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DNA, also known as deoxyribonucleic acid, is a molecule made up of two polynucleotide chains that form a double helix and bear genetic instructions for all known organisms and many viruses' development, function, growth, and reproduction. The nucleic acids present include DNA and ribonucleic acid.This particular extract tells us all about what DNA is, what they are made of and their structure. It also tells us about what DNA packaging is, how nucleosomes play an important role in DNA packaging, steps to DNA packaging and what makes the whole process so important.
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Keyterms: DNA, Deoxyribonucleic acid, Nucleic acids, Ribonucleic acid, DNA packaging, Reproduction, Polynucleotide chain, Double helix
Read Also: Genome Important Notes
DNA Structure
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Watson and Crick suggested the DNA structure in the year of 1953. They said that DNA is a double-helical structure with two polynucleotide strands that run antiparallel to one another. Due to the presence of phosphate groups in the DNA backbone, this double helix is negatively charged. To combat the negative charge, the cell produces histone proteins that bind to the DNA.
Each DNA strand is a long, linear molecule made up of smaller units called nucleotides that join together to form a chain within the double helix. The structure of a DNA molecule is defined as a double helix. A DNA molecule is made up of two strands that form a twisted ladder around each other. The backbone of each strand is made up of alternating sugar (deoxyribose) and phosphate groups.
But have you ever wondered how a DNA molecule can live in a nucleus that is a fraction of its size? The method of DNA packaging may clarify this.
The video below explains this:
Packaging of DNA Detailed Video Explanation:
Read also: Central dogma
DNA Packaging
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DNA is a complex organic molecular structure that can be present in both prokaryotic and eukaryotic cells, as well as in many viruses. It is an inherited material located in the cell nucleus that is primarily responsible for carrying genetic information.
The DNA structure has these following main highlights:
- The DNA strands are helically injured, with each strand forming a right-handed coil.
- Each helix has a 3.32 nm pitch, and one turn is made up of around 10 nucleotides.
- Two base pairs are separated by 0.34 nanometers.
- The gap between two succeeding base pairs and the product of the total number of base pairs make up a DNA's total length.
- A standard strand of DNA is about 2.2 metres long, much longer than a nucleus.
If the distance between two consecutive base pairs is 0.34 nm, the length of DNA double helix in a standard mammalian cell is approximately 2.2 metres (calculated by multiplying the total number of bp by the gap between two consecutive bp i.e. 6.6 109 bp 0.34 10-9m/bp). It is the length that is a lot greater than the dimension of a standard nucleus (approximately 10–6 m).
Though prokaryotes like Escherichia coli lack a fixed nucleus, their DNA is not dispersed throughout the cell. DNA (which is negatively charged) is kept together with proteins (which have positive charges) in a nucleoid region. The nucleoid's DNA is arranged into large loops kept together by proteins. This organisation is even more complicated in eukaryotes. Histones are a group of positively charged, essential proteins. The abundance of amino acid residues with charged side chains determines the charge of a protein. The essential amino acid residues lysines and arginines are abundant in histones. The side chains of both amino acid residues are positively charged. Histones are arranged into eight-molecule units known as histone octamers. The nucleosome is created when negatively charged DNA is wrapped around a positively charged histone octamer.
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| Related Topics | ||
|---|---|---|
| DNA Replication | Human Genome Project | Lac Operon |
| Molecular Basis of Inheritance | Structure of RNA | Transcription |
Why are Nucleosomes considered to be the central player in DNA Packaging?
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A nucleosome is made up of 200 bp of DNA helix. Nucleosomes are the repeated units of chromatin, the thread-like stained (coloured) bodies that can be found in the nucleus. When viewed under an electron microscope, nucleosomes in chromatin appear to be like beads on a string (EM). The beads-on-string arrangement of chromatin is packaged to form chromatin fibres, which are then coiled and condensed to form chromosomes during the metaphase stage of cell division. An additional collection of proteins known as Non-histone Chromosomal (NHC) proteins is needed for the packaging of chromatin at a higher level. Some chromatin regions in a standard nucleus are loosely packed (and stain light) and are referred to as euchromatin. Heterochromatin is more heavily packed chromatin that stains black. Heterochromatin has no transcriptional activity, and is inactive whereas euchromatin is active.
Read More: Structure of DNA
Why is DNA packing important?
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The DNA is approximately 3 metres long and must fit inside the nucleus, which is just a few micrometres in diameter. The DNA molecules must be bundled into an extremely compressed and compact form called chromatin in order to fit into the nucleus.
The DNA is reduced to an 11 nm fibre during the initial stages of packaging, which reflects approximately 5-6 folds of compaction. This is accomplished by wrapping nucleosomes in a specific order.
There are three steps of DNA packaging:
- The first step of DNA packaging is Nucleosome.
- The second step of DNA packaging is Solenoid fibre.
- The third order of DNA packaging is Scaffold loop Chromatids Chromosome.
One of the advantages of DNA packaging is that it can be divided into what we use often and what we don't use at all. There are some parts of DNA that are only needed at specific times. Euchromatin is the loosely packed region of the genome that is mostly necessary for protein synthesis. This makes it easier for DNA to enter and make RNA. The tightly packed DNA in heterochromatin is rarely needed.
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Sample Questions
Ques. Explain the mechanism of DNA replication with the help of a replication fork. What role does the enzyme DNA-ligase play in a DNA replication fork? (2019)
Ans. There is a set of enzymes which are required for the process of replication and the most essential is DNA polymerase. Since it uses the catalysing to polymerise the deoxynucleotides through DNA template these polymerases are quite effective, quick and also helps in attaining a very high level of accuracy through catalysing the reaction. A small level of mistake can also lead to mutations. Along with performing as a substratum, they supply energy required for the polymerisation of the reaction. It is impossible to separate two strands of the DNA molecule in their full length when it comes to a long strand of DNA molecule. The energy needed for the replication is quite high, hence the replication takes place inside a minor opening of the DNA helix, known as the replication fork.
The catalysing of polymerase through the DNA-dependent DNA polymerase is done only in a single direction that is 5’3’. It helps in the creation of certain further complications at the replication fork. As a result the replication on one strand (template that has the polarity 3’5’), isn’t started randomly at a single place and it begins at the base of the replication.
The DNA ligase adds the disrupted synthesised pieces by the generation of the phosphodiester bond through catalyzation.
Ques. Describe the formation of recombinant DNA by the action of EcoRI. (2019)
Ans. The EcoRI helps in splitting the DNA of the two bases G and A only at the time when the order GAATTC is available in the DNA. This process leaves the portions that are single stranded at the end which are protruding stretches and these are known as the sticky ends.
Hydrogen bonds take place between the sticky ends and their correspondingly detached equivalent part. The action that helps in the enzyme DNA ligase is enabled by the stickiness present at the end. Through this procedure the Recombinant DNA is created.
Ques. Explain the roles of the following with the help of an example each in recombinant DNA technology:
(i) Restriction Enzymes
(ii) Plasmids(2018)
Ans.(i) The Restriction Enzyme recognises a particular order of the primary pair or the palindromes and detaches the strand of the DNA at a particular location.
Example: EcoRI
(ii) Since the Plasmids are small in size and self-replicating in nature they are employed in genetic engineering as cloning vectors.
Example: Ti Plasmid.
Ques. Describe Meselson and Stahl's experiment that was carried in 1958 on E.Coli. Write the conclusion they arrived at after the experiment. (2016)
Ans. To assimilate 15N into DNA, Meselon and Stahl grew E.coli in 14NH4Cl for a prolonged number of generations. After the assimilation is done, cells are moved into 14NH4Cl, then the DNA which has been drawn out is separated in CsCl and calculated to get their density. The DNA drawn out, following the culture of one generation exhibited intermediate hybrid density, DNA drawn out following two generations exhibited light DNA and hybrid DNA.
Ques. What exactly do you mean by DNA packaging? (1 mark)
Ans. The folding of an organism's DNA into a very compact form that can fit inside the nucleus of a cell is known as DNA packaging.
Ques. What part of DNA packaging do histones play? (1 mark)
Ans. Histones are those proteins that help DNA in the process of packaging. The DNA encircles the histones. Histones are the positively charged proteins that bind to negatively charged DNA with ease. Histones are also very active in the regulation of gene expression.
Ques. What are the effects of acetylation and phosphorylation on DNA packaging? (1 mark)
Ans. Acetylation and phosphorylation loosen the wrapping of DNA by making it more negatively charged. Acetyltransferases are the enzymes that bind acetyl groups to histones.
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