Elements necessary for humans

At present there are 118 elements listed in the periodic table. Some of these elements are commonly found on the earth in the form of ores. Some are radioactive and have very short half lives. Many such elements have been synthesized in the laboratory and live for a very short time.

Human body like other things existing is made of compounds which are made from the elements. Out of these 118 only some elements are connected with the human body.

Although elements as such don’t make up the body it is the combined form that is molecules constitute the human body. But elemental composition is as follows by mass.

Oxygen: 65%

Carbon: 18%

Hydrogen: 10%

Nitrogen: 3%

Other elements: 4%

Other elements include Calcium, Potassium, Phosphorus, Sulphur, Sodium, Chlorine, Magnesium, Boron, Chromium, Cobalt, Copper,  Fluorine, Iodine, Iron, Manganese, Molybdenum, Selenium, Silicon, Tin, Vanadium and Zinc.

Although these elements are used in very minor amount, they are crucial to some body processes.

Elements can be divided into different groups according to the functions they perform.

Building Blocks

The main building blocks of the body are proteins which are synthesized from amino acids. For these elements used are Hydrogen, Carbon, Nitrogen, Oxygen, Phosphorus and Sulphur. DNA also contains these elements except Sulphur. DNA is the genetic code.

Enzymes

Enzymes are chemicals which are catalysts for carrying out chemical reactions like breakdown of sugars and other macro molecules. Such enzymes use some elements like Magnesium, Manganese, Copper, Zinc, Selenium and Molybdenum. Enzymes play role in respiration, digestion, metabolism and immune system.

Nerves and Control

Brain sends messages to different parts of the body and this is a two way communication. Electrical signals are carried through electrolytic solutions like brines. Sodium, Potassium and Calcium ions this play the role of transmitting the signals. Similarly Chloride ions regulate the water in and out of cells. Iodine is used to make hormones which regulate metabolism.

Bones and Teeth

Bones make the template on which our body is hoisted. Strong bones and teeth are essential for the healthy body.  Bones and Teeth are made of Calcium and phosphate. Phosphate contains Phosphorus and Oxygen. Manganese element makes more stronger and resistance to breaking.

Blood

Blood is the lifeline of the body. Blood carries oxygen to the cells and removes the carbon-dioxide gas which is the byproduct of combustion reaction. Oxygen is carried by blood due to the presence of iron which binds the Oxygen. Other elements which are constituents of blood are Carbon, Oxygen, Iron and Cobalt. Cobalt is essential to make red blood cells.

Respiration and Energy

Respiration is inhalation of Oxygen. Adinosine Triphosphate (ATP) is formed during respiration which is the compound used by body as energy. Main elements involved here are Carbon, Nitrogen, Phosphorus and Oxygen.

Source: c&en magazine of American Chemical Society (ACS)

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Concept of pH in Chemistry

Although the pH of a lake or polluted stream is seldom reported in the media, the people who are monitoring the health of the lake water record it daily religiously. But pH is quite an important physical property of water. pH of a stream gives an indication about the salts and other soluble matter present in the water. These soluble salts affect the organisms living in the water. Also changing pH in a stream can be an indicator of increasing pollution or some other environmental factor.

As we know life on our planet is based on the water. Water is a unique solvent as it dissolves a number of chemicals in it. Water molecule is a simple one with H2O as its formula indicating 2 hydrogen atoms joined to 1 oxygen atom. It V shaped geometry imparts it high polarity with which it is able to break down many salt molecules into individual ions called cations and anions. As such water is slightly ionized into equivalent amounts of hydrogen and hydroxyl ions. The value is 10-07 equivalents, a very very tiny value indeed. But this small value is enough to do all the chemistry. When chemicals dissolve in it, the values of hydrogen and hydroxyl ions become unequal. Particularly when any compound containing hydrogen ions is added to water, hydrogen ions become predominant and solution is said to become acidic and such chemicals are called acids. Examples of acids are hydrochloric acid, nitric acid, citric acid and sulphuric acid. On the other hand, when any chemical which have hydroxyl ions is added to water, hydroxyl ions predominate and water becomes basic and such chemicals are called bases.  Examples of bases are sodium hydroxide, washing soda and potassium hydroxide.

pH is a measure of how acidic/basic water is. It is defined as the minus logarithm of hydrogen ions concentration. Since -log[10-07] is 7, the pH of pure water is 7. The range goes from 0-14. Any solution having pH value less than 7 is acidic and above 7 is basic in nature.

The pH of any natural water determines availability of nutrients like phosphorus, nitrogen, and carbon for aquatic life. Many nutrients like phosphorous are very sensitive to pH since it exists in different forms at different pH values. Only a particualr form is assimilated by the organism.

Similarly, pH determines the solubility of heavy metals which are generally toxic in nature. Heavy metals are generally more soluble at lower pH and hence lower pH gives a warning about the possibility of these heavier and poisonous metals.

pH of Battery acid is 1, vinegar is about 3, milk slightly above 6, baking soda between 8 and 9 & ammonia solution about 12.Diagram of pH. pH 1=battery acid, 2=lemon juice, 3-vinegar, 6.5=milk, 8.5=baking soda, sea water, 10.5=Milk of Magnesia, 12=ammonia, 13=lye. ph 3 to 4=Adult fish die. ph 4-5=Fish reproductionaffected. pH 5-6.5=Normal range for precipitat on. pH 6-8=Normal range of stream pH. pH 1-5=Acid rain.

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.

450px-Phylogenetic_tree

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.

Antoine Laurent Lavoisier: Father of Modern Chemistry

Antoine Lavoisier, son of a wealthy lawyer,  was a social climber, tax collector and widely held to be the founder of modern chemistry. He was born in 1743 and was put to guillotine in 1794 on the charges of selling the adulterated tobacco which was a luxury and was very costly. It came from colonies in South America established by Europeans and employed black people as captives.

Antoine-Laurent Lavoisier and His Wife (Marie-...

He discovered oxygen gas and named it so. Joseph Priestly, English scientist had also discovered this gas but named it “dephlogisticated air“. Both knew that the gas was closely associated with combustion in or around 1774. Priestly even demonstrated the synthesis of the gas by heating the mercury oxide with focused sun rays before Lavoisier when the former was a guest of the latter’s family on a tour to France. After some time of this event, Lavoisier also synthesized oxygen by an entirely different method.

He also demonstrated that water which was considered an element to be made of two elements oxygen and hydrogen. He devised a very brilliant method to split the water into

Chem ical ex pe ri ments in In tro duc tion to...
Chem ical ex pe ri ments in In tro duc tion to Chem istry (Seimi Kaisō). (Photo credit: Wikipedia)

its forming elements. The water was boiled and steam was passed through a coiled pipe made of iron. The box containing the coil was joined to another pipe which was dipped into the water at other end.The steam reacted with iron forming oxide thus subtracting the oxygen from water. Another component, namely Hydrogen, went out and bubbled through water and was collected by displacement above water.

Similarly he showed that air which again was considered an element was in fact a mixture of gases.

He is credited with starting the nomenclature of the elements known during his time. He even put the heat also among the elements list. He is thus responsible for initiating the process of documentation of chemsitry.

His another great achievement was what is now known as Stochiometry in chemistry. It is in a way is conservation of mass. He decomposed the salts of known weight and weighed the products and found that total amount remains the same. This audit of the mass has been responsible for the discovery of new compounds and elements and research chemists regularly make use of the this technique to pinpoint the missing mass.

Such a great scientist met with a very sad end. He was hanged when he was barely 50 years old.

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.

Cyclohexane: A Chemical Chair

Cyclohexane belongs to the category of hydrocarbons called naphthenes. It has a chemical formula of C6H12. Naphthenes are found in crude oil. Most abundant are mono ring compounds of which cyclohexane is the perfect example. In fact, the poly ring naphthenes are found in the high boiling fractions of naphtha and the name seems to have been derived from naphtha. The term Naphthene has become almost redundant except in petroleum industry.The other fractions present in the crude oil are paraffins which are long chain alkanes  with formula CnH2n+1. For example, when n=6, then we have hexane with formula C6H14. High molecular weight paraffins are the main constituents of waxes. Another important category of compounds present in the crude oil is called aromatics. The most celebrated and simplest molecule of the category is Benzene with chemical formula C6H6. The overall properties of crude oil depend on the relative amounts of these fractions.

So, we observe that normal hexane, cyclohexane and benzene have six carbons but number of hydrogen atoms go on decreasing while going from paraffins to aromatics. This indicates that we are progressing towards graphite with the loss of hydrogen atoms. Crude oils derived from the marine sources are lighter in nature meaning they have lesser amounts of waxy paraffins. This helps them to be lighter and survive in under sea hydrostatic pressure. On the other hand, plants in the arid climates have wax on their leaves which helps in the prevention of moisture evaporation and is absolutely necessary for the survival of plants under harsh conditions. Thus the crude derived from terrestrial plants have higher wax content.

Anyway, we come to cyclohexane. The carbon atoms try to have tetrahedral geometry around them when combining to 4 atoms. But this is not possible here. So they settle for a compromise for stability. Cyclohexane twists to have a shape like a chair with alternate carbons in two parallel planes and hydrogen atoms arranged in two directions. They are in positions called axial and equatorial positions with axial hydrogen atoms almost perpendicular to the carbon atoms plane with alternating up and down positions.

How was this structure confirmed? It was confirmed by using the tool called Nuclear Magnetic Resonance (NMR) which is used these days in the medical science under the name of MRI. The protons  (hydrogen atoms) behave like tiny magnets and spin around their axis. As we know from the magnets, when we place a small magnet near a strong magnet, smaller one aligns itself along the axis of stronger magnet. Energy is required to flip it back to its original position. Thus the principle of NMR is that molecules are placed in a powerful magnetic field and swept with electromagnetic energy. This will be of no useful tool if all the hydrogen atoms absorb the energy at same wavelength. Fortunately, the magnetic moments of hydrogen atoms are modified by the electronic environment around it a molecule which may be due to the presence of hetero atoms and groups or different number of groups. Thus due to the different environment, the hydrogen atoms absorb energy at different wavelengths. From this we come to know the chemical environment of different hydrogen atoms and thus elucidate its structure. In our brain, we have so many molecules which contain hydrogen atoms and these are affected by the state of our mind.

When cyclohexane is placed in a NMR cell, we get only a single signal indicating that all the hydrogen atoms are equivalent. But this is true only at normal temperature. The reason is that axial and equatorial hydrogen atoms flip up and down because energy required for this is very small and room temperature provides it. But as we cool the sample, less energy is available and a temperature reaches 40K, the atoms sort of freeze in their locations and two peaks begin to appear. These peaks are indicative of up and down orientation hydrogen atoms. This confirms a chair configuration of cyclohexane.