Chemistry and Metabolism of Biomolecules #7: Chemistry of Nucleic Acids

in steemstem •  22 days ago

The nucleic acids. The most important of all biomolecules highlighted in the former installments of this series. The DNA, which is a nucleic acid is instrumental for the passage of information from one generation to another.

Think for a moment, how random we would look without information stored in our parents being passed on to us. Without the DNA, we wouldn’t share traits with our parents.

There’s also the argument that most genetic diseases like diabetes and haemophilia won’t affect us if there was no means of passing information from parents to offspring. A fair argument I’ll say.

The ATP (Adenosine monophosphate), the energy currency of the cell is a very important nucleotide and also a medium cells can store large amounts of energy for future utilization.

But I’ll like to let you know what nucleic acids really are, what they are made of, the types out there while highlighting their relevance to life in the process.


What are Nucleic Acids anyway


Nucleic acids: The most important biomolecule in nature (License: Public Domain]: Pixabay

Nucleic Acids are simply polymers of nucleotides. The nucleotides are molecules that contain a nitrogenous base (molecules which possess nitrogen atoms in their structure and act as bases), a phosphate group and a sugar unit (Ribose in RNA, Deoxyribose in DNA).

The nitrogenous bases found in nucleic acids are classified into;

  1. The pyrimidine bases
  2. The purine bases

The purine and pyrimidine bases (License: Public Domain]: Wikicommons

The pyrimidine bases have simple structures. They specifically have nitrogen atoms at positions 1 and 3 of their structure. They have a close resemblance to the structure; pyridine. There are three pyrimidine bases known to man. They include; Cytosine, Uracil and Thymine. They are denoted by C, U and T respectively. They exist in pairs with purine bases in DNA and RNA.

The purine bases are just pyrimidine bases with imidazole rings fused to their structures. It is the most widely occurring nitrogen containing heterocyclic compound in nature. The only two known purine bases are; Adenine and Guanine.


Chargaff’s Rule


The chargaff’s rule states that in a DNA molecule, the number of purine bases must be equal to the number of pyrimidine bases. The million dollar question is; How is this constancy maintained ?

The purine and pyrimidine bases have self activating and self inhibiting properties. When enough pyrimidine bases are produced for example. The pyrimidine bases inhibit enzymes necessary for its further production while activating enzymes necessary for the further production of purine bases. This way, constancy is easily achieved.

The process by which pyrimidine inhibits its further production is known as feed-back inhibition while the process by which it activates the production of more purine bases is known as feed-forward activation.

The purine and pyrimidine bases pair in a complimentary manner and thus, knowing the number of one purine base is a reliable way of knowing the number of its complimentary pyrimidine base. Guanine always pairs with cytosine while adenine always pairs with thymine in DNA or uracil in RNA. These base pairs must be in equal amounts according to Chargaff’s rule.

The Sugar moiety in both DNA and RNA is a five-carbon sugar. In RNA, the Sugar moiety is Ribose. In DNA, the Sugar moiety is a derivative of Ribose; Deoxyribose. I’ll highlight where they differ in the next section.


Types of Nucleic Acids


The two types of Nucleic acids are:

  1. The Deoxyribonucleic Acid
  2. The Ribonucleic Acid


Deoxyribonucleic acid (DNA)


The double helical structure of DNA (License: Public Domain]: Wikicommons

DNA is a polynucleotide. It consists of monomers of either one of these four nitrogenous bases (Adenine, Guanine, Cytosine and Thymine). These nitrogenous bases pair in a complimentary manner. Adenine pairs with Thymine. Guanine pairs with Cytosine.

DNA is a double helical structure. It has genetic information stored in it, actually, at certain regions known as genes. The DNA is the starter molecule in the central dogma of molecular biology (where information stored in DNA is expressed as proteins).

The two DNA strands contain the same information and during replication, they are passed on differently to two daughter DNAs. Thus, a daughter DNA has its first strand from one parent DNA and the second strand from another parent DNA.

Illustrative Representation of the Difference between a Ribose and a Deoxyribose Sugar (License: CC-BY-SA 3.0, Author: Boumphreyfr]: Wikicommons

It is particularly interesting to note that DNA contains deoxyribose. This is the case when the ~OH group at carbon-2 is replaced by a hydrogen (H) atom giving rise to the structure seen above. This is one of the areas where DNA differs from RNA.

DNA is known to code for proteins but it’s important to note that about 98% of a total DNA strand codes for nothing. This region is referred to as The non-coding region. They are practically not involved in transcription.

The DNA is almost totally resistant to cleavage so that biological information can be preserved. Mutation however messes this up and we tend to get wrong info sometimes.

DNA is packed as chromosome in cells of eukaryotes and are largely duplicated during DNA replication. The proteins known as histones are largely responsible for keeping DNA in this organized state.

The two DNA strands in a typical DNA molecule is known to run in opposite directions. This is why the DNA strands are described as complimentary but opposite running strands. A DNA strand is known to have 3’ OH end and a 5’ phosphate end. Thus, DNA can exhibit bi-directionality since it can run in either the 3’ to 5’ or 5’ to 3’ direction.

The stability of DNA is large due to hydrogen bonds that exist between its base pairs as well as interactions between the individual nucleobases. This confers a huge stability on the DNA molecule.

The DNA molecule is largely confined to the nucleus in eukaryotes but there are cases where they can be found in chloroplasts or chloroplasts. In prokaryotes however, the DNA is found exclusively in the cytoplasm.

DNA molecules are also mostly circular in prokaryotes but linear in eukaryotes.

It has been hypothesized that the human genome has three BILLION base pairs arranged into 46 different chromosomes. Matter-of-factly speaking, if the DNA in one human cell was stretched out over a distance it will be approximately be over 2 meters long. Sounds unbelievable ? I know. This quote from sciencefocus.com goes ahead to blow your mind

If you stretched the DNA in one cell all the way out, it would be about 2m long and all the DNA in all your cells put together would be about twice the diameter of the Solar System.

How can the cell fit such length in just 6 microns of space ? Well, thank the topoisomerases. These enzymes can induce and remove supercoils in DNA. Supercoiling is the process where a molecule is continuously coiled upon itself until it assumes a super tight and compact structure.

Supercoiling of DNA is necessary for its appropriate fitting into the cell. However, during replication and transcription, DNA must be present in a stretched out form so its sequence can be read by enzymes necessary for those two processes. DNA gyrase and DNA helicase come in here leading to the unfolding and stabilizing of the unfolded DNA to aid the process of transcription and replication.

I will illustrate the process of DNA synthesis with time and trust me, you’ll appreciate it. Right now, let’s move on to the other type of nucleic acid.


Ribonucleic acid (RNA)


A comparative look at the DNA and RNA (License: CC-BY-SA 3.0, Author: Sponk]: Wikicommons

RNA is a product of DNA transcription. Not totally correct. In proper biochemical terms, the messenger RNA (mRNA) is the product of DNA transcription. The RNA is very similar to the DNA structurally but there are notable differences.

Firstly, RNA contains Ribose and not deoxyribose as seen in DNA as it’s five carbon Sugar moiety.

Secondly, RNA is mostly single stranded molecule which is totally opposite to the DNA which is mostly double stranded.

Thirdly, RNA contains Adenine, Guanine, Cytosine and Uracil while DNA contains Adenine, Guanine, Cytosine and Thymine. The difference being the substitution of Uracil for Thymine or vice versa in either of them.

The RNA are of different types; the messenger RNA (mRNA), the transfer RNA (tRNA) and the ribosomal RNA (rRNA).

The mRNA is produced during transcription. It solely carries information from the DNA to the ribosome where it is translated to protein.

tRNA is instrumental for translation. It contains anticodons which is specific for a particular codon and aids the tRNA in recognizing a particular codon. It also has an arm where amino acids are attached before it is transported to the polypeptide chain according the particular codon read by the tRNA.

The rRNA bind to the mRNA and generally aid the process of protein synthesis. They actually aid the formation of peptide bonds between amino acids elongating the polypeptide chain. The rRNA has a large subunit and a small subunit which possess ribozyme activity. The mRNA is held between the subunits while peptide bonds are being formed between aligning amino acids simultaneously. Quite dynamic I’ll say.


Summary


Nucleic acids are vital components in biological systems. They are the most important biological molecules in nature. DNA and RNA are vital for protein synthesis. The central dogma illustrates that perfectly. The chemistry part of this series is done. The metabolism will come up much later. I’ll introduce novel topics in biochemistry which will most likely blow your minds in my future posts or just complete the metabolism installments. I’m in a limbo. Thank you for doing this with me anyway. Till next time


References


DNA. Wikipedia articles (accessed on May 3rd, 2018)
RNA. Wikipedia articles (accessed May 3rd, 2018)
Chargaff’s Rule. Wikipedia articles (accessed May 4th, 2018).
Chatterjea, M. N. (2012). Textbook of Medical Biochemistry. (8th Edition). Jaypee Brothers Medical Publishers. New Delhi. India. pp. 215 - 225.
Vasudevan et al. (2011). Textbook of Biochemistry. (6th Edition). Jaypee Brothers Medical Publishers. New Delhi. India. pp. 457-468.


Image Sources
All images are from pixabay and wikicommons licensed under creative commons and eligible for commercial use.


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The process by which pyrimidine inhibits its further production is known as feed-back inhibition while the process by which it activates the production of more purine bases is known as feed-forward activation.

feedback!! I first heard this term in my control-engineering classes. It seems that lot of engineering processes are happening inside cells. :)

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Ah yes. Everything is just interconnected at some point.

Chemistry lessons always makes me scared. I just get tangled up on those atomic bonds and their structure too easily, lol. But the DNA, RNA thing always been like a 'next gen tech' to me.

Thirdly, RNA contains Adenine, Guanine, Cytosine and Uracil while DNA contains Adenine, Guanine, Cytosine and Thymine.

I remember memorizing the parts of DNA & RNA back in 11th grade. Thank God that I don't have to deal with chemistry or biology things anymore, hehehe.
A good post, KING. Cheers!

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Thanks a lot for such an amazing comment, @ied. Oops you located me this time😆

Well, chemistry is amazing. You would love it if you dedicated more time to it

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you see another Bangladeshi is afraid of chemistry :D

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Lol. I think it’s a Bangladesh thing 😂

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:D hehe

First off, it is not just Bangladesh that is afraid of Organic Chemistry. When I took my last class Watson and Crick were just in the process of turning the whole field upside down.

This is just a stupendous article. Thank you for it.

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LOL 😆

Your post has been selected as #adsactlyspostoftheday :)

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Thank you :)

I remember when you mentioned that I'll start loving BCH when you start your series and without mincing words, I'm beginning to appreciate the contributions of Biochemist to helping us understanding the basic building blocks of our body.

The DNA at least is one I'm quite familiar with, to an extent sha. Now, I'm beaming with confidence learning more about it and the RNA knowledge bagged too.

Thanks @kingabesh. You're really an authority in this field

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Thanks for the nice words man. I’m glad you got to learn a lot

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You made it easy...

Always a pleasure buddy..

You took me back to school on this one, I never liked biochemistry, I'm always forgetting how to spell the compounds, most of their spellings looked alike to me.

In cases of DNA mutations, how exactly does mutation occur?

I can't wait to have my mind blown by your future novel articles.

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I hope to have your mind blown. Mutation occurs when a nucleotide in the DNA sequence is altered by any means. Could be by chemicals, ultraviolet rays or a genetic defect. When that happens, wrong proteins are synthesized and that manifests phenotypically in most cases. In some cases, there are no obvious effects. I’ll talk about mutation soon. You’ll appreciate it.

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The way you explained shows you have perfect understanding of the subject in particular. I applaud your intelligence.
Following you right away.

You must be a strong man to handle that book by "chatterjea" still have it in my shelf as a reference book, quite difficult to get info from it.
Nice post bro, that was a fantastic write up on nucleic acids

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Thanks for the kind words man. Glad you loved it

Hey @kingabesh, thank you for the education regarding Nucleic Acids. I must admit that I never studied Chemistry but I feel like I'm learning a lot from your blogs.

I knew a little something about DNA and RNA, however I didn't know there were three different types of RNA (mRNA - tRNA - rRNA).

Looking forward to your future Metabolism posts.
Take care!

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Thanks for dropping by, LordNero. Im glad youve learned something from my blog 😁

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I don't understand this part

When enough pyrimidine bases are produced for example. The pyrimidine bases inhibit enzymes necessary for its further production while activating enzymes necessary for the further production of purine bases.

Shouldn't be that when enough is produced it inhibits and when there is not enough it activates.

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Actually that’s what I’m trying to say but it doesn’t stop at inhibiting it’s own synthesis, it goes ahead to activate the synthesis of another molecule. It’s particularly not very common to see a molecule inhibit and activate at the same time but the purine and pyrimidine bases seem to do this interchangeably.

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Ah I see. So then there must be a relation between the concentration of the activating and inhibiting enzyme.

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actually, there's a relation between the concentration of purine and pyrimidine bases.

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Ah so the concentration between purine is kept constant because they need to be paired.

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Exactly. You get the drill 😄

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