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55-415: Deoxycytidine diphosphate is a nucleoside diphosphate . It is related to the common nucleic acid CTP, or cytidine triphosphate , with the -OH ( hydroxyl ) group on the 2' carbon on the nucleotide's pentose removed (hence the deoxy- part of the name), and with one fewer phosphoryl group than CTP . 2'-Deoxycytidine diphosphate is abbreviated as dCDP . Deoxycytidine diphosphate is synthesized through

110-659: A nucleobase , a five-carbon sugar ( ribose or deoxyribose ), and a phosphate group consisting of one to three phosphates . The four nucleobases in DNA are guanine , adenine , cytosine , and thymine ; in RNA, uracil is used in place of thymine. Nucleotides also play a central role in metabolism at a fundamental, cellular level. They provide chemical energy—in the form of the nucleoside triphosphates , adenosine triphosphate (ATP), guanosine triphosphate (GTP), cytidine triphosphate (CTP), and uridine triphosphate (UTP)—throughout

165-401: A pentose sugar and a phosphate . They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecules within all life-forms on Earth . Nucleotides are obtained in the diet and are also synthesized from common nutrients by the liver . Nucleotides are composed of three subunit molecules:

220-416: A purine or pyrimidine nucleobase (sometimes termed nitrogenous base or simply base ), a pentose sugar , and a phosphate group which makes the molecule acidic. 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 (where the only difference

275-419: A (d5SICS–dNaM) complex or base pair in DNA. E. coli have been induced to replicate a plasmid containing UBPs through multiple generations. This is the first known example of a living organism passing along an expanded genetic code to subsequent generations. The applications of synthetic nucleotides vary widely and include disease diagnosis, treatment, or precision medicine. Nucleotide (abbreviated "nt")

330-466: A double helix, the two strands are oriented in opposite directions, which permits base pairing and complementarity between the base-pairs, all which is essential for replicating or transcribing the encoded information found in DNA. 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

385-483: A phosphorylated ribosyl unit. The covalent linkage between the ribose and pyrimidine occurs at position C 1 of the ribose unit, which contains a pyrophosphate , and N 1 of the pyrimidine ring. Orotate phosphoribosyltransferase (PRPP transferase) catalyzes the net reaction yielding orotidine monophosphate (OMP): Orotidine 5'-monophosphate is decarboxylated by orotidine-5'-phosphate decarboxylase to form uridine monophosphate (UMP). PRPP transferase catalyzes both

440-526: A regular double helix, and can adopt highly complex three-dimensional structures that are based on short stretches of intramolecular base-paired sequences including both Watson-Crick and noncanonical base pairs, and a wide range of complex tertiary interactions. Nucleic acid molecules are usually unbranched and may occur as linear and circular molecules. For example, bacterial chromosomes, plasmids , mitochondrial DNA , and chloroplast DNA are usually circular double-stranded DNA molecules, while chromosomes of

495-399: A second one-carbon unit from formyl-THF is added to the nitrogen group and the ring is covalently closed to form the common purine precursor inosine monophosphate (IMP). Inosine monophosphate is converted to adenosine monophosphate in two steps. First, GTP hydrolysis fuels the addition of aspartate to IMP by adenylosuccinate synthase, substituting the carbonyl oxygen for a nitrogen and forming

550-432: Is a common unit of length for single-stranded nucleic acids, similar to how base pair is a unit of length for double-stranded nucleic acids. The IUPAC has designated the symbols for nucleotides. Apart from the five (A, G, C, T/U) bases, often degenerate bases are used especially for designing PCR primers . These nucleotide codes are listed here. Some primer sequences may also include the character "I", which codes for

605-528: Is a single molecule that contains 247 million base pairs ). In most cases, naturally occurring DNA molecules are double-stranded and RNA molecules are single-stranded. There are numerous exceptions, however—some viruses have genomes made of double-stranded RNA and other viruses have single-stranded DNA genomes, and, in some circumstances, nucleic acid structures with three or four strands can form. Nucleic acids are linear polymers (chains) of nucleotides. Each nucleotide consists of three components:

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660-411: Is fueled by ATP hydrolysis. In humans, pyrimidine rings (C, T, U) can be degraded completely to CO 2 and NH 3 (urea excretion). That having been said, purine rings (G, A) cannot. Instead, they are degraded to the metabolically inert uric acid which is then excreted from the body. Uric acid is formed when GMP is split into the base guanine and ribose. Guanine is deaminated to xanthine which in turn

715-411: Is one of four types of molecules called nucleobases (informally, bases). It is the sequence of these four nucleobases along the backbone that encodes genetic information. This information specifies the sequence of the amino acids within proteins according to the genetic code . The code is read by copying stretches of DNA into the related nucleic acid RNA in a process called transcription. Within cells, DNA

770-453: Is organized into long sequences called chromosomes. During cell division these chromosomes are duplicated in the process of DNA replication, providing each cell its own complete set of chromosomes. Eukaryotic organisms (animals, plants, fungi, and protists) store most of their DNA inside the cell nucleus and some of their DNA in organelles, such as mitochondria or chloroplasts. In contrast, prokaryotes (bacteria and archaea) store their DNA only in

825-432: Is oxidized to uric acid. This last reaction is irreversible. Similarly, uric acid can be formed when AMP is deaminated to IMP from which the ribose unit is removed to form hypoxanthine. Hypoxanthine is oxidized to xanthine and finally to uric acid. Instead of uric acid secretion, guanine and IMP can be used for recycling purposes and nucleic acid synthesis in the presence of PRPP and aspartate (NH 3 donor). Theories about

880-543: Is protected to create a phosphoramidite , which can then be used to obtain analogues not found in nature and/or to synthesize an oligonucleotide . 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. Recently it has been also demonstrated that cellular bicarbonate metabolism can be regulated by mTORC1 signaling. The liver

935-530: Is subsequently formed by the amination of UTP by the catalytic activity of CTP synthetase . Glutamine is the NH 3 donor and the reaction is fueled by ATP hydrolysis, too: Cytidine monophosphate (CMP) is derived from cytidine triphosphate (CTP) with subsequent loss of two phosphates. The atoms that are used to build the purine nucleotides come from a variety of sources: The de novo synthesis of purine nucleotides by which these precursors are incorporated into

990-561: Is the nucleotide , each of which contains a pentose sugar ( ribose or deoxyribose ), a phosphate group, and a nucleobase . Nucleic acids are also generated within the laboratory, through the use of enzymes (DNA and RNA polymerases) and by solid-phase chemical synthesis . 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 ( small interfering RNA ) to large chromosomes ( human chromosome 1

1045-435: Is the committed step in purine synthesis. The reaction occurs with the inversion of configuration about ribose C 1 , thereby forming β - 5-phosphorybosylamine (5-PRA) and establishing the anomeric form of the future nucleotide. Next, a glycine is incorporated fueled by ATP hydrolysis, and the carboxyl group forms an amine bond to the NH 2 previously introduced. A one-carbon unit from folic acid coenzyme N 10 -formyl-THF

1100-421: Is the major organ of de novo synthesis of all four nucleotides. De novo synthesis of pyrimidines and purines follows two different pathways. Pyrimidines are synthesized first from aspartate and carbamoyl-phosphate in the cytoplasm to the common precursor ring structure orotic acid, onto which a phosphorylated ribosyl unit is covalently linked. Purines, however, are first synthesized from the sugar template onto which

1155-431: Is the presence of a hydroxyl group ). Also, the nucleobases 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 each other in an alternating chain (sugar-phosphate backbone) through phosphodiester linkages. In conventional nomenclature ,

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1210-413: Is then added to the amino group of the substituted glycine followed by the closure of the imidazole ring. Next, a second NH 2 group is transferred from glutamine to the first carbon of the glycine unit. A carboxylation of the second carbon of the glycin unit is concomitantly added. This new carbon is modified by the addition of a third NH 2 unit, this time transferred from an aspartate residue. Finally,

1265-484: The University of Tübingen , Germany. He discovered a new substance, which he called nuclein and which - depending on how his results are interpreted in detail - can be seen in modern terms either as a nucleid acid- histone complex or as the actual nucleid acid. Phoeber Aaron Theodor Levene, an American biochemist determined the basic structure of nucleic acids. In the early 1880s, Albrecht Kossel further purified

1320-574: The nucleus , and for the presence of phosphate groups (related to phosphoric acid). Although first discovered within the nucleus of eukaryotic cells, nucleic acids are now known to be found in all life forms including within bacteria , archaea , mitochondria , chloroplasts , and viruses (There is debate as to whether viruses are living or non-living ). All living cells contain both DNA and RNA (except some cells such as mature red blood cells), while viruses contain either DNA or RNA, but usually not both. The basic component of biological nucleic acids

1375-407: The origin of life require knowledge of chemical pathways that permit formation of life's key building blocks under plausible prebiotic conditions. The RNA world hypothesis holds that in the primordial soup there existed free-floating ribonucleotides , the fundamental molecules that combine in series to form RNA . Complex molecules like RNA must have arisen from small molecules whose reactivity

1430-406: The pyrimidine nucleotides . Being on a major metabolic crossroad and requiring much energy, this reaction is highly regulated. In the first reaction unique to purine nucleotide biosynthesis, PPAT catalyzes the displacement of PRPP's pyrophosphate group (PP i ) by an amide nitrogen donated from either glutamine (N), glycine (N&C), aspartate (N), folic acid (C 1 ), or CO 2 . This

1485-599: The sequence of nucleotides . Nucleotide sequences are of great importance in biology since they carry the ultimate instructions that encode all biological molecules, molecular assemblies, subcellular and cellular structures, organs, and organisms, and directly enable cognition, memory, and behavior. Enormous efforts have gone into the development of experimental methods to determine the nucleotide sequence of biological DNA and RNA molecules, and today hundreds of millions of nucleotides are sequenced daily at genome centers and smaller laboratories worldwide. In addition to maintaining

1540-441: The umami taste, often in the form of a yeast extract. A nucleo tide is composed of three distinctive chemical sub-units: a five-carbon sugar molecule, a nucleobase (the two of which together are called a nucleo side ), and one phosphate group . With all three joined, a nucleotide is also termed a "nucleo side mono phosphate", "nucleoside di phosphate" or "nucleoside tri phosphate", depending on how many phosphates make up

1595-579: The GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI web site. Deoxyribonucleic acid (DNA) is a nucleic acid containing the genetic instructions used in the development and functioning of all known living organisms. The chemical DNA

1650-453: The activity of proteins and other signaling molecules, and as enzymatic cofactors , often carrying out redox reactions. Signaling cyclic nucleotides are formed by binding the phosphate group twice to the same sugar molecule , bridging the 5'- and 3'- hydroxyl groups of the sugar. Some signaling nucleotides differ from the standard single-phosphate group configuration, in having multiple phosphate groups attached to different positions on

1705-520: The carbons to which the phosphate groups attach are the 3'-end and the 5'-end carbons of the sugar. This gives nucleic acids directionality , and the ends of nucleic acid molecules are referred to as 5'-end and 3'-end. The nucleobases are joined to the sugars via an N -glycosidic linkage involving a nucleobase ring nitrogen ( N -1 for pyrimidines and N -9 for purines) and the 1' carbon of the pentose sugar ring. Non-standard nucleosides are also found in both RNA and DNA and usually arise from modification of

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1760-692: The cell for the many cellular functions that demand energy, including: amino acid , protein and cell membrane synthesis, moving the cell and cell parts (both internally and intercellularly), cell division, etc.. In addition, nucleotides participate in cell signaling ( cyclic guanosine monophosphate or cGMP and cyclic adenosine monophosphate or cAMP) and are incorporated into important cofactors of enzymatic reactions (e.g., coenzyme A , FAD , FMN , NAD , and NADP ). In experimental biochemistry , nucleotides can be radiolabeled using radionuclides to yield radionucleotides. 5-nucleotides are also used in flavour enhancers as food additive to enhance

1815-446: The cell nucleus. From the inner workings of the cell to the young of a living thing, they contain and provide information via the nucleic acid sequence . This gives the RNA and DNA their unmistakable 'ladder-step' order of nucleotides within their molecules. Both play a crucial role in directing protein synthesis . Strings of nucleotides are bonded to form spiraling backbones and assembled into chains of bases or base-pairs selected from

1870-621: The cytoplasm. Within the 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. Ribonucleic acid (RNA) functions in converting genetic information from genes into the amino acid sequences of proteins. The three universal types of RNA include transfer RNA (tRNA), messenger RNA (mRNA), and ribosomal RNA (rRNA). Messenger RNA acts to carry genetic sequence information between DNA and ribosomes, directing protein synthesis and carries instructions from DNA in

1925-465: The double-helix structure of DNA . Experimental studies of nucleic acids constitute a major part of modern biological and medical research , and form a foundation for genome and forensic science , and the biotechnology and pharmaceutical industries . The term nucleic acid is the overall name for DNA and RNA, members of a family of biopolymers , and is a type of polynucleotide . Nucleic acids were named for their initial discovery within

1980-425: The eukaryotic nucleus are usually linear double-stranded DNA molecules. Most RNA molecules are linear, single-stranded molecules, but both circular and branched molecules can result from RNA splicing reactions. The total amount of pyrimidines in a double-stranded DNA molecule is equal to the total amount of purines. The diameter of the helix is about 20 Å . One DNA or RNA molecule differs from another primarily in

2035-632: The five primary, or canonical, nucleobases . RNA usually forms a chain of single bases, whereas DNA forms a chain of base pairs. The bases found in RNA and DNA are: adenine , cytosine , guanine , thymine , and uracil . Thymine occurs only in DNA and uracil only in RNA. Using amino acids and protein synthesis , the specific sequence in DNA of these nucleobase-pairs helps to keep and send coded instructions as genes . In RNA, base-pair sequencing helps to make new proteins that determine most chemical processes of all life forms. Nucleic acid was, partially, first discovered by Friedrich Miescher in 1869 at

2090-415: The formation of PRPP . PRPS1 is the enzyme that activates R5P , which is formed primarily by the pentose phosphate pathway , to PRPP by reacting it with ATP . The reaction is unusual in that a pyrophosphoryl group is directly transferred from ATP to C 1 of R5P and that the product has the α configuration about C1. This reaction is also shared with the pathways for the synthesis of Trp , His , and

2145-412: The formation of carbamoyl phosphate from glutamine and CO 2 . Next, aspartate carbamoyltransferase catalyzes a condensation reaction between aspartate and carbamoyl phosphate to form carbamoyl aspartic acid , which is cyclized into 4,5-dihydroorotic acid by dihydroorotase . The latter is converted to orotate by dihydroorotate oxidase . The net reaction is: Orotate is covalently linked with

2200-407: The intermediate adenylosuccinate. Fumarate is then cleaved off forming adenosine monophosphate. This step is catalyzed by adenylosuccinate lyase. Inosine monophosphate is converted to guanosine monophosphate by the oxidation of IMP forming xanthylate, followed by the insertion of an amino group at C 2 . NAD is the electron acceptor in the oxidation reaction. The amide group transfer from glutamine

2255-781: The non-standard nucleotide inosine . Inosine occurs in tRNAs and will pair with adenine, cytosine, or thymine. This character does not appear in the following table, however, because it does not represent a degeneracy. While inosine can serve a similar function as the degeneracy "H", it is an actual nucleotide, rather than a representation of a mix of nucleotides that covers each possible pairing needed. Nucleic acid Nucleic acids are chemical compounds that are found in nature. They carry information in cells and make up genetic material. These acids are very common in all living things, where they create, encode, and store information in every living cell of every life-form on Earth. In turn, they send and express that information inside and outside

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2310-515: The nucleid acid substance and discovered its highly acidic properties. He later also identified the nucleobases . In 1889 Richard Altmann created the term nucleic acid – at that time DNA and RNA were not differentiated. In 1938 Astbury and Bell published the first X-ray diffraction pattern of DNA. In 1944 the Avery–MacLeod–McCarty experiment showed that DNA is the carrier of genetic information and in 1953 Watson and Crick proposed

2365-422: The nucleotide monomers of a nucleic acid end-to-end into a long chain. 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 ( directionality ) of the chain-joins runs from the 5'-end to the 3'-end ( read : 5 prime-end to 3 prime-end)—referring to the five carbon sites on sugar molecules in adjacent nucleotides. In

2420-515: The nucleus to ribosome . Ribosomal RNA reads the DNA sequence, and catalyzes peptide bond formation. Transfer RNA serves as the carrier molecule for amino acids to be used in protein synthesis, and is responsible for decoding the mRNA. In addition, many other classes of RNA are now known. Artificial nucleic acid analogues have been designed and synthesized. They include peptide nucleic acid , morpholino - and locked nucleic acid , glycol nucleic acid , and threose nucleic acid . Each of these

2475-401: The oxidation-reduction reaction of cytidine 5'-diphosphocholine which is catalyzed by the presence of ribonucleoside-diphosphate reductase . Additionally, ribonucleoside-diphosphate reductase is capable of binding and catalyzing both the formation of deoxyribonucleotides from ribonucleotide. Nucleoside diphosphate Nucleotides are organic molecules composed of a nitrogenous base,

2530-415: The phosphate group. 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 ribo nucleotides if the sugar is ribose, or deoxyribo nucleotides if the sugar is deoxyribose. Individual phosphate molecules repetitively connect the sugar-ring molecules in two adjacent nucleotide monomers, thereby connecting

2585-478: The purine and pyrimidine bases. Thus a reaction network towards the purine and pyrimidine RNA building blocks can be established starting from simple atmospheric or volcanic molecules. An unnatural base pair (UBP) is a designed subunit (or nucleobase ) of DNA which is created in a laboratory and does not occur in nature. Examples include d5SICS and dNaM . These artificial nucleotides bearing hydrophobic nucleobases , feature two fused aromatic rings that form

2640-488: The purine ring proceeds by a 10-step pathway to the branch-point intermediate IMP , the nucleotide of the base hypoxanthine . AMP and GMP are subsequently synthesized from this intermediate via separate, two-step pathways. Thus, purine moieties are initially formed as part of the ribonucleotides rather than as free bases . Six enzymes take part in IMP synthesis. Three of them are multifunctional: The pathway starts with

2695-534: The pyrimidine bases thymine (in DNA) and uracil (in RNA) occur in just one. Adenine forms a base pair with thymine with two hydrogen bonds, while guanine pairs with cytosine with three hydrogen bonds. In addition to being building blocks for the construction of nucleic acid polymers, singular nucleotides play roles in cellular energy storage and provision, cellular signaling, as a source of phosphate groups used to modulate

2750-403: The ribosylation and decarboxylation reactions, forming UMP from orotic acid in the presence of PRPP. It is from UMP that other pyrimidine nucleotides are derived. UMP is phosphorylated by two kinases to uridine triphosphate (UTP) via two sequential reactions with ATP. First, the diphosphate from UDP is produced, which in turn is phosphorylated to UTP. Both steps are fueled by ATP hydrolysis: CTP

2805-407: 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, not within a specific organelle . Nucleotides undergo breakdown such that useful parts can be reused in synthesis reactions to create new nucleotides. The synthesis of the pyrimidines CTP and UTP occurs in the cytoplasm and starts with

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2860-483: The standard nucleosides within the DNA molecule or the primary (initial) RNA transcript. Transfer RNA (tRNA) molecules contain a particularly large number of modified nucleosides. Double-stranded nucleic acids are made up of complementary sequences, in which extensive Watson-Crick base pairing results in a highly repeated and quite uniform nucleic acid double-helical three-dimensional structure. In contrast, single-stranded RNA and DNA molecules are not constrained to

2915-471: The sugar. Nucleotide cofactors include a wider range of chemical groups attached to the sugar via the glycosidic bond , including nicotinamide and flavin , and in the latter case, the ribose sugar is linear rather than forming the ring seen in other nucleotides. Nucleotides can be synthesized by a variety of means, both in vitro and in vivo . In vitro, protecting groups may be used during laboratory production of nucleotides. A purified nucleoside

2970-672: Was discovered in 1869, but its role in genetic inheritance was not demonstrated until 1943. The DNA segments that carry this genetic information are called genes. Other DNA sequences have structural purposes, or are involved in regulating the use of this genetic information. Along with RNA and proteins, DNA is one of the three major macromolecules that are essential for all known forms of life. DNA consists of two long polymers of monomer units called nucleotides, with backbones made of sugars and phosphate groups joined by ester bonds. These two strands are oriented in opposite directions to each other and are, therefore, antiparallel . Attached to each sugar

3025-548: Was governed by physico-chemical processes. RNA is composed of purine and pyrimidine nucleotides, both of which are necessary for reliable information transfer, and thus Darwinian evolution . Becker et al. showed how pyrimidine nucleosides can be synthesized from small molecules and ribose , driven solely by wet-dry cycles. Purine nucleosides can be synthesized by a similar pathway. 5'-mono- and di-phosphates also form selectively from phosphate-containing minerals, allowing concurrent formation of polyribonucleotides with both

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