THE PROOF OF BEING WATERPROOF

Have you ever wondered how raindrops simply bead-up and slide off from taro leaves? Have you ever thought the reason behind the leaf’s waterproof ability? The cuticle or waxy layer on the epidermis of the leaf caused the extreme water-shedding preventing it from getting wet. 

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This phenomenon is called the “lotus effect” referring to the same water repelling characteristic exhibited by the lotus leaves. This is also present in other insects and birds, notice how butterfly wings don’t get drenched from the rain and how water gently rolls off a duck’s back.

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The lotus effect refers to self-cleaning properties that are a result of very high water repellence (superhydrophobicity), as exhibited by the leaves of the lotus flower. Dirt particles are picked up by water droplets due to the micro- and nanoscopic architecture on the surface, which minimizes the droplet's adhesion to that surface. Superhydrophobicity and self-cleaning properties are also found in other plants and also on the wings of certain insects.

The high surface tension of water causes droplets to assume a nearly spherical shape, since a sphere has minimal surface area, and this shape therefore has least surface energy. On contact with a surface, adhesion forces result in wetting of the surface. Either complete or incomplete wetting may occur depending on the structure of the surface and the fluid tension of the droplet. The cause of self-cleaning properties is the hydrophobic water-repellent double structure of the surface. This enables the contact area and the adhesion force between surface and droplet to be significantly reduced resulting in a self-cleaning process. This hierarchical double structure is formed out of a characteristic epidermis (its outermost layer called the cuticle) and the covering waxes. The waxes are hydrophobic and form the second layer of the double structure. This system regenerates. This bio-chemical property is responsible for the functioning of the water repellency of the surface.

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Dirt particles with an extremely reduced contact area are picked up by water droplets and are thus easily cleaned off the surface. If a water droplet rolls across such a contaminated surface the adhesion between the dirt particle, irrespective of its chemistry, and the droplet is higher than between the particle and the surface. As this self-cleaning effect is based on the high surface tension of water it does not work with organic solvents. Therefore, the hydrophobicity of a surface is no protection against graffiti.

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The cuticle minimizes transpiration from the leaf. The cuticle is hydrophobic so water beads up and rolls off just like water does on a freshly waxed car. This effect is of a great importance for plants as a protection against pathogens like fungi or algae growth, and also for animals like butterflies, dragonflies and other insects not able to cleanse all their body parts. Another positive effect of self-cleaning is the prevention of contamination of the area of a plant surface exposed to light resulting in reduced photosynthesis.

References

http://www.worldngayon.com/2013/05/waterproof-technology/

https://en.wikipedia.org/wiki/Lotus_effectl

http://www.madsci.org/posts/archives/2000-11/973301398.Bt.r.html

21st and 22nd Amino Acids?

Proteins are key players in many vital processes in living organisms. Functionally, they transport substances like hemoglobin, which carries oxygen to cells; some are enzymes, which catalyze metabolic reactions; hormones, which regulate body activities; pump ions or recognize signalling molecules; and some are antibodies, which protect our body. The complexity and variety of proteins is really unusually large, for example, there are more than 100,000 different proteins at work in our body. But almost all of them are made up of 20 different amino acids only.

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The 20 amino acids that are encoded directly by the codons of the universal genetic code are called standard or canonical amino acids. The others are called non-standard or non-canonical. Most of the non-standard amino acids are also non-proteinogenic (i.e. they cannot be used to build proteins), but there are non-standard proteinogenic amino acids, as they can be used to build proteins by exploiting information not encoded in the universal genetic code.

The truth that there are amino acids, except for the 20 standard amino acids, that can be used for protein production in certain cases is really amazing. These non-standard proteinogenic amino acids: selenocysteine (21st) which is present in many non-eukaryotes as well as most eukaryotes, but not coded directly by DNA and pyrrolysine (22nd) which can be found only in some archaea and one bacterium). For example, 25 human proteins include selenocysteine (Sec) in their primary structure, and the structurally characterized enzymes (selenoenzymes) employ Sec as the catalytic moiety in their active sites. Pyl and Sec are encoded via variant codons. For example, Sec is encoded by stop codon and SECIS element.

Twenty-two amino acids are naturally incorporated into polypeptides and encoded by the universal genetic code while Sec and Pyl are incorporated into proteins by unique synthetic mechanisms. Sec is incorporated when the mRNA being translated includes a SECIS element, which causes the UGA codon to encode Sec instead of a stop codon.

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It has been shown that in the case of selenocysteine, termination of translation is inhibited in the presence of a specific mRNA sequence in the 3'-region after the UGA-codon that forms a hairpin like structure (called "Sec insertion sequence" (SECIS)).

Pyl is used by some methanogenic archaea in enzymes that they use to produce methane. It is coded for with the codon UAG, which is normally a stop codon in other organisms. This UAG codon is followed by a PYLIS downstream sequence.

Sec and Pyl are rare amino acids that are co-translationally inserted into proteins and known as the 21st and 22nd amino acids in the genetic code. Sec and Pyl are encoded by UGA and UAG codons, respectively, which normally serve as stop signals.

Only a few highly specialized proteins additionally contain selenocysteine, the very rare 21st amino acid discovered in 1986. The researchers at the Technische Universitaet Muenchen have elucidated the structure of an important enzyme in the production of Pyl.

PYRROLYSINE
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In 2002, the discovery of the 22nd amino acid in methane-producing archaea of the family Methanosarcinaceae was really a big surprise: Pyl. It is genetically encoded in a similar manner as that of Sec and the other 20. The archaea use the unusual amino acid in proteins that they need for energy conversion. Pyl is located in the catalytic center of the proteins and is essential for their function. The energy generation process of the archaebacteria would not work without Pyl.

The scientists at Ohio State University succeeded in deciphering parts of the manufacturing process of Pyl in March 2011. They proposed a reaction mechanism suggesting that the enzyme PylB catalyzes the first step of Pyl biosynthesis by converting the amino acid lysine to the intermediate product methylornithine. Scientists headed by Michael Groll, Professor of Biochemistry at the TUM-Department of Chemistry, could now determine the crystalline structure of PylB by X-ray using structure analysis.

PYRROLYSINE

www.chemspider.com

To their great surprise, they caught the enzyme in action: at the time of crystallization the reaction product, methylornithine, had not left the enzyme. It adhered to a confined space, a kind of "reaction vessel," still in connection with the centers of the enzyme responsible for its creation. "That the product was still present in the enzyme, was something special and a great stroke of luck," says Felix Quitterer, a member of the scientific staff at the Department of Biochemistry and lead author of the publication. "We were not only able to directly detect the methylornithine, but also retroactively reconstruct how it is created from the source amino acid lysine."

This reaction was not only unknown until now, it is also very difficult to catalyze. It is a cluster of four iron and four sulfur atoms in the active site that is the key to the conversion. "This is a really unusual enzymatic reaction. Up to now no chemist in the laboratory is able to synthesize methylornithine in a one-step reaction starting from lysine," says Groll.

The conversion of lysine to methylornithine is helping scientists to understand how archaebacteria can modify an existing system to enable the formation of a tailored amino acid that, when installed in the appropriate protein, catalyzes a very specific reaction.

As surfing over the net, this question really caught my attention, “Why does the vast complexity of proteins in living organisms come from only a few natural amino acids, even though the genetic code would be able to encode many more?” I’ve just thought to myself, He really put things in order. Some are capable for this, and some are for that.

References:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1976440/ Retrieved: 05-28-16

https://en.wikipedia.org/wiki/Amino_acid Retrieved: 05-28-16

http://pubs.acs.org/cen/topstory/8021/8021notw1.html Retrieved: 05-28-16

http://www.albany.edu/faculty/cs812/bio366/selenocysteine_ppt.pdf Retrieved: 05-28-16

https://www.sciencedaily.com/releases/2011/11/111118133052.htm Retrieved: 05-28-16

Mimosa pudica: The Defensive Revelations Behind “Shyness”

The “shyness” of Mimosa pudica is really an astounding floral behavior in the botanical world. You, I and everyone might have enjoyed playing, touching and shaking its leaves to make them fold inward and droop right before one’s eye, and might have associated that this amazing plant is “sleeping” and/or just “shy” as it feels being tickled. As curiosity have driven me off, I’ve gathered information and found out the how’s and why’s of this plant’s shyness.

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Mimosa pudica, called by numerous names such as sensitive plant, sleepy plant, humble plant, touch-me-not, TickleMe plant, shame plant or shy plant, is often grown for its great characteristic: the compound leaves fold inward and droop when touched or shaken, and re-open a few minutes later. The species are native to South America and Central America, but is now a pantropical weed. It can also be found in Asia in countries such as Thailand, Indonesia, Malaysia, Philippines, and Jamaica. It grows mostly in undisturbed shady areas, under trees or shrubs.

CREDIT: www.pondkoi.com

The leaves-closing mechanism is caused by various stimuli, such as touching, warming, blowing, or shaking. These movements have been termed seismonastic movements, the reaction to physical shock. The movement occurs when specific regions of cells lose turgor pressure, which is the force that is applied onto the cell wall by water within the cell (mostly in the central vacuole) which, in turn, this turgor pressure exerts inwardly a mechanical wall pressure against the protoplast. The two equal and opposing pressures give strength to the cell and columns of water-

filled cells keep the plant erect.

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When the plant is disturbed and tickled, an electrical signal goes through the plant cells. These electrical signals stimulated specific regions on the stems to release chemicals including potassium ions which force water out of the cell vacuoles and the water diffuses out of the cells, producing a loss of cell pressure and cell collapse hence, causes the leaflets and stalks to wilt; this differential turgidity between different regions of cells results in the closing of the leaflets and the collapse of the leaf petiole. The stimulus can also be transmitted to neighboring leaves. This reaction to touch or being tickled is called thigmonasty or thigmotropism.

The changes in leaf orientation termed "sleep" also happens at night. The leaves will also fold and bend in movements known as nyctitropism or nyctinastic movements (the changing of the position of the leaves of plants at night). It then reopens as the sun rises.

CREDIT: www.growsonyou.com

The plant’s nyctitropism may be a way to reduce water loss by transpiration as the leaves fold down upon each other.  During cold weather, the leaves will close as well, could this be a way to maintain its body temperature?

Many scientists think that the plant mainly uses its ability to shrink as
a defense mechanism against different predators. Grazing animals tend to be frightened of the moving plant’s leaves just enough to stop them from eating the leaves. The sudden movement also dislodges harmful insects. It`s one of the nature’s wonderful floral defense mechanisms ever created by God, isn’t it?

References:

https://answers.yahoo.com/question/index?qid=20070828022305AAJRso2 Retrieved: 05/11/16

https://en.wikipedia.org/wiki/Mimosa_pudica Retrieved: 05/11/16

http://biology.stackexchange.com/questions/1114/why-did-the-sensitive-plant-mimosa-pudica-evolve-its-leaf-closing-mechanism Retrieved: 05/11/16

LIFELIGHT: The Chemical Secrets of Flickering Fireflies

Fireflies’ summertime glow is really a fascinating nature’s show to watch. And we might have wondered - how and why do these little creatures produce light? The chemical reaction within fireflies’ bodies allows them to make and emit light. 

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This kind of light production is called bioluminescence, the conversion of chemical energy into light energy, and is quite characterized by many other organisms, mostly marine organisms. Perchance an epitome of bioluminescence is the manner how fireflies produce light. To be able to do this, they contain photic organs on their lower abdomen that make light. Generally, luciferin chemical reacts with ATP, and when exposed to oxygen, light is produced and emitted.

CREDIT: www.firefly.org

Fireflies contain an organic compound called luciferin in their bodies. Luc represents firefly luciferase, adenosine triphosphate (ATP), the universal biochemical energy source, and PPi is inorganic pyrophosphate. Firefly luciferase has extraordinary specificity for this nucleotide triphosphate. The adenylate is the true substrate of the subsequent oxidative chemistry. Luciferase converts firefly D-luciferin (LH2) into the corresponding enzyme-bound luciferyl adenylate. In fact, D-LH2-AMP produced synthetically reacts with oxygen in the presence of luciferase to produce light emission identical to that obtained with the natural substrates D-luciferin and Mg-ATP. (Bruce R. Branchini, CHEMISTRY OF FIREFLY BIOLUMINESCENCE)

The luciferase enzyme functions as a mono-oxygenase, although it does so in a very unusual manner without the apparent involvement of a metal or cofactor. In some way that has not been yet determined, luciferase amino acid residues are recruited to promote the addition of molecular oxygen to the D-luciferin adenylate, which is then transformed to an electronically excited state oxyluciferin molecule and carbon dioxide, each containing one oxygen atom from molecular oxygen. Visible light emission results from the rapid loss of energy of the excited state oxyluciferin molecule via a fluorescence pathway. The symbol (*) denotes an electronic excited state.

The light wavelength is between 510 and 670 nanometers (pale yellow to reddish green color). To reflect the light away from their abdomen, fireflies’ cells that make the light have uric acid crystals.

credit: www.x-weibo.net

The pulsating pattern is due to the fireflies’ regulation of airflow into their abdomen. When oxygen is available, the firefly’s abdomen lights up and when there is no oxygen, there is no glow. The oxygen transport from outside to the interior cells takes place through abdominal trachea because these organisms do not have lungs. It is really amazing how some firefly species produce a high flash rate, pointing out the relatively slow speed of the muscles for oxygen transport.

Experts believed that in flash control, nitric oxide gas is very important. Without this gas, oxygen that enters is bound to mitochondria’s surface, and is thereby not available for transport further within the light organ. The presence of the gas, which binds to the mitochondria, allows oxygen to flow into the light organ where it combines with the other chemicals needed to create an awesome bioluminescent reaction. Because nitric oxide breaks down very fast, as soon as the chemical is no longer being produced, the oxygen molecules are again trapped by the mitochondria and are not available for the production of light.

A firefly's light is “cold light”, without a lot of energy being lost as heat, contrary to a light bulb which produces a lot of heat in addition to light. This is necessary because if a firefly's light-producing organ got as hot as a light bulb, the firefly would not survive the experience. 

By recreating the firefly’s glow in the lab, scientists continue to tease out the secrets behind how these little guys light up, the American Chemical Society (ACS) announced in a new video. Scientists had known that a compound called luciferase produced the firefly’s glow. A recent article published in the Journal of the American Chemical Society, Dr. Bruce Branchini of Connecticut College, reveals a molecule toxic to most animals, called a superoxide ion, plays a key role in the reactions that cause luciferase to produce light. Superoxide ion is a form of molecular oxygen which contains an extra electron, a very reactive specie. It can cause inflammation and cell damage in humans and other animals but doesn’t appear to harm the bug because the reactions are contained and happen quickly, the scientists say. 

Reasons of Flashing and Flickering

Fireflies’ flashing and flickering acts have a variety of reasons. Other experts think that the firefly’s flashy style may warn predators of their bitter taste and to stay away. Their bodies are equipped with the chemical called lucibufagens, and after a predator gets a mouthful, it quickly learns to associate the firefly's light with a bad taste. 

credit: cleantechnica.com

As adults, many fireflies have flash patterns unique to their species and use them to identify other members of their species as well as to discriminate between members of the opposite sex. Several studies have shown that female fireflies choose mates depending upon specific male flash pattern characteristics. Higher male flash rates, as well as increased flash intensity, have been shown to be more attractive to females in two different firefly species.

The adult fireflies of some species are not luminous at all, instead, they use pheromones to locate mates. The use of pheromones as sexual signals appears to be the ancestral condition in fireflies with the use of luminous sexual signals as being a more recent development. There are species that employ both pheromonal and luminous components in their mating systems. These species appear to be evolutionarily intermediate between the pheromone-only fireflies and flash-only fireflies.

While each firefly species has its own pattern of flashing, some females imitate the patterns of other species. Males land next to them – only to be eaten alive by tricky fireflies. Their light is quite a deadly weapon, not just motivation of romance.

References:

https://en.wikipedia.org/wiki/Firefly (Retrieved: April 28, 2016) 

http://animals.howstuffworks.com/insects/question554.htm (Retrieved: April 28, 2016) 

http://earthsky.org/earth/bugs-firefly-light (Retrieved: April 28, 2016) 

http://www.scientificamerican.com/article/how-and-why-do-fireflies/ (Retrieved: April 28, 2016) 

http://learn.genetics.utah.edu/content/molecules/firefly/ (Retrieved: April 28, 2016) 

https://www.sciencemag.org/news/sifter/watch-chemistry-behind-how-fireflies-glow (Retrieved: April 28, 2016) 

http://news.nationalgeographic.com/2015/07/150724-fireflies-glow-bugs-summer-nation-science/ (Retrieved: April 28, 2016)