it.

Protein formation being under the control of nucleic adds, every organism has got specific types of proteins. Thus if protein from one organism is transferred to the body of another organism, it acts as a foreign body and produces disease. For , example bacteria give rise to disease when they infect a  host. Proteins of one animal when grafted into another, do not heal into place.

Nucleic acids. As we know, these are nudeotide polymers. Nucleotide is a phosphate of a nitrogen-base plus simple sugar pentose. Pentose may be either Ribose or Deoxyribose, the latter containing one oxygen atom less than ribose. On this basis we may distinguish between Ribose-nucleic-acids (RNA) and Deoxyribose-nudeic-adds (DNA). DNA forms genes and RNA functions as an intermediary between genes and the sites of protein synthesis in a cell.

* Formerly fat was considered to be metabolically inactive substance. (For example, in human body it was supposed to be a reservior from which the body could draw calories during starvation or similar conditions. Its main day to day function was one of insulation against temperature changes and mechanical protection of underlying structures against minor trauma. We were also familiar with the aesthetic aspects of fat But it was not considered as an organ in its own right It is nbw known that fat plays a unique and central role in the economy of energy, a fact of which we were ignorant several years ago. To use an analogy, just as the capital of a bank cannot be allowed to be idle, so resources stored in the fatly tissue are not to be regarded as inactive or inert To extend the analogy, although the amount of capital represented by fat may be constant, there is a continuous borrowing and lending of funds, with the result that, provided the weight remains constant, a zero balance is struck.

Other constituents of cell. In addition to fats, carbohydrates, proteins, nucleic acids and Adenosine-phosphates which form the bulk of living matter, a cell contains hundreds of other organic substances. These are present in minute quantities and yet they may be extremely important for the maintenance of life. One category of these substances is known as pigments. Besides their aesthetic aspect in the living world, pigments perform various extremely important roles.

Pigments. Three types are particularly significant-

One group includes pigments known as Tetrapyrrols. A pyrrol contains a skeleton of five atoms of carbon and nitrogen arranged in a ring. Four such rings joined together form a tetrapyrrol. Tetrapyrrols of this type include red, blue, green and other varieties of pigments found, for example, in algae, in the shells of robin and other bird eggs and in mammalian faeces and urine

Fig.24.-PIGMENTS. (Chemical Structure)

In other tetrapyrrols, the four pyrrol rings are joined to form a larger ring in turn and in the centre of this larger ring is usually present a single atom of metal. A major pigment of this type is green chlorophyll, the central metal atom here being of magnesium. This is present in photosynthetic organisms. In another important type of ring-like tetrapyrrol, the central atom is iron and such pigments are red; for example, haemoglobin, the red oxygen-transporting substance in the blood of many animals (man and vertebrates generally).

(b) A second large group of pigments in organisms comprises carotenoids. They produce red, orange, yellow and brown colours. They are long chains of carbon atoms, with carbon rings attached at both ends of the chain. Two subgroups of carotenoids are the Carotenes and the Xanthophylls. Carotenes have a general formula C40 H55 and Vitamin A is its derivative. Named after the carrot in which carotenes are abundant, the pigments also occur widely in all leaves and are reponsible for the red, yellow or cream white colours of, for example, tomatoes, pumpkins, egg yolk, butter, milk and other plant and animal products.

Xanthophylls contain oxygen in addition to carbon and hydrogen. They are also widely distributed. A common Xanthophyll of leaves is lutien (C40H56O2), which is responsible for the yellow colours in autumn foliage( ).

(c) A third major group of pigments comprises the Anthocyanins formed among plants but not animals. An anthocyanin molecule is composed of several rings of atoms, the ring being joined in complex ways. They produce the deep reds and blues of plants as in many flowers, fruits and roots (e.g., beet-root). They are also manufactured in autumn foliage where they account for red colouration. They are water soluble whereas carotenoids and chlorophylls are fat soluble.

Most conspicuous in animals but not in plants is Melanin. It is responsible for yellow-brown, brown and black animal colours. Thus it occurs abundantly in hair, skin, in the inner layers of eyes and also in the interior membrances of some animals. Melanin is a chemical derivative of the amino acid tyrosine. Specialised pigment cells produce melanin, which accumulates in granules within such cells. If only a few melanin granules are present, the cell appears to be yellowish or brownish in colour. A black colour is produced by dense masses of granules.

The Holy Quran says:


“And the things of various colours that He has created for you in the earth, in them is a Sign for those who keep the working of the Divine Laws before them”.


“Do you not see that Allah sends down rains from above and leads it through springs in the Earth? Then He causes to grow therewith produce of various colours. Then it withers and turns yellow. Then He makes it dry up and crumble away. Truly in this is a message to men of understanding”.

These are the wonderful ways of the working of Divine laws in the physical world. We note how the same Carbon, Nitrogen, Hydrogen and Oxygen atoms in a molecule with change in their number and arrangement pattern, produce a variety of pigments. How the inclusion of a single atom of magnesium in a formula produces green colour, and the inclusion of an atom of iron produces red colour. How the addition of oxygen to carbon and hydrogen atoms (C40H56O2) produces lutien, a yellow pigment of autumn foliage ( ) and so on.

Meaning of colour. It would be worthwhile in this connection to describe what we mean when we say that so an and so object has got so and so a colour. For example, we know that a plant is green because it contains a green pigment called chlorophyll. Why does chlorophyll look green?

For this let us recall the electromagnetic radiation, already described in Chapter IV. The constituents of electromagnetic spectrum which are of different wave-lengths extend from radio-waves to cosmic rays. The wave-length decreases from radio-waves, through infrared rays, light rays, ultraviolet rays, X-rays, gamma rays, to cosmic rays. Thus radio-waves are longest and least energetic and cosmic rays are shortest and most energetic. The light rays or the visible spectrum which is a part of the electro-magnetic spectrum described above is again composed of rays of different wavelengths. They range from violet, through indigo, blue, green, yellow, orange, to red in increasing lengths. Thus violet is shortest and most energetic, and red is longest and least energetic.

Colour is not an inherent property of an object. It is a sensation produced by stimulation of optic nerves by particular light vibrations and its interpretation by brain cells. When light from a self-luminous source falls on a particular object the light rays may be absorbed, or transmitted, or reflected by it. The transmitted or reflected rays when they fall into our eyes, are carried by optic nerves to optic lobe area of brain which interprets these vibrations as colour. (Fig. 25).

Fig.25.-LIGHT RAYS. (Light rays reaching an object may be partly reflected, partly absorbed and partly transmitted.)

An object which absorbs all types of light rays (from violet to red) falling on it would be invisible. A black object approaches this theoretical condition very closely. An object which transmits all light rays, would be completely transparent and would thus be invisible. And an object which reflects all light would appear in the colour of light falling on it.

Thus the colour of an object depends on what type of light rays are absorbed, transmitted or reflected. Just as a radio-receiver is sensitive only to a portion of electromagnetic spectrum known as radio-waves, so the human eye is sensitive only to a portion known as visible spectrum or light rays. The optic lobe of the brain is so constructed that it interprets the shortest most energetic light waves as colour violet and the longest least energetic as colour red. Light waves of intermediate increasing wave-lengths are inerpreted as indigo, blue, green, yellow and orange respectively. Viewed together in a properly mixed beam such as sunlight the whole spectrum of visible waves is interpreted as white.

The subjective nature of colour is revealed in colour blind persons. These people can identify certain colours and not others. The defect here lies in the visual mechanism of the viewer and not in the object viewed.

We may conclude therefore that the light waves which chlorophyll reflects and transmits, and which make chlorophyll appear green to us, have intermediate length and energy content; and that the light waves which chlorophyll absorbs must be the other components of the visible spectrum, namely, the long red waves and the short blue-violet waves.

Similarly the colours of plants, animals, rocks, minerals and in fact of all the living and non-living objects around us varies with their respective chemical and physical structure and consequently upon the rays of solar spectrum that each of them reflects, transmits or absorbs. What a beautiful arrangement, for the display of beautiful colours in this beautiful world.

The scientists who explore nature and gain knowledge of natural phenomena are termed  ‘Ulema’ by the Holy Quran:


“Do you not see that Allah sends down rains from above? With it We then bring out produces of various colours. And in the mountains are newly created strata of rocks, white and red of various shades of colour, and intensely black. And so amongst men and crawling creatures and cattle are they of various colours. Those who posses the knowledge of these sciences ( ) really appreciate the mighty powers of the laws of Allah. They know that His law is omnipotent and provides protection for those who abide by it”.

The word  in the above verse is significant. Usually it is translated as “tracts”. But actually it means the newly created strata of the Earth’s crust.

means ‘new, or ‘newly created’.

Let us recall that most sedimentary rocks were formed by erosion of other rocks. The action of air and water causes exposed rocks to crumble and the rainwater gradually moves the pieces downhill. After movement has ceased, some substance in solution in water deposits a cementing material which holds the pieces together to form a rock. If the pieces are large, we call it Conglomerate. Pieces about the size of sand grains form a sandstone. When the mass is like a fine smooth powder, the rock becomes a shale. The normal succession of sedimentary rocks is conglomerate, sandstone, shale and limestone. The limestone which is made principally of the shells of marine animals is formed only in clear water, and indicates the presence of very sluggish streams preceding the rock formation that could not carry even small particles. The sedimentary rocks may be turned into metamorphic rocks under the influence of heat, pressure, water and motion. Thus shale became slate, granite became gneiss, limestone became marble and sandstone became quartz. The changes involve recrystallisation and the formation of new minerals. Rocks are made up of minerals, and minerals themselves are composed of one or more of the natural elements. The compounds of different elements, e.g., carbon, copper, iron, aluminium, calcium etc., produce different colours. The colours of rock strata are further influenced by other factors. For example, limestone is white in colour,

but when quite near the shores, mud may be mixed with it to give it a grey colour. Metamorphosis may change colours: for example, sedimentary coal is brown in colour, and when subjected to heat and pressure bituminous coals are formed which are dull-black in colour.

In the above-said verse (15:28), the display of various colours in the newly formed strata of the Earth’s crust is referred to. Moreover this is the only verse in the Holy Quran where the word  is used, and here it is used for those who possess knowledge of natural phenomena.


In addition to the above constituents of cells there are other complex substances, such as derivatives of corbohydrates which form cells of animals and plants; and lipid derivatives, such as waxes which form covering films in plants; or cutin and sebrin which function as water-proofing and evaporation-resisting materials. Similarly, ralated to fats are the sterols, complex ring structures which form the molecular framework of a number of vitamins and of animal hormones which play major functional roles.

Weathering also affects the colouration of newly sedimentary rocks. Rocks exposed to weather for a long time assume a different colour. The chief agents responsible for weathering of rocks are (1) Air (2) water (3) Temperature changes and (4) plants and animals. The methods by which they cause changes are of two kinds;

mechanical and chemical. It is only chemicals which cause change of colour. Air alone has no -effect on rocks but air and water together are the chief agents of weathering. Oxygen and carbon dioxide are the gases of the air which with water cause important chemical changes in rocks of all kinds. Oxygen and water attack the iron found as a constituent of many dark coloured minerals, changing it to ferric oxide (rust). That accounts for the yellow, brown and red colours of most rocks and soils. The carbonaceous materias of plants also cause change in the colour of soils. The red colour is due to oxidised iron, produced by the chemical weathering of some rocks. There are two classes of iron compounds, ferric and ferrous. The ferric are red, yellow and brown in colour. Ferrous compounds are almost colourless. Hence a reduction of ferric to ferrous compounds by the carbonacous material of the humus, results in a change from red soils to colourless and finally black soils.

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