Why Uracil is present in RNA and Thymine in DNA? Let’s Know!

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Ever wondered, why uracil is present in RNA and Thymine in DNA. What’s the reason for this change in DNA & RNA?

Both Thymine and Uracil are nitrogenous bases, both are pyrimidines, both are large having a single ring structure.

We all know that nucleic acids DNA or RNA can contain anyone of the four Nitrogenous bases: Adenine(A), Guanine(G), Cytosine(C), and Thymine(T) / Uracil (U).

The change is that RNA has Uracil instead of Thymine. The other three nitrogenous bases viz. Adenine, Guanine, and Cytosine are the same as in the case of DNA.

Uracil (U) base is a pyrimidine and is very similar to that of DNA Thymine (T).

Uracil is energetically less expensive to produce than thymine, which may account for its use in RNA.

That’s evidence of evolution in the molecular biology of RNA and shows how RNA emerged first, before DNA.

Let’s first know about the difference of Uracil and Thymine then you will better understand the correct answer… So, let’s get started!


Nitrogenous Bases
Nitrogenous Bases

What is Uracil?

Uracil is one of the four nitrogenous bases in RNA molecule that is represented by the letter U. It’s a pyrimidine and has a large single ring structure.

The chemical formula of Uracil is C4H4N2O2 and its IUPAC name is Pyrimidine-2,4(1H,3H)-dione.

A uracil is a demethylated form of a thymine, meaning that a methyl group (CH3) is removed from a molecule of thymine at the 5′ Carbon.

In RNA, Uracil binds to Adenine using two hydrogen bonds. Thus, uracil acts as both a hydrogen bond acceptor and a hydrogen bond donor when bonded with Adenine.

This Uracil binds with a ribose pentose sugar to form the ribonucleoside uridine. And, as soon as the phosphate group attaches to uridine, then uridine 5′-monophosphate is produced.

Uracil is a weak acid and it is very resistant to oxidation and so allows the RNA to exist outside of the nucleus freely without any hassle. This DNA can’t do.

Uracil with its bond with riboses and phosphates performs various biological functions like acting as allosteric regulators, coenzymes for reactions, involved in the biosynthesis of polysaccharides, and the transportation of sugars containing aldehydes, etc.

The presence of Uracil in RNA like mRNA helps in the production of amino acid chains to produce proteins. Almost 37 codons out of the 64 total codons of mRNA have Uracil that helps to encode proteins.

The function of Uracil for termination of protein synthesis can’t also be ignored. Uracil is present in all of the 3 stop codons: UAA, UAG, and UGA.


What is Thymine?

Thymine is one of the four nitrogenous bases in DNA molecule that is represented by the letter T. It’s a pyrimidine and has a large single ring structure.

The chemical formula of Thymine is C5H6N2O2 and its IUPAC name is 5-Methylpyrimidine-2,4(1H,3H)-dione. It is also known as 5-methyluracil.

In DNA, Thymine binds to Adenine using two hydrogen bonds. Thymine is derived by methylation (addition of CH3) of Uracil at the 5′ Carbon position.

The hydrogen bonding between Thymine and Adenine is so strong that it stabilizes the DNA structure more than that of the RNA.

This Thymine binds with a deoxyribose pentose sugar to form the nucleoside deoxythymidine.

When the phosphate group attaches to nucleoside deoxythymidine, then it produces dTMP (deoxythymidine monophosphate), dTDP (Thymidine diphosphate), or dTTP (Thymidine triphosphate).

The presence of Thymine doesn’t allow the DNA to be directly translated to proteins. When the need arises for translation, an mRNA copy is generated from DNA in which the Thymine gets replaced with Uracil.

Thymine-Adenine paring is much common in the DNA of the cell. But, under specific conditions, such as exposure to ultraviolet light, Thymine-Thymine paring (thymine dimers) may also occur, and this can even lead to skin cancer.

Thymine is both beneficial and harmful. That is if the natural chemical structure of thymine gets defected then, the DNA gets mutated leading to the formation of melanoma skin cancer. And, if thymine’s structure is perfect then the DNA is better stabilized.


Thymine Vs. Uracil: What’s the difference?

1. Thymine is the pyrimidine base of the DNA, whereas Uracil is the pyrimidine base of the RNA.

2. Methyl group (CH3) is absent in Uracil whereas, it’s present in thymine at the 5′ Carbon position.

3. Methylation of Uracil leads to Thymine whereas, the demethylation of Thymine leads to Uracil.

4. In RNA, uracil binds to adenine by two hydrogen bonds. In DNA, the uracil is replaced by thymine and thus, adenine binds to thymine by two hydrogen bonds.

5. The chemical formula of Thymine is C5H6N2O2. And, the chemical formula of Uracil is C4H4N2O2.

6. Thymine binds with deoxyribose sugar and phosphate group to form dTMP, dTDP, and dTTP. Whereas, Uracil binds to form uridine 5′-monophosphate.

7. Thymine has a molar mass of 126.1133 g/mol and Uracil has a molar mass of 112.0868 g/mol.


ANSWERED: Why Uracil is present in RNA and Thymine in DNA?

There are so many appropriate reasons to answer it. Let’s know these reasons:

Reason 1: We all know that RNA was first formed before DNA and so its structure is very simple and unstable. And, that Uracil is energetically less expensive to produce than Thymine, which may account for its use in RNA.

Reason 2: Deamination of Cytosine or rarely Adenine or Guanine can create Uracil very easily. Such deamination can cause mutation in DNA that can be detected due to the production of Uracil. And, so to help the DNA repair system to identify the mutated cytosine through the deamination process Thymine is present in DNA.

Reason 3: Thymine has greater resistance to photochemical mutation than Uracil, making the genetic message of DNA more stable. It is seen that the excitation energy in DNA is mobile, and is eventually transferred to thymine residues, which are the sites of radiation damage. So, the presence of Thymine in DNA is a selective advantage.

Reason 4: Evidence of evolution in molecular biology shows why DNA has evolved from RNA. This can be well-understood as, to get rid of mutations the DNA repair system needs to detect the errors of excessive Uracil formation due to Cytosine deamination in DNA. And so, this may be one reason why DNA had evolved to contain Thymine instead of Uracil to make the DNA repair system better.

Reason 5: We all know that RNA is short-lived having an average lifespan of only two minutes. And, that DNA has a life-span of about 6.8 million years, after which all the bonds would be broken. Thus, uracil being unstable is appropriate for RNA, because stability doesn’t matter for RNA as it is very short-lived. Whereas Thymine is very appropriate for DNA where maintaining the genetic sequence with very high stability is necessary.

Reason 6: If Uracil has been there in DNA, then Cytosine deamination would gradually lead to a decrease in G≡C base pairs and an increase in A꞊U base pairs in the DNA of all cells. This would have eliminated various genes and their gene expressions during the course of time. So, having Thymine in place of DNA solved this problem.

Reason 7: As life was evolving from simpler to more complex forms, the need for genetic stability was nature’s first choice and importance. Nature wanted to transform simple ones to present-day complex ones and so the need to transform the primitive RNA containing organisms to the present-day more stable and energy-efficient DNA containing organisms was necessary. This was achieved by simple substitution of DNA as genetic material and making RNA as just an intermediate and in order to attain this goal, Uracil remained in RNA and Thymine in DNA.

Reason 8: Uracil seems to be able to pair with itself and many other bases and this can terminate the gene expression processes if incorporated into DNA making the DNA error-prone. The reason for this behavior of uracil was its freedom with respect to steric factors and hydrophilicity. So, adding a methyl group in 5′ Carbon position of uracil resolved this problem by making Thymine. This enabled an organism to save its genetic information in complimentary copies adding redundancy and more stability to genetic information. This gave DNA the stability to mutate but in a more controlled manner to sustain evolution.


tRNA only has Thymine

It is seen that tRNA is the only type of RNA that contains Thymine. The reason for this is still a tRNA controversy in the molecular biology world.

It’s because there are modified nucleotides in tRNA’s that are specific and are not found in other RNA or DNA. tRNA is 3D complex RNA having unpaired Thymine on its T loop.

The tRNA 3D structure has a complicated conformation showing the other bases along with Thymine in the T loop. This helps in providing stability to these structures.

The T-arm or T-loop is a specialized region on the tRNA molecule which acts as a special recognition site for the ribosome to form a tRNA-ribosome complex during protein biosynthesis or translation.

The T-arm has two components to it; the T-stems and the T-loop. There are two T-stems of five base pairs each.

The T arm is a 5 base pairs stem contains the sequence TΨC where Ψ is a pseudouridine and T is Thymine.

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