A macromolecule is a large molecule, such as protein created by the polymerization of smaller subunits. They are composed of thousands of atoms or more; the most common macromolecules in biochemistry are large non-polymeric molecules. Synthetic macromolecules include common plastics and synthetic fibers as well as experimental materials such as carbon nanotubes; the term macromolecule was coined by Nobel laureate Hermann Staudinger in the 1920s, although his first relevant publication on this field only mentions high molecular compounds. At that time the phrase polymer, as introduced by Berzelius in 1833, had a different meaning from that of today: it was another form of isomerism for example with benzene and acetylene and had little to do with size. Usage of the term to describe large molecules varies among the disciplines. For example, while biology refers to macromolecules as the four large molecules comprising living things, in chemistry, the term may refer to aggregates of two or more molecules held together by intermolecular forces rather than covalent bonds but which do not dissociate.
According to the standard IUPAC definition, the term macromolecule as used in polymer science refers only to a single molecule. For example, a single polymeric molecule is appropriately described as a "macromolecule" or "polymer molecule" rather than a "polymer," which suggests a substance composed of macromolecules; because of their size, macromolecules are not conveniently described in terms of stoichiometry alone. The structure of simple macromolecules, such as homopolymers, may be described in terms of the individual monomer subunit and total molecular mass. Complicated biomacromolecules, on the other hand, require multi-faceted structural description such as the hierarchy of structures used to describe proteins. In British English, the word "macromolecule" tends to be called "high polymer". Macromolecules have unusual physical properties that do not occur for smaller molecules. Another common macromolecular property that does not characterize smaller molecules is their relative insolubility in water and similar solvents, instead forming colloids.
Many require particular ions to dissolve in water. Many proteins will denature if the solute concentration of their solution is too high or too low. High concentrations of macromolecules in a solution can alter the rates and equilibrium constants of the reactions of other macromolecules, through an effect known as macromolecular crowding; this comes from macromolecules excluding other molecules from a large part of the volume of the solution, thereby increasing the effective concentrations of these molecules. All living organisms are dependent on three essential biopolymers for their biological functions: DNA, RNA and proteins; each of these molecules is required for life since each plays a distinct, indispensable role in the cell. The simple summary is that DNA makes RNA, RNA makes proteins. DNA, RNA, proteins all consist of a repeating structure of related building blocks. In general, they are all unbranched polymers, so can be represented in the form of a string. Indeed, they can be viewed as a string of beads, with each bead representing a single nucleotide or amino acid monomer linked together through covalent chemical bonds into a long chain.
In most cases, the monomers within the chain have a strong propensity to interact with other amino acids or nucleotides. In DNA and RNA, this can take the form of Watson-Crick base pairs, although many more complicated interactions can and do occur; because of the double-stranded nature of DNA all of the nucleotides take the form of Watson-Crick base pairs between nucleotides on the two complementary strands of the double-helix. In contrast, both RNA and proteins are single-stranded. Therefore, they are not constrained by the regular geometry of the DNA double helix, so fold into complex three-dimensional shapes dependent on their sequence; these different shapes are responsible for many of the common properties of RNA and proteins, including the formation of specific binding pockets, the ability to catalyse biochemical reactions. DNA is an information storage macromolecule that encodes the complete set of instructions that are required to assemble and reproduce every living organism. DNA and RNA are both capable of encoding genetic information, because there are biochemical mechanisms which read the information coded within a DNA or RNA sequence and use it to generate a specified protein.
On the other hand, the sequence information of a protein molecule is not used by cells to functionally encode genetic information. DNA has three primary attributes that allow it to be far better than RNA at encoding genetic information. First, it is double-stranded, so that there are a minimum of two copies of the information encoding each gene in every cell. Second, DNA has a much greater stability against breakdown than does RNA, an attribute associated with the absence of the 2'-hydroxyl group within every nucleotide of DNA. Third sophisticated DNA surveillance and repair systems are present which monitor damage to the DNA and repair the sequence when necessary. Analogous systems have not evolved for repairing damaged RNA molecules. Chromosomes can contain many billions of atoms, arranged in a specific chemical structure. Proteins are functional macromolecules responsible for catalysing the biochemical reactions that sustain life. Proteins carry out all functions of an organism, for example p
Dioxins and dioxin-like compounds
Dioxins and dioxin-like compounds are compounds that are toxic environmental persistent organic pollutants. They are by-products of various industrial processes - or, in case of dioxin-like PCBs and PBBs, part of intentionally produced mixtures, they include: Polychlorinated dibenzo-p-dioxins, or dioxins. PCDDs are derivatives of dibenzo-p-dioxin. There are 75 PCDD congeners, differing in the number and location of chlorine atoms, seven of them are toxic, the most dangerous being 2,3,7,8-Tetrachlorodibenzodioxin Polychlorinated dibenzofurans, or furans. PCDFs are derivatives of dibenzofuran. There are 135 isomers, ten have dioxin-like properties. Polychlorinated/polybrominated biphenyls, derived from biphenyl, of which twelve are "dioxin-like". Under certain conditions PCBs may form dibenzofurans/dioxins through partial oxidation. Dioxin may refer to 1,4-Dioxin proper, the basic chemical unit of the more complex dioxins; this simple compound has no PCDD-like toxicity. Dioxins have different toxicity depending on the position of the chlorine atoms.
Because dioxins refer to such a broad class of compounds that vary in toxicity, the concept of toxic equivalency factor has been developed to facilitate risk assessment and regulatory control. Toxic equivalence factors exist for seven congeners of ten furans and twelve PCBs; the reference congener is the most toxic dioxin 2,3,7,8-tetrachlorodibenzo-p-dioxin which per definition has a TEF of one. This compound is stable and tends to accumulate in the food chain having a half-life of 7 to 9 years in humans The main characteristics of dioxins are that they are insoluble in water but have a high affinity for lipids. In addition, they tend to associate with organic matter, such as ash and plant leaves. In reference to their importance as environmental toxicants the term dioxins is used exclusively to refer to the sum of compounds from the above groups which demonstrate the same specific toxic mode of action associated with TCDD; these include 12 PCBs. Incidents of contamination with PCBs are often reported as dioxin contamination incidents since it is this toxic characteristic, of most public and regulatory concern.
The toxic effects of dioxins are measured in fractional equivalencies of TCDD, the most toxic and best studied member of its class. The toxicity is mediated through the interaction with a specific intracellular protein, the aryl hydrocarbon receptor, a transcriptional enhancer, affecting a number of other regulatory proteins; this receptor is a transcription factor, involved in expression of many genes. TCDD binding to the AH receptor induces the cytochrome P450 1A class of enzymes which function to break down toxic compounds, e.g. carcinogenic polycyclic hydrocarbons such as benzopyrene. While the affinity of dioxins and related industrial toxicants to this receptor may not explain all their toxic effects including immunotoxicity, endocrine effects and tumor promotion, toxic responses appear to be dose-dependent within certain concentration ranges. A multiphasic dose-response relationship has been reported, leading to uncertainty and debate about the true role of dioxins in cancer rates; the endocrine disrupting activity of dioxins is thought to occur as a down-stream function of AH receptor activation, with thyroid status in particular being a sensitive marker of exposure.
It is important to note that TCDD, along with the other PCDDs, PCDFs and dioxin-like coplanar PCBs are not direct agonists or antagonists of hormones, are not active in assays which directly screen for these activities such as ER-CALUX and AR-CALUX. These compounds have not been shown to have any direct mutagenic or genotoxic activity, their main action in causing cancer is cancer promotion. A mixture of PCBs such as Aroclor may contain PCB compounds which are known estrogen agonists, but on the other hand are not classified as dioxin-like in terms of toxicity. Mutagenic effects have been established for some lower chlorinated chemicals such as 3-chlorodibenzofuran, neither persistent nor an AH receptor agonist; the symptoms reported to be associated with dioxin toxicity in animal studies are wide-ranging, both in the scope of the biological systems affected and in the range of dosage needed to bring these about. Acute effects of single high dose dioxin exposure include wasting syndrome, a delayed death of the animal in 1 to 6 weeks.
By far most toxicity studies have been performed using 2,3,7,8-tetrachlorodibenzo-p-dioxin. The LD50 of TCDD varies wildly between species and strains of the same species, with the most notable disparity being between the similar species of hamster and guinea pig; the oral LD50 for guinea pigs is as low as 0.5 to 2 μg/kg body weight, whereas the oral LD50 for hamsters can be as high as 1 to 5 mg/kg body weight. Between different mouse or rat strains there may be tenfold to thousandfold differences in acute toxicity. Many pathological findings are seen in the liver and other organs; some chronic and sub-chronic exposures can be harmful at much lower levels at particular developmental stages including foetal and pubescent stages. Well established developmental effects are cleft palate, disturbances in tooth development and sexual development as well as endocrine effects. Dioxins have been considered toxic and able to cause reproductive and developmental problems, damage the immune system, inte
Cytochromes P450 are proteins of the superfamily containing heme as a cofactor and, are hemeproteins. CYPs use a variety of large molecules as substrates in enzymatic reactions, they are, in general, the terminal oxidase enzymes in electron transfer chains, broadly categorized as P450-containing systems. The term "P450" is derived from the spectrophotometric peak at the wavelength of the absorption maximum of the enzyme when it is in the reduced state and complexed with carbon monoxide. CYP enzymes have been identified in all kingdoms of life: animals, fungi, bacteria, in viruses. However, they are not omnipresent. More than 50,000 distinct CYP proteins are known. Most CYPs require a protein partner to deliver one or more electrons to reduce the iron. Based on the nature of the electron transfer proteins, CYPs can be classified into several groups: Microsomal P450 systems, in which electrons are transferred from NADPH via cytochrome P450 reductase. Cytochrome b5 can contribute reducing power to this system after being reduced by cytochrome b5 reductase.
Mitochondrial P450 systems, which employ adrenodoxin reductase and adrenodoxin to transfer electrons from NADPH to P450. Bacterial P450 systems, which employ a ferredoxin reductase and a ferredoxin to transfer electrons to P450. CYB5R/cyb5/P450 systems, in which both electrons required by the CYP come from cytochrome b5. FMN/Fd/P450 systems found in Rhodococcus species, in which a FMN-domain-containing reductase is fused to the CYP. P450 only systems, which do not require external reducing power. Notable ones include thromboxane synthase, prostacyclin synthase, CYP74A; the most common reaction catalyzed by cytochromes P450 is a monooxygenase reaction, e.g. insertion of one atom of oxygen into the aliphatic position of an organic substrate while the other oxygen atom is reduced to water: RH + O2 + NADPH + H+ → ROH + H2O + NADP+ Many hydroxylation reactions use CYP enzymes. Genes encoding CYP enzymes, the enzymes themselves, are designated with the root symbol CYP for the superfamily, followed by a number indicating the gene family, a capital letter indicating the subfamily, another numeral for the individual gene.
The convention is to italicise the name. For example, CYP2E1 is the gene that encodes the enzyme CYP2E1—one of the enzymes involved in paracetamol metabolism; the CYP nomenclature is the official naming convention, although CYP450 or CYP450 is used synonymously. However, some gene or enzyme names for CYPs may differ from this nomenclature, denoting the catalytic activity and the name of the compound used as substrate. Examples include CYP5A1, thromboxane A2 synthase, abbreviated to TBXAS1, CYP51A1, lanosterol 14-α-demethylase, sometimes unofficially abbreviated to LDM according to its substrate and activity; the current nomenclature guidelines suggest that members of new CYP families share at least 40% amino acid identity, while members of subfamilies must share at least 55% amino acid identity. There are nomenclature committees that track both base gene names and allele names; the active site of cytochrome P450 contains a heme-iron center. The iron is tethered to the protein via a cysteine thiolate ligand.
This cysteine and several flanking residues are conserved in known CYPs and have the formal PROSITE signature consensus pattern - - x - - - - - C - -. Because of the vast variety of reactions catalyzed by CYPs, the activities and properties of the many CYPs differ in many aspects. In general, the P450 catalytic cycle proceeds as follows: Substrate binds in proximity to the heme group, on the side opposite to the axial thiolate. Substrate binding induces a change in the conformation of the active site displacing a water molecule from the distal axial coordination position of the heme iron, changing the state of the heme iron from low-spin to high-spin. Substrate binding induces electron transfer from NADH via cytochrome P450 reductase or another associated reductase. Molecular oxygen binds to the resulting ferrous heme center at the distal axial coordination position giving a dioxygen adduct not unlike oxy-myoglobin. A second electron is transferred, from either cytochrome P450 reductase, ferredoxins, or cytochrome b5, reducing the Fe-O2 adduct to give a short-lived peroxo state.
The peroxo group formed in step 4 is protonated twice, releasing one molecule of water and forming the reactive species referred to as P450 Compound 1. This reactive intermediate was isolated in 2010, P450 Compound 1 is an iron oxo species with an additional oxidizing equivalent delocalized over the porphyrin and thiolate ligands. Evidence for the alternative perferryl iron-oxo is lacking. Depending on the substrate and enzyme involved, P450 enzymes can catalyze any of a wide variety of reactions. A hypothetical hydroxylation is shown in this illustration. After the product has been released from the active site, the enzyme returns to its original state, with a water molecule returning to occupy the distal coordination position of the iron nucleus. An alternative route for mono-oxygenation is via the "peroxide shunt"; this pathway entails oxidation of the ferric-substrate complex with oxygen-atom donors such as peroxides and hypochlorites. A hypothetical peroxide "XOOH" is shown in the di
Drug metabolism is the metabolic breakdown of drugs by living organisms through specialized enzymatic systems. More xenobiotic metabolism is the set of metabolic pathways that modify the chemical structure of xenobiotics, which are compounds foreign to an organism's normal biochemistry, such as any drug or poison; these pathways are a form of biotransformation present in all major groups of organisms, are considered to be of ancient origin. These reactions act to detoxify poisonous compounds; the study of drug metabolism is called pharmacokinetics. The metabolism of pharmaceutical drugs is an important aspect of medicine. For example, the rate of metabolism determines the duration and intensity of a drug's pharmacologic action. Drug metabolism affects multidrug resistance in infectious diseases and in chemotherapy for cancer, the actions of some drugs as substrates or inhibitors of enzymes involved in xenobiotic metabolism are a common reason for hazardous drug interactions; these pathways are important in environmental science, with the xenobiotic metabolism of microorganisms determining whether a pollutant will be broken down during bioremediation, or persist in the environment.
The enzymes of xenobiotic metabolism the glutathione S-transferases are important in agriculture, since they may produce resistance to pesticides and herbicides. Drug metabolism is divided into three phases. In phase I, enzymes such as cytochrome P450 oxidases introduce reactive or polar groups into xenobiotics; these modified compounds are conjugated to polar compounds in phase II reactions. These reactions are catalysed by transferase enzymes such as glutathione S-transferases. In phase III, the conjugated xenobiotics may be further processed, before being recognised by efflux transporters and pumped out of cells. Drug metabolism converts lipophilic compounds into hydrophilic products that are more excreted; the exact compounds an organism is exposed to will be unpredictable, may differ over time. The major challenge faced by xenobiotic detoxification systems is that they must be able to remove the almost-limitless number of xenobiotic compounds from the complex mixture of chemicals involved in normal metabolism.
The solution that has evolved to address this problem is an elegant combination of physical barriers and low-specificity enzymatic systems. All organisms use cell membranes as hydrophobic permeability barriers to control access to their internal environment. Polar compounds cannot diffuse across these cell membranes, the uptake of useful molecules is mediated through transport proteins that select substrates from the extracellular mixture; this selective uptake means that most hydrophilic molecules cannot enter cells, since they are not recognised by any specific transporters. In contrast, the diffusion of hydrophobic compounds across these barriers cannot be controlled, organisms, cannot exclude lipid-soluble xenobiotics using membrane barriers. However, the existence of a permeability barrier means that organisms were able to evolve detoxification systems that exploit the hydrophobicity common to membrane-permeable xenobiotics; these systems therefore solve the specificity problem by possessing such broad substrate specificities that they metabolise any non-polar compound.
Useful metabolites are excluded since they are polar, in general contain one or more charged groups. The detoxification of the reactive by-products of normal metabolism cannot be achieved by the systems outlined above, because these species are derived from normal cellular constituents and share their polar characteristics. However, since these compounds are few in number, specific enzymes can remove them. Examples of these specific detoxification systems are the glyoxalase system, which removes the reactive aldehyde methylglyoxal, the various antioxidant systems that eliminate reactive oxygen species; the metabolism of xenobiotics is divided into three phases:- modification and excretion. These reactions act in concert to remove them from cells. In phase I, a variety of enzymes act to introduce polar groups into their substrates. One of the most common modifications is hydroxylation catalysed by the cytochrome P-450-dependent mixed-function oxidase system; these enzyme complexes act to incorporate an atom of oxygen into nonactivated hydrocarbons, which can result in either the introduction of hydroxyl groups or N-, O- and S-dealkylation of substrates.
The reaction mechanism of the P-450 oxidases proceeds through the reduction of cytochrome-bound oxygen and the generation of a highly-reactive oxyferryl species, according to the following scheme: O2 + NADPH + H+ + RH → NADP+ + H2O + ROHPhase I reactions may occur by oxidation, hydrolysis, cyclization and addition of oxygen or removal of hydrogen, carried out by mixed function oxidases in the liver. These oxidative reactions involve a cytochrome P450 monooxygenase, NADPH and oxygen; the classes of pharmaceutical drugs that utilize this method for their metabolism include phenothiazines and steroids. If the metabolites of phase I reactions are sufficiently polar, they may be excreted at this point. However, many phase I products are not eliminated and undergo a subsequent reaction in which an endogenous substrate combines with the newly incorporated functional group to
Structural biology is a branch of molecular biology and biophysics concerned with the molecular structure of biological macromolecules, how they acquire the structures they have, how alterations in their structures affect their function. This subject is of great interest to biologists because macromolecules carry out most of the functions of cells, it is only by coiling into specific three-dimensional shapes that they are able to perform these functions; this architecture, the "tertiary structure" of molecules, depends in a complicated way on each molecule's basic composition, or "primary structure." Biomolecules are too small to see in detail with the most advanced light microscopes. The methods that structural biologists use to determine their structures involve measurements on vast numbers of identical molecules at the same time; these methods include: Mass spectrometry Macromolecular crystallography Proteolysis Nuclear magnetic resonance spectroscopy of proteins Electron paramagnetic resonance Cryo-electron microscopy Multiangle light scattering Small angle scattering Ultrafast laser spectroscopy Dual-polarization interferometry and circular dichroismMost researchers use them to study the "native states" of macromolecules.
But variations on these methods are used to watch nascent or denatured molecules assume or reassume their native states. See protein folding. A third approach that structural biologists take to understanding structure is bioinformatics to look for patterns among the diverse sequences that give rise to particular shapes. Researchers can deduce aspects of the structure of integral membrane proteins based on the membrane topology predicted by hydrophobicity analysis. See protein structure prediction. In the past few years it has become possible for accurate physical molecular models to complement the in silico study of biological structures. Examples of these models can be found in the Protein Data Bank. Primary structure Secondary structure Tertiary structure Quaternary structure Structural domain Structural motif Protein subunit Molecular model Cooperativity Chaperonin Structural genomics Stereochemistry Resolution Proteopedia The collaborative, 3D encyclopedia of proteins and other molecules.
Protein structure prediction Media related to Structural biology at Wikimedia Commons Nature: Structural & Molecular Biology magazine website Journal of Structural Biology Structural Biology - The Virtual Library of Biochemistry, Molecular Biology and Cell Biology Structural Biology in Europe
Biochemistry, sometimes called biological chemistry, is the study of chemical processes within and relating to living organisms. Biochemical processes give rise to the complexity of life. A sub-discipline of both biology and chemistry, biochemistry can be divided in three fields. Over the last decades of the 20th century, biochemistry has through these three disciplines become successful at explaining living processes. All areas of the life sciences are being uncovered and developed by biochemical methodology and research. Biochemistry focuses on understanding how biological molecules give rise to the processes that occur within living cells and between cells, which in turn relates to the study and understanding of tissues and organism structure and function. Biochemistry is related to molecular biology, the study of the molecular mechanisms by which genetic information encoded in DNA is able to result in the processes of life. Much of biochemistry deals with the structures and interactions of biological macromolecules, such as proteins, nucleic acids and lipids, which provide the structure of cells and perform many of the functions associated with life.
The chemistry of the cell depends on the reactions of smaller molecules and ions. These can be inorganic, for example water and metal ions, or organic, for example the amino acids, which are used to synthesize proteins; the mechanisms by which cells harness energy from their environment via chemical reactions are known as metabolism. The findings of biochemistry are applied in medicine and agriculture. In medicine, biochemists investigate the cures of diseases. In nutrition, they study how to maintain health wellness and study the effects of nutritional deficiencies. In agriculture, biochemists investigate soil and fertilizers, try to discover ways to improve crop cultivation, crop storage and pest control. At its broadest definition, biochemistry can be seen as a study of the components and composition of living things and how they come together to become life, in this sense the history of biochemistry may therefore go back as far as the ancient Greeks. However, biochemistry as a specific scientific discipline has its beginning sometime in the 19th century, or a little earlier, depending on which aspect of biochemistry is being focused on.
Some argued that the beginning of biochemistry may have been the discovery of the first enzyme, diastase, in 1833 by Anselme Payen, while others considered Eduard Buchner's first demonstration of a complex biochemical process alcoholic fermentation in cell-free extracts in 1897 to be the birth of biochemistry. Some might point as its beginning to the influential 1842 work by Justus von Liebig, Animal chemistry, or, Organic chemistry in its applications to physiology and pathology, which presented a chemical theory of metabolism, or earlier to the 18th century studies on fermentation and respiration by Antoine Lavoisier. Many other pioneers in the field who helped to uncover the layers of complexity of biochemistry have been proclaimed founders of modern biochemistry, for example Emil Fischer for his work on the chemistry of proteins, F. Gowland Hopkins on enzymes and the dynamic nature of biochemistry; the term "biochemistry" itself is derived from a combination of chemistry. In 1877, Felix Hoppe-Seyler used the term as a synonym for physiological chemistry in the foreword to the first issue of Zeitschrift für Physiologische Chemie where he argued for the setting up of institutes dedicated to this field of study.
The German chemist Carl Neuberg however is cited to have coined the word in 1903, while some credited it to Franz Hofmeister. It was once believed that life and its materials had some essential property or substance distinct from any found in non-living matter, it was thought that only living beings could produce the molecules of life. In 1828, Friedrich Wöhler published a paper on the synthesis of urea, proving that organic compounds can be created artificially. Since biochemistry has advanced since the mid-20th century, with the development of new techniques such as chromatography, X-ray diffraction, dual polarisation interferometry, NMR spectroscopy, radioisotopic labeling, electron microscopy, molecular dynamics simulations; these techniques allowed for the discovery and detailed analysis of many molecules and metabolic pathways of the cell, such as glycolysis and the Krebs cycle, led to an understanding of biochemistry on a molecular level. Philip Randle is well known for his discovery in diabetes research is the glucose-fatty acid cycle in 1963.
He confirmed. High fat oxidation was responsible for the insulin resistance. Another significant historic event in biochemistry is the discovery of the gene, its role in the transfer of information in the cell; this part of biochemistry is called molecular biology. In the 1950s, James D. Watson, Francis Crick, Rosalind Franklin, Maurice Wilkins were instrumental in solving DNA structure and suggesting its relationship with genetic transfer of information. In 1958, George Beadle and Edward Tatum received the Nobel Prize for work in fungi showing that one gene produces one enzyme. In 1988, Colin Pitchfork was the first person convicted of murder with DNA evidence, which led to the growth of forensic science. More Andrew Z. Fire and Craig C. Mello received the 2006 Nobel Prize for discovering the role of RNA interference, in the silencing of gene expression. Around two dozen of the 92
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