The DNA

You may have had a relative say to you, “You look exactly like your father” or “You have the same eyes as your mother!” Have you ever wondered what is the reason for this? It is because of your DNA! You get 50% of your DNA from your father and the other 50% from your mother. Want to learn more about the components and structure of this interesting molecule? Let’s dive in.

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Structure of DNA

The genetic material in most organisms is DNA or Deoxyribonucleic acid; whereas in some viruses, it is RNA or Ribonucleic acid. A DNA molecule consists of two polynucleotide chains i.e. chains with multiple nucleotides. Let’s understand the structure of this chain in detail.

Structure Of Polynucleotide Chain

A nucleotide is made of the following components:

• Pentose sugar – A pentose sugar is a 5-carbon sugar. In case of DNA, this sugar is deoxyribose whereas, in RNA, it is ribose.
• Phosphate group
• Nitrogenous base – These can be of two types – Purines and Pyrimidines. Purines include Adenine and Guanine whereas pyrimidines include Cytosine and Thymine. In RNA, thymine is replaced by Uracil.

Nitrogenous base + pentose sugar (via N-glycosidic linkage) = Nucleoside.

Nucleoside + phosphate group (via phosphoester linkage) = Nucleotide.

Nucleotide + Nucleotide (via 3′-5′ phosphodiester linkage) = Dinucleotide.

Many nucleotides linked together = Polynucleotide.

A polynucleotide has a free phosphate group at the 5′ end of the sugar and this is called the 5′ end. Similarly, the sugar also has a free 3′-OH group at the other end of the polynucleotide which is called the 3′ end. The backbone of a polynucleotide chain consists of pentose sugars and phosphate groups; whereas the nitrogenous bases project out of this backbone.

Check out our other article on DNA here.

Double Helix Structure

DNA is a long polymer and therefore, difficult to isolate from cells in an intact form. This is why it is difficult to study its structure. However, in 1953, James Watson and Francis revealed the ‘double helix’ model of the structure of DNA, based on X-ray diffraction data from Maurice Wilkins and Rosalind Franklin.

This model also reveals a unique property of polynucleotide chains – Base pairing. It refers to the hydrogen bonds that connect the nitrogen bases on opposite DNA strands. This pairing gives rise to complementary strands i.e. if you know the sequence of bases on one strand, you can predict the bases on the other strand. Additionally, if each DNA strand acts as a template for synthesis (parent) of a new strand, then the new double-stranded DNA (daughters) produced are identical to the parental DNA strand.

Salient Features of DNA Double-Helix

• It consists of two polynucleotide chains where the sugar and phosphate group form the backbone and the nitrogenous bases project inside the helix.
• The two polynucleotide chains have anti-parallel polarity i.e. if one strand has 5′ → 3′ polarity, the other strand has 3′ → 5′ polarity.
• The bases on the opposite strands are connected through hydrogen bonds forming base pairs (bp). Adenine always forms two hydrogen bonds with thymine from the opposite strand and vice-versa. Guanine forms three hydrogen bonds with cytosine from the opposite strand and vice-versa. Therefore, a purine always pairs with a pyrimidine on the other strand, giving rise to a uniform distance between the two strands of the helix.
• The two strands coil in a right-handed fashion. Each turn of the helix is 3.4nm (or 34 Angstrom units) consisting of 10 nucleotides. These nucleotides are at a distance of 0.34nm (or 3.4 Angstrom units).
• The helix is stable because of the base pairs that stack over one another and hydrogen bonds that hold the bases together.

Packaging of DNA Helix

If you calculate the length of DNA in a typical mammalian cell, it is approximately 2.2 meters. The dimension of a typical nucleus is only about 10^-6 meters! Then, how does such a long polymer fit in the nucleus of a cell?

Prokaryotes like E. coli, do not have a defined nucleus. Here, the negatively-charged DNA is held together in large loops by positively-charged proteins in a structure called ‘nucleoid’. In Eukaryotes, however, the organization of DNA in the nucleus is much more complex and is as follows:

• The negatively-charged DNA is wrapped around a positively-charged histone octamer i.e. a unit of 8 histone molecules. This forms a ‘Nucleosome‘. Histones are positively-charged proteins that are rich in basic amino acids – arginines and lysines. A typical nucleosome has 200bp of DNA helix.
• Many nucleosomes join together to form a thread-like structure – Chromatin in the nucleus. The nucleosomes in chromatin appear as ‘beads-on-string’ under the electron microscope.
• The chromatin is packaged to form chromatin fibres which are further coiled and condensed to form chromosomes. The higher level packaging of chromatin requires another set of proteins – Non-histone Chromosomal (NHC) proteins.

Note: Euchromatin is the region of chromatin that is loosely packed and therefore stains lightly; whereas Heterochromatin is the densely packed region and therefore stains dark.

Solved Example For You

Q1: In DNA, adenine pairs with thymine. What does adenine pair with, in RNA?

1. Cytosine
2. Uracil
3. Thymine
4. Guanine

Solution: The answer is ‘b’. Adenine pairs with Uracil in RNA.