1.
Base pair
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A base pair is a unit consisting of two nucleobases bound to each other by hydrogen bonds. They form the blocks of the DNA double helix. Dictated by specific hydrogen bonding patterns, Watson-Crick base pairs allow the DNA helix to maintain a regular helical structure that is dependent on its nucleotide sequence. The complementary nature of this structure provides a backup copy of all genetic information encoded within double-stranded DNA. Many DNA-binding proteins can recognize specific base pairing patterns that identify particular regulatory regions of genes, intramolecular base pairs can occur within single-stranded nucleic acids. The size of a gene or an organisms entire genome is often measured in base pairs because DNA is usually double-stranded. Hence, the number of base pairs is equal to the number of nucleotides in one of the strands. The haploid human genome is estimated to be about 3.2 billion bases long and to contain 20, a kilobase is a unit of measurement in molecular biology equal to 1000 base pairs of DNA or RNA. The total amount of related DNA base pairs on Earth is estimated at 5.0 x 1037, in comparison, the total mass of the biosphere has been estimated to be as much as 4 TtC. Hydrogen bonding is the interaction that underlies the base-pairing rules described above. Appropriate geometrical correspondence of hydrogen donors and acceptors allows only the right pairs to form stably. Purine-pyrimidine base pairing of AT or GC or UA results in proper duplex structure, the only other purine-pyrimidine pairings would be AC and GT and UG, these pairings are mismatches because the patterns of hydrogen donors and acceptors do not correspond. The GU pairing, with two bonds, does occur fairly often in RNA. Higher GC content results in higher melting temperatures, it is, therefore, on the converse, regions of a genome that need to separate frequently — for example, the promoter regions for often-transcribed genes — are comparatively GC-poor. GC content and melting temperature must also be taken into account when designing primers for PCR reactions, the following DNA sequences illustrate pair double-stranded patterns. By convention, the top strand is written from the 5 end to the 3 end, thus and this is due to their isosteric chemistry. One common mutagenic base analog is 5-bromouracil, which resembles thymine, most intercalators are large polyaromatic compounds and are known or suspected carcinogens. Examples include ethidium bromide and acridine, an unnatural base pair is a designed subunit of DNA which is created in a laboratory and does not occur in nature
2.
Hydrogen bond
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Hydrogen bonds can occur between molecules or within different parts of a single molecule. Depending on geometry and environment, the hydrogen bond free energy content is between 1 and 5 kcal/mol and this makes it stronger than a van der Waals interaction, but weaker than covalent or ionic bonds. This type of bond can occur in molecules such as water and in organic molecules like DNA. Intermolecular hydrogen bonding is responsible for the boiling point of water compared to the other group 16 hydrides that have much weaker hydrogen bonds. Intramolecular hydrogen bonding is responsible for the secondary and tertiary structures of proteins. It also plays an important role in the structure of polymers, in 2011, an IUPAC Task Group recommended a modern evidence-based definition of hydrogen bonding, which was published in the IUPAC journal Pure and Applied Chemistry. An accompanying detailed technical report provides the rationale behind the new definition, a hydrogen atom attached to a relatively electronegative atom will play the role of the hydrogen bond donor. This electronegative atom is usually fluorine, oxygen, or nitrogen, a hydrogen attached to carbon can also participate in hydrogen bonding when the carbon atom is bound to electronegative atoms, as is the case in chloroform, CHCl3. An example of a hydrogen donor is the hydrogen from the hydroxyl group of ethanol. In a hydrogen bond, the electronegative atom not covalently attached to the hydrogen is named proton acceptor, because of the small size of hydrogen relative to other atoms and molecules, the resulting charge, though only partial, represents a large charge density. A hydrogen bond results when this positive charge density attracts a lone pair of electrons on another heteroatom. The hydrogen bond is described as an electrostatic dipole-dipole interaction. These covalent features are more substantial when acceptors bind hydrogens from more electronegative donors, the partially covalent nature of a hydrogen bond raises the following questions, To which molecule or atom does the hydrogen nucleus belong. And Which should be labeled donor and which acceptor, liquids that display hydrogen bonding are called associated liquids. Hydrogen bonds can vary in strength from weak to extremely strong. For example, the central interresidue N−H···N hydrogen bond between guanine and cytosine is much stronger in comparison to the N−H···N bond between the adenine-thymine pair, the length of hydrogen bonds depends on bond strength, temperature, and pressure. The bond strength itself is dependent on temperature, pressure, bond angle, the typical length of a hydrogen bond in water is 197 pm. The ideal bond angle depends on the nature of the hydrogen bond donor, moore and Winmill used the hydrogen bond to account for the fact that trimethylammonium hydroxide is a weaker base than tetramethylammonium hydroxide
3.
Nucleoside
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Nucleosides are glycosylamines that can be thought of as nucleotides without a phosphate group. A nucleoside consists simply of a nucleobase and a sugar, whereas a nucleotide is composed of a nucleobase, a five-carbon sugar. In a nucleoside, the base is bound to either ribose or deoxyribose via a beta-glycosidic linkage, examples of nucleosides include cytidine, uridine, adenosine, guanosine, thymidine and inosine. While a nucleoside is a linked to a sugar, a nucleotide is composed of a nucleoside. Thus, nucleosides can be phosphorylated by specific kinases in the cell on the primary alcohol group to produce nucleotides. Nucleotides are the molecular building-blocks of DNA and RNA, the nucleosides, in turn, are subsequently broken down, in the lumen of the digestive system by nucleosidases into nucleobases and ribose or deoxyribose. In addition, nucleotides can be broken down, inside the cell into nitrogenous bases, in medicine several nucleoside analogues are used as antiviral or anticancer agents. The viral polymerase incorporates these compounds with non-canonical bases and these compounds are activated in the cells by being converted into nucleotides. They are administered as nucleosides since charged nucleotides cannot easily cross cell membranes, in molecular biology, several analogues of the sugar backbone exist. Due to the low stability of RNA, which is prone to hydrolysis and this is achieved by using a different backbone sugar. These analogues include LNA, morpholino, PNA and these nucleotides possess the non-canonical sugar dideoxyribose, which lacks 3 hydroxyl group. It therefore cannot bond with the base and terminates the chain. Arabinosyl nucleosides Nucleobase Synthesis of nucleosides
4.
Nucleotide
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Nucleotides are organic molecules that serve as the monomer units for forming the nucleic acid polymers DNA and RNA, both of which are essential biomolecules in all life-forms on Earth. Nucleotides are the blocks of nucleic acids, they are composed of three subunit molecules, a nitrogenous base, a five-carbon sugar, and at least one phosphate group. They are also known as phosphate nucleotides, a nucleoside is a nitrogenuous base and a 5-carbon sugar. Thus a nucleoside plus a group yields a nucleotide. Nucleotides also play a role in life-form metabolism at the fundamental. In addition, nucleotides participate in signaling, and are incorporated into important cofactors of enzymatic reactions. In experimental biochemistry, nucleotides can be radiolabeled with radionuclides to yield radionucleotides, a nucleotide is composed of three distinctive chemical sub-units, a five-carbon sugar molecule, a nitrogenous base—which two together are called a nucleoside—and one phosphate group. With all three joined, a nucleotide is also termed a nucleoside monophosphate, thus, the terms nucleoside diphosphate or nucleoside triphosphate may also indicate nucleotides. Nucleotides contain either a purine or a pyrimidine base—i. e, the nitrogenous base molecule, also known as a nucleobase—and are termed ribonucleotides if the sugar is ribose, or deoxyribonucleotides if the sugar is deoxyribose. These chain-joins of sugar and phosphate molecules create a backbone strand for a single- or double helix, in any one strand, the chemical orientation of the chain-joins runs from the 5-end to the 3-end —referring to the five carbon sites on sugar molecules in adjacent nucleotides. Unlike in nucleic acid nucleotides, singular cyclic nucleotides are formed when the group is bound twice to the same sugar molecule. These individual nucleotides function in cell metabolism rather than the nucleic acid structures of long-chain molecules, nucleic acids then are polymeric macromolecules assembled from nucleotides, the monomer-units of nucleic acids. The purine bases adenine and guanine and pyrimidine base cytosine occur in both DNA and RNA, while the pyrimidine bases thymine and uracil in just one, adenine forms a base pair with thymine with two hydrogen bonds, while guanine pairs with cytosine with three hydrogen bonds. Nucleotides can be synthesized by a variety of both in vitro and in vivo. In vivo, nucleotides can be synthesized de novo or recycled through salvage pathways, the components used in de novo nucleotide synthesis are derived from biosynthetic precursors of carbohydrate and amino acid metabolism, and from ammonia and carbon dioxide. The liver is the organ of de novo synthesis of all four nucleotides. De novo synthesis of pyrimidines and purines follows two different pathways, purines, however, are first synthesized from the sugar template onto which the ring synthesis occurs. For reference, the syntheses of the purine and pyrimidine nucleotides are carried out by several enzymes in the cytoplasm of the cell, nucleotides undergo breakdown such that useful parts can be reused in synthesis reactions to create new nucleotides
5.
Nucleic acid
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Nucleic acids are biopolymers, or large biomolecules, essential to all known forms of life. They are composed of monomers, which are made of three components, a 5-carbon sugar, a phosphate group, and a nitrogenous base. If the sugar is a simple ribose, the polymer is RNA, if the sugar is derived from ribose as deoxyribose, Nucleic acids are arguably the most important of all biomolecules. They are found in abundance in all living things, where they function to create and encode, the encoded information is contained and conveyed via the nucleic acid sequence, which provides the ladder-step ordering of nucleotides within the molecules of RNA and DNA. Using amino acids and the known as protein synthesis, the specific sequencing in DNA of these nucleobase-pairs enables storing and transmitting coded instructions as genes. In RNA, base-pair sequencing provides for manufacturing new proteins that determine the frames and parts, Nucleic acids were discovered by Friedrich Miescher in 1869. In 1889 Richard Altmann discovered that nuclein has acidic properties, and it became called nucleic acid In 1938 Astbury, in 1953 Watson and Crick determined the structure of DNA. The term nucleic acid is the name for DNA and RNA, members of a family of biopolymers. Nucleic acids were named for their initial discovery within the nucleus, all living cells contain both DNA and RNA, while viruses contain either DNA or RNA, but usually not both. The basic component of nucleic acids is the nucleotide, each of which contains a pentose sugar, a phosphate group. Nucleic acids are generated within the laboratory, through the use of enzymes. The chemical methods also enable the generation of altered nucleic acids that are not found in nature, Nucleic acids are generally very large molecules. Indeed, DNA molecules are probably the largest individual molecules known, well-studied biological nucleic acid molecules range in size from 21 nucleotides to large chromosomes. In most cases, naturally occurring DNA molecules are double-stranded and RNA molecules are single-stranded, Nucleic acids are linear polymers of nucleotides. Each nucleotide consists of three components, a purine or pyrimidine nucleobase, a sugar, and a phosphate group. The substructure consisting of a nucleobase plus sugar is termed a nucleoside, Nucleic acid types differ in the structure of the sugar in their nucleotides–DNA contains 2-deoxyribose while RNA contains ribose. Also, the found in the two nucleic acid types are different, adenine, cytosine, and guanine are found in both RNA and DNA, while thymine occurs in DNA and uracil occurs in RNA. The sugars and phosphates in nucleic acids are connected to other in an alternating chain through phosphodiester linkages
6.
RNA
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Ribonucleic acid is a polymeric molecule essential in various biological roles in coding, decoding, regulation, and expression of genes. RNA and DNA are nucleic acids, and, along with proteins and carbohydrates, like DNA, RNA is assembled as a chain of nucleotides, but unlike DNA it is more often found in nature as a single-strand folded onto itself, rather than a paired double-strand. Cellular organisms use messenger RNA to convey information that directs synthesis of specific proteins. Many viruses encode their genetic information using an RNA genome, some RNA molecules play an active role within cells by catalyzing biological reactions, controlling gene expression, or sensing and communicating responses to cellular signals. One of these processes is protein synthesis, a universal function where RNA molecules direct the assembly of proteins on ribosomes. This process uses transfer RNA molecules to deliver amino acids to the ribosome, analysis of these RNAs has revealed that they are highly structured. Unlike DNA, their structures do not consist of long double helices, in this fashion, RNAs can achieve chemical catalysis. For instance, determination of the structure of the enzyme that catalyzes peptide bond formation—revealed that its active site is composed entirely of RNA. Each nucleotide in RNA contains a sugar, with carbons numbered 1 through 5. A base is attached to the 1 position, in general, adenine, cytosine, guanine, adenine and guanine are purines, cytosine and uracil are pyrimidines. A phosphate group is attached to the 3 position of one ribose, the phosphate groups have a negative charge each, making RNA a charged molecule. The bases form hydrogen bonds between cytosine and guanine, between adenine and uracil and between guanine and uracil, however, other interactions are possible, such as a group of adenine bases binding to each other in a bulge, or the GNRA tetraloop that has a guanine–adenine base-pair. An important structural feature of RNA that distinguishes it from DNA is the presence of a group at the 2 position of the ribose sugar. The A-form geometry results in a deep and narrow major groove. RNA is transcribed with only four bases, but these bases, pseudouridine, in which the linkage between uracil and ribose is changed from a C–N bond to a C–C bond, and ribothymidine are found in various places. Another notable modified base is hypoxanthine, a deaminated adenine base whose nucleoside is called inosine, inosine plays a key role in the wobble hypothesis of the genetic code. The specific roles of many of these modifications in RNA are not fully understood, the functional form of single-stranded RNA molecules, just like proteins, frequently requires a specific tertiary structure. The scaffold for this structure is provided by secondary structural elements that are hydrogen bonds within the molecule and this leads to several recognizable domains of secondary structure like hairpin loops, bulges, and internal loops
7.
DNA
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Deoxyribonucleic acid is a molecule that carries the genetic instructions used in the growth, development, functioning and reproduction of all known living organisms and many viruses. DNA and RNA are nucleic acids, alongside proteins, lipids and complex carbohydrates, most DNA molecules consist of two biopolymer strands coiled around each other to form a double helix. The two DNA strands are termed polynucleotides since they are composed of simpler units called nucleotides. Each nucleotide is composed of one of four nitrogen-containing nucleobases—cytosine, guanine, adenine, or thymine —a sugar called deoxyribose, and a phosphate group. The nucleotides are joined to one another in a chain by covalent bonds between the sugar of one nucleotide and the phosphate of the next, resulting in an alternating sugar-phosphate backbone. The nitrogenous bases of the two polynucleotide strands are bound together, according to base pairing rules, with hydrogen bonds to make double-stranded DNA. The total amount of related DNA base pairs on Earth is estimated at 5.0 x 1037, in comparison the total mass of the biosphere has been estimated to be as much as 4 trillion tons of carbon. The DNA backbone is resistant to cleavage, and both strands of the double-stranded structure store the same biological information and this information is replicated as and when the two strands separate. A large part of DNA is non-coding, meaning that these sections do not serve as patterns for protein sequences, the two strands of DNA run in opposite directions to each other and are thus antiparallel. Attached to each sugar is one of four types of nucleobases and it is the sequence of these four nucleobases along the backbone that encodes biological information. RNA strands are created using DNA strands as a template in a process called transcription, under the genetic code, these RNA strands are translated to specify the sequence of amino acids within proteins in a process called translation. Within eukaryotic cells DNA is organized into structures called chromosomes. During cell division these chromosomes are duplicated in the process of DNA replication, eukaryotic organisms store most of their DNA inside the cell nucleus and some of their DNA in organelles, such as mitochondria or chloroplasts. In contrast prokaryotes store their DNA only in the cytoplasm, within the eukaryotic chromosomes, chromatin proteins such as histones compact and organize DNA. These compact structures guide the interactions between DNA and other proteins, helping control which parts of the DNA are transcribed, DNA was first isolated by Friedrich Miescher in 1869. DNA is used by researchers as a tool to explore physical laws and theories, such as the ergodic theorem. The unique material properties of DNA have made it an attractive molecule for material scientists and engineers interested in micro-, among notable advances in this field are DNA origami and DNA-based hybrid materials. DNA is a polymer made from repeating units called nucleotides
8.
Adenine
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It also has functions in protein synthesis and as a chemical component of DNA and RNA. The shape of adenine is complementary to either thymine in DNA or uracil in RNA, the image on the right shows pure adenine, as an independent molecule. When connected into DNA, a covalent bond is formed between deoxyribose sugar and the bottom left nitrogen, so removing the hydrogen, the remaining structure is called an adenine residue, as part of a larger molecule. Adenosine is adenine reacted with ribose as used in RNA and ATP, deoxyadenosine adenine attached to deoxyribose, adenine forms several tautomers, compounds that can be rapidly interconverted and are often considered equivalent. However, in isolated conditions, i. e. in an inert gas matrix and in the gas phase, purine metabolism involves the formation of adenine and guanine. Adenine is one of the two purine nucleobases used in forming nucleotides of the nucleic acids, in DNA, adenine binds to thymine via two hydrogen bonds to assist in stabilizing the nucleic acid structures. In RNA, which is used for synthesis, adenine binds to uracil. Adenine forms adenosine, a nucleoside, when attached to ribose and it forms adenosine triphosphate, a nucleoside triphosphate, when three phosphate groups are added to adenosine. Adenosine triphosphate is used in cellular metabolism as one of the methods of transferring chemical energy between chemical reactions. In older literature, adenine was sometimes called Vitamin B4 and it is no longer considered a true vitamin or part of the Vitamin B complex. However, two B vitamins, niacin and riboflavin, bind with adenine to form the essential cofactors nicotinamide adenine dinucleotide and flavin adenine dinucleotide, hermann Emil Fischer was one of the early scientists to study adenine. It was named in 1885 by Albrecht Kossel, in reference to the pancreas from which Kossels sample had been extracted. On August 8,2011, a report, based on NASA studies with meteorites found on Earth, was published suggesting building blocks of DNA and RNA may have been formed extraterrestrially in outer space
