Peptides are short chains of amino acid monomers linked by peptide bonds. The covalent chemical bonds are formed when the carboxyl group of one amino acid reacts with the amino group of another; the shortest peptides are dipeptides, consisting of 2 amino acids joined by a single peptide bond, followed by tripeptides, etc. A polypeptide is a long and unbranched peptide chain. Hence, peptides fall under the broad chemical classes of biological oligomers and polymers, alongside nucleic acids and polysaccharides, etc. Peptides are distinguished from proteins on the basis of size, as an arbitrary benchmark can be understood to contain 50 or fewer amino acids. Proteins consist of one or more polypeptides arranged in a biologically functional way bound to ligands such as coenzymes and cofactors, or to another protein or other macromolecule, or to complex macromolecular assemblies. While aspects of the lab techniques applied to peptides versus polypeptides and proteins differ, the size boundaries that distinguish peptides from polypeptides and proteins are not absolute: long peptides such as amyloid beta have been referred to as proteins, smaller proteins like insulin have been considered peptides.
Amino acids that have been incorporated into peptides are termed "residues" due to the release of either a hydrogen ion from the amine end or a hydroxyl ion from the carboxyl end, or both, as a water molecule is released during formation of each amide bond. All peptides except cyclic peptides have an N-terminal and C-terminal residue at the end of the peptide. Many kinds of peptides are known, they have been categorized according to their sources and function. According to the Handbook of Biologically Active Peptides, some groups of peptides include plant peptides, bacterial/antibiotic peptides, fungal peptides, invertebrate peptides, amphibian/skin peptides, venom peptides, cancer/anticancer peptides, vaccine peptides, immune/inflammatory peptides, brain peptides, endocrine peptides, ingestive peptides, gastrointestinal peptides, cardiovascular peptides, renal peptides, respiratory peptides, opiate peptides, neurotrophic peptides, blood–brain peptides; some ribosomal peptides are subject to proteolysis.
These function in higher organisms, as hormones and signaling molecules. Some organisms produce peptides as antibiotics, such as microcins. Peptides have posttranslational modifications such as phosphorylation, sulfonation, palmitoylation and disulfide formation. In general, peptides are linear. More exotic manipulations do occur, such as racemization of L-amino acids to D-amino acids in platypus venom. Nonribosomal peptides are assembled by enzymes, not the ribosome. A common non-ribosomal peptide is glutathione, a component of the antioxidant defenses of most aerobic organisms. Other nonribosomal peptides are most common in unicellular organisms and fungi and are synthesized by modular enzyme complexes called nonribosomal peptide synthetases; these complexes are laid out in a similar fashion, they can contain many different modules to perform a diverse set of chemical manipulations on the developing product. These peptides are cyclic and can have complex cyclic structures, although linear nonribosomal peptides are common.
Since the system is related to the machinery for building fatty acids and polyketides, hybrid compounds are found. The presence of oxazoles or thiazoles indicates that the compound was synthesized in this fashion. Peptide fragments refer to fragments of proteins that are used to identify or quantify the source protein; these are the products of enzymatic degradation performed in the laboratory on a controlled sample, but can be forensic or paleontological samples that have been degraded by natural effects. Use of peptides received prominence in molecular biology for several reasons; the first is that peptides allow the creation of peptide antibodies in animals without the need of purifying the protein of interest. This involves synthesizing antigenic peptides of sections of the protein of interest; these will be used to make antibodies in a rabbit or mouse against the protein. Another reason is that techniques such as mass spectrometry enable the identification of proteins based on the peptide masses and sequence that result from their fragmentation.
Peptides have been used in the study of protein structure and function. For example, synthetic peptides can be used as probes to see where protein-peptide interactions occur- see the page on Protein tags. Inhibitory peptides are used in clinical research to examine the effects of peptides on the inhibition of cancer proteins and other diseases. For example, one of the most promising application is through peptides that target LHRH; these particular peptides act as an agonist, meaning that they bind to a cell in a way that regulates LHRH receptors. The process of inhibiting the cell receptors suggests that peptides could be beneficial in treating prostate cancer, but additional investigations and experiments are required before their cancer-fighting attributes can be considered definitive; the peptide families in this section are ribosomal peptides with hormonal activity. All of these peptides are synthesized by cells as longer "propeptides" or "proproteins" and truncated prior to exiting the cell.
They are released into the bloodstream. Magainin family Cecropin famil
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
Chemistry is the scientific discipline involved with elements and compounds composed of atoms and ions: their composition, properties and the changes they undergo during a reaction with other substances. In the scope of its subject, chemistry occupies an intermediate position between physics and biology, it is sometimes called the central science because it provides a foundation for understanding both basic and applied scientific disciplines at a fundamental level. For example, chemistry explains aspects of plant chemistry, the formation of igneous rocks, how atmospheric ozone is formed and how environmental pollutants are degraded, the properties of the soil on the moon, how medications work, how to collect DNA evidence at a crime scene. Chemistry addresses topics such as how atoms and molecules interact via chemical bonds to form new chemical compounds. There are four types of chemical bonds: covalent bonds, in which compounds share one or more electron; the word chemistry comes from alchemy, which referred to an earlier set of practices that encompassed elements of chemistry, philosophy, astronomy and medicine.
It is seen as linked to the quest to turn lead or another common starting material into gold, though in ancient times the study encompassed many of the questions of modern chemistry being defined as the study of the composition of waters, growth, disembodying, drawing the spirits from bodies and bonding the spirits within bodies by the early 4th century Greek-Egyptian alchemist Zosimos. An alchemist was called a'chemist' in popular speech, the suffix "-ry" was added to this to describe the art of the chemist as "chemistry"; the modern word alchemy in turn is derived from the Arabic word al-kīmīā. In origin, the term is borrowed from the Greek χημία or χημεία; this may have Egyptian origins since al-kīmīā is derived from the Greek χημία, in turn derived from the word Kemet, the ancient name of Egypt in the Egyptian language. Alternately, al-kīmīā may derive from χημεία, meaning "cast together"; the current model of atomic structure is the quantum mechanical model. Traditional chemistry starts with the study of elementary particles, molecules, metals and other aggregates of matter.
This matter can be studied in isolation or in combination. The interactions and transformations that are studied in chemistry are the result of interactions between atoms, leading to rearrangements of the chemical bonds which hold atoms together; such behaviors are studied in a chemistry laboratory. The chemistry laboratory stereotypically uses various forms of laboratory glassware; however glassware is not central to chemistry, a great deal of experimental chemistry is done without it. A chemical reaction is a transformation of some substances into one or more different substances; the basis of such a chemical transformation is the rearrangement of electrons in the chemical bonds between atoms. It can be symbolically depicted through a chemical equation, which involves atoms as subjects; the number of atoms on the left and the right in the equation for a chemical transformation is equal. The type of chemical reactions a substance may undergo and the energy changes that may accompany it are constrained by certain basic rules, known as chemical laws.
Energy and entropy considerations are invariably important in all chemical studies. Chemical substances are classified in terms of their structure, phase, as well as their chemical compositions, they can be analyzed using the tools of e.g. spectroscopy and chromatography. Scientists engaged in chemical research are known as chemists. Most chemists specialize in one or more sub-disciplines. Several concepts are essential for the study of chemistry; the particles that make up matter have rest mass as well – not all particles have rest mass, such as the photon. Matter can be a mixture of substances; the atom is the basic unit of chemistry. It consists of a dense core called the atomic nucleus surrounded by a space occupied by an electron cloud; the nucleus is made up of positively charged protons and uncharged neutrons, while the electron cloud consists of negatively charged electrons which orbit the nucleus. In a neutral atom, the negatively charged electrons balance out the positive charge of the protons.
The nucleus is dense. The atom is the smallest entity that can be envisaged to retain the chemical properties of the element, such as electronegativity, ionization potential, preferred oxidation state, coordination number, preferred types of bonds to form. A chemical element is a pure substance, composed of a single type of atom, characterized by its particular number of protons in the nuclei of its atoms, known as the atomic number and represented by the symbol Z; the mass number is the sum of the number of neutrons in a nucleus. Although all the nuclei of all atoms belonging to one element will have the same
Speed of light
The speed of light in vacuum denoted c, is a universal physical constant important in many areas of physics. Its exact value is 299,792,458 metres per second, it is exact because by international agreement a metre is defined as the length of the path travelled by light in vacuum during a time interval of 1/299792458 second. According to special relativity, c is the maximum speed at which all conventional matter and hence all known forms of information in the universe can travel. Though this speed is most associated with light, it is in fact the speed at which all massless particles and changes of the associated fields travel in vacuum; such particles and waves travel at c regardless of the motion of the source or the inertial reference frame of the observer. In the special and general theories of relativity, c interrelates space and time, appears in the famous equation of mass–energy equivalence E = mc2; the speed at which light propagates through transparent materials, such as glass or air, is less than c.
The ratio between c and the speed v at which light travels in a material is called the refractive index n of the material. For example, for visible light the refractive index of glass is around 1.5, meaning that light in glass travels at c / 1.5 ≈ 200,000 km/s. For many practical purposes and other electromagnetic waves will appear to propagate instantaneously, but for long distances and sensitive measurements, their finite speed has noticeable effects. In communicating with distant space probes, it can take minutes to hours for a message to get from Earth to the spacecraft, or vice versa; the light seen from stars left them many years ago, allowing the study of the history of the universe by looking at distant objects. The finite speed of light limits the theoretical maximum speed of computers, since information must be sent within the computer from chip to chip; the speed of light can be used with time of flight measurements to measure large distances to high precision. Ole Rømer first demonstrated in 1676 that light travels at a finite speed by studying the apparent motion of Jupiter's moon Io.
In 1865, James Clerk Maxwell proposed that light was an electromagnetic wave, therefore travelled at the speed c appearing in his theory of electromagnetism. In 1905, Albert Einstein postulated that the speed of light c with respect to any inertial frame is a constant and is independent of the motion of the light source, he explored the consequences of that postulate by deriving the theory of relativity and in doing so showed that the parameter c had relevance outside of the context of light and electromagnetism. After centuries of precise measurements, in 1975 the speed of light was known to be 299792458 m/s with a measurement uncertainty of 4 parts per billion. In 1983, the metre was redefined in the International System of Units as the distance travelled by light in vacuum in 1/299792458 of a second; the speed of light in vacuum is denoted by a lowercase c, for "constant" or the Latin celeritas. In 1856, Wilhelm Eduard Weber and Rudolf Kohlrausch had used c for a different constant shown to equal √2 times the speed of light in vacuum.
The symbol V was used as an alternative symbol for the speed of light, introduced by James Clerk Maxwell in 1865. In 1894, Paul Drude redefined c with its modern meaning. Einstein used V in his original German-language papers on special relativity in 1905, but in 1907 he switched to c, which by had become the standard symbol for the speed of light. Sometimes c is used for the speed of waves in any material medium, c0 for the speed of light in vacuum; this subscripted notation, endorsed in official SI literature, has the same form as other related constants: namely, μ0 for the vacuum permeability or magnetic constant, ε0 for the vacuum permittivity or electric constant, Z0 for the impedance of free space. This article uses c for the speed of light in vacuum. Since 1983, the metre has been defined in the International System of Units as the distance light travels in vacuum in 1⁄299792458 of a second; this definition fixes the speed of light in vacuum at 299,792,458 m/s. As a dimensional physical constant, the numerical value of c is different for different unit systems.
In branches of physics in which c appears such as in relativity, it is common to use systems of natural units of measurement or the geometrized unit system where c = 1. Using these units, c does not appear explicitly because multiplication or division by 1 does not affect the result; the speed at which light waves propagate in vacuum is independent both of the motion of the wave source and of the inertial frame of reference of the observer. This invariance of the speed of light was postulated by Einstein in 1905, after being motivated by Maxwell's theory of electromagnetism and the lack of evidence for the luminiferous aether, it is only possible to verify experimentally that the two-way speed of light is frame-independent, because it is impossible to measure the one-way speed of light without some convention as to how clocks at the source and at the detector should be synchronized. However
High-temperature superconductors are materials that behave as superconductors at unusually high temperatures. The first high-Tc superconductor was discovered in 1986 by IBM researchers Georg Bednorz and K. Alex Müller, who were awarded the 1987 Nobel Prize in Physics "for their important break-through in the discovery of superconductivity in ceramic materials". Whereas "ordinary" or metallic superconductors have transition temperatures below 30 K and must be cooled using liquid helium in order to achieve superconductivity, HTS have been observed with transition temperatures as high as 138 K, can be cooled to superconductivity using liquid nitrogen; until 2008, only certain compounds of copper and oxygen were known to have HTS properties, the term high-temperature superconductor was used interchangeably with cuprate superconductor for compounds such as bismuth strontium calcium copper oxide and yttrium barium copper oxide. Several iron-based compounds are now known to be superconducting at high temperatures.
In 2015, hydrogen sulfide under high pressure was found to undergo superconducting transition near 203 K, due the formation of H3S, a new record high temperature superconductor. For an explanation about Tc, see Superconductivity § Superconducting phase transition and the second bullet item of BCS theory § Successes of the BCS theory; the phenomenon of superconductivity was discovered by Kamerlingh Onnes in 1911, in metallic mercury below 4 K. Since, researchers have attempted to observe superconductivity at increasing temperatures with the goal of finding a room-temperature superconductor. By the late 1970s, superconductivity was observed in several metallic compounds at temperatures that were much higher than those for elemental metals and which could exceed 20 K. In 1986, J. Georg Bednorz and K. Alex Müller, working at the IBM research lab near Zurich, Switzerland were exploring a new class of ceramics for superconductivity. Bednorz encountered a barium-doped compound of lanthanum and copper oxide whose resistance dropped to zero at a temperature around 35 K.
Their results were soon confirmed by many groups, notably Paul Chu at the University of Houston and Shoji Tanaka at the University of Tokyo. Shortly after, P. W. Anderson, at Princeton University came up with the first theoretical description of these materials, using the resonating valence bond theory, but a full understanding of these materials is still developing today; these superconductors are now known to possess a d-wave pair symmetry. The first proposal that high-temperature cuprate superconductivity involves d-wave pairing was made in 1987 by Bickers and Scalettar, followed by three subsequent theories in 1988 by Inui, Doniach and Ruckenstein, using spin-fluctuation theory, by Gros, Poilblanc and Zhang, by Kotliar and Liu identifying d-wave pairing as a natural consequence of the RVB theory; the confirmation of the d-wave nature of the cuprate superconductors was made by a variety of experiments, including the direct observation of the d-wave nodes in the excitation spectrum through Angle Resolved Photoemission Spectroscopy, the observation of a half-integer flux in tunneling experiments, indirectly from the temperature dependence of the penetration depth, specific heat and thermal conductivity.
Until 2015 the superconductor with the highest transition temperature, confirmed by multiple independent research groups was mercury barium calcium copper oxide at around 133 K. After more than twenty years of intensive research, the origin of high-temperature superconductivity is still not clear, but it seems that instead of electron-phonon attraction mechanisms, as in conventional superconductivity, one is dealing with genuine electronic mechanisms, instead of conventional, purely s-wave pairing, more exotic pairing symmetries are thought to be involved. In 2014, evidence showing that fractional particles can happen in quasi two-dimensional magnetic materials, was found by EPFL scientists lending support for Anderson's theory of high-temperature superconductivity; the structure of high-Tc copper oxide or cuprate superconductors are closely related to perovskite structure, the structure of these compounds has been described as a distorted, oxygen deficient multi-layered perovskite structure.
One of the properties of the crystal structure of oxide superconductors is an alternating multi-layer of CuO2 planes with superconductivity taking place between these layers. The more layers of CuO2, the higher Tc; this structure causes a large anisotropy in normal conducting and superconducting properties, since electrical currents are carried by holes induced in the oxygen sites of the CuO2 sheets. The electrical conduction is anisotropic, with a much higher conductivity parallel to the CuO2 plane than in the perpendicular direction. Critical temperatures depend on the chemical compositions, cations substitutions and oxygen content, they can be classified as superstripes. The first superconductor found with Tc > 77 K (liquid nitrogen b
Amino acids are organic compounds containing amine and carboxyl functional groups, along with a side chain specific to each amino acid. The key elements of an amino acid are carbon, hydrogen and nitrogen, although other elements are found in the side chains of certain amino acids. About 500 occurring amino acids are known and can be classified in many ways, they can be classified according to the core structural functional groups' locations as alpha-, beta-, gamma- or delta- amino acids. In the form of proteins, amino acid residues form the second-largest component of human muscles and other tissues. Beyond their role as residues in proteins, amino acids participate in a number of processes such as neurotransmitter transport and biosynthesis. In biochemistry, amino acids having both the amine and the carboxylic acid groups attached to the first carbon atom have particular importance, they are known as α-amino acids. They include the 22 proteinogenic amino acids, which combine into peptide chains to form the building-blocks of a vast array of proteins.
These are all L-stereoisomers, although a few D-amino acids occur in bacterial envelopes, as a neuromodulator, in some antibiotics. Twenty of the proteinogenic amino acids are encoded directly by triplet codons in the genetic code and are known as "standard" amino acids; the other two are selenocysteine, pyrrolysine. Pyrrolysine and selenocysteine are encoded via variant codons. N-formylmethionine is considered as a form of methionine rather than as a separate proteinogenic amino acid. Codon–tRNA combinations not found in nature can be used to "expand" the genetic code and form novel proteins known as alloproteins incorporating non-proteinogenic amino acids. Many important proteinogenic and non-proteinogenic amino acids have biological functions. For example, in the human brain and gamma-amino-butyric acid are the main excitatory and inhibitory neurotransmitters. Hydroxyproline, a major component of the connective tissue collagen, is synthesised from proline. Glycine is a biosynthetic precursor to porphyrins used in red blood cells.
Carnitine is used in lipid transport. Nine proteinogenic amino acids are called "essential" for humans because they cannot be produced from other compounds by the human body and so must be taken in as food. Others may be conditionally essential for medical conditions. Essential amino acids may differ between species; because of their biological significance, amino acids are important in nutrition and are used in nutritional supplements, fertilizers and food technology. Industrial uses include the production of drugs, biodegradable plastics, chiral catalysts; the first few amino acids were discovered in the early 19th century. In 1806, French chemists Louis-Nicolas Vauquelin and Pierre Jean Robiquet isolated a compound in asparagus, subsequently named asparagine, the first amino acid to be discovered. Cystine was discovered in 1810, although its monomer, remained undiscovered until 1884. Glycine and leucine were discovered in 1820; the last of the 20 common amino acids to be discovered was threonine in 1935 by William Cumming Rose, who determined the essential amino acids and established the minimum daily requirements of all amino acids for optimal growth.
The unity of the chemical category was recognized by Wurtz in 1865, but he gave no particular name to it. Usage of the term "amino acid" in the English language is from 1898, while the German term, Aminosäure, was used earlier. Proteins were found to yield amino acids after enzymatic acid hydrolysis. In 1902, Emil Fischer and Franz Hofmeister independently proposed that proteins are formed from many amino acids, whereby bonds are formed between the amino group of one amino acid with the carboxyl group of another, resulting in a linear structure that Fischer termed "peptide". In the structure shown at the top of the page, R represents a side chain specific to each amino acid; the carbon atom next to the carboxyl group is called the α–carbon. Amino acids containing an amino group bonded directly to the alpha carbon are referred to as alpha amino acids; these include amino acids such as proline which contain secondary amines, which used to be referred to as "imino acids". The alpha amino acids are the most common form found in nature, but only when occurring in the L-isomer.
The alpha carbon is a chiral carbon atom, with the exception of glycine which has two indistinguishable hydrogen atoms on the alpha carbon. Therefore, all alpha amino acids but glycine can exist in either of two enantiomers, called L or D amino acids, which are mirror images of each other. While L-amino acids represent all of the amino acids found in proteins during translation in the ribosome, D-amin
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