Discovering The Mystery Of DNA

Deoxyribonucleic acid (DNA), is sometimes called the most important chemical on earth, because it makes up our genes. But did you know the tale of its discovery was a long journey, involving many scientists?

Father Mendel and the hunt for the ‘gene’
Father Gregor Mendel, a Catholic monk, carried out experiments in the 19th century which laid the principles of modern genetics. His findings were later confirmed and extended by Hugo de Vries, Carl Correns, Erich von Tschermak and Thomas Hunt Morgan. The most critical finding was that different traits were inherited independently, as if each was a particle (now called a ‘gene’). This set off a hunt to find the chemical nature of the gene.

The chromosome theory
Theodor Boveri was a biologist who showed that chromosomes were necessary for inheritance in sea urchins. Walter Sutton demonstrated this in a grasshopper. Soon evidence mounted that chromosomes were the bearers of heredity, and it was established beyond doubt in 1915.

Chromosomes are very complicated structures in the cell, and contain both proteins and DNA. For a long time, it was a matter of hot debate as to which was the actual carrier of heredity. The debate was finally put to rest in 1944 by Oswald Avery, Colin MacLeod, and Maclyn McCarty, who showed that it was DNA and not protein that caused heredity.

The structure of DNA
A race began to determine the structure of DNA and the chemical basis of how genes work. It was already known that DNA is made of four ‘bases’ – adenine, guanine, thymine and cytosine. In 1950, Erwin Chargaff demonstrated that the total amount of adenine in any DNA molecule equals the total amount of thymine. He showed that the amount of guanine equals that of Cytosine. These are now called Chargaff’s rules.

At the same time Rosalind Franklin, Maurice Wilkins, James Watson and Francis Crick were using a new method for determining chemical structures – X-ray diffraction. Rosalind Franklin carried out many experiments and obtained many X-rays that showed a distinct, repetitive pattern. From this, Crick (who was originally trained as an engineer) deduced that DNA existed in two intertwined strands – called the double helix. The discovery was announced in 1953.

The foundation of a new science
The double helix made it clear how Chargaff’s rules apply. Each strand is a chain made of a combination of the four bases. Every adenine on one strand pairs with a thymine on the other strand, while guanine pairs with cytosine.

Since then, a very large number of advances have been made and a whole science has emerged at the interface of chemistry and genetics. Called molecular biology, it has led to discoveries as to how genes work physically, the basis of genetic disorders and the new fields of gene therapy and genetic engineering.

Ancient red dye powers new ‘green’ battery

A natural plant dye once prized throughout the Old World to make fiery red textiles – has found a second life as the basis for a new “green” battery. Chemists from The City College of New York teamed with researchers from Rice University and the U.S. Army Research Laboratory to develop a non-toxic and sustainable lithium-ion battery powered by purpurin, a dye extracted from the roots of the madder plant.

“Purpurin,” on the other hand, said team member and City College Professor of Chemistry George John, “comes from nature and it will go back to nature.” The team reports their results in the journal Nature’s online and open access publication, Scientific Reports, on December 11, 2012.

Most Li-ion batteries today rely on finite supplies of mined metal ores, such as cobalt. “Thirty percent of globally produced cobalt is fed into battery technology,” noted Dr. Leela Reddy, lead author and a research scientist in Professor Ajayan’s lab in the Department of Mechanical Engineering and Material Science at Rice University. The cobalt salt and lithium are combined at high temperatures to make a battery’s cathode, the electrode through which the electric current flows.

Fortunately, biologically based color molecules, like purpurin and its relatives, seem pre-adapted to act as a battery’s electrode. In the case of purpurin, the molecule’s six-membered (aromatic) rings are festooned with carbonyl and hydroxyl groups adept at passing electrons back and forth, just as traditional electrodes do. “These aromatic systems are electron-rich molecules that easily coordinate with lithium,” explained Professor John.

Moreover, growing madder or other biomass crops to make batteries would soak up carbon dioxide and eliminate the disposal problem – without its toxic components, a lithium-ion battery could be thrown away. Best of all, purpurin also turns out to be a no-fuss ingredient. “In the literature there are one or two other natural organic molecules in development for batteries, but the process to make them is much more tedious and complicated,” noted Professor John.

Made and stored at room temperature, the purpurin electrode is made in just a few easy steps: dissolve the purpurin in an alcohol solvent and add lithium salt. When the salt’s lithium ion binds with purpurin the solution turns from reddish yellow to pink. “The chemistry is quite simple,” coauthor and City College postdoctoral researcher Dr. Nagarajan explained.

The team estimates that a commercial green Li-ion battery may be only a few years away, counting the time needed to ramp up purpurin’s efficiency or hunt down and synthesize similar molecules. “We can say it is definitely going to happen, and sometime soon, because in this case we are fully aware of the mechanism,” said Professor John.

Onion Can Soak Up Heavy Metal

Onion and garlic waste from the food industry could be used to mop up hazardous heavy metals, including arsenic, cadmium, iron, lead, mercury and tin in contaminated materials, according to a research paper published in the International Journal of Environment and Pollution.

Biotechnologists Rahul Negi, Gouri Satpathy, Yogesh Tyagi and Rajinder Gupta of the GGS Indraprastha University in Delhi, India, explain how waste from the processing and canning of onion (Allium cepa L.) and garlic (Allium sativum L.) could be used as an alternative remediation material for removing toxic elements from contaminated materials including industrial effluent. The team has studies the influence of acidity or alkalinity, contact time, temperature and concentration of the different materials present to optimize conditions for making a biological heavy metal filter for industrial-scale decontamination.

They have found that at 50 Celsius (122 Fahrenheit), the efficiency of the clean-up process is largely dependent on pH (acidity or alkalinity) and equilibration time usually occurs within half an hour; a pH of 5 was optimal. They demonstrated the maximum extraction was achievable for lead, one of the most troublesome metallic environmental pollutants. They could extract more than 10 milligrams per gram of Allium material from a test solution containing 5 grams per liter of mixed metal ion solution, amounting to recovery efficiency of more than 70%. The absorbed metals can be released into a collecting vessel using nitric acid(HNO3, the CAS number is 7697-37-2) and the biomass reused.

The team experimented with Allium biomass to demonstrated effective removal of heavy metals from both simulated and actual industrial effluents. “The technique appears to be industrially applicable and viable,” they suggest. “This may provide an affordable, environmental friendly and low maintenance technology for small and medium scale industries in developing countries,” they conclude.

A sad tale to TEL

You may have heard an elder asking for unleaded petrol at a pump. Do you know why lead was once added to petrol? And why it was discontinued later?

The problem of ‘knocking’ in engines
In the early days of automobiles, ‘knocking’ was a major problem. In a car’s engine, the petrol is injected into a ‘fuel chamber’, where it mixes with air. A spark plug then creates an electric spark, which causes the fuel-air mixture to burn and produce heat. This causes the air to expand and push a piston, which drives the wheel.

However, one problem was that the fuel would catch fire even when the spark was not provided. This often led to engine problems; sometimes it even exploded!

The search for an anti-knock
Many people tried to find a solution. One way was to find a chemical that could be added to petrol, so that it would not combust until the spark was provided. In 1921, Thomas Midgley discovered that a compound called tetra-ethyl lead (TEL) prevented knocking when added to fuel. Midgley is also famous as the discoverer of CFCs.

TEL was soon adopted by fuel companies around the world as an additive to fuels. However, it soon proved to be one of the world’s biggest chemical disasters.

TEL and Lead poisoning
Lead is very dangerous to human beings. It causes anaemia, memory loss, abdominal pain, bone weakening, depression and finally death. It can be identified by ‘lead hue’, i.e. pale colouration of the skin. As the use of TEL spread around the world, it led to lead poisoning among petrol pump workers as well as users.

Lead also poisons the ‘catalytic converters’ that all modern car engines must be fitted with. This is a small device that removes dangerous substances like carbon monoxide and nitrogen oxides. However, even tiny amounts of lead can damage the converter.

Sadly, TEL continued to be used for a very long time as there was no other alternative available. However, many improvements were made to engine design over the years, reducing or eliminating ‘knocking’. With the need for leaded fuel slowly decreased. Lead poisoning causes anaemia, memory loss, abdominal pain, bone weakening, depression and finally death.

A lesson learnt
has since been banned in many countries around the world. India banned the use of it in 2000. Alongside, the government introduced rules called the Bharat Stage standards. These rules require car manufacturers to implement technologies that reduce or eliminate the need for unleaded fuels.

The story of TEL highlights the nature of chemistry. What seems like a reasonable solution to a problem can unfortunately create terrible problems. Luckily, scientists today have adopted many methods to make science safer. In chemistry, such methods are called Green Chemistry.

New Drug Cuts Risk of Deadly Transplant Side Effect in Half

A new class of drugs reduced the risk of patients contracting a serious and often deadly side effect of lifesaving bone marrow transplant treatments, according to a study from researchers at the University of Michigan Comprehensive Cancer Center.

The study, the first to test this treatment in people, combined the drug vorinostat with standard medications given after transplant, resulting in 21 percent of patients developing graft-vs.-host disease compared to 42 percent of patients who typically develop this condition with standard medications alone.

“Graft-vs.-host disease is the most serious complication from transplant that limits our ability to offer it more broadly. Current prevention strategies have remained mostly unchanged over the past 20 years. This study has us cautiously excited that there may be a potential new way to prevent this condition,” says lead study author Sung Choi, M.D., assistant professor of pediatrics at the U-M Medical School.

Vorinostat is currently approved by the U.S. Food and Drug Administration to treat certain types of cancer. But U-M researchers, led by senior study author Pavan Reddy, M.D., found in laboratory studies that the drug had anti-inflammatory effects as well — which they hypothesized could be useful in preventing graft-vs.-host disease, a condition in which the new donor cells begin attacking other cells in the patient’s body.

The researchers found vorinostat was safe and tolerable to give to this vulnerable population, with manageable side effects. In addition, rates of patient death and cancer relapse among the study participants were similar to historical averages.
The results mirror those found in the laboratory using mice. Reddy, an associate professor of internal medicine at the U-M Medical School, has been studying this approach in the lab for eight years.

“This is an entirely new approach to preventing graft-vs.-host disease,” Choi says. Specifically, vorinostat targets histone deacetylases, which are different from the usual molecules targeted by traditional treatments.

Vorinostat has a dual effect as an anti-cancer and an anti-inflammatory agent. That’s what’s potentially great about using it to prevent graft-vs.-host, because it may also help prevent the leukemia from returning,” Choi says.

The study is continuing to enroll participants. The researchers hope next to test vorinostat in patients receiving a transplant from an unrelated donor, which carries an even greater risk of graft-vs.-host disease. This approach is not currently available outside of this clinical trial.

The History of Matches

From history books, we know that Stone Age people would rub two pieces of flint very hard to produce a fire. Nowdays we just strike a match, and it lights up immediately. Ever wondered how we came this far?

The ‘light-bringing slaves’
The first matches in recorded history come from China – a land known for its
invention of fireworks. It was known that sulphur, when subjected to mechanical force, ignites instantly. By coating small pine sticks with sulphur, women developed a primitive kind of match. They were so useful that the Chinese poet Tao Gu called them ‘light-bringing slaves’.

The invention of the ‘noiseless match’
In the Middle Ages, the match travelled from China to Europe. Though being useful,
it was still expensive, unreliable and dangerous.

In the 19th century, scientists discovered that matches could be made to light reliably by adding potassium chlorate. When a match is struck, heat is produced due to friction. This causes the potassium chlorate to decompose and release oxygen, which ignites the sulphur.These matches were still dangerous, as potassium chlorate tends to be explosive.

In 1836, Janos Irinyi, a Hungarian chemist, replaced potassium chlorate with lead dioxide, which works in the same way, but is less explosive.Irinyi sold the invention to Istvan Romer, who set up the first commercial match factories, and these were a great success.

When a match is struck, heat is produced due to friction.This causes the potassium chlorate to decompose and release oxygen, which ignites the sulphur.

White phosphorus and the ‘safety match’
Irinyi and Romer’s matches contained white phosphorus, a toxic chemical. As match-
making spread, many match workers caught a debilitating illness called phossy jaw. A safer alternative was sought.

It was found by the famous scientist J.J. Berzelius who discovered that red phosphorus was equally effective and yet less toxic. His student Gustaf Pasch went a step further by separating the explosive chemicals into the match head and the striking surface. The match head consisted of potassium chlorate mixed with binding agents. The striking surface is coated with red phosphorus. Only when the match is struck against the surface, will it will burst into flame.

Factories for making safety matches were set up in Sweden in 1847 first, but soon spread throughout the world. Matches were packed into boxes, the sides of which formed the striking surface. And this is how safety matches are made even today!

Reforming in Supercritical Water

Almost everything we use today – plastics, medicines, synthetic fabrics – is made by some chemical process or the other. Many of these require organic solvents like benzene or acetone, which are environmental pollutants. How nice would it be if there was a way to make these useful things without needing harmful solvents?

Enter Supercritical Fluids
A supercritical fluid is a special state of a substance that exists above its critical point. For water, that’s 374°C. At this temperature, water loses many peculiar properties it has in its liquid state, such as hydrogen bonding and repelling non-polar substances.

Imagine an unbreakable glass ball, half-full of water, and the rest a vacuum above it. Some of the empty space will be filled by water vapour. Now let’s heat this ball. As water boils, it forms steam. The density of liquid water decreases, while that of steam increases. As you keep heating it, at one point, the density of water will be equal to the density of steam. This temperature is called the critical point. At this point both liquid and gas states merge into a state called supercritical water (SCW).

Reactions in supercritical water
Now let’s understand why supercritical water is different. In its liquid state, water forms many ‘hydrogen bonds’ between its molecules. These are what make water expand when freezing, making ice lighter than water. However, as water is heated, the molecules move more and more about and the hydrogen bonds break. At the critical point, they disappear completely.

Many chemicals used to make plastics, medicines etc. are not soluble in water because its hydrogen bonds do not allow water molecules to mix with those molecules. That’s why they need to be dissolved in solvents like benzene or acetone. However, when hydrogen bonds are broken, water molecules can dissolve chemicals that were previously insoluble. Now you’ll be thinking, why not use SCW as a solvent instead of benzene or acetone?

Putting supercritical water to work
Some factories have started making acetophenone, using SCW as the solvent. Acetophenone is a precursor molecule used to make many drugs and perfumes. Another important reaction carried out with SCW as solvent is the breakdown of triglycerides (commonly found in animal & vegetable fats) to glycerine and fatty acids. Fatty acids are used in the making of soap and biodiesel. It is also being thought of as a substitute for steam in thermal power plants.

The supercritical form of carbon dioxide is also useful. It is used nowadays in manufacturing decaffeinated coffee powder, and for creating nano-materials. When you become a scientist yourself, we’re sure you’ll find an exciting use for supercritical materials!

The structure of vetiver odorants

Approximately one third of all fragrances on the market contain vetiver oil as a key ingredient, for which no synthetic odorant is commercially available. Instead it has to be distilled from the dried roots of vetiver grass.

To find out about the structural requirements of vetiver odorants, researchers in Switzerland devised a synthesis to a 7,8-seco-khusimone, which still contained all the structural features held responsible for the vetiver odour. As they report in the European Journal of Organic Chemistry, however, the final product displayed none of the expected olfactory characteristics, thus proving the vetiver rule wrong.

Vetiver oil has a distinct and characteristic suave and sweet woody-earthy odour with additional green grapefruit and rhubarb-type facets. In perfumery it is often used to provide the woody base note in combination with rather inexpensive bergamot oil, or its synthetic counterparts, which provides a fresh citrus component. Currently, there is no synthetic vetiver perfumery material available commercially. This lack of availability is partially due to the complex sesquiterpene nature of its constituents, and partially due to the lack of consensus as to which constituents contribute to its characteristic odour. One component for which there is consensus is (–)-khusimone, which forms only up to 2% of the essential oil, but does present a typical vetiver odour and is, so far, the only genuine natural lead structure.

Syntheses of related structures led to the development of a vetiver rule, which postulates that the woody odour of vetiver is a result of the presence of an alpha-branched carbonyl osmophore at a specific distance from a bulky group, with an overall dimension of 13–15 carbon atoms. Philip Kraft and Natacha Denizot (Givaudan, Switzerland) thus decided to apply this vetiver rule to the genuine lead structure khusimone itself in order to design a new vetiver odorant with even improved olfactory properties, and in addition an easier synthetic access. The target structure, 7,8-seco-khusimone, was obtained as a mixture of diastereomers in a 10-step sequence starting from commercially available allyl alcohol(the CAS No. is 107-18-6) and isovaleric acid.

A key advantage of the sequence is that it fairly easily allows further modifications of the target structure. Although the desired compound was synthesised successfully it was 10 times less intense than (–)-khusimone and displayed a floral, rosy, green, germanium-like odour with no woody or vetiver character. Kraft and Denizot, therefore, conclude that the vetiver rule has been proved wrong, or at least that the structural requirements are more complex than first suggested.

Facts About Plasma

Like fish in the ocean, we humans too, live in a giant ocean. We spend all our lives in a gigantic ocean of plasma, but we’re barely aware what it is! Physicist Max Babi explains all about plasma – the fourth state of matter.

Just what is plasma?
‘Plasma’ is a Greek word meaning ‘that which is diffuse’ i.e. unclear, or semi-
transparent. It is also defined by physicists as ‘ionized matter’. This is the plasma of physics. Don’t confuse it with ‘biological plasma’ which is a colourless jellylike liquid in our blood.

All matter is composed of atoms which are ‘neutral’. That means they do not carry any electrical charge. Sometimes a flash of high voltage, or heating to extreme temperature will cause the ‘outermost’ electrons to get knocked off. These electrons will then knock off electrons from neighbouring atoms. This creates a mass of ionized matter, which is called plasma. Plasma is considered the 4th state of matter.

The other three states of matter are solids, liquids and gases, all of which are neutral in normal conditions. The plasma state is similar to the gaseous state, and yet it is very different. How?

Gases are electrically neutral, but plasmas contain both positive and negative charges. Gases cannot conduct electricity, plasmas can. Gases are not influenced by electromagnetic fields; plasmas can be deflected, focused or diverged by such fields.

The uses of plasmas
Micro-plasma welding is a method used to join paper thin sheets of metals. The
joint becomes invisible after polishing. Stainless steel water storage tanks and other kitchen implements are made this way.

Plasma spray process is a most magical use of thermal plasmas it is the only coating process that can apply any material on to any material.

Non-metal on to non-metal: Teflon on to magnesia (ceramic, also called as Magnesium oxide). Some chemicals like hydrofluoric acid can corrode the ceramic vessels they are kept in; coating them with Teflon prevents corrosion.

Metal on to metal: Titanium on to mild steel, to prevent corrosion of steel.
Non-metal on to metal: alumina on to stainless steel. Alumina reduces the wear and
tear on the stainless steel vessel due to industrial processes.

Metal on to non-metal: copper on to porcelain used in capacitors. Plasma-spraying copper onto the porcelain makes it ‘solderable’, so that electric wires can be attached to it.

Gluten Free and Tasty!

Cereals are good for you, supplying the body with carbohydrates, proteins and vitamins. Yet some people are intolerant to the gluten protein they contain. Now, researchers are developing new recipes for tasty, gluten-free pasta and pastries.

Not every person can eat what they like; far from it, one in every 250 people in Germany is intolerant to the protein gluten, which is chiefly found in the cereals wheat, spelt, barley and rye. Experts call this intolerance coeliac disease. For those affected, this means giving up bread, pizza, pasta and cakes, while ice cream wafers, dumplings and pretzels also pass onto the list of banned foods. Those suffering from coeliac disease, a chronic bowel disorder, must keep to a strict diet if they are to avoid diarrhea, stomach ache, vomiting and other symptoms. Accordingly, only gluten-free products make it onto the menu.

Indeed, demand for these food products, mainly offered by small and medium-sized enterprises (SMEs), has risen steadily over the past years. Nevertheless, many consumers dislike gluten-free pasta and bakery products because they are unappetizing, lacking in texture and leave a disagreeable sensation in the mouth. This is a view confirmed in consumer tests involving coeliac disease sufferers and healthy volunteers. Partners include ingredient providers and food producers as well as research institutes from Germany, Ireland, Italy and Sweden. The aim of the project is to enable SMEs to develop premium, tasty gluten-free products that the consumer will eat with real enjoyment and satisfaction. The focus is primarily on bread and pasta, and on improving their taste, smell, appearance, texture and sensation in the mouth.

Gluten is good for baking because it holds the dough together. Hydrocolloids like xanthan gum, HPMC(the full name is Hydroxypropyl methyl cellulose and CAS No. is 9004-65-3) and dextran have all been examined carefully, as well as seeds taken from cereals and pseudocereals like amaranth, quinoa and buckwheat. In addition, scientists analyzed protein isolates taken from potatoes and pulses like lupins, broad beans and peas, as well as investigating the interaction of a variety of recipe ingredients during the production process, and the ways in which this affected texture, sensory properties and aroma profile. A whole range of recipes were tested; for example, researchers combined proteins with soluble fibers like xanthan gum and HPMC or with insoluble citrus fibers.

Bez considers the project a success, pointing to project partners’ success in producing a range of new and improved gluten-free breads, including toast bread, leavened bread and oat wholemeal bread, ciabatta, baguettes and pizza dough. Four of the baked goods producers involved in the project are already using the recipes for ciabatta, wholemeal bread and pizza dough. Furthermore, researchers were able to produce tasty, gluten-free spaghetti with a high fiber and protein content. Bez is confident that it won’t be long now before we see some of the new products lining bakery and supermarket shelves.