Purine | Its fundamental Structure

Contents

Purine definition

Purines are generally organic compounds consisting of two aromatic heterocyclic rings. They are usually water-soluble and contains nitrogen and carbon atoms in their rings. Hence they are known as heterocyclic. They are broadly classified into normal purines, substituted purines and tautomeric purines.

Purine base

Generally, two nitrogenous bases in the DNA and RNA are found to contain purine rings 

Adenine which is known as 6-aminopurine                      

Guanine, which is known as 6-oxy-2-amonipurine

The amino group in Adenine is present at the C6 position (carbon atom present at the 6th position of the ring). Whereas guanine’s amino group is present at the C2 position, guanine also contains a carbonyl group at the C6 position.

Purine nucleotides

Nucleotides are chemically the phosphate esters of nucleosides. Nucleotides are the monomeric units present in nucleic acids such as DNA and RNA. Hence they are called polynucleotides.

Nucleotides are composed of three essential structural components:

  1. A purine base (Adenine or Guanine)
  2. A 5 C sugar (Deoxyribose or Ribose)
  3. A phosphate group
Figure: Structure of purine nucleotide and its importance in DNA double helical structure https://commons.wikimedia.org/wiki/File:0322_DNA_Nucleotides.jpg

Purine structure

Purines are generally double-ringed structures comprising nine members (five carbon atoms and four nitrogen atoms). The giant ring consists of six atoms (two nitrogen atoms and four carbon atoms), while the smaller ring consists of five atoms (three carbon atoms and two nitrogen atoms). Two carbon atoms are common in the bigger and smaller ring.

purine
Figure: Purine Structure
https://commons.wikimedia.org/wiki/File:Blausen_0323_DNA_Purines.png

Purine adenine

Adenine is a purine derived nitrogenous base represented by the letter “A”. The IUPAC name of Adenine is 6-aminopurine. Adenine forms complementary base pairing with thymine and Uracil in DNA and RNA, respectively. Adenine reacts with a ribose sugar to form adenosine nucleoside, which is found in RNA and ATP. Whereas, when Adenine reacts with deoxyribose, it comprises deoxyadenosine nucleoside, which is present in DNA. Adenine forms various tautomeric compounds having the ability of interconversion. 

Derivatives of Adenine perform a variety of essential functions in various biochemical pathways. The cell’s energy currency, “the ATP” (Adenosine triphosphate), is also an adenine derivative. Several Adenine derivatives such as FAD (Flavin adenine dinucleotide) and NAD (Nicotinamide adenine dinucleotide) act as coenzymes for several biochemically essential enzymes. Purine derivatives also have specific roles in proteins synthesis and DNA replication as well.

Purines and pyrimidines

These are the primary structural and fundamental constituents of DNA and RNA, vital for storing genetic information inside the cell. The impairments in the cellular metabolism of purines and pyrimidines result in various consequences. 

Malignant cells exhibit a property of divide and synthesize DNA and RNA at an exceptionally faster rate. The nucleotide synthesis inhibitors play a significant role in inhibiting DNA replication in rapidly dividing malignant cells and ultimately resulting in a decrease in malignant cell growth.

Purines and pyrimidines are often involved in the enzyme catalysis as they act as a coenzyme. Some essential purine derivative like NAD (Nicotinamide adenine dinucleotide) and FAD (Flavin Adenine Dinucleotide) acts as a coenzyme for several enzymes that belongs to the class of oxidoreductases and hydrolases. In general, such as enzymes of glycolysis and Kreb’s cycle. NAD is often used in various other forms in the reactions such as NAD+ (oxidized form of NAD), NADP (Phosphate conjugated form of NAD), NADH (A reduced form of NAD) etc. 

Purine vs pyrimidine

Nucleotides are classified based on basic fundamental structure into purines and pyrimidines. They hold together both the strands of the DNA via hydrogen bonds which are formed between purines and pyrimidines. The nitrogenous base pairing occurs following Chargaff’s rule, which states that Adenine pairs with Thymine while Guanine pairs with Cytosine. 

PurinesPyrimidines
Purines are bigger in sizePyrimidines are smaller in size
Contains two rings made up of carbon and nitrogen atomsContain only one ring made up of carbon and nitrogen atoms
They are of two types: Adenine (A) and Guanine (G) Both are common in DNA as well as RNAThey are of three basic types: Thymine (T), Cytosine (C) and Uracil (U) Cytosine is common in both DNA and RNA Thymine is specifically found in DNA While Uracil is only present in RNA
Table: Basic difference between purines and pyrimidines

Purine hydrogen bonds

Purine nitrogenous bases usually contain nitrogen and oxygen, which are considered among the most electronegative elements. The lone pair of electrons present in oxygen and nitrogen atoms acts as the hydrogen bond acceptors. In contrast, the hydrogen attached with the oxygen and nitrogen develops a partial positive charge because of the oxygen and nitrogen atom’s electronegativity. This hydrogen atom acts as the hydrogen bond donor. 

The non-covalent attractive forces hold together the hydrogen bond donor as well as the hydrogen bond acceptor. This non-covalent attractive force is known as a hydrogen bond. Let’s look into the case of deoxyguanosine. The oxygen atom attached to the C6 acts as hydrogen bond acceptor while the hydrogen atoms attached to the N1 and N2 acts as hydrogen bond donor.  

Why do purines bond with pyrimidines

The structural framework of purines and pyrimidines enables them to form H-bonds with each other. For example, guanine (purine) and Cytosine (pyrimidine) have certain atoms which are capable of forming a Hydrogen bond (they can either provide acidic hydrogen or electronegative atom for the formation of Hydrogen bond). Guanine and Cytosine have three such pairs of atoms. Hence, they form three hydrogen bonds. Whereas Adenine and thymine have two such pairs, they can form two hydrogen bonds.

Purine to purine hydrogen bond or pyrimidine to pyrimidine hydrogen bond is not possible because of the difference in the atoms’ orientation capable of forming Hydrogen bonds. Purine-Purine or Pyrimidine-Pyrimidine cannot form complementary base pairs because of the difference in their tautomeric forms. 

Figure: AT base pairing https://commons.wikimedia.org/wiki/File:AT_DNA_base_pair.svg
Figure: GC base pairing https://commons.wikimedia.org/wiki/File:Base_pair_GC.svg

Purine pyrimidine mnemonic

To remember the basic information related to purines and pyrimidines, people have designed some phrases resembling the information regarding purines and pyrimidines.

“Pure as gold” we can remember the types of purines by this mnemonic. 

Here, 

Pure resembles “Purine.” 

as resembles “Adenine.”

gold resembles “guanine.”

“Cut the pie” we can remember the types of pyrimidines by this mnemonic.

Here,

CUT means “Cytosine, Uracil and Thymine.”

Pie resembles “pyrimidines.”

Conclusions

In this article we have discussed about the purine structure, nature of bonding and their complementary base pairing with pyrimidines in details. to know more about purines and their biosynthesis click here

FAQs

Q1. what purine means

Answer: Purines are crystalline nitrogenous compounds with a general formula C5H4N4. They are one of the main constituents of nucleic acids, such as deoxyribonucleic acids and ribonucleic acids. Purines are abundantly found in meat. Adenine and guanine are the purines nucleotides present in DNA and RNA. Purines are the precursor compounds in uric acid formation and are excreted out from the body from urine. The increased levels of uric acid inside the body often invites various physiological abnormalities.

Q2. what purine is found in DNA

Answer: Two types of purines (double-ringed nitrogenous bases) are found in deoxyribonucleic acid (DNA), namely:

Adenine: it is also known as 6-aminopurine, chemical formula: C5H5N5, molecular mass = 135.13 grams per mole

Guanine: it is also known as 2-aminopurin-6-one, chemical formula: C5H5N5O, molecular mass = 151.13 grams per mole

Q3. what purine pyrimidine pairs can you form.

Answer: Purine forms a complementary base pair with pyrimidine by following Chargaff’s rule, which states that Adenine will always base pairs with thymine, and guanine will always base pairs with Cytosine. This pairing pattern is also known as Watson-Crick base pairing. Purine always pairs with pyrimidine because the space between two nucleotide strands of the DNA is only 20 Å in which only 3 rings can accommodate if purine forms a base pair with another purine. There will be 4 rings between both the strands of the DNA. If pyrimidine includes a base pair with another pyrimidine, there will be 2 rings between the DNA strands. Both conditions will be unstable for the DNA structure. 

Q4. purine vs pyrimidine

Answer: Purines contains double-ringed structures, while pyrimidines contains single ringed structures. Rings of purines and pyrimidines are composed of nitrogen and carbon atoms. Two basic types of purines (Adenine and Guanine) are found in DNA/RNA while, three basic types of pyrimidines (Thymine, Cytosine and Uracil) are found in DNA/RNA.

Q5. purine vs protein

Answer: the constituent atoms of general proteins are similar to the purines; both are composed of C, H, O and N atoms. But, purine contains amino and keto groups, while proteins have amino and carboxylic acid groups (as they are the polymers of amino acids).

Purines are the components of nucleic acids, while proteins are the components of other cellular structures.

Q6. Is purine a protein

Answer: Purine is not a protein because it is not made up of amino acids. But, some of the purine derivatives like Xanthine and Hypoxanthine are known as purine amino acids.

Q7. What is the difference between a nucleotide and a nucleoside?

Answer:  Nucleotide contains a nitrogenous base, a ribose sugar and a phosphate group, while nucleoside contains nitrogenous base and ribose sugar.

Nucleotides are the monomer of the DNA/RNA, while nucleosides are the precursors molecules of nucleotides.

Nucleotides are involved in various biochemical pathways, but nucleoside does not.

Q8. Does single-stranded DNA exist?

Answer: Yes, single-stranded DNA does exist; some viruses have ss DNA as their genome. But the ss DNA is less stable than double-stranded or dsDNA.

Q9. Which is more stable? DNA or RNA

Answer: The deoxyribose sugar is much more stable than ribose sugar. Since DNA contains deoxyribose sugar; thus, it is much stable than RNA. RNA has a lifetime of a few minutes after completing its lifetime; RNA degrades while in the DNA is functional throughout that cell’s life, even for decades.

Q10. Which base pair is more stable among AT and GC?

Answer: Guanine and Cytosine form three hydrogen bonds, while Adenine and Thymine form only two hydrogen bonds. Hence, the GC base pair is more stable, and the DNA containing a higher amount of GC base pair is also more durable.

About Dr. Abdullah Arsalan

I am Abdullah Arsalan , Completed my PhD in Biotechnology. I have 7 years of research experience. I have published 6 papers so far in the journals of international repute with an average impact factor of 4.5 and few more are in consideration. I have presented research papers in various national and international conferences. My subject area of interest is biotechnology and biochemistry with special emphasis on Protein chemistry, enzymology, immunology, biophysical techniques and molecular biology.

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