Packaging of DNA Helix- Discovery, Structure and Importance

“The process of tightly packing the DNA molecule to fit into the nucleus of a cell is known as Packaging of DNA Helix“. DNA is known to be the blueprint of life. You might be shocked to know that the length of a DNA molecule is around 2.2m2.2m, whereas the nucleus in which it is packed is just 10–6m10–6m. 

You might wonder how such a long molecule fits into a small nucleus? How does DNA packaging take place in a cell? Get answers to all your questions related to the packaging of DNA. This article will learn about DNA, its composition, terminologies associated with DNA packaging, DNA packaging in Eukaryotic and Prokaryotic cells, and much more.

Define DNA

DNA, also known as Deoxyribonucleic Acid, can be defined as a biopolymer of deoxyribonucleotides joined with each other by phosphodiester bonds. It is genetic material found in the majority of organisms, including certain classes of viruses. Only a few other viruses, all viroids and prions, have genetic materials other than DNA. It contains all the genetic information of an organism and instructions required to make important proteins and has the ability to replicate itself.

Composition of DNA

1. A DNA molecule is made up of two DNA strands known as polynucleotide chains.
2. These polynucleotide chains are composed of smaller units that are called nucleotides joined by phosphodiester bonds.
3. Each nucleotide consists of three subunit molecules, a phosphate group, a sugar group and one of the four types of nitrogen bases.
4. The four nitrogen bases in DNA are guanine, adenine, cytosine and thymine.
5. The nucleotides are connected together into chains along with phosphate and sugar groups alternating with each other to form a strand of DNA.
6. DNA is acidic in nature and negatively charged due to the presence of phosphate groups.

What is Packaging of DNA Helix?

DNA packaging is the method of folding the DNA molecule to fit into the nucleus of a cell. Chromosomal DNA packaged inside ultramicroscopic nuclei of a cell with the assistance of histones is named packaging of DNA Helix. Nucleosomes are positively charged proteins that are closely attached to DNA which is negatively charged in nature to form complex compounds. Each nucleosome consists of DNA wound \(1.65\) times around eight histone proteins.

Discovery of DNA Helix

American biologist Watson and English physicist Francis Crick based on previous information proposed a very simple but famous double helix model for the structure of DNA. Salient features of the double helix structure of DNA are:

1. DNA consists of two polynucleotide chains. The backbone is constituted by sugar-phosphate, and the bases project inside.
2. The two chains of DNA run in anti-parallel fashion with \(5′ \to 3’\) polarity in one and \(3 \to 5’\) polarity in the other chain.
3. One complete turn is called pitch or gyre. Each turn of the double helix or the pitch of the helix is \(3.4\,nm\left({34\,\overset{o}{\mathop A} } \right).\)
4. It has roughly \(10\) base pairs in each turn. The distance between two adjacent base pairs is approximately equal to \(0.34\,nm\left({3.4\,\overset{o}{\mathop A} } \right)\) The diameter of the double helix is \(2\,nm\) \(\left( {20\,\mathop A\limits^0 } \right).\)
5. Distance between two bases present in opposite strands is \(1.1\,nm\left({11\,\overset{o}{\mathop A} } \right).\)
6. Sugar and phosphate form the backbone of the helix, while bases are aligned towards the axis.
7. The bases are \(H\)-bonded with each other based on Chargaff’s rule, i.e. Adenine binds to Thymine by \(2H\) -bonds, while Cytosine binds to Guanine by \(3H\)-bonds.
8. The plane of one base pair stacks over the other in a double helix. This, in addition to \(H\)-bonds, confers stability to the helical structure.
9. The turn of the helix forms a larger groove called a major groove which is \(2.2\,nm\left({22\,\overset{o}{\mathop A} } \right)\) and a minor groove which is about \(1.2\,nm\left({12\,\overset{o}{\mathop A} } \right).\)
10. These grooves are responsible for binding with proteins and enzymes to regulate functions of DNA and provide stability to the structure of DNA.

Fig: Watson and Crick Double helix model

Terminologies Associated with Packaging of DNA Helix

Chromosomes

Chromosomes are the structures in which DNA and histone proteins are closely packed. In the nucleus of every cell, the DNA molecule is packaged into thread-like structures called chromosomes with the help of histone proteins. Each chromosome has two chromatids joined together, a constriction point called the centromere. Centromere divides the chromosome into two sections or arms. The two arms of the chromosome are ‘p arm’ and ‘q arm’, where ‘p arm’ is referred to as short arm and ‘q arm’ is referred to as the long arm. The location of the centromere on each chromosome gives the chromosome its specific characteristic shape and can be used to locate the position of its specific genes.

Histones

Histones are basic proteins that are positively charged. The charge of a protein depends on the presence of the types of ammo acids with charged side chains. Histones are rich in basic amino acid units like lysines and arginines. Both these amino acids carry positive charges in their side chains. Histones are organised to form a group of eight molecules called a histone octamer. Every nucleosome is composed of DNA wrapped around a core of eight histone proteins. Each core consists of four different types of histone are \(H2A,\,H2B,\,H3\) and \(H4\) each of these are present in two copies. Another form of histone, \(H1\) binds to both the nucleosome and also the linker DNA.

Chromatin

A number of nucleosomes together form a structure called chromatin. Chromatin is a fibre or a string with beads of nucleosomes that are arranged at a regular distance from one another. It has a diameter of about \(10\,nm.\) It is visible as thread-like stained or coloured bodies in the nucleus.

Nucleosome

The negatively charged DNA is wrapped around the positively charged histone octamer to form a structure called a nucleosome. The nucleosomes in chromatin look like beads-on-string structures when seen under the electron microscope. The nucleosome is the fundamental subunit of chromatin.

Linker DNA

Linker DNA is double-stranded DNA present between two nucleosome cores and holds the cores together in cooperation with histone \(H1.\)

Linker Histone

The linker histone is a protein that binds with the nucleosome, while the core histones from the octamer core of the nucleosome around which the DNA is wrapped.

Fig: Cell to DNA and Structure of DNA Helix

Packing of DNA Helix in Prokaryotes

In terms of DNA helix packaging, packaging in prokaryotes is relatively simpler as compared to eukaryotic packaging. The features of prokaryotic packaging of DNA helix is as follows:

1. In prokaryotic bacteria like E.coli, the size of DNA is \({\rm{4}}{\rm{.6}}\) million base pairs, i.e. approximately \(1.36\,mm\) in length, when cut and stretched out.
2. It is packed inside a small bacterial cell with a phenomenon called supercoiling which means that DNA is either under-wound (less than one turn of the helix per \({\rm{10}}\) base pairs) or over-wound (more than \({\rm{1}}\) turn per \({\rm{10}}\) base pairs) from its normal relaxed state.
3. In most prokaryotes, stored genetic material is a single, circular chromosome located in an area of the cytoplasm and protected only by the outer membranes or the cell wall.
4. Such an organisation is called nucleoid or genophore.
5. Other proteins and enzymes such as DNA gyrase aid in supporting the supercoiled structure.

Packaging of DNA Double Helix in Eukaryotes

The packing of DNA is much more complex than in prokaryotes. The arrangement of DNA helix in Eukaryotes is as follows:

1. In Eukaryotes, each chromosome consists of a long DNA molecule and have a different type of packing to compress their DNA inside the nucleus.
2. DNA is wrapped around histone proteins, and forms structures called nucleosomes.
3. The DNA is negatively charged due to the presence of phosphate groups.
4. The histone proteins that are rich in basic amino acids (mainly lysine and arginine) are organised to form an octamer.
5. Octamer core or nucleosome core or nu-body is made up of two subunits of \(H2A,\,H2B,\,H3\) and \(H4\) histones.
6. The opposite charges of DNA and histones facilitate the tightly wrapping of DNA around the nucleosome core, i.e. histones, by the development of electrostatic forces between them.
7. About \(200\,bp\) of DNA is wrapped over nu-body to complete about \({\rm{1}}\frac{3}{4}\) turns. This forms a nucleosome of size \(110 \times 60\overset{o}{\mathop A}. \)
8. The adjacent nucleosomes are bound to each other with the help of linker DNA, having a length of about \(80\,bp.\)
9. The linker DNA is held in place by the \(H1\) histone.
10. The nucleosomes undergo stacking over each other to form solenoid or chromatin fibre.
11. The stacking and further coiling is supported by non-histone proteins.
12. Each helix of solenoid consists of approximately \({\rm{6}}\) nucleosomes stacked over each other.
13. This causes the length of the solenoid to become around \(30\,nm.\)
14. There are mainly two types of chromatin fibres, euchromatin and heterochromatin.
15. The euchromatin fibres are \({\rm{30}}\) to \(80\,nm\) in diameter and are loosely packed and stain light. These fibres make up about \({\rm{2\% }}\) of the genome and mainly consist of genes.
16. Heterochromatin fibres are about \(300\,nm\) in diameter and are more densely packed and stained dark. These fibres make up about \({\rm{98\% }}\) of the genome and mainly consist of repetitive DNA.
17. The solenoid undergoes further condensing during the metaphase stage to form chromosomes.

Fig: Structure of a Nucleosome

Difference Between Packaging of DNA Helix in Eukaryotes and Prokaryotes

Significance of DNA Helix Packaging

DNA packaging is a crucial process in the living cell. A large amount of DNA is closely packed in the small nucleus of every cell by DNA packaging.

1. DNA packaging helps the DNA to fit well within the small size of a cell nucleus.
2. DNA packaging is essential during cell division which facilitates the condensation of chromatin to form chromosomes.
3. Due to highly packed DNA due to DNA packaging, it is easy to turn genes on or off as per requirement.
4. DNA helix packaging not only protects the cells but also regulates genes that are accessed.

Summary

DNA is a biopolymer of deoxyribonucleotides that are joined by phosphodiester bonds. The DNA packaging helps in folding the DNA in an appropriate fashion to reduce its size sufficiently small enough to fit inside the nucleus of a eukaryotic cell and cytoplasm of a prokaryotic cell. The packaging of DNA helix in eukaryotes is more complex than prokaryotes. In a eukaryotic cell, the packaging of DNA helix requires a histone octamer core called the nu-body or nucleosome core. Prokaryotic DNA helix packaging doesn’t require such an assembly.

FAQs

Q.1. What is the major function of a Packaging of DNA Helix?
Ans: DNA packaging is a crucial process in the living cell. A large amount of DNA is closely packed in the small nucleus of every cell by DNA packaging.
1. DNA packaging helps the DNA to fit well within the small size of a cell nucleus.
2. DNA packaging is essential during cell division which facilitates the condensation of chromatin to form chromosomes.
3. Due to highly packed DNA due to DNA packaging, it is easy to turn genes on or off as per requirement.
4. DNA helix packaging not only protects the cells but also regulates genes that are accessed.

Q.2. Define DNA.
Ans: DNA, also known as deoxyribonucleic acid, can be defined as a biopolymer of deoxyribonucleotides joined with each other by phosphodiester bonds.

Q.3. What is Packaging of DNA Helix?
Ans: Chromosomal DNA packaged inside ultramicroscopic nuclei of a cell with the help of histones proteins in a eukaryotic cell is called packaging of DNA Helix.

Q.4. What is the correct order of DNA packaging?
Ans: DNA is packed into a compressed structure called chromatin during DNA packaging. This process occurs through a specific order of packaging. The correct order of DNA packaging in eukaryotic chromosomes is \({\rm{Nucleosome}} \to {\rm{looped}}\,{\rm{domains}} \to {\rm{chromatin}}\,{\rm{fibre}} \to {\rm{heterochromatin}}{\rm{.}}\)

Q.5. How is DNA packaging different in eukaryotes from prokaryotes?
Ans: In eukaryotes, DNA is wrapped around proteins called histones to help package the DNA into smaller spaces. Most prokaryotes do not have histones. They contain a single, circular chromosome that is found in an area of the cytoplasm called the nucleoid or genophore, where the chromosomal DNA is located.

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