Magnesium in biology
Magnesium is an essential element in biological systems. Magnesium occurs as the Mg2+ ion, it is present in every cell type in every organism. For example, ATP, the main source of energy in cells, must bind to a magnesium ion in order to be biologically active. What is called ATP is actually Mg-ATP; as such, magnesium plays a role in the stability of all polyphosphate compounds in the cells, including those associated with the synthesis of DNA and RNA. Over 300 enzymes require the presence of magnesium ions for their catalytic action, including all enzymes utilizing or synthesizing ATP, or those that use other nucleotides to synthesize DNA and RNA. In plants, magnesium is necessary for synthesis of photosynthesis. A balance of magnesium is vital to the well-being of all organisms. Magnesium is a abundant ion in Earth's crust and mantle and is bioavailable in the hydrosphere; this availability, in combination with a useful and unusual chemistry, may have led to its utilization in evolution as an ion for signaling, enzyme activation, catalysis.
However, the unusual nature of ionic magnesium has led to a major challenge in the use of the ion in biological systems. Biological membranes are impermeable to magnesium, so transport proteins must facilitate the flow of magnesium, both into and out of cells and intracellular compartments. Chlorophyll in plants converts water to oxygen as O2. Hemoglobin in vertebrate animals transports oxygen as O2 in the blood. Chlorophyll is similar to hemoglobin, except magnesium is at the center of the chlorophyll molecule and iron is at the center of the hemoglobin molecule, with other variations; this process keeps living cells on earth alive and maintains baseline levels of CO2 and O2 in the atmosphere. Inadequate magnesium intake causes muscle spasms, has been associated with cardiovascular disease, high blood pressure, anxiety disorders, migraines and cerebral infarction. Acute deficiency is rare, is more common as a drug side-effect than from low food intake per se, but it can occur in people fed intravenously for extended periods of time.
The most common symptom of excess oral magnesium intake is diarrhea. Supplements based on amino acid chelates are much better-tolerated by the digestive system and do not have the side-effects of the older compounds used, while sustained-release dietary supplements prevent the occurrence of diarrhea. Since the kidneys of adult humans excrete excess magnesium efficiently, oral magnesium poisoning in adults with normal renal function is rare. Infants, which have less ability to excrete excess magnesium when healthy, should not be given magnesium supplements, except under a physician's care. Pharmaceutical preparations with magnesium are used to treat conditions including magnesium deficiency and hypomagnesemia, as well as eclampsia; such preparations are in the form of magnesium sulfate or chloride when given parenterally. Magnesium is absorbed with reasonable efficiency by the body from any soluble magnesium salt, such as the chloride or citrate. Magnesium is absorbed from Epsom salts, although the sulfate in these salts adds to their laxative effect at higher doses.
Magnesium absorption from the insoluble oxide and hydroxide salts is erratic and of poorer efficiency, since it depends on the neutralization and solution of the salt by the acid of the stomach, which may not be complete. Magnesium orotate may be used as adjuvant therapy in patients on optimal treatment for severe congestive heart failure, increasing survival rate and improving clinical symptoms and patient's quality of life. Magnesium can affect muscle relaxation through direct action on cell membranes. Mg2+ ions close certain types of calcium channels, which conduct positively charged calcium ions into neurons. With an excess of magnesium, more channels will be blocked and nerve cells activity will decrease. Intravenous magnesium sulphate is used in treating pre-eclampsia. For other than pregnancy-related hypertension, a meta-analysis of 22 clinical trials with dose ranges of 120 to 973 mg/day and a mean dose of 410 mg, concluded that magnesium supplementation had a small but statistically significant effect, lowering systolic blood pressure by 3–4 mm Hg and diastolic blood pressure by 2–3 mm Hg.
The effect was larger. Higher dietary intakes of magnesium correspond to lower diabetes incidence. For people with diabetes or at high risk of diabetes, magnesium supplementation lowers fasting glucose; the U. S. Institute of Medicine updated Estimated Average Requirements and Recommended Dietary Allowances for magnesium in 1997. If there is not sufficient information to establish EARs and RDAs, an estimate designated Adequate Intake is used instead; the current EARs for magnesium for women and men ages 31 and up are 265 mg/day and 350 mg/day, respectively. The RDAs are 420 mg/day. RDAs are higher than EARs so as to identify amounts that will cover people with higher than average requirements. RDA for pregnancy is 350 to 400 mg/day depending on age of the woman. RDA for lactation ranges 310 to 360 mg/day for same reason. For children ages 1–13 years the RDA increases with age from 65 to 200 mg/day; as for safety, the IOM sets Tolerable upper intake levels for vitamins and minerals when evidence is sufficient.
In the case of magnesium the UL is set at 350 mg/day. The UL is specific to magnesium consumed as a dietary supplement, the reason being that too much magnesium consumed at one time can caus
Enzymes are macromolecular biological catalysts. Enzymes accelerate chemical reactions; the molecules upon which enzymes may act are called substrates and the enzyme converts the substrates into different molecules known as products. All metabolic processes in the cell need enzyme catalysis in order to occur at rates fast enough to sustain life. Metabolic pathways depend upon enzymes to catalyze individual steps; the study of enzymes is called enzymology and a new field of pseudoenzyme analysis has grown up, recognising that during evolution, some enzymes have lost the ability to carry out biological catalysis, reflected in their amino acid sequences and unusual'pseudocatalytic' properties. Enzymes are known to catalyze more than 5,000 biochemical reaction types. Most enzymes are proteins; the latter are called ribozymes. Enzymes' specificity comes from their unique three-dimensional structures. Like all catalysts, enzymes increase the reaction rate by lowering its activation energy; some enzymes can make their conversion of substrate to product occur many millions of times faster.
An extreme example is orotidine 5'-phosphate decarboxylase, which allows a reaction that would otherwise take millions of years to occur in milliseconds. Chemically, enzymes are like any catalyst and are not consumed in chemical reactions, nor do they alter the equilibrium of a reaction. Enzymes differ from most other catalysts by being much more specific. Enzyme activity can be affected by other molecules: inhibitors are molecules that decrease enzyme activity, activators are molecules that increase activity. Many therapeutic drugs and poisons are enzyme inhibitors. An enzyme's activity decreases markedly outside its optimal temperature and pH, many enzymes are denatured when exposed to excessive heat, losing their structure and catalytic properties; some enzymes are used commercially, in the synthesis of antibiotics. Some household products use enzymes to speed up chemical reactions: enzymes in biological washing powders break down protein, starch or fat stains on clothes, enzymes in meat tenderizer break down proteins into smaller molecules, making the meat easier to chew.
By the late 17th and early 18th centuries, the digestion of meat by stomach secretions and the conversion of starch to sugars by plant extracts and saliva were known but the mechanisms by which these occurred had not been identified. French chemist Anselme Payen was the first to discover an enzyme, diastase, in 1833. A few decades when studying the fermentation of sugar to alcohol by yeast, Louis Pasteur concluded that this fermentation was caused by a vital force contained within the yeast cells called "ferments", which were thought to function only within living organisms, he wrote that "alcoholic fermentation is an act correlated with the life and organization of the yeast cells, not with the death or putrefaction of the cells."In 1877, German physiologist Wilhelm Kühne first used the term enzyme, which comes from Greek ἔνζυμον, "leavened" or "in yeast", to describe this process. The word enzyme was used to refer to nonliving substances such as pepsin, the word ferment was used to refer to chemical activity produced by living organisms.
Eduard Buchner submitted his first paper on the study of yeast extracts in 1897. In a series of experiments at the University of Berlin, he found that sugar was fermented by yeast extracts when there were no living yeast cells in the mixture, he named the enzyme that brought about the fermentation of sucrose "zymase". In 1907, he received the Nobel Prize in Chemistry for "his discovery of cell-free fermentation". Following Buchner's example, enzymes are named according to the reaction they carry out: the suffix -ase is combined with the name of the substrate or to the type of reaction; the biochemical identity of enzymes was still unknown in the early 1900s. Many scientists observed that enzymatic activity was associated with proteins, but others argued that proteins were carriers for the true enzymes and that proteins per se were incapable of catalysis. In 1926, James B. Sumner crystallized it; the conclusion that pure proteins can be enzymes was definitively demonstrated by John Howard Northrop and Wendell Meredith Stanley, who worked on the digestive enzymes pepsin and chymotrypsin.
These three scientists were awarded the 1946 Nobel Prize in Chemistry. The discovery that enzymes could be crystallized allowed their structures to be solved by x-ray crystallography; this was first done for lysozyme, an enzyme found in tears and egg whites that digests the coating of some bacteria. This high-resolution structure of lysozyme marked the beginning of the field of structural biology and the effort to understand how enzymes work at an atomic level of detail. An enzyme's name is derived from its substrate or the chemical reaction it catalyzes, with the word ending in -ase. Examples are alcohol dehydrogenase and DNA polymerase. Different enzymes that catalyze the same chemical reaction are called isozymes; the International Union of Biochemistry and Molecular Biology have developed a nomenclature for enzymes, the EC numbers. The first number broadly classifies the enzyme based on its mechanism; the top-level classification is: EC 1, Oxidoreductases: catalyze oxidation/reducti
In molecular biology, DNA replication is the biological process of producing two identical replicas of DNA from one original DNA molecule. DNA replication occurs in all living organisms acting as the basis for biological inheritance; the cell possesses the distinctive property of division. DNA is made up of a double helix of two complementary strands. During replication, these strands are separated; each strand of the original DNA molecule serves as a template for the production of its counterpart, a process referred to as semiconservative replication. As a result of semi-conservative replication, the new helix will be composed of an original DNA strand as well as a newly synthesized strand. Cellular proofreading and error-checking mechanisms ensure near perfect fidelity for DNA replication. In a cell, DNA replication begins at origins of replication, in the genome. Unwinding of DNA at the origin and synthesis of new strands, accommodated by an enzyme known as helicase, results in replication forks growing bi-directionally from the origin.
A number of proteins are associated with the replication fork to help in the initiation and continuation of DNA synthesis. Most prominently, DNA polymerase synthesizes the new strands by adding nucleotides that complement each strand. DNA replication occurs during the S-stage of interphase. DNA replication can be performed in vitro. DNA polymerases isolated from cells and artificial DNA primers can be used to start DNA synthesis at known sequences in a template DNA molecule. Polymerase chain reaction, ligase chain reaction, transcription-mediated amplification are examples. DNA exists as a double-stranded structure, with both strands coiled together to form the characteristic double-helix; each single strand of DNA is a chain of four types of nucleotides. Nucleotides in DNA contain a deoxyribose sugar, a phosphate, a nucleobase; the four types of nucleotide correspond to the four nucleobases adenine, cytosine and thymine abbreviated as A, C, G and T. Adenine and guanine are purine bases, while cytosine and thymine are pyrimidines.
These nucleotides form phosphodiester bonds, creating the phosphate-deoxyribose backbone of the DNA double helix with the nucleobases pointing inward. Nucleobases are matched between strands through hydrogen bonds to form base pairs. Adenine pairs with thymine, guanine pairs with cytosine. DNA strands have a directionality, the different ends of a single strand are called the "3′ end" and the "5′ end". By convention, if the base sequence of a single strand of DNA is given, the left end of the sequence is the 5′ end, while the right end of the sequence is the 3′ end; the strands of the double helix are anti-parallel with one being 5′ to 3′, the opposite strand 3′ to 5′. These terms refer to the carbon atom in deoxyribose to which the next phosphate in the chain attaches. Directionality has consequences in DNA synthesis, because DNA polymerase can synthesize DNA in only one direction by adding nucleotides to the 3′ end of a DNA strand; the pairing of complementary bases in DNA means that the information contained within each strand is redundant.
Phosphodiester bonds are stronger than hydrogen bonds. This allows the strands to be separated from one another; the nucleotides on a single strand can therefore be used to reconstruct nucleotides on a newly synthesized partner strand. DNA polymerases are a family of enzymes. DNA polymerases in general cannot initiate synthesis of new strands, but can only extend an existing DNA or RNA strand paired with a template strand. To begin synthesis, a short fragment of RNA, called a primer, must be created and paired with the template DNA strand. DNA polymerase adds a new strand of DNA by extending the 3′ end of an existing nucleotide chain, adding new nucleotides matched to the template strand one at a time via the creation of phosphodiester bonds; the energy for this process of DNA polymerization comes from hydrolysis of the high-energy phosphate bonds between the three phosphates attached to each unincorporated base. Free bases with their attached phosphate groups are called nucleotides; when a nucleotide is being added to a growing DNA strand, the formation of a phosphodiester bond between the proximal phosphate of the nucleotide to the growing chain is accompanied by hydrolysis of a high-energy phosphate bond with release of the two distal phosphates as a pyrophosphate.
Enzymatic hydrolysis of the resulting pyrophosphate into inorganic phosphate consumes a second high-energy phosphate bond and renders the reaction irreversible. In general, DNA polymerases are accurate, with an intrinsic error rate of less than one mistake for every 107 nucleotides added. In addition, some DNA polymerases have proofreading ability. Post-replication mismatch repair mechanisms monitor the DNA for errors, being capable of distinguishing mismatches in the newly synthesized DNA strand from the original strand sequence. Together, these three discrimination steps enable replication fidelity of less than one mistake for every 109 nucleotides added; the rate of DNA replication in a living cell was first measured as the rate of phage T4 DNA elongation in phage-infected E. coli. During the period of exponential DNA increase at 37 °C, the rate was 749 nucleotides per second
DNA ligase is a specific type of enzyme, a ligase, that facilitates the joining of DNA strands together by catalyzing the formation of a phosphodiester bond. It plays a role in repairing single-strand breaks in duplex DNA in living organisms, but some forms may repair double-strand breaks. Single-strand breaks are repaired by DNA ligase using the complementary strand of the double helix as a template, with DNA ligase creating the final phosphodiester bond to repair the DNA. DNA ligase is used in both DNA DNA replication. In addition, DNA ligase has extensive use in molecular biology laboratories for recombinant DNA experiments. Purified DNA ligase is used in gene cloning to join DNA molecules together to form recombinant DNA; the mechanism of DNA ligase is to form two covalent phosphodiester bonds between 3' hydroxyl ends of one nucleotide, with the 5' phosphate end of another. Two ATP molecules are consumed for each phosphodiester bond formed. AMP is required for the ligase reaction, which proceeds in four steps: Reorganization of activity site such as nicks in DNA segments or Okazaki fragments etc.
Adenylation of a lysine residue in the active center of the enzyme, pyrophosphate is released. Ligase will work with blunt ends, although higher enzyme concentrations and different reaction conditions are required; the E. coli DNA ligase is encoded by the lig gene. DNA ligase in E. coli, as well as most prokaryotes, uses energy gained by cleaving nicotinamide adenine dinucleotide to create the phosphodiester bond. It does not ligate blunt-ended DNA except under conditions of molecular crowding with polyethylene glycol, cannot join RNA to DNA efficiently; the activity of E. coli DNA ligase can be enhanced by DNA polymerase at the right concentrations. Enhancement only works when the concentrations of the DNA polymerase 1 are much lower than the DNA fragments to be ligated; when the concentrations of Pol I DNA polymerases are higher, it has an adverse effect on E. coli DNA ligase The DNA ligase from bacteriophage T4. The T4 ligase is the most-commonly used in laboratory research, it can ligate either cohesive or blunt ends of DNA, oligonucleotides, as well as RNA and RNA-DNA hybrids, but not single-stranded nucleic acids.
It can ligate blunt-ended DNA with much greater efficiency than E. coli DNA ligase. Unlike E. coli DNA ligase, T4 DNA ligase cannot utilize NAD and it has an absolute requirement for ATP as a cofactor. Some engineering has been done to improve the in vitro activity of T4 DNA ligase. A typical reaction for inserting a fragment into a plasmid vector would use about 0.01 to 1 units of ligase. The optimal incubation temperature for T4 DNA ligase is 16 °C. In mammals, there are four specific types of ligase. DNA ligase I: ligates the nascent DNA of the lagging strand after the Ribonuclease H has removed the RNA primer from the Okazaki fragments. DNA ligase III: complexes with DNA repair protein XRCC1 to aid in sealing DNA during the process of nucleotide excision repair and recombinant fragments. Of the all known mammalian DNA ligases, only Lig III has been found to be present in mitochondria. DNA ligase IV: complexes with XRCC4, it catalyzes the final step in the non-homologous end joining DNA double-strand break repair pathway.
It is required for VJ recombination, the process that generates diversity in immunoglobulin and T-cell receptor loci during immune system development. DNA ligase II: appears to be used in repair, it is formed by alternative splicing of a proteolytic fragment of DNA ligase III and does not have its own gene, therefore it is considered to be identical to DNA ligase III. DNA ligase from eukaryotes and some microbes uses adenosine triphosphate rather than NAD. Derived from a thermophilic bacterium, the enzyme is stable and active at much higher temperatures than conventional DNA ligases, its half-life is 48 hours at 65°C and greater than 1 hour at 95°C. Ampligase DNA Ligase has been shown to be active for at least 500 thermal cycles or 16 hours of cycling.10 This exceptional thermostability permits high hybridization stringency and ligation specificity. There are at least three different units used to measure the activity of DNA ligase: Weiss unit - the amount of ligase that catalyzes the exchange of 1 nmole of 32P from inorganic pyrophosphate to ATP in 20 minutes at 37°C.
This is the one most used. Modrich-Lehman unit - this is used, one unit is defined as the amount of enzyme required to convert 100 nmoles of dn to an exonuclease-III resistant form in 30 minutes under standard conditions. Many commercial suppliers of ligases use an arbitrary unit based on the ability of ligase to ligate cohesive ends; these units are more subjective than quantitative and lack precision. DNA ligases have become indispensable tools in modern molecular biology research for generating recombinant DNA sequences. For example, DNA ligases are used with restriction enzymes to insert DNA fragments genes, into plasmids. Controlling the optimal temperature is a vital aspect of performing effi
Nucleic acids are the biopolymers, or small biomolecules, essential to all known forms of life. The term nucleic acid is the overall name for DNA and RNA, they are composed of nucleotides, which are the monomers made of three components: a 5-carbon sugar, a phosphate group and a nitrogenous base. If the sugar is a compound ribose, the polymer is RNA. Nucleic acids are the most important of all biomolecules, they are found in abundance in all living things, where they function to create and encode and store information in the nucleus of every living cell of every life-form organism on Earth. In turn, they function to transmit and express that information inside and outside the cell nucleus—to the interior operations of the cell and to the next generation of each living organism; 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. Strings of nucleotides are bonded to form helical backbones—typically, one for RNA, two for DNA—and assembled into chains of base-pairs selected from the five primary, or canonical, which are: adenine, guanine and uracil.
Using amino acids and the process 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 and most chemical processes of all life forms. Nuclein were discovered by Friedrich Miescher in 1869. In the early 1880s Albrecht Kossel further purifies the substance and discovers its acidic properties, he also identifies the nucleobases. In 1889 Richard Altmann creates the term nucleic acid In 1938 Astbury and Bell published the first X-ray diffraction pattern of DNA. In 1953 Watson and Crick determined the structure of DNA. Experimental studies of nucleic acids constitute a major part of modern biological and medical research, form a foundation for genome and forensic science, the biotechnology and pharmaceutical industries; the term nucleic acid is the overall name for DNA and RNA, members of a family of biopolymers, is synonymous with polynucleotide.
Nucleic acids were named for their initial discovery within the nucleus, for the presence of phosphate groups. Although first discovered within the nucleus of eukaryotic cells, nucleic acids are now known to be found in all life forms including within bacteria, mitochondria, chloroplasts and viroids.. All living cells contain both DNA and RNA, while viruses contain either DNA or RNA, but not both; the basic component of biological nucleic acids is the nucleotide, each of which contains a pentose sugar, a phosphate group, a nucleobase. Nucleic acids are generated within the laboratory, through the use of enzymes and by solid-phase chemical synthesis; the chemical methods enable the generation of altered nucleic acids that are not found in nature, for example peptide nucleic acids. Nucleic acids are very large molecules. Indeed, DNA molecules are the largest individual molecules known. Well-studied biological nucleic acid molecules range in size from 21 nucleotides to large chromosomes. In most cases 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 of nucleotides; each nucleotide consists of three components: a purine or pyrimidine nucleobase, a pentose sugar, 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; the nucleobases found in the two nucleic acid types are different: adenine 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 through phosphodiester linkages. In conventional nomenclature, 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, 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 and the 1' carbon of the pentose sugar ring. Non-standard nucleosides are found in both RNA and DNA and arise from modification of the standard nucleosides within the DNA molecule or the primary RNA transcript. Transfer RNA molecules contain a 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 repeated and quite uniform double-helical three-dimensional structure. In contrast, single-stranded
Ribonucleic acid is a polymeric molecule essential in various biological roles in coding, decoding and expression of genes. RNA and DNA are nucleic acids, along with lipids and carbohydrates, constitute the four major macromolecules essential for all known forms of life. Like DNA, RNA is assembled as a chain of nucleotides, but unlike DNA it is more found in nature as a single-strand folded onto itself, rather than a paired double-strand. Cellular organisms use messenger RNA to convey genetic 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 active processes is protein synthesis, a universal function in which RNA molecules direct the assembly of proteins on ribosomes; this process uses transfer RNA molecules to deliver amino acids to the ribosome, where ribosomal RNA links amino acids together to form proteins.
Like DNA, most biologically active RNAs, including mRNA, tRNA, rRNA, snRNAs, other non-coding RNAs, contain self-complementary sequences that allow parts of the RNA to fold and pair with itself to form double helices. Analysis of these RNAs has revealed that they are structured. Unlike DNA, their structures do not consist of long double helices, but rather collections of short helices packed together into structures akin to proteins. In this fashion, RNAs can achieve chemical catalysis. For instance, determination of the structure of the ribosome—an RNA-protein complex that catalyzes peptide bond formation—revealed that its active site is composed of RNA; each nucleotide in RNA contains a ribose sugar, with carbons numbered 1' through 5'. A base is attached to the 1' position, in general, cytosine, guanine, or uracil. Adenine and guanine are purines and uracil are pyrimidines. A phosphate group is attached to the 5' position of the next; the phosphate groups have a negative charge each. 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 component of RNA that distinguishes it from DNA is the presence of a hydroxyl group at the 2' position of the ribose sugar; the presence of this functional group causes the helix to take the A-form geometry, although in single strand dinucleotide contexts, RNA can also adopt the B-form most observed in DNA. The A-form geometry results in a deep and narrow major groove and a shallow and wide minor groove. A second consequence of the presence of the 2'-hydroxyl group is that in conformationally flexible regions of an RNA molecule, it can chemically attack the adjacent phosphodiester bond to cleave the backbone. RNA is transcribed with only four bases, but these bases and attached sugars can be modified in numerous ways as the RNAs mature. Pseudouridine, in which the linkage between uracil and ribose is changed from a C–N bond to a C–C bond, 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. There are more than 100 other occurring modified nucleosides; the greatest structural diversity of modifications can be found in tRNA, while pseudouridine and nucleosides with 2'-O-methylribose present in rRNA are the most common. The specific roles of many of these modifications in RNA are not understood. However, it is notable that, in ribosomal RNA, many of the post-transcriptional modifications occur in functional regions, such as the peptidyl transferase center and the subunit interface, implying that they are important for normal function; the functional form of single-stranded RNA molecules, just like proteins requires a specific tertiary structure. The scaffold for this structure is provided by secondary structural elements that are hydrogen bonds within the molecule; this leads to several recognizable "domains" of secondary structure like hairpin loops and internal loops.
Since RNA is charged, metal ions such as Mg2+ are needed to stabilise many secondary and tertiary structures. The occurring enantiomer of RNA is D-RNA composed of D-ribonucleotides. All chirality centers are located in the D-ribose. By the use of L-ribose or rather L-ribonucleotides, L-RNA can be synthesized. L-RNA is much more stable against degradation by RNase. Like other structured biopolymers such as proteins, one can define topology of a folded RNA molecule; this is done based on arrangement of intra-chain contacts within a folded RNA, termed as circuit topology. Synthesis of RNA is catalyzed by an enzyme—RNA polymerase—using DNA as a template, a process known as transcription. Initiation of transcription begins with the binding of the enzyme to a promoter sequence in the DNA; the DNA double helix is unwound by the helicase activity of the enzyme. The enzyme progresses along the template strand in the 3’ to 5’ direction, synthesizing a complementary RNA molecule with elongation occ
Deoxyribonucleic acid is a molecule composed of two chains that coil around each other to form a double helix carrying the genetic instructions used in the growth, development and reproduction of all known organisms and many viruses. DNA and ribonucleic acid are nucleic acids; the two DNA strands are known as polynucleotides as they are composed of simpler monomeric units called nucleotides. Each nucleotide is composed of one of four nitrogen-containing nucleobases, a sugar called deoxyribose, 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 separate polynucleotide strands are bound together, according to base pairing rules, with hydrogen bonds to make double-stranded DNA; the complementary nitrogenous bases are divided into two groups and purines. In DNA, the pyrimidines are cytosine. Both strands of double-stranded DNA store the same biological information.
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 are thus antiparallel. Attached to each sugar is one of four types of nucleobases, it is the sequence of these four nucleobases along the backbone. RNA strands are created using DNA strands as a template in a process called transcription. Under the genetic code, these RNA strands specify the sequence of amino acids within proteins in a process called translation. Within eukaryotic cells, DNA is organized into long structures called chromosomes. Before typical cell division, these chromosomes are duplicated in the process of DNA replication, providing a complete set of chromosomes for each daughter cell. Eukaryotic organisms store most of their DNA inside the cell nucleus as nuclear DNA, some in the mitochondria as mitochondrial DNA, or in chloroplasts as chloroplast DNA. In contrast, prokaryotes store their DNA only in circular chromosomes.
Within eukaryotic chromosomes, chromatin proteins, such as histones and organize DNA. These compacting 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, its molecular structure was first identified by Francis Crick and James Watson at the Cavendish Laboratory within the University of Cambridge in 1953, whose model-building efforts were guided by X-ray diffraction data acquired by Raymond Gosling, a post-graduate student of Rosalind Franklin. DNA is used by researchers as a molecular tool to explore physical laws and theories, such as the ergodic theorem and the theory of elasticity; the unique material properties of DNA have made it an attractive molecule for material scientists and engineers interested in micro- and nano-fabrication. Among notable advances in this field are DNA origami and DNA-based hybrid materials. DNA is a long polymer made from repeating units called nucleotides.
The structure of DNA is dynamic along its length, being capable of coiling into tight loops and other shapes. In all species it is composed of two helical chains, bound to each other by hydrogen bonds. Both chains are coiled around the same axis, have the same pitch of 34 angstroms; the pair of chains has a radius of 10 angstroms. According to another study, when measured in a different solution, the DNA chain measured 22 to 26 angstroms wide, one nucleotide unit measured 3.3 Å long. Although each individual nucleotide is small, a DNA polymer can be large and contain hundreds of millions, such as in chromosome 1. Chromosome 1 is the largest human chromosome with 220 million base pairs, would be 85 mm long if straightened. DNA does not exist as a single strand, but instead as a pair of strands that are held together; these two long strands coil in the shape of a double helix. The nucleotide contains both a segment of the backbone of a nucleobase. A nucleobase linked to a sugar is called a nucleoside, a base linked to a sugar and to one or more phosphate groups is called a nucleotide.
A biopolymer comprising multiple linked nucleotides is called a polynucleotide. The backbone of the DNA strand is made from alternating sugar residues; the sugar in DNA is 2-deoxyribose, a pentose sugar. The sugars are joined together by phosphate groups that form phosphodiester bonds between the third and fifth carbon atoms of adjacent sugar rings; these are known as the 3′-end, 5′-end carbons, the prime symbol being used to distinguish these carbon atoms from those of the base to which the deoxyribose forms a glycosidic bond. When imagining DNA, each phosphoryl is considered to "belong" to the nucleotide whose 5′ carbon forms a bond therewith. Any DNA strand therefore has one end at which there is a phosphoryl attached to the 5′ carbon of a ribose and another end a