Tag Archives: Oxygen

Changing Colors of Leaves

Nature is a great chemist. It is playing with chemical pigments to present vivid colors. Even a single leaf is a piece of art. There are many classes of pigments present inside it but their amount and times of breakdown and synthesis decides the resultant color. The different colors are on display during autumn season. The leaves begin to look less and less green. They can take yellow, orange and red hues depending upon the ratios of the amounts of different pigments present in the leaves.

Most important pigment in the leaves is the chlorophyll. It is this pigment which imparts the green color to the leaf. It’s amount is dictated by the warmth and amount of sunlight the plant receives. It’s presence is the indication that plant is alive and carrying out photosynthesis to convert carbondioxide and water into sugars and oxygen. Sugars contain energy from the sun which is harvested by tree or plant during photosynthesis.


What happens when it is not sunny. We see a kaleidoscope of different colors in leaves. There are yellow, orange and red hues. These colors are attributed to other pigments present inside the leaves. These were there throughout the life of the leaf but there colors were masked by the strong green color.

In the autumn, when sunlight is not available in plenty, the production of chlorophyll is halted. On the other hand, the chlorophyll present begins to breakdown. At this time, color contribution from other pigments begin to show up.

Chlorophyll is a type of chlorine with magnesium as the central metallic ion. There are 4 nitrogen atoms which are Lewis bases and thus trap the positively charged magnesium ion. Chlorophyll is synthesized in the warm and sunny conditions by the plants. It’s green color dominates the color in the leaves. During autumn, the sunlight is not fully available and hence the production of chlorophyll halts and since it is not required the already present chlorophyll in the leaves begins to breakdown and hence result is the decrease in green color of the leaves.

Carotenoids and flavonoids are pigments which are always present in the leaves but there color is masked by the green color of the chlorophyll. When during autumn, the chlorophyll begins to breakdown, the color of these two classes of compounds begins to show up.

Xanthophylls which are oxygenated carotenoids are responsible for the yellow color of leaves. They do not require light for synthesis, so that xanthophylls are present in all young leaves as well as in etiolated leaves.


A class of carotenoids known as beta carotene is responsible for the orange color in leaves. It absorb light of green and blue wavelengths and reflects red and yellow wavelengths light thus causing the orange color in leaves during autumn. Beta-carotene are also responsible for this color in carrots. They begin to degrade at the same time as chlorophyll but at a slower rate thus showing up the orange color gradually.


There is another class of compounds called anthocyanins which begins to get synthesized in the mature leaves due to the high amount of sugars in them. These are red in color. These are thought to prolong the falling of leaves.



Ice hides memories of past climate!!!!

Almost all the elements in the universe are composed of atoms siblings though are chemically equivalent but have slightly different weight. Atom is composed of equal number of electrons and protons to make it electrically neutral and stable. There are also neutrons which are electrically neutral but have weight almost equal to the proton. Protons and neutrons reside in the centre of atom and called jointly nucleus. This is due to the different numbers of neutrons in these atoms. More the neutrons more shall be the weight of the isotope.
Oxygen has two prominent isotopes. The lighter one contains 8 neutrons and the heavier one contains 10 neutrons this is exactly 2 neutron heavier. The ratio of the heavier atoms to the lighter ones is 1:500 or 0.2%. The number and ratio of the oxygen isotopes is constant if water was present at one place only. But the distribution changes due to physical and biological processes. These two phenomena fractionated the distribution. The oxygen atoms are labeled 18O and 16O.
Since heavier oxygen has lower tendency to evaporate than the lighter and higher tendency to precipitate, the distribution changes continuously with the movement and phase changes of the water.
Originally in the sea water there was a given ratio. Now suppose sun heats the sea and evaporation takes place initiating the water cycle. But notice, the ratio of heavier atoms to lighter atoms will change both is the sea water left behind as well as the vapours. Sea water will become richer in heavier isotope and vapours poorer. Now these vapours rise and starts migrating towards the poles. Temperature gradually begins to fall triggering the precipitation but again further fractionation will take place. In the beginning, some of the heavier atoms will precipitate thus further depleting the pole ward moving water vapours in heavier atoms. So when the snow will start falling, it will be containing the least numbers of heavier atoms.
The snow will settle down. Future years will bring more snow, thus snowflakes shall begin to compact at the lower layers. Snowflakes contain roughly 80% air. After compaction, the air will be expelled and firn will form having only about 20% air. Ultimately lowest layers shall become ice containing only 2% air or less. Layer upon layer will build.
The snow precipitated in the relatively warmer climates shall have more heavier oxygen than the snow precipitated in cooler climates. This phenomena is used to measure the temperature at which a particular layer was deposited. This provides a tool for temperature records in the history of the earth.
For this purpose, scientists take out the continuous cylindrical cores of the ice and measure the abundance of heavier oxygen atoms relative to the lighter ones using ratio recording mass spectrometer and plot this against depth. From the calibration curves with temperature, scientists are able to measure the temperature records.
Knowing the past climatic history of the earth can help in understanding the ice ages epochs, chemical and biological reactions and thus the abundance or otherwise of minerals like petroleum.
Thus the ice deposited over millions of years preserves the memories of the climate in the past. They have been able to recreate the 4 million years record of temperatures.

Our Body is a Wonder Machine

Photosynthesis is the process by which plants make two essential things on which the very survival of animals is hinged. These are namely a sugar called Glucose and oxygen. In the beginning oxygen was a poison to many microbes. But since it was a question of survive or perish, slowly they adapted to respiration using oxygen. Those which could not change receded to great depth where oxygen cannot reach.

Glucose is a like a charged battery which stores energy. Where does this energy come from? Obviously it is the Sun on which the life on the Earth is based upon. Plants use carbon dioxide and water and a mediator called chlorophyll to make glucose and oxygen. Anyone familiar with thermodynamics knows that this reaction is not favorable as its overall Gibbs free energy is positive. Second law of thermodynamics requires that only those reactions are spontaneous for which this energy change is negative. In simple words the energy of products should be lower than that of reactants. Here the energy content of the products is higher by 2880 Kilo Joules per mole. It is the Sun who provides this energy and plants store it in the glucose.

Many of the reactions that take place in living organisms require a source of free energy to drive them. The immediate source of this energy in heterotrophic organisms, which include animals, fungi, and most bacteria, is the sugar glucose. Now reverse reaction that is the oxidation of glucose to carbon dioxide and water takes place when animals consume glucose and oxygen. Thus 2880 KJ/mole energy is liberated.

Of course it would not do to simply “burn” the glucose in the normal way; the energy change would be wasted as heat, and rather too quickly for the well-being of the organism! Effective utilization of this free energy requires a means of capturing it from the glucose and then releasing it in small amounts when and where it is needed. This is accomplished by breaking down the glucose in a series of a dozen or more steps in which the energy liberated in each stage is captured by an “energy carrier” molecule, of which the most important is adenosine diphosphate, known shortly as ADP. At each step in the breakdown of glucose, an ADP molecule reacts with inorganic phosphate and changes into adenosine triphosphate ATP

The 30 kJ mol–1 of free energy stored in each ATP molecule is released when the molecule travels to a site where it is needed and loses one of its phosphate groups, yielding inorganic phosphate and ADP, which eventually finds its way back the site of glucose metabolism for recycling back into ATP. The complete breakdown of one molecule of glucose is coupled with the production of 38 molecules of ATP according to the overall reaction

For each mole of glucose metabolized, 38 × (30 kJ) = 1140 kJ of free energy is captured as ATP, representing an energy efficiency of 1140/2880 = 0.4. That is, 40% of the free energy obtainable from the oxidation of glucose is made available to drive other metabolic processes. The rest is liberated as heat.

Stomatal Index and Level of Carbondioxide in Atmosphere

There was a time when things started rolling on with advent of photosynthesis by cyano-bacteria or green algae which began preparing its food from carbon dioxide and water which were the only substances available in plenty. They paved the way for introduction of oxygen into the atmosphere and for beginning of life dependent on oxygen.

In fact, both the products made by photosynthesis namely sugar and oxygen are used by animals including humans for sustaining their life. We animals are thus the species who learned to make use of the leg work of others to their own advantage. Of course, in today’s world, human beings who do this are termed smarter than the others.

So what the plants and algae used for making their food is being recycled back to the atmosphere in the form of green house gases. Plants use CO2 and H2O and took energy from the Sun to convert these to sugars and animals extract that energy from the food synthesized by plants and algae and return the CO2 and H2O back to the atmosphere.

CO2 is in fact one of the end products of burning the fossil fuels like coal and petroleum which are the preserved forms of energy of Sun due to being buried away from the reach of oxygen. Since all industrial activities use extensively these fuels, levels of CO2 are rising in the atmosphere to alarming levels.

Trees breathe the CO2 through the stomatal pores present in their leaves. They also lose the water through these pores during the day. They are smart enough to adjust the size of their leaves so as to optimize the intake of CO2 and loss of H2O for proper growth.

One such tree was born in 1948 in a isolated place on the edge of a pit 30 kilometers from Dutch city called Eindhoven. By 1990 it was a big majestic tree as most of the Birch family trees are. Scientists from the laboratory of Paleo-botany and Palynology named it fondly “Big Betty”.

During each autumn, the tree will shed a carpet of dry leaves into the pit. So layer after layer is deposited inside the pit. But scientists noticed a peculiar thing about the leave size. Each year the leave size began becoming smaller thus reducing the stomatal index. This was due to the fact that as levels of CO2 rose, the tree needed fewer number of stomata to inhale the same quantity as required and thus avoided the undue loss of moisture from the leaves. In fact when the levels of CO2 were plotted against the stomatal indices of leaves over these years, they matched the patterns of levels of CO2 variations. So the stomatal index was used to calibrate and interpolate the results to guess the levels of CO2 in the past.

Blood: Our lifeline

Blood is the lifeline of bodies. It performs the vital functions to keep our body healthy. It is vehicle for transporting the oxygen which we breathe to the individual cells without which they will perish. Oxygen is bound to the iron present in the red blood cells and the metalloprotein is called hemoglobin. It also collects the resultant carbon dioxide to bring it back to the respiratory organs to be dispensed from the organism.

English: Two drops of blood are shown with a b...

When the supply of oxygen to the body is low at high altitudes, you can see the reddish spots in the cheeks of many people because the blood is not called upon to carry proper amounts of oxygen, some of it stays in the cheeks.

English: Animation of hemoglobin t-r state tra...

Second important component of the blood is white cells. These cells protect us from the infections. Third important component is the platelets. These along with some proteins and vitamin K help in forming the blood clots to stop the loss of blood when we are wounded. White cells also aid in the wound healing because there are bacteria lurking to infect the wound. Interestingly, some particular strains of the dreaded E.Coli bacteria which inhabits our body synthesize vitamin K which our bodies cannot synthesize themselves.

All blood cells are made within your bone marrow. Stem cells exist inside the marrow and can form into red blood cells, white blood cells, platelets and more stem cells. Leukemia is cancer that relates to abnormal cell production in the bone marrow. One form of treatment involves replacing some of the bone marrow with healthy bone marrow.

Remember some fun facts about blood. There is no substitute for blood. Red blood cells live about 120 days. Plasma, which is 90 percent water, is a pale yellow mixture of water, proteins and salts. Thirteen tests are performed on donated blood, 11 are for infectious disease. Newborn baby has about one cup of blood in his or her body.

Simply Mind Boggling

Scientists speculate that all the fundamental particles were created from the energy immediately after the Big Bang event in which Universe was formed. Then these atoms combined in different permutations and combinations and molecules were born. Context of immediately in the cosmic events is not similar to the usual terms with which define our world. It may be millions of years.

Earth was formed but its climate was not like the present day. There was no life except one algae namely “Blue Algae” known in the scientific language as “Cyanobacteria” where “Cyano” stands for blue color. It thrived in the water which occupied 70% surface of the Earth. All around in the atmosphere was carbondioxide and metals existed in the solution form because there was no oxygen to react with them and precipitate them as ores. Iron was the most abundant of them. So this was the scene about 3.5 billions of years ago.

How did these small living beings sustain themselves? Where from did they get the energy? .

They developed the photosynthesis and harvested the energy of Sun. They also did much of the chemistry which resulted in critically changing the composition of gases in the atmosphere. They learned to break the water molecules into hydrogen and oxygen. They then used the hydrogen along with carbon dioxide to make carbohydrates which are the store house of energy. The oxygen gas which was generated was very reactive and reacted with the metal ions especially iron species and got fixed up and ores were formed. This went on for millions of years. Iron acted as a perfect sink for oxygen which was poison for these bacteria themselves because they thrived in the anaerobic conditions.

But a stage reached when no more free iron ions were available. So the concentration of oxygen began building up in the atmosphere and setting a stage in which the new species of life which use oxygen for breathing to evolve. The life started in the real earnest. The oxygen content stabilized at about 20% by volume in the air. Carbon dioxide has very small percentage. So these humble microbes were responsible for the life as we see today on this Earth.

The algae learned to live with the existing conditions.

How big is the cyanobacteria? It has been estimated that its diameter is about 2 microns if we consider it as a sphere which it is not. But for the sake of simplicity and bring home the point as is done in all the scientific inquiry let us assume that. Such a small size !! But is it really small in comparison to the smaller things nature can go to. Let us compare it to the size of carbon atom. If we calculate the volume of bacteria and volume of carbon atom, and calculate how many atoms of carbon can fit into the bacteria, you shall be surprised that a mind boggling 1000000000000 atoms is the answer. You are in for more surprise if you go down to fundamental particles like electrons and leptons.

So this is the scale at which the machinery of the Nature works. On one side are the atomic sized particles and on the other are gigantic stars. But one thing is sure that at the base of everything are the fundamental particles. It is also a fact that things behave very differently on the different scale levels. Electrons can behave as particles under one set of conditions and as a wave in the diffraction experiments. Or they may be behaving as they are but with our existing knowledge  we try to explain the things the way which give reasonable answers.

So let us salute to the “Cyanobacteria” to create favorable conditions for the existing worlds to forms and initiation of the diverse kinds of species on this Earth.

The Mighty Microbes

Microbes may be very small in size but their sheer numbers and remarkable adaptability to the existing climates is astounding. The word microbe is derived from micro-organisms meaning they are so small that they can be seen with the help of a microscope. But these tiny organisms are so active that they can bring about mammoth changes into the environment in which they live.

When the earth first formed, the atmosphere consisted of carbon dioxide and water. Due to this iron existed in the soluble ionic forms in the water. And also there was organic matter. But in the water lived the earliest bacteria called cyanobacteria which were the first photo synthesizers. They combined carbon dioxide and water using sunlight and turned it into their food. Oxygen was the byproduct of this process. Then why did we said there was no free oxygen in the atmosphere and anaerobic conditions existed. Sure oxygen was produced but hungry sinks for it readily available. Iron in the ionic form immediately captured the produced oxygen and got precipitated and iron ore. Similarly organic matter acquired its share of oxygen.Thus all the iron ore we see on the earth is the handiwork of microbes.

Slowly and slowly, all the available iron was precipitated. Now nothing was there to capture the free oxygen and over the period of time, atmosphere was enriched with oxygen. This free oxygen was poison to many microbes which were adapted to conditions devoid of oxygen. Thus they were exterminated. But as we said in the beginning, some of them got buried deep along with organic matter and survived.

It has been reported that amongst these microbe consortia exist a class which uses carbon dioxide and hydrogen to synthesize methane gas. So far it was thought that methane was produced under aerobic conditions but evidence now indicates to the anaerobic bacteria. These bacteria are the terminal stage actors. Before them are a variety of other bacteria which breakdown the organic matter and provide carbondioxide and hydrogen to these bacteria.

The methane in the gas hydrates which hold the promise to solve the energy requirements of the ever hungry industrial world is formed by these microbes and has been trapped in the ice lattices in the form of clathrate compounds which are nothing but cages formed by the water molecule and methane is trapped inside. These bacteria are thought to be starved for food and are ready to pounce on the reactants as soon as they are available.

Microbes are thus omnipresent and affect the life on our planet since the life began with them.

The story of H2O Molecule

I am a molecule of water. Hydrogen and Oxygen are two elements which combine in the ratio of 2 to 1 to create me. I have abundant siblings on the earth. In fact we make up for about 70% of the earth. I am so small that I can enter into smallest of spaces. My birth place is in the space. We all are so identical that it is impossible to label us with names. We all have only one name and that is water. there are species called homo sapiens  After birth I along with my other brothers began living in a place which people started calling the seas. In the beginning we all lived in one place but many upheavals separated us and we were divided into many parts.

We are always in the ceaseless state of movement. Never had time to rest. We chase each other, collide with each other and collide with surroundings. Some of us move and dance faster than others. When the agile ones get tired, they slow down and hand over the baton to sluggards who in turn become agile. But we are bound to each other. But when the Sun is angry and it is hot, some of us are thrown out from the sea and fly up and up. Then we float aimlessly in the atmosphere. We wander from here and there. But we again come together at places which are cool such as above the mountains and rich vegetation. We join one another so tightly that we cannot remain afloat. We begin to fall towards earth.

So of us fall on the mountains where temperatures are so low that we become hibernated and enter a deeper and longer sleep. Others fall directly on the earth where they flow collectively as one body and travels from high altitudes to low altitudes. Some of us are very curious and collect inside the depression and become confined there for very long periods.  Other more adventurous even penetrate the earth and go deep inside it and remain there for thousands of years. During our journey on the land we take with us members of other communities which disintegrate inside us into their individual entities. Some of us joined on the way with others become a mammoth creature called the river and flow towards our home at sea. It can take us 2 to 6 months time for reaching back.

Our brothers in the confined places called lakes and ponds have to wait  much much longer to reach home. When Sun smiles benignly on them, some of us again escape into the atmosphere and if lucky go back either falling directly into the sea or falling again on the earth and joining the other which have already begun their journey towards home in the form of river.