Nucleoside | Its important structural properties with 10 FAQs

Nucleoside | Its important structural properties with 10 FAQs

Contents

What is nucleoside?

The two structural components of the nucleoside are a nitrogenous base (also known as nucleobase) and a five-carbon ribose sugar (ribose in RNA and deoxyribose in case of DNA). Due to nitrogenous base and sugar moieties, nucleosides are often regarded as glycosamines.

Nucleoside structure | base nucleoside nucleotide | DNA nucleoside | nucleoside diphosphate

The nitrogenous base present in the nucleoside could be purine or pyrimidine. These nitrogenous bases are bonded to the ribose sugar at fixed positions. The purines are linked to ribose sugar through a glycosidic bond through their N9 work, while pyrimidines link through their N1 position.

The anomeric carbon (the carbon atom associated with the carbonyl group of aldehyde and ketone) of the ribose sugar forms a glycosidic bond with the nitrogenous base.

Nucleoside
Figure: Nucleoside deoxyadenosine https://commons.wikimedia.org/wiki/File:Desoxyadenosin.svg

Types of nucleosides

Six basic types of nucleosides are synthesized in our body

  • Adenosine
  • Guanosine
  • Thymidine
  • Cytidine
  • Uridine
  • Inosine

Nucleoside vs nucleotide | nucleoside 5 monophosphate | nucleoside monophosphate

The simplest way to differentiate between a nucleotide and a nucleoside is as follows:

Nucleoside = Nitrogenous base + Ribose sugar

Nucleotide = Nitrogenous base + Ribose sugar + Phosphate group

Important note: All the bonds among the constituent species (base, sugar and phosphate group) are purely covalent. The ribose sugar lies at the middle position (covalently bound to the nitrogenous base on one side and phosphate group on the other side) inside a nucleotide. 

The nucleic acids (DNA; deoxyribonucleic acid, RNA; ribonucleic acid) found in every organism are chemically nucleotide polymers. 

A nucleoside is the nucleotide lacking a phosphate group.

A nucleoside can be converted into a nucleotide just by a process of phosphorylation (addition of phosphate group). Furthermore, nucleotide can be converted into nucleoside by the process of dephosphorylation (removal of a phosphate group).

FeaturesNucleosidesNucleotides
RoleCapable of forming nucleotides by the process of phosphorylationThey are the monomeric units of the nucleic acids (DNA or RNA) present in almost every cells of an organism
Structural CompositionThey are composed of a ribose sugar and a nitrogenous baseThey are composed of a ribose sugar, a nitrogenous base and a phosphate group
Physiological importanceThey have immense anti-viral and anti-cancer potentialAny change in the sequence or structure of nucleotides can lead to various mutations in an organism which may result into several abnormalities (absence of a protein or an enzyme which alters the physiology)
Table: Difference between nucleoside and nucleotide

Nucleoside triphosphate

The nucleoside triphosphates are chemical substances that contain a nitrogenous base (purine or pyrimidine), a five-carbon sugar molecule (deoxyribose or ribose) and three phosphate groups. Nucleoside triphosphates serve as the monomeric unit to synthesize nucleic acids (DNA or RNA).

The nucleoside triphosphates are involved in the cellular signalling pathways. They also act as a source of energy for carrying out vital body functions (ATP; Adenosine triphosphate is a nucleoside triphosphate referred to as the cell’s energy currency).

The nucleoside triphosphates are generally formed inside our body cells as they have very poor intestinal absorption. 

Figure: Purines and Pyrimidines forms nucleoside mono, di and triphosphates https://upload.wikimedia.org/wikipedia/commons/c/c4/Figure_14_02_01.jpg

The nucleosides can be converted into nucleotides through the process of phosphorylation facilitated by the action of specific cellular kinases. In phosphorylation, the phosphate group is added to the primary alcohol group of the ribose sugar.

Deoxyribose nucleoside triphosphate | nucleoside 5 triphosphate | nucleoside triphosphate dna replication

The nucleoside triphosphates containing deoxyribose are known as the deoxyribonucleoside triphosphate (dNTPs). Before incorporating into the DNA, the two phosphate groups from the nucleoside triphosphate are cleaved. The resulting nucleoside monophosphate (nucleotide) enters into the DNA fragment under synthesis during DNA replication.

There are generally five types of nucleotides found in the DNA or RNA

  •            deoxyuridine triphosphate (dUTP) is found exclusively in RNA
  •            deoxythymidine triphosphate (dTTP) is found only in DNA
  •            deoxyguanosine triphosphate (dGTP) is found in both DNA and RNA
  •            deoxycytidine triphosphate (dCTP) is found in both DNA and RNA
  •            deoxyadenosine triphosphate (dATP) is found in both DNA and RNA

The above-mentioned deoxyribose nucleoside triphosphates are abundantly found in every organism’s genome, while some less common dNTPs are introduced in the DNA for various purposes. The less common dNTPs includes the artificial nucleotides and tautomeric forms of naturally occurring dNTPs.

Incorporating the tautomeric forms of dNTPs in the DNA results in the mismatch of the base pairs during the DNA replication process. 

Suppose the tautomeric form of cytosine gets incorporated into the DNA instead of the cytosine. In that case, the tautomeric form of cytosine forms three bonds with the adenine. It results in a mismatch (cytosine forms complementary base pair with the guanine, if it is forming a pair with adenine, then it will be considered a mismatch). This mismatch changes the sequence of DNA base pairs in the individual and ultimately results in a mutation. 

The thymine is produced by the deamination of the 5-methylcytosine in eukaryotes. It also makes a mismatch that can be recognized by DNA polymerase III and excised by its 3′ to 5′ prime exonuclease activity. The exonuclease activity is also known as proofreading activity which identifies the mismatch and replaces it with correct dNTP.

The four kinds of dNTPs (dGTPs, dCTPs, dTTPs and dATPs) are solely involved in the replication and repair process of the DNA. the proper balance, and the correct complementary base pairing is required for the synthesis of DNA accurately. 

The above-mentioned dNTPs are present only in minute amounts in a eukaryotic cell, sufficient for the DNA replication process. They are present in small quantities because the enzyme ribonucleotide reductase (RNR) gets activated only when the cells enter into the S-phase of the cell cycle. RNR is responsible for converting ribonucleotides into deoxyribonucleotides and ribonucleotide diphosphates into deoxyribonucleotide diphosphates. A slight increase or decrease in the amounts of these dNTPs can result in mutations in the DNA. 

The activity of RNR enzyme is highly regulated. The RNR activity is allosterically regulated by dATP. It gets activated in the presence of dGTPs, dTTPs and dATPs, and it undergoes feedback inhibition by dATP. The expression of RNR and the activity is relatively low in cells present in the G1 phase and non-dividing cells. The activity of RNR and expression level increases during the DNA repair process and the S-phase of the cell cycle.

The RNR activity is also regulated by the stability of RNR subunit proteins, transcription of several genes associated with the cell cycle, and some inhibitory proteins specific to RNR.

Besides their function in DNA synthesis, the adenosine-5-triphosphate, along with other nucleoside-5-triphosphates, acts as substrate in the enzyme-catalyzed reactions of the central metabolic process. 

Is ATP a nucleoside?

An ATP molecule has three structural components: a nitrogenous base (adenine), a ribose sugar and three phosphate groups; hence it is a nucleotide. The ATP or adenosine-5-triphosphate is the prime molecule for transferring and storing energy for cellular processes (therefore called energy currency). Inside the pyrophosphate bond (high energy bond present in ATP), the energy is stored, used for the cellular metabolic reactions, active transport and other energy-consuming cellular processes.

Every organism consume food to obtain energy through the process of respiration. This received energy is stored in the form of ATP. Whereas plants transduce light energy into chemical energy, this energy is stored and utilized in ATP as well. 

The three phosphate groups are joined together through phosphoanhydride bonds (high energy bonds). Breaking of the phosphoanhydride bond through the process of hydrolysis to release energy. The same reaction course of ATP hydrolysis is mentioned below:

ATP –> ADP + Pi + Energy

Furthermore, the ADP (adenosine diphosphate) also has one phosphoanhydride bond; thus, it can also undergo hydrolysis to release more energy. The same reaction course of ADP hydrolysis is mentioned below:

ADP –> AMP + Pi + Energy

The AMP (adenosine monophosphate) formed in the reaction cannot undergo hydrolysis since it lacks a phosphoanhydride bond. This AMP is again recycled into ADP and ATP when the cell gains energy through respiration. The cellular metabolic reactions utilize and recycle AMP, ADP and ATP continuously. 

Guanine nucleoside | deoxyguanosine nucleoside | nucleoside nucleotide and nucleic acid

Among the four nucleo-bases found in the RNA or DNA, Guanine is one of them. Guanine forms complementary base pair with the cytosine of other polynucleotide strand by three hydrogen bonds. The guanine nucleoside is also known as guanosine. The guanine is a purine derivative with a general formula C5H5N5O. The guanine contains imidazole and pyrimidine rings fused via conjugated double bonds. The bicyclic molecule of guanine is a planer because of its unsaturated arrangement.

Deoxyguanosine is one of the four constituent Deoxyribonucleosides found in the DNA. the deoxyguanosine is composed of nitrogenous base guanine (purine nucleobase) and five-carbon deoxyribose sugar. The guanine base is linked through the N9 nitrogen atom to the C1 carbon atom of the deoxyribose sugar. 

Deoxyguanosine has a basic framework structure similar to guanosine, but at the 2′ position of the ribose sugar, the hydroxyl group is missing (thus known as deoxyribose). The deoxyguanosine forms deoxyguanosine monophosphate when a phosphate group gets attached to the 5′ position of the deoxyribose sugar present in deoxyguanosine.

Nucleoside diphosphate kinase

It is also known as nucleoside diphosphokinase or polynucleotide kinase. It is a homo-hexameric protein (consisting of 6 identical subunits) composed of 152 amino acids. It has 17.7 kilodaltons (KDa) (one dalton is equal to one atomic mass unit). This enzyme is found in mitochondria and cytoplasm. 

Nucleoside diphosphate kinase catalyzes the reversible transfer of phosphate group between different nucleoside diphosphate (NDP) and nucleoside triphosphate (NTP). The nucleoside triphosphate donates the phosphate group (donor) while nucleoside diphosphate accepts the phosphate group (acceptor).

The nucleoside diphosphate kinase catalyzed reaction follows a ping pong mechanism.

YDP + ZTP –> YTP + ZDP

Here, Y and Z represent different nitrogenous bases

Figure: Crystal structure of nucleoside diphosphate kinase
https://commons.wikimedia.org/wiki/File:NDPK_structure_.jpg

The equilibrium between different nucleoside triphosphates is maintained by nucleoside diphosphate kinase; it also impacts gene expression, endocytosis, signal transduction and other cellular processes. 

Concentrative nucleoside transporter

The Concentrative nucleoside transporters comprise three structural proteins in humans which are namely, SLC28A1, SLC28A2 and SLC28A3. SLC28A2 is the co-transporter for the purine-specific Na+-nucleoside among these three constituent proteins. The concentrative nucleoside transporter is located on the bile canalicular membrane. However, SLC28A1 selectively transports adenosine and pyrimidine nucleosides. SLC28A1 is a sodium dependent nucleoside transporter. SLC28A1 is also involved in transporting anti-viral nucleoside analogues like zalcitanine, zidovudine, etc.

Alpha mem without nucleosides

The minimum essential medium alpha (MEM- α) is extensively used for the transfected DHFR-negative cells (dihydrofolate reductase) and mammalian cell culture. The MEM- α can be used with adherent mammalian cells, human melanoma cells, primary rat astrocytes, keratinocytes, and various suspensions. MEM- α is usually modified for a various purposes for their extensive cell culture applications.

The general modifications performed in MEM- α are as follows:

  •            MEM- α is often used with L-glutamine and phenol red
  •            L-glutamine can also be used without Deoxyribonucleosides and Ribonucleosides

The minimum essential medium (MEM) is modified by adding ascorbic acid, biotin, vitamin-B12, lipoic acid, sodium pyruvate and other non-essential amino acids to produce MEM- α. 

MEM- α without nucleosides is also available as a selective medium for DHFR-negative cells and DG44 cells [derived from Chinese Hamster Ovary (CHO) cells].

MEM- α is made up of Earle’s salts (salts of calcium and magnesium, bicarbonate buffer and phenol red) and do not contains growth factors, lipids and proteins. Thus, MEM- α requires 10% FBS (Fetal Bovine Serum) supplementation for proper cell growth. MEM- α also needs a 5–10% CO2 environment for maintaining the physiological pH of the culture medium and a bicarbonate buffer system. 

Conclusions

In this article the basic structure of nucleoside is been discussed along with its importance as growth medium.

FAQs

Q1 What are nucleotide and nucleoside?

Answer: The most basic difference between a nucleotide and a nucleoside is the presence of a phosphate group. Nucleoside has a nitrogenous base and a ribose sugar while, a nucleotide has a nitrogenous base, a ribose sugar and a phosphate group.

 Q2 What is the primary function of nucleic acid?

Answer: the primary function of nucleic acids is to store the entire genetic information of an organism. 

Nucleic acid is also responsible for transmitting genetic information from parents to offsprings.

Q3 What are the three main functions of nucleic acids?

Answer: The three main functions of nucleic acids are as follows:

  • It store genetic information
  • It transmits genetic information from parents to off-springs
  • It is involved in the synthesis of RNA, which has a direct role in protein synthesis.

Q4 Uses of nucleoside triphosphates?

Answer: The nucleoside triphosphates or nucleotides (phosphorylated nucleoside) serve as the monomeric units for the synthesis of DNA or RNA by the process of replication and transcription, respectively. Nucleoside triphosphates also have a role in cell signalling and metabolic reactions.

Q5 List the commonly synthesized nucleosides inside our body?

Answer: There are six types of fundamental nucleosides that are synthesized in our body. Inosine, Uridine, Cytidine, Thymidine, Guanosine, and adenosine are the most synthesized nucleosides in our body.

Q6 How are nucleosides transported?

Answer: The nucleosides are transported through Concentrative nucleoside transporters. Some of the nucleosides reach their target via co-transport, like in transport through SLC28A2. While SLC28A1 selectively transport pyrimidine nucleosides and adenine.

Q7 The function of nucleoside diphosphate kinase?

Answer: Nucleoside diphosphate kinase catalyzes the phosphate group transfer between NTP (nucleoside triphosphate) and NDP (nucleoside diphosphate). It is also known as polynucleotide kinase. Nucleoside diphosphate kinase catalyzes a reaction by a ping-pong mechanism.

Q8 What is MEM?

Answer: The minimum essential medium (MEM) is widely accepted for growing cells. It contains a basal medium known as Eagle medium with essential nutrients. MEM is used to cultivate cells in monolayers.     

Q9 Why FBS is used with MEM

Answer: The MEM is often used with the 10% FBS (Fetal Bovine Serum) to supplement proper cell growth. Sometimes it also requires a 5-10% CO2 atmosphere for maintaining the proper physiological pH.

Q10 Composition of MEM alpha

Answer: The MEM alpha generally contains L-glutamine, phenol red, 10% FBS (Fetal Bovine Serum) and 5-10% CO2 environment. It does not include lipids, proteins and growth factors. MEM also contains Earle’s salts (salts of calcium and magnesium with bicarbonate buffer).

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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