Nucleic Acids- Nucleosides and Nucleotides

Nucleotides are the basic units of nucleic acids, such as DNA and RNA. They are composed of three parts: a nitrogenous base, a pentose sugar, and a phosphate group. The nitrogenous base can be either a purine or a pyrimidine, which are heterocyclic aromatic compounds with nitrogen atoms in their rings. The pentose sugar can be either ribose or deoxyribose, which are five-carbon monosaccharides with an oxygen atom attached to each carbon atom. The phosphate group is a phosphorus atom bonded to four oxygen atoms, one of which is also bonded to the sugar.

The structure of a nucleotide can be represented by the following general formula:

The nitrogenous base is attached to the 1` carbon of the sugar by a beta-glycosidic bond, which is a covalent bond formed between the anomeric carbon of the sugar and a nitrogen atom of the base. The phosphate group is attached to the 5` carbon of the sugar by an ester bond, which is a covalent bond formed between the hydroxyl group of the sugar and the phosphorus atom of the phosphate. The phosphate group can also be attached to another nucleotide at the 3` carbon of the sugar by another ester bond, forming a phosphodiester linkage. This linkage connects nucleotides into a linear chain, forming a polynucleotide or a nucleic acid.

The structure of a nucleotide determines its properties and functions in living organisms. The nitrogenous base is responsible for carrying genetic information and forming complementary base pairs with other nucleotides. The pentose sugar provides structural stability and flexibility to the nucleic acid backbone. The phosphate group provides negative charge and polarity to the nucleic acid molecule and participates in energy transfer reactions.

Nucleotides can be classified into different types based on their nitrogenous base, pentose sugar, and number of phosphate groups. For example, adenosine triphosphate (ATP) is a nucleotide with adenine as the base, ribose as the sugar, and three phosphate groups. Cytidine monophosphate (CMP) is a nucleotide with cytosine as the base, ribose as the sugar, and one phosphate group. Deoxythymidine diphosphate (dTDP) is a nucleotide with thymine as the base, deoxyribose as the sugar, and two phosphate groups.

In summary, nucleotides are the building blocks of nucleic acids that store and transmit genetic information in living cells. They consist of three components: a nitrogenous base, a pentose sugar, and a phosphate group. They are linked by covalent bonds into linear chains that form complex structures and perform various functions in cellular metabolism.

Nitrogenous bases, also called nucleobases, are organic molecules that contain nitrogen and act as bases in chemical reactions. They are essential components of nucleotides, which are the building blocks of nucleic acids such as DNA and RNA.

There are two major classes of nitrogenous bases: purines and pyrimidines. Purines have a double-ring structure with a six-membered ring fused to a five-membered ring. The two purines found in nucleic acids are adenine (A) and guanine (G). Pyrimidines have a single six-membered ring structure. The three pyrimidines found in nucleic acids are cytosine (C), thymine (T), and uracil (U).

The nitrogenous bases form complementary pairs in DNA and RNA by forming hydrogen bonds between them. In DNA, adenine pairs with thymine and guanine pairs with cytosine. In RNA, adenine pairs with uracil and guanine pairs with cytosine. The pairing of the bases is specific and follows the rule of A-T/U and G-C. This rule ensures that the genetic information encoded in the sequence of bases is preserved during replication and transcription.

The nitrogenous bases also have different chemical properties that affect their interactions with other molecules. For example, purines are more soluble in water than pyrimidines, and they absorb light in the ultraviolet region at 260 nm. This allows for the detection and quantification of nucleic acids using spectrophotometry. The nitrogenous bases also have different functional groups attached to their rings, such as amino, keto, or methyl groups. These groups influence the stability and reactivity of the bases.

The nitrogenous bases are derived from simple organic compounds such as pyridine and imidazole. They can be synthesized by living organisms or obtained from dietary sources. Purines are abundant in meat products, especially from internal organs, while pyrimidines are more common in plants, such as peas, beans, and lentils. The metabolism of nitrogenous bases involves various enzymes and pathways that regulate their synthesis and degradation.

DNA stands for deoxyribonucleic acid. It is the molecule that carries the genetic information of all living organisms. DNA is composed of two strands of nucleotides that are coiled around each other to form a double helix. Each strand has a backbone of deoxyribose sugar and phosphate groups, and a sequence of nitrogenous bases that are complementary to each other. The four bases in DNA are adenine (A), thymine (T), guanine (G) and cytosine (C). A pairs with T and G pairs with C through hydrogen bonds, forming the base pairs that hold the two strands together.

The structure of DNA was first discovered by James Watson and Francis Crick in 1953, based on the X-ray diffraction data of Rosalind Franklin and Maurice Wilkins. They proposed that DNA has a right-handed helical structure with 10 base pairs per turn and a diameter of about 2 nm. The two strands run in opposite directions, meaning that they are antiparallel. The sugar-phosphate backbone is on the outside of the helix, while the bases are on the inside, facing each other. The distance between adjacent base pairs is about 0.34 nm, and the length of one turn of the helix is about 3.4 nm.

The structure of DNA allows it to store and transmit genetic information. The sequence of bases in one strand determines the sequence of bases in the other strand, which means that each strand can serve as a template for copying or replicating the other strand. This process is called DNA replication and it occurs before cell division to ensure that each daughter cell inherits an identical copy of DNA from the parent cell. The sequence of bases also encodes the information for making proteins, which are the molecules that perform most of the functions in living cells. The process of converting DNA information into protein is called gene expression and it involves two steps: transcription and translation. Transcription is the synthesis of a messenger RNA (mRNA) molecule that is complementary to a segment of DNA called a gene. Translation is the synthesis of a protein molecule that is determined by the sequence of nucleotides in the mRNA.

DNA is organized into structures called chromosomes, which are located in the nucleus of eukaryotic cells or in the cytoplasm of prokaryotic cells. Each chromosome consists of a long molecule of DNA that is tightly coiled around proteins called histones to form a compact structure called chromatin. Chromatin can be further condensed into visible structures during cell division. Humans have 23 pairs of chromosomes, one pair inherited from each parent. Each chromosome has a specific number and location of genes that determine the traits or characteristics of an organism.

DNA is also present in some organelles outside the nucleus, such as mitochondria and chloroplasts. These organelles have their own circular DNA molecules that are independent from the nuclear DNA. Mitochondrial DNA (mtDNA) is inherited from the mother only, while chloroplast DNA (cpDNA) is inherited from either parent depending on the species. These organelle DNAs encode some proteins that are essential for their functions, such as cellular respiration and photosynthesis.

DNA is a remarkable molecule that has shaped life on Earth for billions of years. It is responsible for storing and transmitting genetic information, encoding proteins, organizing chromosomes, and regulating cellular processes. Understanding the structure and function of DNA is essential for understanding biology, medicine, evolution, and biotechnology.

• A pentose sugar is a monosaccharide (simple sugar) with five carbon atoms .
• The chemical formula of many pentoses is C₅H₁₀O₅, and their molecular weight is 150.13 g/mol.
• Pentoses are very important in biochemistry. Ribose is a constituent of RNA, and the related molecule, deoxyribose, is a constituent of DNA .
• In nucleotides, both types of pentose sugars are in their beta-furanose (closed five-membered ring) form .
• The linear form of a pentose, which usually exists only in solutions, has an open-chain backbone of five carbons. Four of these carbons have one hydroxyl functional group (–OH) each, connected by a single bond, and one has an oxygen atom connected by a double bond (=O), forming a carbonyl group (C=O). The remaining bonds of the carbon atoms are satisfied by six hydrogen atoms.
• Thus the structure of the linear form is H–(CHOH)x–C(=O)–(CHOH)4-x–H, where x is 0, 1, or 2.
• The term "pentose" sometimes is assumed to include deoxypentoses, such as deoxyribose: compounds with general formula C5H10O5-y that can be described as derived from pentoses by replacement of one or more hydroxyl groups with hydrogen atoms.
• Ribose has an OH group at the 2` position of the sugar ring, whereas deoxyribose has an H instead. This difference affects the stability and flexibility of the nucleic acids.
• The aldehyde functional group in the carbohydrates react with neighbouring hydroxyl functional groups to form intramolecular hemiacetals. The resulting ring structure is related to furan, and is termed a furanose. The ring spontaneously opens and closes, allowing rotation to occur about the bond between the carbonyl group and the neighboring carbon atom yielding two distinct configurations (alpha and beta). This process is termed mutarotation.

Structure of ribose and deoxyribose

 H OH H H
| | | |
H - C - C - OH H - C - C - OH
| | | |
OH -C<--| H - C<--|
| | | |
H - C - OH H - C - OH
| |
H H
Ribose Deoxyribose

While a nucleotide is composed of a nucleobase, a five-carbon sugar, and one or more phosphate groups, a nucleoside has only a nitrogenous base and a five-carbon sugar. In a nucleoside, the base is bound to either ribose or deoxyribose via a beta-glycosidic linkage at 1’ position. This means that the anomeric carbon of the sugar (the one that was part of the carbonyl group before cyclization) is attached to the nitrogen atom of the base.

The name of a nucleoside is derived from the name of the base by adding the suffix -idine for pyrimidines and -osine for purines. For example, cytosine becomes cytidine and adenine becomes adenosine. Some common nucleosides are shown below:

Nucleosides can also have modified bases or sugars, such as inosine (which has hypoxanthine instead of adenine), pseudouridine (which has an extra carbon-carbon bond in uracil), and ribothymidine (which has thymine instead of uracil in RNA).

Nucleosides are important precursors for nucleotide synthesis, as they can be phosphorylated by kinases to form nucleotides. They can also be degraded by nucleosidases to release free bases and sugars. Nucleosides have various biological functions, such as acting as neurotransmitters (e.g., adenosine), regulating gene expression (e.g., 5-methylcytidine), and participating in metabolic pathways (e.g., S-adenosylmethionine).

Nucleotides are organic molecules composed of three subunits: a nitrogenous base, a pentose sugar and a phosphate group. They serve as the building blocks of nucleic acids, such as DNA and RNA, which store and transmit genetic information in living organisms. Nucleotides also have various roles in cellular metabolism and signaling, such as providing chemical energy, acting as cofactors, mediating hormone responses and regulating enzyme activities. Some of the properties of nucleotides are:

• Solubility: Nucleotides are soluble at body pH, which is around 7.4. This allows them to dissolve in the aqueous environment of the cell and participate in biochemical reactions.
• Absorption: Nucleotides absorb ultraviolet (UV) light at 260 nm, which is the wavelength that corresponds to the maximum energy transition of the nitrogenous bases. This property can be used to detect and quantify nucleotides in biological samples.
• Hydrogen bonding: Nucleotides can form hydrogen bonds with each other and with other molecules through their nitrogenous bases and phosphate groups. Hydrogen bonds are weak electrostatic interactions that stabilize the structure of nucleic acids and facilitate their interactions with proteins and other molecules. For example, DNA consists of two strands of nucleotides that are held together by hydrogen bonds between complementary bases: adenine (A) pairs with thymine (T) and guanine (G) pairs with cytosine (C). RNA can also form hydrogen bonds within itself or with other molecules, such as DNA or proteins.
• Phosphorylation: Nucleotides can be phosphorylated or dephosphorylated by enzymes that add or remove phosphate groups from them. Phosphorylation is a key mechanism that regulates the activity and function of nucleotides and their derivatives. For example, adenosine triphosphate (ATP) is the main energy currency of the cell that transfers phosphate groups to other molecules to drive metabolic processes. ATP can be synthesized from adenosine diphosphate (ADP) and inorganic phosphate by phosphorylation, or hydrolyzed back to ADP and phosphate by dephosphorylation. Similarly, cyclic adenosine monophosphate (cAMP) is a nucleotide derivative that acts as a second messenger in hormone signaling pathways. cAMP can be synthesized from ATP by phosphorylation, or degraded to AMP by dephosphorylation.

Purine and pyrimidine bases are the nitrogenous bases that form part of the nucleotides, which are the building blocks of nucleic acids. Purine and pyrimidine bases differ in their structure, properties and functions.

• Structure: Purine bases have a double-ring structure composed of a six-membered pyrimidine ring fused to a five-membered imidazole ring. The two purine bases found in nucleic acids are adenine and guanine. Pyrimidine bases have a single-ring structure composed of a six-membered ring with two nitrogen atoms. The three pyrimidine bases found in nucleic acids are cytosine, thymine and uracil .
• Properties: Purine and pyrimidine bases have different physical and chemical properties that affect their interactions with other molecules. Some of these properties are :
  • Solubility: Purine bases are sparingly soluble in water, while pyrimidine bases are more soluble at body pH.
  • Absorption: Purine and pyrimidine bases absorb light in the ultraviolet region at 260 nm, which can be used for their detection and quantitation.
  • Hydrogen bonding: Purine and pyrimidine bases can form hydrogen bonds with each other through their nitrogen and oxygen atoms. The specific pairing of purine and pyrimidine bases in DNA and RNA is determined by the number and location of hydrogen bonds. For example, adenine pairs with thymine (in DNA) or uracil (in RNA) by forming two hydrogen bonds, while guanine pairs with cytosine by forming three hydrogen bonds.
  • Acidity: Purine and pyrimidine bases have acidic properties due to the presence of nitrogen atoms that can donate protons. The acid dissociation constants (pKa) of purine and pyrimidine bases vary depending on their structure and environment. For example, cytosine has a pKa of 12.16, while thymine has a pKa of 9.7.
  • Tautomerism: Purine and pyrimidine bases can exist in different tautomeric forms, which are interconvertible by the movement of protons or electrons. Tautomers are isomers that differ in the position of a double bond or a hydrogen atom. For example, guanine can exist as a lactam or lactim form, while cytosine can exist as an amino or imino form. Tautomerism affects the base pairing and mutagenesis of nucleic acids.
• Functions: Purine and pyrimidine bases have various roles in cellular metabolism besides being part of nucleic acids. Some of these functions are :
  • Energy transfer: Purine nucleotides such as adenosine triphosphate (ATP) and guanosine triphosphate (GTP) are involved in energy transfer reactions in various metabolic pathways.
  • Signal transduction: Purine nucleotides such as cyclic adenosine monophosphate (cAMP) and cyclic guanosine monophosphate (cGMP) act as second messengers in signal transduction events mediated by hormones and other extracellular stimuli.
  • Coenzyme formation: Purine nucleotides are part of several important coenzymes such as nicotinamide adenine dinucleotide (NAD+), flavin adenine dinucleotide (FAD), coenzyme A (CoA) and tetrahydrofolate (THF), which participate in various enzymatic reactions.
  • Neurotransmission: Purine nucleosides such as adenosine and purine nucleotides such as ATP can function as neurotransmitters or neuromodulators in the central and peripheral nervous systems.
  • Allosteric regulation: Purine nucleotides can bind to allosteric sites on some enzymes and affect their activity by changing their conformation or affinity for substrates.
  • Activated intermediates: Purine nucleotides can serve as activated intermediates in various biosynthetic reactions such as methylation, sulfation, glycosylation and phosphorylation.

A pentose sugar is a monosaccharide with five carbon atoms and the chemical formula C5H10O5. Pentose sugars are very important in biochemistry, as they are the components of the five-carbon sugar backbone of nucleic acids. The two most common pentose sugars in nucleic acids are ribose and deoxyribose, which differ by the presence or absence of an oxygen atom at the 2` position of the sugar ring.

Pentose sugars can exist in two forms: open-chain (linear) or closed-chain (cyclic). The open-chain form has a carbonyl group (C=O) at one end of the carbon chain and four hydroxyl groups (OH) attached to the other carbon atoms. The closed-chain form has a five-membered ring structure that resembles furan, and is therefore called a furanose. The ring can open and close spontaneously in aqueous solutions, allowing the rotation of the carbon atoms around the bond between the carbonyl group and the adjacent carbon atom. This rotation results in two distinct configurations: alpha (α) and beta (β), depending on whether the hydroxyl group at the anomeric carbon (the one attached to the carbonyl group) is below or above the plane of the ring.

The pentose sugars can also form esters with phosphate groups, which are important for linking nucleotides together by phosphodiester bonds. The phosphate group can attach to any hydroxyl group of the sugar, but usually it is at the 5` position in nucleic acids. The phosphate group gives a negative charge to the nucleotide, which affects its interactions with other molecules.

Some of the properties of pentose sugars are :

• They are monosaccharides that contain five carbon atoms.
• They can form esters with phosphate groups, which are essential for nucleic acid synthesis and structure.
• They can exist in two forms: open-chain or closed-chain (furanose).
• They can have two configurations: alpha or beta, depending on the orientation of the hydroxyl group at the anomeric carbon.
• They are different in DNA and RNA: DNA has deoxyribose, which lacks an oxygen atom at the 2` position, while RNA has ribose, which has an oxygen atom at the 2` position.
• They are important for photosynthesis, respiration, and nucleic acid synthesis.

In nucleic acids, nucleotides contain either a purine or a pyrimidine base—i.e., the nucleobase molecule, also known as a nitrogenous base—and are termed ribonucleotides if the sugar is ribose, or deoxyribonucleotides if the sugar is deoxyribose . Ribose is a five-carbon sugar with one oxygen atom attached to each carbon atom. Deoxyribose is derived from ribose by the loss of an oxygen atom at the 2` position. The difference between ribose and deoxyribose is shown below:

The type of sugar determines the type of nucleic acid that the nucleotides form. Ribonucleotides are the building blocks of ribonucleic acid (RNA), which is involved in protein synthesis, gene expression, and regulation. Deoxyribonucleotides are the building blocks of deoxyribonucleic acid (DNA), which stores and transmits genetic information. The structure of RNA and DNA is shown below:

The type of sugar also affects the stability and function of the nucleic acids. RNA is more prone to hydrolysis than DNA because of the presence of the 2` hydroxyl group in ribose, which can act as a nucleophile and attack the phosphodiester bond. This makes RNA more reactive and versatile than DNA, but also more susceptible to degradation by enzymes and chemicals. DNA is more stable and durable than RNA because of the absence of the 2` hydroxyl group in deoxyribose, which reduces the reactivity and increases the resistance to hydrolysis. This makes DNA more suitable for long-term storage and transmission of genetic information.

Nucleosides are molecules that consist of a nitrogenous base and a pentose sugar. The nitrogenous base can be either a purine or a pyrimidine. Based on the type of nitrogenous base, nucleosides can be classified into two major groups:

• Purine nucleosides: These are nucleosides that have a purine base, such as adenine or guanine, attached to the sugar. Examples of purine nucleosides are adenosine, guanosine, inosine, and xanthosine. Adenosine and guanosine are the most common purine nucleosides in nucleic acids. Inosine is a modified nucleoside that can base pair with any of the four bases in RNA. Xanthosine is a rare nucleoside that can be formed by deamination of guanosine.

• Pyrimidine nucleosides: These are nucleosides that have a pyrimidine base, such as cytosine, thymine, or uracil, attached to the sugar. Examples of pyrimidine nucleosides are cytidine, uridine, thymidine, and pseudouridine. Cytidine and uridine are the most common pyrimidine nucleosides in nucleic acids. Thymidine is a modified nucleoside that is found only in DNA. Pseudouridine is another modified nucleoside that is formed by isomerization of uridine and is found in some types of RNA.

The classification of nucleosides based on nitrogenous base type is useful for understanding the structure and function of nucleic acids. For example, the ratio of purine to pyrimidine nucleosides in a nucleic acid reflects its stability and specificity. The presence of modified nucleosides in a nucleic acid indicates its role in regulation and modification of gene expression.

Nucleotides are organic molecules that serve as the basic structural units for DNA and RNA, the substances that control all hereditary characteristics. They also have a variety of roles in cellular metabolism, such as:

• Providing chemical energy in the form of nucleoside triphosphates, such as ATP, GTP, CTP, and UTP, for many cellular functions that demand energy . Energy is stored in our body as ATP, which can be converted to ADP or AMP when there is a need for energy.
• Participating in cell signaling and acting as essential chemical links in the response of cells to hormones and other extracellular stimuli. The predominant second messenger is cyclic-AMP (cAMP), a cyclic derivative of AMP formed from ATP.
• Acting as coenzymes, which are required to catalyze many biochemical reactions by enzymes . For example, a dinucleotide, nicotinamide adenine dinucleotide (NAD), participates in many oxidation reactions as an electron carrier, along with the related compound nicotinamide adenine dinucleotide phosphate (NADP).
• Serving as neurotransmitters and as signal receptor ligands. Adenosine can function as an inhibitory neurotransmitter, while ATP also affects synaptic neurotransmission throughout the central and peripheral nervous systems. ADP is an important activator of platelet functions resulting in control of blood coagulation.
• Controlling numerous enzymatic reactions through allosteric effects on enzyme activity.
• Serving as activated intermediates in numerous biosynthetic reactions. These activated intermediates include S-adenosylmethionine (SAM) involved in methyl transfer reactions as well as the many sugar coupled nucleotides involved in glycogen and glycoprotein synthesis.

The structure of every protein, and ultimately of every biomolecule and cellular component, is a product of information programmed into the nucleotide sequence of a cell’s nucleic acids. Polynucleotides consist of nucleosides joined by 3′,5′-phosphodiester bridges. The genetic message resides in the sequence of bases along the polynucleotide chain.

Nucleotides are distributed in the nucleus and cytoplasm of various organs, tissues, and cells along with nucleic acids, and are used as components of nucleic acids to participate in basic life activities such as genetics, development, and growth of organisms.

Nucleotides are essential for all the functions performed by a living cell and for transferring information to new cells or the next generation of living organisms.

We are Compiling this Section. Thanks for your understanding.