Structure And Functions Of DNA

Introduction to DNA

DNA is a fundamental component that drives many life processes in the form of genetic material. The genetic material makes each organism unique as the genetic composition of the material varies among each of us. In layman terms, DNA is the information found in the molecular form that helps in storing and distributing the instructions for making Proteins, which are the lifeblood of the survival. Chromosomes provide space for the storage of molecular instructions necessary for inheritance. There are 46 chromosomes in our body, each one of which is the consequence of thousands of  DNA being assimilated in a sequential manner.  The terms genes, genome, nucleic acids, DNA and RNA are frequently used in the biological sciences. Although they have been used frequently, the context which we use may slightly differ for each. This article is designed to brief the structure, functions and double-helical model of DNA. The scope of DNA  goes beyond biology because many scientific disciplines accommodate the knowledge of DNA and chromosomes as their fundamental aspect. However, modern medicine and biotechnology often use procedures related to DNA and chromosomes. DNA technology is being extensively used in diagnosing many genetic diseases, including sickle-cell disease and Huntington's disease. Not only that, many of the long-term treatment options such as therapeutic hormones, insulin and human growth hormone, are developed as a result of DNA technology.

 

 

 

Discovery of DNA

In the year 1869,  German biochemist  Frederich Miescher has observed the DNA for the first time. At the time, many scientists were unclear about the complete picture of DNA as there were poor evidence about its exact molecular biology. In the year 1953, group of scientists;  James Watson, Francis Crick, Maurice Wilkins and Rosalind Franklin have identified the DNA double helix. Nine years later, Watson  Crick and Wilkins received the Nobel Prize for the discovery of the DNA hence the structural model was named after Watson Crick. DNA (deoxyribonucleic acid) is one of the macromolecules essential for many cellular functions.

 

 

 

Structure of DNA

A brief outline

A number of questions still remains unanswered with regard to the molecular basis of genetic materials. However, it is comprehensively agreed that the DNA is a  polymer holding a long polymerase chain which is made up of reverse spiral nucleotides. A single strand of DNA  is called the helix while the combination of 2 single strands forms a double helical molecule. The twisting of a long chain of a double-helical structure forms a major and a minor grove as shown in th eimage below. The major groove occurs when the polynucleotide backbones are far apart, whereas the minor groove is formed due to the closed arrangement of backbones. The grooves twist around the molecule on opposite sides. Certain proteins bind to DNA to alter its structure or to regulate transcription (copying DNA to RNA) or replication (copying DNA to DNA). The double helical strands run in a parallel direction with each strand containing a series of polynucleotides. A polynucleotide molecule is a biopolymer comprising  13 or more nucleotide monomers bonded by covalent bonds with distinct biological function. The arrangement of polynucleotides in a chin is highly unique and is the essence of genetics. 

 

 

 

 

 

 

Structure of nucleotides

Nucleotides that compose DNA are called deoxyribonucleotides while that of RNA is termed ribonucleotides.  A nucleotide is made up of 3 major elements; pentose sugar, a phosphate group, and a nitrogenous baseA pentose sugar is a simple monosaccharide named so because it contains 5 carbon atoms arranged as 1ʹ, 2ʹ, 3ʹ, 4ʹ, and 5ʹ while 1ʹ is read as “one prime”. The sugars are found bonded with the phosphate groups to form sugar-phosphate backbones which lie on the outside of the nucleotide chain which can be seen in the image below. Phosphate-sugar backbones are present throughout the wall of the double helix on either side. In a molecule of DNA, sugar-phosphate complex acts as a backbone of the structural framework of the genetic material. To create the sugar-phosphate backbone, dNTP releases the two terminal phosphates as a pyrophosphate. The resulting strand of nucleic acid holds a free phosphate group at the 5ʹ carbon end while another free hydroxyl group at the 3ʹ carbon end. The 2 unused phosphate groups from the nucleotide triphosphate are released as pyrophosphate during phosphodiester bond formation. The hydrolysis of pyrophosphate releases the energy necessary to drive nucleotide polymerization.

 

 

 

 

 

 

 

 

Nitrogenous bases

The nitrogenous bases are found in between the 2 helices of polynucleotide chains supported by a hydrogen bond in the middle. There are 2 types of nitrogenous bases; purines and pyrimidines in which the permutation and combination of these 2  types form a series of codons. DNA of humans has 64 varieties of codons which forms a variety of combinations of nitrogenous bases.  Purine bases are indicated as ATGC in DNA  ( In the case of DNA adenine (A) pairs with thymine (T) while cytosine (C) pairs with guanine (G) whereas in the  RNA molecule, uracil takes the place of thymine forming AUGC instead of ATGC. Purines and pyrimidines are otherwise called the base pairs found lying between the double helices. The nitrogenous base is an information-carrying part of the nucleotide structure. For more information on genetic code Click here.

 

 

 

Bonding pattern of purines and pyrimidines

Adenine is a purine, bonding with thymine,  Guanine is also a purine that bonds with cytosine. The bonding between the two strands is enabled by 2 types of hydrogen bonds. Triple hydrogen resulting in a strong adherence between cytosine-guanine while the thymine-adenine bond is supported by a double hydrogen bond. One common aspect found in the nitrogenous bonds of DNA and RNA is the cytosine to guanine bond.

 

 

Functions of Nucleotides

Nucleotides assist in a range of functions. They are the precursors of DNA and RNS in many ways. Nucleotides act as  fundamental catalysts in many biological reactions including the formation of ATP . Some of them work as intermediaries during normal cellular physiology .  Nucleotides assist as metabolic regulators during some hormonal actions 

 

 

 

Types of DNA 

A-DNA is  a right-handed double helix model much comparable to the B-DNA form. A- DNA is a variant of regular DNA that  protects the DNA  during extreme condition such as desiccation.  B-DNA , the most common type with a right-handed helix. Under normal conditions, the majority of DNA demonstrates  B type conformation . On the contrary, the third type, Z-DNA is a left-handed version in which  the double helix winds from right to left in a zig-zag pattern. It was discovered by Andres Wang and Alexander Rich.

 

 

 

Double Helical model of DNA

In the year 1953, James Watson and Francis published a descriptive model for DNA popularly known as ‘double helix’ DNA model.  The model has clearly explained the properties of polynucleotide chains. The double-helical model of DNA  postulated that the 2 types of hydrogen bonds between the 2  opposite sides of nitrogenous bases help them in holding together.  The pairing formula of nitrogenous bases givesthem a unique double-helical formation. The double-helical model is characterized by right-handed coiling or twisting with each twist of the helix measuring 3.4nm or 34 Angstrom units. In an  individual twist, 10 nucleotides are embedded forming 2 groves- the minor groove and the major groove.  The 2 grooves appear like they are twisted around base pairs as shown in the picture. In a double-helical model, the 2 strands run in an antiparallelfashion where the 2 strands are placed in a way that the 5' end (phosphate-bearing end) of one strand joins the 3' end (hydroxyl-bearing end) and vice versa. This is called an antiparallel polarity organization.

 

 

 

Packaging of DNA Helix( Selenoid model of DNA packing)

 

                                

 

 

 

The biological phenomenon of the formation of a chromosome lies behind the packaging of DNA and the entire process is known as the SELENOID model of DNA packing. The sequence of  the formation of chromosomes is  indicated as DNA → nucleosome → solenoid → chromatin fibre → chromatid → chromosome. DNA is compactly packed into nucleosomes while multiple nucleosomes join together forming a long, beaded and thread-like structure; chromatin. The chromatin further recoils to form chromatin fibres. Several chromatin fibres undergoes coiling to form the final unit -chromosomes.  For more information on genetics and heredity Click here.

 

 

 

Note:

The packaging system differs between different species , in Escherichia coli, the total length of its DNA is 1.36 mm whereas the human DNA  measures about 2.2 meters. Similarly, the average distance between the 2  adjacent bases in an E-coli is about 0.34nm when compared to that of the human`s  6 micrometres (µm). In a prokaryote like E. coli, the genetic material is double-coiled (coiled and recoiled) with the help of RNAs. However, in the case of eukaryotes, the packing of DNA is carried out by a positively-charged histone octamer ( 8 histone molecules) closely wrapped around a negatively-charged DNA forming a  nucleosome.  

 

 

 

Further reading

1.      

Differences between DNA and RNA

2.

Replication of DNA

3.

Mechanism of transcription

4.

Introduction to genetics and gene therapy

5.

Gene therapy

 

 

 

 

Questions

  1. Who discovered DNA?

  2. Explain the double-helical structure of DNA

  3. What are nucleotides?

  4. Explain the packaging of DNA.

  5. Explain the Bonding pattern of purines and pyrimidine.

 

 

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