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what is rna

Ribonucleic acid (abbreviated RNA) is a nucleic acid present in all living cells that has structural similarities to DNA. Unlike DNA, however, RNA is most often single-stranded. An RNA molecule has a backbone made of alternating phosphate groups and the sugar ribose, rather than the deoxyribose found in DNA. Attached to each sugar is one of four bases: adenine (A), uracil (U), cytosine (C) or guanine (G). Different types of RNA exist in cells: messenger RNA (mRNA), ribosomal RNA (rRNA) and transfer RNA (tRNA). In addition, some RNAs are involved in regulating gene expression. Certain viruses use RNA as their genomic material.

Ribonucleic acid, or RNA. I often think of RNA as being the less well-known cousin of DNA, particularly for people outside the field of biology or genomics. But really, when you think about it, RNA, in so many ways, is the actual functional form of nucleic acids that really the body uses to do the business of, you know, constructing cells or responding to immune challenges, of carrying amino acids from one part of the cell to the other, that quite often I feel that RNA doesn’t get the respect it deserves. So what I think we can share is that the different forms of RNA — mRNA, tRNA, rRNA — each in their own way have absolutely fundamental functions without which the biology of the genome could not be translated into practice. And I guess the most obvious one here might be mRNAs, because these are the transcribed forms of genes, the form in which a gene gets read by the cell. But really, I would encourage everyone to learn about the unique roles that tRNAs and rRNAs have as well, because each of these fits into the puzzle of life in a wonderfully unique way.

Types and functions of RNA

Of the many types of RNA, the three most well-known and most commonly studied are messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA), which are present in all organisms. These and other types of RNAs primarily carry out biochemical reactions, similar to enzymes. Some, however, also have complex regulatory functions in cells. Owing to their involvement in many regulatory processes, to their abundance, and to their diverse functions, RNAs play important roles in both normal cellular processes and diseases.

In protein synthesis, mRNA carries genetic codes from the DNA in the nucleus to ribosomes, the sites of protein translation in the cytoplasm. Ribosomes are composed of rRNA and protein. The ribosome protein subunits are encoded by rRNA and are synthesized in the nucleolus. Once fully assembled, they move to the cytoplasm, where, as key regulators of translation, they “read” the code carried by mRNA. A sequence of three nitrogenous bases in mRNA specifies incorporation of a specific amino acid in the sequence that makes up the protein. Molecules of tRNA (sometimes also called soluble, or activator, RNA), which contain fewer than 100 nucleotides, bring the specified amino acids to the ribosomes, where they are linked to form proteins.

In addition to mRNA, tRNA, and rRNA, RNAs can be broadly divided into coding (cRNA) and noncoding RNA (ncRNA). There are two types of ncRNAs, housekeeping ncRNAs (tRNA and rRNA) and regulatory ncRNAs, which are further classified according to their size. Long ncRNAs (lncRNA) have at least 200 nucleotides, while small ncRNAs have fewer than 200 nucleotides. Small ncRNAs are subdivided into micro RNA (miRNA), small nucleolar RNA (snoRNA), small nuclear RNA (snRNA), small-interfering RNA (siRNA), and PIWI-interacting RNA (piRNA).

The miRNAs are of particular importance. They are about 22 nucleotides long and function in gene regulation in most eukaryotes. They can inhibit (silence) gene expression by binding to target mRNA and inhibiting translation, thereby preventing functional proteins from being produced. Many miRNAs play significant roles in cancer and other diseases. For example, tumour suppressor and oncogenic (cancer-initiating) miRNAs can regulate unique target genes, leading to tumorigenesis and tumour progression.

Also of functional significance are the piRNAs, which are about 26 to 31 nucleotides long and exist in most animals. They regulate the expression of transposons (jumping genes) by keeping the genes from being transcribed in the germ cells (sperm and eggs). Most piRNA are complementary to different transposons and can specifically target those transposons.

Circular RNA (circRNA) is unique from other RNA types because its 5′ and 3′ ends are bonded together, creating a loop. The circRNAs are generated from many protein-encoding genes, and some can serve as templates for protein synthesis, similar to mRNA. They can also bind miRNA, acting as “sponges” that prevent miRNA molecules from binding to their targets. In addition, circRNAs play an important role in regulating the transcription and alternative splicing of the genes from which circRNAs were derived.

Important connections have been discovered between RNA and human disease. For example, as described previously, some miRNAs are capable of regulating cancer-associated genes in ways that facilitate tumour development. In addition, the dysregulation of miRNA metabolism has been linked to various neurodegenerative diseases, including Alzheimer disease. In the case of other RNA types, tRNAs can bind to specialized proteins known as caspases, which are involved in apoptosis (programmed cell death). By binding to caspase proteins, tRNAs inhibit apoptosis; the ability of cells to escape programmed death signaling is a hallmark of cancer. Noncoding RNAs known as tRNA-derived fragments (tRFs) are also suspected to play a role in cancer. The emergence of techniques such as RNA sequencing has led to the identification of novel classes of tumour-specific RNA transcripts, such as MALAT1 (metastasis associated lung adenocarcinoma transcript 1), increased levels of which have been found in various cancerous tissues and are associated with the proliferation and metastasis (spread) of tumour cells.

A class of RNAs containing repeat sequences is known to sequester RNA-binding proteins (RBPs), resulting in the formation of foci or aggregates in neural tissues. These aggregates play a role in the development of neurological diseases such as amyotrophic lateral sclerosis (ALS) and myotonic dystrophy. The loss of function, dysregulation, and mutation of various RBPs has been implicated in a host of human diseases.

The discovery of additional links between RNA and disease is expected. Increased understanding of RNA and its functions, combined with the continued development of sequencing technologies and efforts to screen RNA and RBPs as therapeutic targets, are likely to facilitate such discoveries.

phase, in thermodynamics, chemically and physically uniform or homogeneous quantity of matter that can be separated mechanically from a nonhomogeneous mixture and that may consist of a single substance or a mixture of substances. The three fundamental phases of matter are solid, liquid, and gas (vapour), but others are considered to exist, including crystalline, colloid, glassy, amorphous, and plasma phases. When a phase in one form is altered to another form, a phase change is said to have occurred.

General considerations

A system is a portion of the universe that has been chosen for studying the changes that take place within it in response to varying conditions. A system may be complex, such as a planet, or relatively simple, as the liquid within a glass. Those portions of a system that are physically distinct and mechanically separable from other portions of the system are called phases.

Phases within a system exist in a gaseous, liquid, or solid state. Solids are characterized by strong atomic bonding and high viscosity, resulting in a rigid shape. Most solids are crystalline, inasmuch as they have a three-dimensional periodic atomic arrangement; some solids (such as glass) lack this periodic arrangement and are noncrystalline, or amorphous. Gases consist of weakly bonded atoms with no long-range periodicity; gases expand to fill any available space. Liquids have properties intermediate between those of solids and gases. The molecules of a liquid are condensed like those of a solid. Liquids have a definite volume, but their low viscosity enables them to change shape as a function of time. The matter within a system may consist of more than one solid or liquid phase, but a system can contain only a single gas phase, which must be of homogeneous composition because the molecules of gases mix completely in all proportions.

System variables

Systems respond to changes in pressuretemperature, and chemical composition, and, as this happens, phases may be created, eliminated, or altered in composition. For example, an increase in pressure may cause a low-density liquid to convert to a denser solid, while an increase in temperature may cause a solid to melt. A change of composition might result in the compositional modification of a preexisting phase or in the gain or loss of a phase.

The phase rule

The classification and limitations of phase changes are described by the phase rule, as proposed by the American chemist J. Willard Gibbs in 1876 and based on a rigorous thermodynamic relationship. The phase rule is commonly given in the form P + F = C + 2. The term P refers to the number of phases that are present within the system, and C is the minimum number of independent chemical components that are necessary to describe the composition of all phases within the system. The term F, called the variance, or degrees of freedom, describes the minimum number of variables that must be fixed in order to define a particular condition of the system.

Phase diagrams

Unary systems

Phase relations are commonly described graphically in terms of phase diagrams (see Figure 1). Each point within the diagram indicates a particular combination of pressure and temperature, as well as the phase or phases that exist stably at this pressure and temperature. All phases in Figure 1 have the same composition—that of silicon dioxide, SiO2. The diagram is a representation of a one-component (unary) system, in contrast to a two-component (binary), three-component (ternary), or four-component (quaternary) system. The phases coesite, low quartz, high quartz, tridymite, and cristobalite are solid phases composed of silicon dioxide; each has its own atomic arrangement and distinctive set of physical and chemical properties. The most common form of quartz (found in beach sands and granites) is low quartz. The region labeled anhydrous melt consists of silicon dioxide liquid.

Different portions of the silicon dioxide system may be examined in terms of the phase rule. At point A a single solid phase exists—low quartz. Substituting the appropriate values into the phase rule P + F = C + 2 yields 1 + F = 1 + 2, so F = 2. For point A (or any point in which only a single phase is stable) the system is divariant—i.e., two degrees of freedom exist. Thus, the two variables (pressure and temperature) can be changed independently, and the same phase assemblage continues to exist.

Point B is located on the boundary curve between the stability fields of low quartz and high quartz. At all points along this curve, these two phases coexist. Substituting values in the phase rule (2 + F = 1 + 2) will cause a variance of 1 to be obtained. This indicates that one independent variable can be changed such that the same pair of phases will be retained. A second variable must be changed to conform to the first in order for the phase assemblage to remain on the boundary between low and high quartz. The same result holds for the other boundary curves in this system.

Point C is located at a triple point, a condition in which three stability fields intersect. The phase rule (3 + F = 1 + 2) indicates that the variance is 0. Point C is therefore an invariant point; a change in either pressure or temperature results in the loss of one or more phases. The phase rule also reveals that no more than three phases can stably coexist in a one-component system because additional phases would lead to negative variance.

Binary systems

Consider the binary system (Figure 2) that describes the freezing and melting of the minerals titanite (CaSiTiO5) and anorthite feldspar (CaAl2Si2O8). The melt can range in composition from pure CaSiTiO5 to pure CaAl2Si2O8, but the solids show no compositional substitution. All phases therefore have the composition of CaSiTiO5, CaAl2Si2O8, or a liquid mixture of the two. The system in the figure has been examined at atmospheric pressure; because the pressure variable is fixed, the phase rule is expressed as P + F = C + 1. In this form it is called the condensed phase rule, for any gas phase is either condensed to a liquid or is present in negligible amounts. The phase diagram shows a vertical temperature coordinate and a horizontal compositional coordinate (ranging from pure CaSiTiO5 at the left to pure CaAl2Si2O8 at the right).

The phase fields (separated by the solid curves) contain either one or two phases. Any point in a one-phase field corresponds to a single phase whose composition is indicated directly below on the horizontal axis. For example, point A presents a liquid whose composition is 70 percent CaAl2Si2O8 and 30 percent CaSiTiO5. The compositions of phases in a two-phase field are determined by construction of a horizontal (constant-temperature) line from the point of interest to the extremities of the two-phase field. Thus, a sample with composition B consists of liquid C (43 percent CaSiTiO5 and 57 percent CaAl2Si2O8) and solid anorthite D. A sample at point E at a lower temperature consists of the solids titanite (F) and anorthite (G).

Liquid CaAl2Si2O8 cools to produce solid anorthite at 1,550 °C, whereas liquid CaSiTiO5 cools to produce solid titanite at 1,390 °C. If the batch were a mixture of the two components, the freezing temperature of each of these minerals would be depressed. In a melt consisting of a single component, such as CaSiTiO5, all atoms could add to titanite nuclei to form crystals of titanite. If, however, the melt contained 30 percent CaAl2Si2O8, the rate of formation of titanite nuclei would be decreased, as 30 percent of the melt could not contribute to their formation. In order to increase the rate of formation of titanite nuclei and promote crystallization, the temperature of the melt must be decreased below the freezing point of pure CaSiTiO5. When cooled, liquid A does not begin crystallization until temperature H is reached. Pure anorthite crystals precipitate from the melt. Depletion of CaAl2Si2O8 from the melt causes the melt composition to become relatively enriched in CaSiTiO5, with consequent additional depression of the anorthite freezing point. As freezing continues, the liquid composition changes until the minimum point is reached at I. This point is called the eutectic. It is the lowest temperature at which a liquid can exist in this system. At the eutectic, both anorthite and titanite crystallize together at a fixed temperature and in a fixed ratio until the remaining liquid is consumed. All intermediate liquid compositions migrate during crystallization to the eutectic. The melting sequence of titanite-anorthite mixtures is exactly the opposite of the freezing sequence (i.e., melting of any anorthite-titanite mixture begins at the eutectic).

Depression of the freezing point of a compound by the addition of a second component is common in both binary and more complex systems. This usually occurs when the solid phases either have a fixed composition or show limited solid solution. Common examples are the mixing of ice and salt (NaCl) or the use of ethylene glycol (antifreeze) to depress the freezing point of water.

Applications to petrology

Systematic investigation of the phase changes of the more common anhydrous mineral groups was initiated by the Canadian-born American petrologist Norman L. Bowen and his coworkers at the Geophysical Laboratory of the Carnegie Institution of Washington, D.C., in the early 20th century. This work was generally limited to systems at atmospheric pressure. Subsequent advances in technology have permitted the examination of rock systems in the presence of water pressure and ultrahigh confining pressures. Materials can now be systematically examined under conditions that range from those at Earth’s surface to those simulating conditions that exist at the core. This has led to a vast increase in knowledge about the conditions of formation of both igneous and metamorphic rocksSynthetic equivalents of almost every mineral or rock system can now be produced in the laboratory. Even gemstones such as diamonds are routinely synthesized.

Typical of the data now available are the freezing-melting curves (Figure 3) of the common volcanic rock basalt (and its coarse-grained equivalent, gabbro). Figure 3A shows the crystallization range (shaded) for basaltic melts as a function of lithostatic pressure; this pressure is due to depth of burial. The two short lines show the approximate position of a transition region between gabbro and its denser solid equivalent, eclogite (a sodium-pyroxene + garnet rock). The melting curves have a positive slope, as the solids are denser than their equivalent melts and are thus favoured (enlarged) with increasing pressure.

In the presence of water pressure (PH2O), the freezing-melting curves are depressed (Figure 3B) because the water acts as another component. The slope of the curves is also influenced by the presence of a hydrous solid phase, hornblende, whose approximate stability field is indicated by the dashed line. The changes in liquid composition and crystallization sequences have been determined. Similar information is available for most common igneous rocks.

In 1915 the Finnish petrologist Pentii E. Eskola set up a classification scheme for metamorphic rocks that was based on metamorphic facies. Each facies was defined by the presence of one or more common mineral assemblages. The stability limits of these assemblages subsequently have been determined by laboratory studies. As a result, placing a metamorphic rock within a particular facies indicates the broad pressure-temperature region in which the rock formed. (See metamorphic rock: Metamorphic facies for the pressure-temperature regions of the major metamorphic facies.) For example, a rock containing sodium-rich pyroxene and garnet is placed within the eclogite facies, which indicates that it formed at pressures greater than about 12 kilobars and temperatures above approximately 600 °C. Rocks in the blueschist facies contain the blue amphibole glaucophane; such rocks are stable at high pressures and relatively low temperatures.

A large variety of schemes are available to provide more detailed information on the temperatures and pressures of formation of both igneous and metamorphic rocks. These may use phase relations, stable isotopes, or the compositions of coexisting mineral pairs.

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