Tag Archives: Carbon dioxide

Energy efficiency of human machine

Living organisms require energy for every activity they perform. As I am keying in from the keyboard, energy is being used for movement of fingers, thought and coordination processes running in the brain. The immediate source of this energy in heterotrophic organisms, which include animals, fungi, and most bacteria, is the sugar glucose. Glucose is oxidized into carbon dioxide and water with the help of inhaled oxygen and in the process 2880 KJ/mol energy is released.

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.

Mechanism of breakdown of glucose occurs in controlled manner 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 as ADP. At each step in the breakdown of glucose, an ADP molecule reacts with inorganic phosphate and changes into ATP. Each such step require 30 kJ/mol

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.

Where does the glucose come from? Animals obtain their glucose from their food, especially cellulose and starches that, like glucose have similar skeletal structure. Animals obtain this food by eating plants or other animals. Ultimately, all food comes from plants, most of which are able to make their own glucose from CO2 and H2O through the process of photosynthesis.

This describes aerobic respiration, which evolved after the development of photosynthetic life on Earth began to raise the concentration of atmospheric oxygen. Oxygen is a poison to most life processes at the cellular level, and it is believed that aerobic respiration developed as a means to protect organisms from this peril. Those that did not adapt have literally to deep down strata where oxygen cannot reach. These organism constitute the more primitive anaerobic bacteria.

The function of oxygen in respiration is to serve as an acceptor of the electrons that glucose loses when it undergoes oxidation. Other electron acceptors can fulfill the same function when oxygen is not available, but none yields nearly as much free energy. For example, if oxygen cannot be supplied to mammalian muscle cells as rapidly as it is needed, they switch over to an anaerobic process yielding lactic acid instead of CO2. In this process, only (2 × 30 kJ/mol) = 60 kJ/mol of free energy is captured, so the efficiency is only 28% on the basis of this reaction, and it is even lower in relation to glucose. In “aerobic” exercising, one tries to maintain sufficient lung capacity and cardiac output to supply oxygen to muscle cells at a rate that promotes the aerobic pathway.


Bread: Most Basic Necessity

One’s “Bread and Butter” means the major occupation which provides him the sustenance for life. “breaking bread” is a community custom which is sharing the food and sitting together. It is thus more than eating but a way to bring the members of a community closer to one another. The importance of bread cannot be overemphasized. Primitive man was a nomad and it was the wheat grass for which womenfolk are credited to have grown, which gave the man a reason to stay put at a place and bring the stability in the life which was almost akin to animals. It provided him with spare time in which to hone his skills and rise above the animals. When he discovered the fire, he learned to cook and roast and thus bread must have been discovered.

From Chinese baozi to Armenian lavash, bread comes in thousands of forms. But the basic ingredients are same world over: milled grains and water.

Imagine a continuum of breads, ranging from the thinnest flat breads to the fluffiest brioche. Some are amazingly simple: Matzoh, for example, is nothing more than flour and water, baked until crisp. Raised breads, on the other hand, involve the complex interactions between flour and the leaveners that give them their porous, tender quality.

Leaveners come in two main forms: baking powder or soda and yeast.

Baking powder or baking soda is used for faster results as it is based on the chemical reactions of the soda with acidic substances present or released during heating and resulted in the production of carbon dioxide necessary to inflate dough or batter. Baking powder and baking soda are used to leaven baked goods that have a delicate structure, ones that rise quickly as carbon dioxide is produced, such as quick breads like cornbread and biscuits.

Yeast, on the other hand, is a live, single-celled fungus. There are about 160 species of yeast, and many of them live all around us. It is stored in the optimum conditions and activated by availability of sugars present in the milled grains. They release carbon dioxide which makes the bread rise. The reactions are slow in comparison to the baking soda.

Leavening will make the bubbles for sure but some structure is required to contain these bubble and stop them from leaving. This is done by glutton which forms a three dimensional network and trap the produced carbon dioxide. Besides this there is plenty of starch present in the grains. This is attacked by enzymes which break it into the sugars, the food for the yeast to consume and release carbon dioxide and also help absorb the moisture. This is the chemistry behind making of the bread.

Is there life on Mars? Again Microbes hold the key

Earliest life of single cell evolved into 3 branches having distinct traits. The branches further subdivide into more branches on the evolutionary tree of life called Phylogenetic tree of life. The first three branches are called Bacteria, archaea and Eucaryota.


As we can see in this tree, there is a member of archaea family with the name Methanogen. This microbe holds the answer for presence of vast quantities of methane which is trapped inside the ice cages called methane hydrates. These hydrates are found on Earth in the permafrost regions having very low temperatures or under the deep sea floor. Water molecules arrange themselves into octahedral cubes in which molecules of many compounds can fit into them. These are called clathrate compounds. These structures are very fragile and as soon as the overhead pressure is reduced or temperature increases, the structure crumbles and gas is released. So special technology is required to produce the methane from hydrates. In US, carbon dioxide was pumped into the hydrate layer. It substituted into the cages releasing the methane free. It served two important purposes. First the production of fuel gas methane and sequestration of unwanted carbon dioxide. These microbes use carbon dioxide and hydrogen to make their food and also generate methane and water. These microbes are very enterprising. They can use alternative sources of carbon like acetates which are the products formed by another kind of bacteria by breaking the macro-molecules present in the buried organic matter, for their food. One thing these tiny beings hate is oxygen. They work in anaerobic environments like deep buried locations.

Now this microbe is being held responsible for the methane gas found on Mars indicating that there is life on the planet. It means Mars is not a dead planet. Professor James Kasting said if there is anything alive on Mars at this time in its history, it would probably be some form of microbial life living deep beneath the planet’s surface. Perhaps the most likely form of microbial life is a type of bacteria known as methanogenic bacteria, or methanogens for short. The CO2 needed by the methanogens could presumably come from the atmosphere. The H2 could come from chemical reactions between water and certain types of rocks, specifically magnesium- and iron-rich basalts. Such rocks are found on certain parts of the seafloor today on Earth. When they react with water, they form minerals called serpentine minerals. In the process, hydrogen is produced. The reaction that produces methane is thermodynamically favorable, so Methanogens could use the energy released by this reaction to drive their metabolism. Microbes can make many reactions happen at much lower temperature by changing the path of reactions through enzyme catalysts which these microbes synthesize.

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.

Bacteria in Oilfields

Bacteria can thrive on almost anything and adapt themselves to very diverse environments. They can eat subsist on substances like cellulose which we humans cannot assimilate. They can breakdown poisonous gases like hydrogen sulfide and absorb nitrogen from atmosphere and fix them into the roots of many plants which plants use as fertilizer.

Bacteria can even breakdown crude oil. Crude oil consists of millions of hydrocarbons which are composed from carbon and hydrogen. These compounds range from the simplest molecule called methane made from 1 carbon atom to giant molecules containing even more than 50 carbon atoms.

Many of these bacteria live in the upper crust of the soil. They have attained the capability to use lighter hydrocarbon gases namely methane, ethane, propane and also the higher molecular hydrocarbons as the source of the carbon nutrient for energy. These are called aerobic bacteria and commonly termed as methanotrophs, propanotrophs and so on. They use like us the atmospheric oxygen to oxidize the hydrocarbons and end result is energy, carbon dioxide and water, the same products as are generated during the digestion of food by us. Of course, they also need so many other nutrients like electrolytes, trace elements which they use to synthesize enzymes which help in carrying out degradation reactions at much lower temperatures.

But this is not the end of story. There are bacteria which can survive in the anoxic (without oxygen) environment such as deeply buried bacteria which breakdown the organic matter. They extract the oxygen required to breakdown the organic matter from the sulfate ions present in the water associated with the organic matter. They breakdown the organic matter to methane and one strain of them is aptly called methanogens.

One may wonder if such bacteria exist deep down and breakdown the oil why have they eaten up all the oil present inside the reservoirs. The answer is that they are sloths in nature. They multiply with speeds nowhere near to the aerobic bacteria. Experimenters working in proliferating and separating the pure strains are often frustrated with there laziness.

The hypothesis that all the biogenic gas has been produced by aerobic bacteria is being challenged because biogenic gas has been found in the deeper sediments generated under anaerobic conditions. Researchers say that the methane trapped inside the ice crystals called gas hydrates has been the handiwork of methanogens.

Algae: A machine to make energy

In the beginning there was carbon dioxide, water and sunlight on our Earth and its environment. The same carbon dioxide which is the end product of today’s industrial processes. The factories spew carbon dioxide. Scientists are finding ways to fix this carbon dioxide which is the major cause of greenhouse effect and results in trapping the heat and disallows it dissipate and result in Global warming.

Whereas in the present climate living beings mostly use oxygen to breakup the food and convert it to glucose and energy, in the beginning only organism that thrived on carbon dioxide was called green algae. It mastered the art of harvesting sunlight by a process called photosynthesis in which it converted the freely available carbon dioxide and water into glucose which it used as food. But along with the glucose, another product was formed which we call oxygen and cannot live without.

Now the families of these algae, again seem to be rescuing us from the crisis of energy. The mineral oil and coal, major sources of energy are not inexhaustible and considering there rate of consumption, there is a concern to find the alternate sources of energy. One example is ethanol manufacturing from the corn.

Algae is holding the promise to save us again. The green covering on the ponds looks very unattractive but these tiny globules contain lipids which can be converted into the biofuels. Some of these also contain hydrocarbons. These algae sequester the carbon dioxide infused into the environment and helps cleaning the atmosphere.

At this stage, efforts are on to increase the yield of biomass and make it commercially viable. For this favorable conditions are being created to grow the algae into the open ponds where yield shall be more due to availability of sunlight also. Algae is attacked by some aquatic species called rotifers. Efforts are on to create the media which shall do away with all these problems.

Besides the energy in the form of lipids, there are algae which are excellent diet supplement because they contain a myriad number of minerals and proteins. One such algae is spirulina which is very popular among the people who want to become slim by shedding the weight.

Eggs: A concoction of Chemicals

Chicken eggs are convenient food item. It is easy to make a number of recipes. They can be scrambled, boiled, fried, or poached. Eggs are used in custards and cakes and so many other confectioneries. The versatility of eggs is a reflection of their intricate chemical makeup. Eggs contain a big list of chemicals including proteins, fats, vitamins, minerals, and water.

We wrongly think that eggshells are impervious. Eggs do have holes. A single eggshell is perforated by 9,000 pores, on average. The shell forms the egg’s container, protecting it and acting as a permeable membrane for air and moisture to pass through.

Eggshell is made mainly of calcium carbonate which is chemical insoluble in water and is also major constituent of limestone. Calcium carbonate content is about 95% and rest  5% is a mix of other minerals, such as calcium phosphate and magnesium carbonate, as well as soluble and insoluble proteins. These components strongly influence the strength of the shell. A hen on a diet low in calcium or vitamin D, for example, lays eggs having thin, soft shells, or no shells at all.

Generally the shell of egg is white or brown but chickens lay eggs of other colors, from pink to green to blue. The colors of eggs come from pigments that are secreted by the hen and deposited on the eggshell’s outer layers during formation in the chicken’s oviduct, the canal that eggs travel through from the ovaries to the outside world. Egg color is a genetic trait, so colors vary from breed to breed. Brown eggshells contain the pigment protoporphyrin, a breakdown product of hemoglobin. Found only on the shell’s surface, the brown pigment can be dissolved by vinegar or rubbed off with sandpaper. Blue and green hues are caused by the pigment oocyanin, a by-product of bile formation. White eggshells are devoid of these pigments.

Surrounded by the eggshell, the slimy, clear fluid of the egg is the albumen, or egg white—the egg’s cytoplasm. It consists of 90% water, seven major proteins, and no fat. Main protein present in the albumen is called ovalbumin and it accounts for 54% of the white.

In a fresh egg, the albumen contains carbon dioxide, which diffuses out of the egg as it ages. With the loss of CO2, the egg white becomes more alkaline and thins. Because of CO2 loss through the shell pores, an egg a few weeks old will be easier to peel after boiling than a fresh egg with a higher CO2 concentration, although the cause of this phenomenon isn’t completely understood.

Yolk makes up one-third of the egg’s weight,  is the near-opposite of albumen in chemical composition. It contains all of the egg’s fat and cholesterol, half of its protein, and four times the calories of the white. A yolk’s golden yellow color is due to the diet of the hen. A diet rich in the yellow and orange plant pigments called xanthophylls leads to a yellow yolk. If the hen’s diet is low in these pigments, the yolk can be almost colorless.

Yolks contain all of the vitamin content in the egg, including six B vitamins, as well as vitamins A, D, and E. The yolk also contains the antioxidants lutein and zeaxanthin and trace amounts of β-carotene, phosphorus, iron, magnesium, and other metals.

The freshness of an egg can be determined from the appearance of its yolk. A fresh egg has a round, firm yolk and a tight surrounding membrane, called the vitelline membrane. As the egg ages, the yolk absorbs water from the albumen, which distends the membrane and results in a looser, flattened yolk.

The greenish gray ring that can form around the yolk of a boiled egg comes from overcooking. The iron and sulfur in the yolk form ferrous sulfides, creating the green ring at the yolk’s surface. Although the color is unappealing, the research proves that the ring does not affect an egg’s flavor and nutritional content.

Contributing to an egg’s normal odor are a number of volatile constituents, including hydrocarbons, phenols, indans, indoles, pyrroles, pyrazines, and sulfides, including hydrogen sulfide. Dimethyl sulfide and dimethyl trisulfide in small amounts contribute to the characteristic odor and flavor of eggs, even fresh ones.

A truly rotten egg is formed when bacteria penetrate the shell and produce foul-smelling hydrogen sulfide.

The complexity of eggs puts them in the spotlight of health debates. Although eggs are high in protein and vitamins and low in fat and sugar, they’re heavy on cholesterol, which could raise a person’s risk of heart disease. An egg can contain up to 250 mg of cholesterol, which is 83% of the U.S. recommended daily allowance of 300 mg.

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.

Chemistry by Nature

Nature is a great chemist. It synthesizes millions of compounds every moment ranging from simple molecules like methane to very complex molecules like carbohydrates, cellulose and proteins. Most of these compounds are synthesized by plants. From the plants they are passed on to animals because the animals cannot synthesize their food by themselves. But there are many chemical reactions occurring inside the cells like breaking down the complex molecules and unlocking the energy which is stored in them.

Where does all the energy locked inside the different molecules come from? Most of it is derived from the Sun light. In many cultures like Hindus and Egyptians, Sun is worshiped as the harbinger of life. They may not be knowing the scientific facts behind it. Energy tries to dissipate and some storage is required to held it at one place and use it whenever required. Cells are the prime example.

How do the plants get hold of the energy. They carry out a reaction called photosynthesis in which they combine carbon dioxide and water in the presence of sunlight. All this work is done with the help of a big organic molecule called Chlorophyll. The products of this reaction are sugar and oxygen. When human beings consume the sugar, they break it down again to carbon dioxide and water and energy absorbed from the sun is unlocked and nourishes our bodies.

This reaction is a fuel burning reaction. But unlike the burning of fuels it happens at a very low temperature (body temperature) in our bodies although both reactions are exothermic in nature. How is this achieved? First of all, only those reactions are possible which results in products having lower energy than the reactants. But to initiate the reaction, the system has to cross a energy hill called energy of activation.

Catalysts are capable of making the reactions occur at low temperatures because they lower the energy of activation. In our bodies there are specialized proteins which are called enzymes which act as catalysts. These are very specific and one enzyme is specialized for only one task.

Catalysts also determine the kind of product that is synthesized. For example, the hydrogenation of unsaturated oils can be carried out by reaction with hydrogen. In the case of using a catalyst, only cis addition to the double bond is allowed whereas without catalyst in addition to elevated temperature and pressure conditions, the product formed is a mixture of both cis and trans products.

Since in the nature most of the reactions are carried out at ambient conditions, enzymes are generally utilized by the nature. In the case of molecules having asymmetric carbon centres a mixture of 50:50 ratio is produced without enzymes. These are called stereo-isomers and rotate the light in left and right direction. But in nature only one of these forms is synthesized. After all animals consume only one form of stereoisomers.

So nature is a great chemist.