Nucleic acid - DNA, RNA, ATP, GTP, dATP의 이해

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Nucleotides as optimal candidates for essential nutrients in living organisms: A review

A phosphodiesterase (PDE) is an enzyme that breaks a phosphodiester bond. Usually, phosphodiesterase refers to cyclic nucleotide phosphodiesterases, which have great clinical significance and are described below. However, there are many other families of phosphodiesterases, including phospholipases C and D, autotaxin, sphingomyelin phosphodiesterase, DNases, RNases, and restriction endonucleases (which all break the phosphodiester backbone of DNA or RNA), as well as numerous less-well-characterized small-molecule phosphodiesterases. The cyclic nucleotide phosphodiesterases comprise a group of enzymes that degrade the phosphodiester bond in the second messenger molecules cAMP and cGMP. They regulate the localization, duration, and amplitude of cyclic nucleotide signaling within subcellular domains. PDEs are therefore important regulators of signal transduction mediated by these second messenger molecules.

A nucleotidase is a hydrolytic enzyme that catalyzes the hydrolysis of a nucleotide into a nucleoside and a phosphate.[1]A nucleotide + H2O = a nucleoside + phosphate

For example, it converts adenosine monophosphate to adenosine, and guanosine monophosphate to guanosine.

Nucleotidases have an important function in digestion in that they break down consumed nucleic acids.

In enzymology, a purine nucleosidase (EC 3.2.2.1) is an enzyme that catalyzes the chemical reaction

a purine nucleoside + H2O  

 D-ribose + a purine base

Thus, the two substrates of this enzyme are purine nucleoside and H2O, whereas its two products are D-ribose and purine base.  This enzyme belongs to the family of hydrolases, specifically those glycosylases that hydrolyse N-glycosyl compounds. The systematic name of this enzyme class is purine-nucleoside ribohydrolase. Other names in common use include nucleosidase, purine beta-ribosidase, purine nucleoside hydrolase, purine ribonucleosidase, ribonucleoside hydrolase, nucleoside hydrolase, N-ribosyl purine ribohydrolase, nucleosidase g, N-D-ribosylpurine ribohydrolase, inosine-adenosine-guanosine preferring nucleoside hydrolase, purine-specific nucleoside N-ribohydrolase, IAG-nucleoside hydrolase, and IAG-NH. This enzyme participates in purine metabolism and nicotinate and nicotinamide metabolism.

Nucleotides as optimal candidates for essential nutrients in living organisms: A review

four nucleobases in DNA are guanine, adenine, cytosine and thymine;

in RNA, uracil is used in place of thymine.

https://kr.iherb.com/pr/bluebonnet-nutrition-nucleotide-complex-rna-dna-60-vegetable-capsules/10147

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 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.[2] 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.

Uracil - Wikipedia

참고) 아데닌과 아데노신의 차이는 adenine + sugar = adenosine

Nucleic acid = DNA(ATGC), RNA(AUGC)

DNA = Deoxyribonucleic acid

RNA = Ribonucleic acid

여기서 Ribo는 ribose는 C5H10O5인 당(sugar), dexoyribose는 C5H10O4인 당

Nucleotide

A nucleotide is composed of three distinctive chemical sub-units: a five-carbon sugar molecule, a nucleobase (the two of which together are called a nucleoside), and one phosphate group. With all three joined, a nucleotide is also termed a "nucleoside monophosphate", "nucleoside diphosphate" or "nucleoside triphosphate", depending on how many phosphates make up 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 ribonucleotides if the sugar is ribose, or deoxyribonucleotides if the sugar is deoxyribose. Individual phosphate molecules repetitively connect the sugar-ring molecules in two adjacent nucleotide monomers, thereby connecting 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 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 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 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.[2] Some signaling nucleotides differ from the standard single-phosphate group configuration, in having multiple phosphate groups attached to different positions on the sugar.[4] 

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.

Nucleoside

Nucleosides are glycosylamines that can be thought of as nucleotides without a phosphate group. A nucleoside consists simply of a nucleobase (also termed a nitrogenous base) and a five-carbon sugar (ribose or 2'-deoxyribose) whereas a nucleotide is composed of a nucleobase, a five-carbon sugar, and one or more phosphate groups. In a nucleoside, the anomeric carbon is linked through a glycosidic bond to the N9 of a purine or the N1 of a pyrimidine. Nucleotides are the molecular building-blocks of DNA and RNA.

Nucleosides are glycosylamines that can be thought of as nucleotides without a phosphate group. A nucleoside consists simply of a nucleobase (also termed a nitrogenous base) and a five-carbon sugar (ribose or 2'-deoxyribose) whereas a nucleotide is composed of a nucleobase, a five-carbon sugar, and one or more phosphate groups. In a nucleoside, the anomeric carbon is linked through a glycosidic bond to the N9 of a purine or the N1 of a pyrimidine. Nucleotides are the molecular building-blocks of DNA and RNA.

Adenosine (symbol A) is an organic compound that occurs widely in nature in the form of diverse derivatives. The molecule consists of an adenine attached to a ribose via a β-N9-glycosidic bond. Adenosine is one of the four nucleoside building blocks of RNA (and its derivative deoxyadenosine is a building block of DNA), which are essential for all life. Its derivatives include the energy carriers adenosine mono-, di-, and triphosphate, also known as AMP/ADP/ATP. Cyclic adenosine monophosphate (cAMP) is pervasive in signal transduction. Adenosine is used as an intravenous medication for some cardiac arrhythmias.

Adenosyl (abbreviated Ado or 5'-dAdo) is the chemical group formed by removal of the 5′-hydroxy (OH) group. It is found in adenosylcobalamin (an active form of vitamin B12[1]) and as a radical in radical SAM enzymes.[2]

Guanosine (symbol G or Guo) is a purine nucleoside comprising guanine attached to a ribose (ribofuranose) ring via a β-N9-glycosidic bond. Guanosine can be phosphorylated to become guanosine monophosphate (GMP), cyclic guanosine monophosphate (cGMP), guanosine diphosphate (GDP), and guanosine triphosphate (GTP). These forms play important roles in various biochemical processes such as synthesis of nucleic acids and proteins, photosynthesis, muscle contraction, and intracellular signal transduction (cGMP). When guanine is attached by its N9 nitrogen to the C1 carbon of a deoxyribose ring it is known as deoxyguanosine.

ATP, ADP, AMP

Adenosine triphosphate (ATP) is an organic compound that provides energy to drive many processes in living cells, such as muscle contraction, nerve impulse propagation, condensate dissolution, and chemical synthesis. Found in all known forms of life, ATP is often referred to as the "molecular unit of currency" of intracellular energy transfer.[2] When consumed in metabolic processes, it converts either to adenosine diphosphate (ADP) or to adenosine monophosphate (AMP). Other processes regenerate ATP. The human body recycles its own body weight equivalent in ATP each day.[3] It is also a precursor to DNA and RNA, and is used as a coenzyme.

From the perspective of biochemistry, ATP is classified as a nucleoside triphosphate, which indicates that it consists of three components: a nitrogenous base (adenine), the sugar ribose, and the triphosphate.

Adenosine diphosphate (ADP), also known as adenosine pyrophosphate (APP), is an important organic compound in metabolism and is essential to the flow of energy in living cells. ADP consists of three important structural components: a sugar backbone attached to adenine and two phosphate groups bonded to the 5 carbon atom of ribose. The diphosphate group of ADP is attached to the 5’ carbon of the sugar backbone, while the adenine attaches to the 1’ carbon.[1]

Adenosine diphosphate - Wikipedia

ADP can be interconverted to adenosine triphosphate (ATP) and adenosine monophosphate (AMP). ATP contains one more phosphate group than does ADP. AMP contains one fewer phosphate group. Energy transfer used by all living things is a result of dephosphorylation of ATP by enzymes known as ATPases. The cleavage of a phosphate group from ATP results in the coupling of energy to metabolic reactions and a by-product of ADP.[1] ATP is continually reformed from lower-energy species ADP and AMP. The biosynthesis of ATP is achieved throughout processes such as substrate-level phosphorylation, oxidative phosphorylation, and photophosphorylation, all of which facilitate the addition of a phosphate group to ADP.

Adenosine monophosphate (AMP), also known as 5'-adenylic acid, is a nucleotide. AMP consists of a phosphate group, the sugar ribose, and the nucleobase adenine; it is an ester of phosphoric acid and the nucleoside adenosine.[1] As a substituent it takes the form of the prefix adenylyl-.[2]

AMP plays an important role in many cellular metabolic processes, being interconverted to ADP and/or ATP. AMP is also a component in the synthesis of RNA.[3] AMP is present in all known forms of life.[4]

Production and degradation[edit]

AMP does not have the high energy phosphoanhydride bond associated with ADP and ATP. AMP can be produced from ADP:

2 ADP → ATP + AMP

Or AMP may be produced by the hydrolysis of one high energy phosphate bond of ADP:

ADP + H2O → AMP + Pi

AMP can also be formed by hydrolysis of ATP into AMP and pyrophosphate:

ATP + H2O → AMP + PPi

When RNA is broken down by living systems, nucleoside monophosphates, including adenosine monophosphate, are formed.

AMP can be regenerated to ATP as follows:

AMP + ATP → 2 ADP (adenylate kinase in the opposite direction)ADP + Pi → ATP (this step is most often performed in aerobes by the ATP synthase during oxidative phosphorylation)

AMP can be converted into IMP by the enzyme myoadenylate deaminase, freeing an ammonia group.

In a catabolic pathway, adenosine monophosphate can be converted to uric acid, which is excreted from the body in mammals.[5]

Physiological role in regulation[edit]

AMP-activated kinase regulation[edit]

The eukaryotic cell enzyme 5' adenosine monophosphate-activated protein kinase, or AMPK, utilizes AMP for homeostatic energy processes during times of high cellular energy expenditure, such as exercise.[6] Since ATP cleavage, and corresponding phosphorylation reactions, are utilized in various processes throughout the body as a source of energy, ATP production is necessary to further create energy for those mammalian cells. AMPK, as a cellular energy sensor, is activated by decreasing levels of ATP, which is naturally accompanied by increasing levels of ADP and AMP.[7]

Though phosphorylation appears to be the main activator for AMPK, some studies suggest that AMP is an allosteric regulator as well as a direct agonist for AMPK.[8] Furthermore, other studies suggest that the high ratio of AMP:ATP levels in cells, rather than just AMP, activate AMPK.[9] For example, the species of Caenorhabditis elegans and Drosophila melanogaster and their AMP-activated kinases were found to have been activated by AMP, while species of yeast and plant kinases were not allosterically activated by AMP.[9]

5' AMP-activated protein kinase or AMPK or 5' adenosine monophosphate-activated protein kinase is an enzyme (EC 2.7.11.31) that plays a role in cellular energy homeostasis, largely to activate glucose and fatty acid uptake and oxidation when cellular energy is low. It belongs to a highly conserved eukaryotic protein family and its orthologues are SNF1 in yeast, and SnRK1 in plants. It consists of three proteins (subunits) that together make a functional enzyme, conserved from yeast to humans. It is expressed in a number of tissues, including the liver, brain, and skeletal muscle. In response to binding AMP and ADP,[1] the net effect of AMPK activation is stimulation of hepatic fatty acid oxidation, ketogenesis, stimulation of skeletal muscle fatty acid oxidation and glucose uptake, inhibition of cholesterol synthesis, lipogenesis, and triglyceride synthesis, inhibition of adipocyte lipogenesis, inhibition of adipocyte lipolysis, and modulation of insulin secretion by pancreatic β-cells.[2] It should not be confused with cyclic AMP-activated protein kinase (protein kinase A).[3]

AMP binds to the γ-subunit of AMPK, leading to the activation of the kinase, and then eventually a cascade of other processes such as the activation of catabolic pathways and inhibition of anabolic pathways to regenerate ATP. Catabolic mechanisms, which generate ATP through the release of energy from breaking down molecules, are activated by the AMPK enzyme while anabolic mechanisms, which utilize energy from ATP to form products, are inhibited.[10] Though the γ-subunit can bind AMP/ADP/ATP, only the binding of AMP/ADP results in a conformational shift of the enzyme protein. This variance in AMP/ADP versus ATP binding leads to a shift in the dephosphorylation state for the enzyme.[11] The dephosphorylation of AMPK through various protein phosphatases completely inactivates catalytic function. AMP/ADP protects AMPK from being inactivated by binding to the γ-subunit and maintaining the dephosphorylation state.[12]

cAMP[edit]

AMP-activated protein kinase (AMPK) regulates a diverse range of cellular processes that are linked to human disease. The major pathways known to be regulated by AMPK in different tissues are highlighted for different organs and cell types within the body. Those that are positively impacted by AMPK are shown in green boxes, while those that are inhibited by AMPK are in red boxes. Diseases that have the potential to be treated by AMPK modulation are shown in yellow boxes. CVD, cardiovascular disease; FA, fatty acid; HCC, hepatocellular carcinoma; NAFLD, non-alcoholic fatty liver disease; NASH, non-alcoholic steatohepatitis; NO, nitric oxide; T2D, type 2 diabetes.

Main article: Cyclic AMP

AMP can also exist as a cyclic structure known as cyclic AMP (or cAMP). Within certain cells the enzyme adenylate cyclase makes cAMP from ATP, and typically this reaction is regulated by hormones such as adrenaline or glucagon. cAMP plays an important role in intracellular signaling.[13]

GTP, GDP, GMP

Guanosine-5'-triphosphate (GTP) is a purine nucleoside triphosphate. It is one of the building blocks needed for the synthesis of RNA during the transcription process. Its structure is similar to that of the guanosine nucleoside, the only difference being that nucleotides like GTP have phosphates on their ribose sugar. GTP has the guanine nucleobase attached to the 1' carbon of the ribose and it has the triphosphate moiety attached to ribose's 5' carbon.

It also has the role of a source of energy or an activator of substrates in metabolic reactions, like that of ATP, but more specific. It is used as a source of energy for protein synthesis and gluconeogenesis.

GTP is essential to signal transduction, in particular with G-proteins, in second-messenger mechanisms where it is converted to guanosine diphosphate (GDP) through the action of GTPases.

Guanosine diphosphate, abbreviated GDP, is a nucleoside diphosphate. It is an ester of pyrophosphoric acid with the nucleoside guanosine. GDP consists of a pyrophosphate group, a pentose sugar ribose, and the nucleobase guanine.[1]

GDP is the product of GTP dephosphorylation by GTPases, e.g., the G-proteins that are involved in signal transduction.

Guanosine monophosphate (GMP), also known as 5′-guanidylic acid or guanylic acid (conjugate base guanylate), is a nucleotide that is used as a monomer in RNA. It is an ester of phosphoric acid with the nucleoside guanosine. GMP consists of the phosphate group, the pentose sugar ribose, and the nucleobase guanine; hence it is a ribonucleoside monophosphate. Guanosine monophosphate is commercially produced by microbial fermentation.[1]

CTP, CDP, CMP

Cytidine triphosphate (CTP) is a pyrimidine nucleoside triphosphate. CTP, much like ATP, consists of a ribose sugar, and three phosphate groups. The major difference between the two molecules is the base used, which in CTP is cytosine.

CTP is a substrate in the synthesis of RNA. CTP is a high-energy molecule similar to ATP, but its role as an energy coupler is limited to a much smaller subset of metabolic reactions. CTP is a coenzyme in metabolic reactions like the synthesis of glycerophospholipids, where it is used for activation and transfer of diacylglycerol and lipid head groups,[1] and glycosylation of proteins. CTP acts as an inhibitor of the enzyme aspartate carbamoyltransferase, which is used in pyrimidine biosynthesis.[2]

Cytidine diphosphate, abbreviated CDP, is a nucleoside diphosphate. It is an ester of pyrophosphoric acid with the nucleoside cytidine. CDP consists of the pyrophosphate group, the pentose sugar ribose, and the nucleobase cytosine.

Cytidine monophosphate, also known as 5'-cytidylic acid or simply cytidylate, and abbreviated CMP, is a nucleotide that is used as a monomer in RNA.[1] It is an ester of phosphoric acid with the nucleoside cytidine. CMP consists of the phosphate group, the pentose sugar ribose, and the nucleobase cytosine; hence, a ribonucleoside monophosphate.

UTP, UDP, UMP

Uridine-5′-triphosphate (UTP) is a pyrimidine nucleoside triphosphate, consisting of the organic base uracil linked to the 1′ carbon of the ribose sugar, and esterified with tri-phosphoric acid at the 5′ position. Its main role is as substrate for the synthesis of RNA during transcription. UTP is the precursor for the production of CTP via the help of CTP Synthetase.[1] UTP can be biosynthesized from UDP by Nucleoside Diphosphate Kinase after using phosphate group from ATP.[2][3] UDP + ATP ⇌ UTP + ADP;[4] both UTP and ATP are energetically equal[4]

The homologue in DNA is thymidine triphosphate (TTP or dTTP). UTP also has a deoxyribose form (dUTP). UTP also has the role of a source of energy or an activator of substrates in metabolic reactions, like that of ATP, but more specific. When UTP activates a substrate (like Glucose-1-phosphate), UDP-glucose is formed and inorganic phosphate is released.[5] UDP-glucose enters the synthesis of glycogen. UTP is used in the metabolism of galactose, where the activated form UDP-galactose is converted to UDP-glucose. UDP-glucuronate is used to conjugate bilirubin to a more water-soluble bilirubin diglucuronide. UTP is also used to activate amino sugars like Glucosamine-1-phosphate to UDP-glucosamine, and N-acetyl-glucosamine-1-phosphate to UDP-N-acetylglucosamine.[6]

Uridine diphosphate, abbreviated UDP, is a nucleotide diphosphate. It is an ester of pyrophosphoric acid with the nucleoside uridine. UDP consists of the pyrophosphate group, the pentose sugar ribose, and the nucleobase uracil.

UDP is an important factor in glycogenesis. Before glucose can be stored as glycogen in the liver and muscles, the enzyme UDP-glucose pyrophosphorylase forms a UDP-glucose unit by combining glucose 1-phosphate with uridine triphosphate, cleaving a pyrophosphate ion in the process. Then, the enzyme glycogen synthase combines UDP-glucose units to form a glycogen chain. The UDP molecule is cleaved from the glucose ring during this process and can be reused by UDP-glucose pyrophosphorylase.[1][2]

Uridine diphosphate - Wikipedia