The real mystery behind the shape of the DNA “MOLECULE OF LIFE”

Looking at the DNA with an electron microscope, you will find a picture of what looks like rubber band staring right back at you in its’ famous B shape. But seriously, do you really know that DNA can actually change its shape from the famous right-sided B shape to any other infamous shape? Believe me this is one of the amazing things I have seen and you won’t believe what mathematicians have to say about this. Now before we discuss any further I would like to introduce you to what I call “The Molecule of Life” (DNA).

WHAT IS DNA?

Deoxyribonucleic acid, or DNA, is a biological macromolecule that carries hereditary information in many organisms. DNA is necessary for the production of proteins, metabolism, and reproduction of the cell. Large compressed DNA molecules with associated proteins called chromatin, are mostly present inside the nucleus. Some cytoplasmic organelles like the mitochondria also contain DNA molecules.

 Does this explanation make any sense to you? Well you don’t have to worry because I will have to break it down for you knowing that not everyone is a Biologist like me. DNA also known as the molecule of life is a molecule that contains the instructions an organism needs to develop, live and reproduce. These instructions are found inside every cell and are passed down from parents to their children. It can also be seen as a long molecule that contains human unique genetic code. Like a recipe book it holds the instructions for making all the proteins in our bodies.

Functions Of DNA

The functions of DNA cannot be over emphasized since it has almost everything to do with human existence. DNA was discovered chemically before its functions became clear. DNA and its related molecule, ribonucleic acid (RNA), were initially identified simply as acidic molecules that were present in the nucleus. When Mendel’s experiments on genetics were rediscovered, it became clear that heredity was probably transmitted through discrete particles and there was a biochemical basis for inheritance. A series of experiments demonstrated that among the four types of macromolecules within the cell (carbohydrates, lipids, proteins and nucleic acids), the only chemicals that were consistently transmitted from one generation to the next were nucleic acids. I shall be explaining some functions of DNA and try my best to break it down. Some of the functions of DNA are:

Replication

Life begins from a single cell, for humans this is the zygote formed by the fertilization of an egg by a sperm. After this, the entire dazzling array of cells and tissue types are produced by cell division. Even the maintenance of normal functions in an adult requires constant mitosis. Each time a cell divides, nuclear genetic material is duplicated. This implies that nearly three billion nucleotides are accurately read and copied. High-fidelity DNA polymerases and a host of error repair mechanisms ensure that there is only one incorrectly incorporated nucleotide for every 10 billion base pairs. When a double-stranded DNA molecule needs to be replicated, the first thing that happens is that the two strands separate along a short stretch, creating a bubble-like structure. In this transient single-stranded region, a number of enzymes and other proteins, including DNA polymerase work to create the complementary strand, with the correct nucleotide being chosen through hydrogen bond formation. These enzymes continue along each strand creating a new polynucleotide molecule until the entire DNA is replicated.

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Transcription

Another important function of genetic material is to direct the physiological activities of the cell. Most catalytic and functional roles in the body are carried out by peptides, proteins and RNA. The structure and function of these molecules is determined by nucleotide sequences in DNA. When a protein or RNA molecule needs to be produced, the first step is transcription. Like DNA replication, this begins with the transient formation of a single-stranded region. The single-stranded region then acts as the template for the polymerization of a complementary polynucleotide RNA molecule. Only one of the two strands of DNA is involved in transcription. This is called the template strand and the other strand is called the coding strand. Since transcription is also dependent on complementary base pairing, the RNA sequence is nearly the same as the coding strand.

Mutation

One of the main functions of any hereditary material is to be replicated and inherited. In order to create a new generation, genetic information needs to be accurately duplicated and then transmitted. The structure of DNA ensures that the information coded within every polynucleotide strand is replicated with astonishing accuracy. Even though it is important for DNA to be duplicated with a very high degree of accuracy, the overall process of evolution requires the presence of genetic variability within every species. One of the ways in which this happens is through mutations in DNA molecules.

The Shape Of The DNA

Understanding what the DNA is can be greatly different from understanding its shape and how it affects life in totality. The shape of the DNA is amazing owing to the fact of how it does its super-coiling, uncoils itself and take totally another different shape at times like the shape of the ladder. Previous research has clearly shown from results gotten from x-ray and crystallography carried out by scientists like Linus Pauling that DNA was perhaps made of three strands, Rosalind Franklin’s data supported the presence of a double helix. The structure of DNA therefore, was elucidated in a step-wise manner through a series of experiments, starting from the chemical isolation of deoxyribonucleic acid by Frederich Miescher to the X-ray crystallography of this macro-molecule by Rosalind Franklin.

But regarding the shape of DNA this is the views of Biologists and Mathematicians. In recent research carried out, it has been found out that In the cell, the DNA helix coils upon itself, or “super-coils.” The way DNA folds and coils encodes valuable geometric information that can be crucial to control the way genes are expressed. DNA molecules, which carry the genetic code of an organism, have to be tightly packed to fit inside a cell. However, every few hours, the cell produces a faithful copy of its genome in preparation for cell division. This replication process puts tremendous stress on the DNA and can change its shape in lethal ways. Mathematicians have found out that mathematics can describe the many shapes.

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Mathematicians observed that;

“Topology describes how an object deforms smoothly, as if made out of clay without making new holes or breaks. For example, imagine a rubber band tumbling around in a whirlpool. As the water swirls, the rubber band twists, stretches and shrinks. All of the shapes adopted by the band as it moves are topologically identical, but geometrically different”.

In regards to this during the cell cycle, each chromosome is replicated into two identical copies. In order for that to happen, the DNA helix must unwind, causing stress on the DNA. DNA responds to this stress by super-coiling, just like an old telephone cord. But the cell cannot tolerate too much super-coiling. If DNA contorts too much, the cell will suffer. DNA knots and links can cause cells to malfunction or even die. But when a circular chromosome is replicated, the process yields two interlinked chromosomes. That is, the new chromosomes form two rings linked through each other. The new chromosomes must loosen before the cell divides into two cells. Otherwise they would either break on the way to their target cell, or one cell would inherit two interlinked copies of one chromosome and the other one would be missing the chromosome altogether. The cell recruits enzymes to loosen the DNA.

Can you really believe this? Enzymes called Topoisomerases and Recombinases act as scissors and glue for DNA. They can change the geometry and topology of DNA, thus maintaining a stable genome. In E. coli, Topoisomerases work tirelessly during and after replication to maintain healthy levels of super-coiling and to safely loosen the chromosomes. Also, Using mathematics and computer simulations to understand how these enzymes loosen DNA molecules. While the local action is well understood on a biochemical level, how exactly enzymes simplify the topology of DNA is still a mystery. In a recent study, E. coli cells were used as case study where the Topoisomerases don’t work. This showed how to untie a replication link in the minimum number of steps. In general, there can be many loosening pathways. Therefore, using computer simulations to assign probabilities to each pathway indicates that, in the case of replication links, the simplest pathway is the one that enzymes most likely take. Other research on DNA shape are still going on to really find out more implications about the varying changes in the shape of the DNA.

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