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DNA- fascinating video

Deoxyribonucleic acid (DNA) is a molecule that encodes the genetic instructions used in the development and functioning of all known living organisms and many viruses. Along with RNA and proteins, DNA is one of the three major macromolecules essential for all known forms of life. Most DNA molecules are double-stranded helices, consisting of two long biopolymers of simpler units called nucleotides—each nucleotide is composed of a nucleobase (guanine, adenine, thymine, and cytosine), recorded using the letters G, A, T, and C, as well as a backbone made of alternating sugars (deoxyribose) and phosphate groups (related to phosphoric acid), with the nucleobases (G, A, T, C) attached to the sugars. DNA is well-suited for biological information storage, since the DNA backbone is resistant to cleavage and the double-stranded structure provides the molecule with a built-in duplicate of the encoded information. The following video shows animations of processes which occur within each one of the 10 trillion cells in our body!

Discovery

In 1927, Nikolai Koltsov proposed that inherited traits would be inherited via a “giant hereditary molecule” made up of “two mirror strands that would replicate in a semi-conservative fashion using each strand as a template”. In 1928, Frederick Griffith discovered that traits of the “smooth” form of Pneumococcus could be transferred to the “rough” form of the same bacteria by mixing killed “smooth” bacteria with the live “rough” form. This system provided the first clear suggestion that DNA carries genetic information—the Avery–MacLeod–McCarty experiment—when Oswald Avery, along with coworkers Colin MacLeod and Maclyn McCarty, identified DNA as the transforming principle in 1943. DNA’s role in heredity was confirmed in 1952, when Alfred Hershey and Martha Chase in the Hershey–Chase experiment showed that DNA is the genetic material of the T2 phage.

In 1953, James Watson and Francis Crick suggested what is now accepted as the first correct double-helix model of DNA structure in the journal Nature. Their double-helix, molecular model of DNA was then based on a single X-ray diffraction image (labeled as “Photo 51”) taken by Rosalind Franklin and Raymond Gosling in May 1952, as well as the information that the DNA bases are paired — also obtained through private communications from Erwin Chargaff in the previous years. Chargaff’s rules played a very important role in establishing double-helix configurations for B-DNA as well as A-DNA.

Experimental evidence supporting the Watson and Crick model was published in a series of five articles in the same issue of Nature. Of these, Franklin and Gosling’s paper was the first publication of their own X-ray diffraction data and original analysis method that partially supported the Watson and Crick model; this issue also contained an article on DNA structure by Maurice Wilkins and two of his colleagues, whose analysis and in vivo B-DNA X-ray patterns also supported the presence in vivo of the double-helical DNA configurations as proposed by Crick and Watson for their double-helix molecular model of DNA in the previous two pages of Nature.

Repairing system

It’s interesting to notice that the DNA molecule is highly reactive, thus, very unstable… On a good day about one million bases in the DNA in a human cell are damaged. These lesions are caused by a combination of normal chemical activity within the cell and exposure to radiation and toxins coming from environmental sources including cigarette smoke, grilled foods and industrial wastes. So, the organisms have a handful of repairing mechanisms, as said in a recent Science Daily article:

A number of environmental toxins and chemotherapy drugs are alkylation agents that can attack DNA.

When a DNA base becomes alkylated, it forms a lesion that distorts the shape of the molecule enough to prevent successful replication. If the lesion occurs within a gene, the gene may stop functioning. To make matters worse, there are dozens of different types of alkylated DNA bases, each of which has a different effect on replication.

One method to repair such damage that all organisms have evolved is called base excision repair. In BER, special enzymes known as DNA glycosylases travel down the DNA molecule scanning for these lesions. When they encounter one, they break the base pair bond and flip the deformed base out of the DNA double helix. The enzyme contains a specially shaped pocket that holds the deformed base in place while detaching it without damaging the backbone. This leaves a gap (called an “abasic site”) in the DNA that is repaired by another set of enzymes.

Human cells contain a single glycosylase, named AAG, that repairs alkylated bases. It is specialized to detect and delete “ethenoadenine” bases, which have been deformed by combining with highly reactive, oxidized lipids in the body. However, AAG also handles many other forms of akylation damage. Many bacteria, however, have several types of glycosylases that handle different types of damage.

“It’s hard to figure out how glycosylases recognize different types of alkylation damage from studying AAG since it recognizes so many,” says Eichman. “So we have been studying bacterial glycosylases to get additional insights into the detection and repair process.”

That is how they discovered the bacterial glycosylase AlkD with its unique detection and deletion scheme. All the known glycosylases work in basically the same fashion: They flip out the deformed base and hold it in a special pocket while they excise it. AlkD, by contrast, forces both the deformed base and the base it is paired with to flip to the outside of the double helix. This appears to work because the enzyme only operates on deformed bases that have picked up an excess positive charge, making these bases very unstable. If left alone, the deformed base will detach spontaneously. But AlkD speeds up the process by about 100 times. Eichman speculates that the enzyme might also remain at the location and attract additional repair enzymes to the site.

AlkD has a molecular structure that is considerably different from that of other known DNA-binding proteins or enzymes. However, its structure may be similar to that of another class of enzymes called DNA-dependent kinases. These are very large molecules that possess a small active site that plays a role in regulating the cells’ response to DNA damage. AlkD uses several rod-like helical structures called HEAT repeats to grab hold of DNA. Similar structures have been found in the portion of DNA-dependent kinases with no known function, raising the possibility that they play an additional, unrecognized role in DNA repair.

It’s impossible to conceive that such unstable, complex molecule could have originated all alone, by chance and lasted any long in a pre-biotic environment. In a primordial Earth, with a free-oxygen atmosphere, it turns out that it would have no ozon layer, or a very thin one. Thus, the UV light from the Sun would freely bombards the Earth without filtering; the most damaging UV light types would face no barrier, and it’s a fact that UV light damages, degrades polymers!

Many natural and synthetic polymers are attacked by ultra-violet radiation and products made using these materials may crack or disintegrate (if they’re not UV-stable). The problem is known as UV degradation, and is a common problem in products exposed to sunlight. Continuous exposure is a more serious problem than intermittent exposure, since attack is dependent on the extent and degree of exposure.

Effect of UV exposure on polypropylene rope (the left one is damaged, the right one is a new rope)

Add to it the oxidation problem, hydrolysis, etc… Any natural origin of RNA/DNA is inconceivable!

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