Chemistry

From Wikipedia, the free encyclopedia

 

Solutions of substances in flasks, including ammonium hydroxide and nitric acid, illuminated in different colors.

Chemistry, a branch of physical science, is the study of the composition, structure, properties and change of matter.^[1][2] Chemistry is chiefly concerned with atoms and molecules and their interactions and transformations, for example, the properties of the chemical bonds formed between atoms to create chemical compounds. As such, chemistry studies the involvement of electrons and various forms of energy in photochemical reactions, oxidation-reduction reactions, changes in phases of matter, and separation of mixtures. Preparation and properties of complex substances, such as alloys, polymers, biological molecules, and pharmaceutical agents are considered in specialized fields of chemistry.

Chemistry is sometimes called the central science because it bridges other natural sciences like physics, geology and biology.^[3][4] Chemistry is a branch of physical science but distinct from physics.^[5]

The etymology of the word chemistry has been much disputed. The history of chemistry can be traced to certain practices, known as alchemy, which had been practiced for several millennia in various parts of the world, particularly the Middle East.^[6]

Etymology

Chemistry
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The word chemistry comes from the word alchemy, an earlier set of practices that encompassed elements of chemistry, metallurgy, philosophy, astrology, astronomy, mysticism and medicine; it is commonly thought of as the quest to turn lead or another common starting material into gold.^[7] Alchemy, which was practiced around 330, is the study of the composition of waters, movement, growth, embodying, disembodying, drawing the spirits from bodies and bonding the spirits within bodies (Zosimos).^[8] An alchemist was called a 'chemist' in popular speech, and later the suffix "-ry" was added to this to describe the art of the chemist as "chemistry".

The word alchemy in turn is derived from the Arabic word al-kīmīā (الکیمیاء). In origin, the term is borrowed from the Greek χημία or χημεία.^[9][10] This may have Egyptian origins. Many believe that al-kīmīā is derived from the Greek χημία, which is in turn derived from the word Chemi or Kimi, which is the ancient name of Egypt in Egyptian.^[9] Alternately, al-kīmīā may be derived from χημεία, meaning "cast together".^[11]

Definition

In retrospect, the definition of chemistry has changed over time, as new discoveries and theories add to the functionality of the science. The term "chymistry", in the view of noted scientist Robert Boyle in 1661, meant the subject of the material principles of mixed bodies.^[12] In 1663, "chymistry" meant a scientific art, by which one learns to dissolve bodies, and draw from them the different substances on their composition, and how to unite them again, and exalt them to a higher perfection - this definition was used by chemist Christopher Glaser.^[13]

The 1730 definition of the word "chemistry", as used by Georg Ernst Stahl, meant the art of resolving mixed, compound, or aggregate bodies into their principles; and of composing such bodies from those principles.^[14] In 1837, Jean-Baptiste Dumas considered the word "chemistry" to refer to the science concerned with the laws and effects of molecular forces.^[15] This definition further evolved until, in 1947, it came to mean the science of substances: their structure, their properties, and the reactions that change them into other substances - a characterization accepted by Linus Pauling.^[16] More recently, in 1998, the definition of "chemistry" was broadened to mean the study of matter and the changes it undergoes, as phrased by Professor Raymond Chang.^[17]

History

 

Democritus' atomist philosophy was later adopted by Epicurus (341–270 BCE).

Early civilizations, such as the Egyptians^[18] and Babylonians amassed practical knowledge concerning the arts of metallurgy, pottery and dyes, but didn't develop a systematic theory.
A basic chemical hypothesis first emerged in Classical Greece with the theory of four elements as propounded definitively by Aristotle stating that that fire, air, earth and water were the fundamental elements from which everything is formed as a combination. Greek atomism dates back to 440 BC, arising in works by philosophers such as Democritus and Epicurus. In 50 BC, the Roman philosopher Lucretius expanded upon the theory in his book De rerum natura (On The Nature of Things).^[19][20] Unlike modern concepts of science, Greek atomism was purely philosophical in nature, with little concern for empirical observations and no concern for chemical experiments.^[21]

In the Hellenistic world the art of alchemy first proliferated, mingling magic and occultism into the study of natural substances with the ultimate goal of transmuting elements into gold and discovering the elixir of eternal life.^[22] Alchemy was discovered and practised widely throughout the Arab world after the Muslim conquests,^[23] and from there, diffused into medieval and Renaissance Europe through Latin translations.^[24]

Chemistry as science

Under the influence of the new empirical methods propounded by Sir Francis Bacon and others, a group of chemists at Oxford, Robert Boyle, Robert Hooke and John Mayow began to reshape the old alchemical traditions into a scientific discipline. Boyle in particular is regarded as the founding father of chemistry due to his most important work, the classic chemistry text The Sceptical Chymist where the differentiation is made between the claims of alchemy and the empirical scientific discoveries of the new chemistry.^[25] He formulated Boyle's law, rejected the classical "four elements" and proposed a mechanistic alternative of atoms and chemical reactions that could be subject to rigorous experiment.^[26]

Antoine-Laurent de Lavoisier is considered the "Father of Modern Chemistry".^[27]

The theory of phlogiston (a substance at the root of all combustion) was propounded by the German Georg Ernst Stahl in the early 18th century and was only overturned by the end of the century by the French chemist Antoine Lavoisier, the chemical analogue of Newton in physics; who did more than any other to establish the new science on proper theoretical footing, by elucidating the principle of conservation of mass and developing a new system of chemical nomenclature used to this day.^[28]

Prior to his work, though, many important discoveries had been made, specifically relating to the nature of 'air' which was discovered to be composed of many different gases. The Scottish chemist Joseph Black (the first experimental chemist) and the Dutchman J. B. van Helmont discovered carbon dioxide, or what Black called 'fixed air' in 1754; Henry Cavendish discovered hydrogen and elucidated its properties and Joseph Priestley and, independently, Carl Wilhelm Scheele isolated pure oxygen.

English scientist John Dalton proposed the modern theory of atoms; that all substances are composed of indivisible 'atoms' of matter and that different atoms have varying atomic weights.

The development of the electrochemical theory of chemical combinations occurred in the early 19th century as the result of the work of two scientists in particular, J. J. Berzelius and Humphry Davy, made possible by the prior invention of the voltaic pile by Alessandro Volta. Davy discovered nine new elements including the alkali metals by extracting them from their oxides with electric current.^[29]

British William Prout first proposed ordering all the elements by their atomic weight as all atoms had a weight that was an exact multiple of the atomic weight of hydrogen. J. A. R. Newlands devised an early table of elements, which was then developed into the modern periodic table of elements^[30] by the German Julius Lothar Meyer and the Russian Dmitri Mendeleev in the 1860s.^[31] The inert gases, later called the noble gases were discovered by William Ramsay in collaboration with Lord Rayleigh at the end of the century, thereby filling in the basic structure of the table.

Organic chemistry was developed by Justus von Liebig and others, following Friedrich Wöhler's synthesis of urea which proved that living organisms were, in theory, reducible to chemistry.^[32] Other crucial 19th century advances were; an understanding of valence bonding (Edward Frankland in 1852) and the application of thermodynamics to chemistry (J. W. Gibbs and Svante Arrhenius in the 1870s).

Chemical structure

Top: Expected results: alpha particles passing through the plum pudding model of the atom undisturbed.
Bottom: Observed results: a small portion of the particles were deflected, indicating a small, concentrated charge.

At the turn of the twentieth century the theoretical underpinnings of chemistry were finally understood due to a series of remarkable discoveries that succeeded in probing and discovering the very nature of the internal structure of atoms. In 1897, J. J. Thomson of Cambridge University discovered the electron and soon after the French scientist Becquerel as well as the couple Pierre and Marie Curie investigated the phenomenon of radioactivity. In a series of pioneering scattering experiments Ernest Rutherford at the University of Manchester discovered the internal structure of the atom and the existence of the proton, classified and explained the different types of radioactivity and successfully transmuted the first element by bombarding nitrogen with alpha particles.

His work on atomic structure was improved on by his students, the Danish physicist Niels Bohr and Henry Moseley. The electronic theory of chemical bonds and molecular orbitals was developed by the American scientists Linus Pauling and Gilbert N. Lewis.

The year 2011 was declared by the United Nations as the International Year of Chemistry.^[33] It was an initiative of the International Union of Pure and Applied Chemistry, and of the United Nations Educational, Scientific, and Cultural Organization and involves chemical societies, academics, and institutions worldwide and relied on individual initiatives to organize local and regional activities.

Principles of modern chemistry

Laboratory, Institute of Biochemistry, University of Cologne.

The current model of atomic structure is the quantum mechanical model.^[34] Traditional chemistry starts with the study of elementary particles, atoms, molecules,^[35] substances, metals, crystals and other aggregates of matter. This matter can be studied in solid, liquid, or gas states, in isolation or in combination. The interactions, reactions and transformations that are studied in chemistry are usually 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, and a great deal of experimental (as well as applied/industrial) chemistry is done without it.

A chemical reaction is a transformation of some substances into one or more different substances.^[36] 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 usually involves atoms as subjects. The number of atoms on the left and the right in the equation for a chemical transformation is equal (when unequal, the transformation by definition is not chemical, but rather a nuclear reaction or radioactive decay). 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 almost 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 chemical analysis, e.g. spectroscopy and chromatography. Scientists engaged in chemical research are known as chemists.^[37] Most chemists specialize in one or more sub-disciplines. Several concepts are essential for the study of chemistry; some of them are:^[38]

Matter

In chemistry, matter is defined as anything that has rest mass and volume (it takes up space) and is made up of particles. 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 pure chemical substance or a mixture of substances.^[39]

Atom

A diagram of an atom based on the Rutherford model

The atom is the basic unit of chemistry. It consists of a dense core called the atomic nucleus surrounded by a space called the electron cloud. The nucleus is made up of positively charged protons and uncharged neutrons (together called nucleons), 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 mass of a nucleon is 1,836 times that of an electron, yet the radius of an atom is about 10,000 times that of its nucleus.^[40][41]

The atom is also the smallest entity that can be envisaged to retain the chemical properties of the element, such as electronegativity, ionization potential, preferred oxidation state(s), coordination number, and preferred types of bonds to form (e.g., metallic, ionic, covalent).

Element

Standard form of the periodic table of chemical elements. The colors represent different categories of elements

Main article: Chemical element

A chemical element is a pure substance which is 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 protons and neutrons in a nucleus. Although all the nuclei of all atoms belonging to one element will have the same atomic number, they may not necessarily have the same mass number; atoms of an element which have different mass numbers are known as isotopes. For example, all atoms with 6 protons in their nuclei are atoms of the chemical element carbon, but atoms of carbon may have mass numbers of 12 or 13.^[41]

The standard presentation of the chemical elements is in the periodic table, which orders elements by atomic number. The periodic table is arranged in groups, or columns, and periods, or rows. The periodic table is useful in identifying periodic trends.^[42]

Compound

Carbon dioxide (CO₂), an example of a chemical compound

A compound is a pure chemical substance composed of more than one element. The properties of a compound bear little similarity to those of its elements.^[43] The standard nomenclature of compounds is set by the International Union of Pure and Applied Chemistry (IUPAC). Organic compounds are named according to the organic nomenclature system.^[44] Inorganic compounds are named according to the inorganic nomenclature system.^[45] In addition the Chemical Abstracts Service has devised a method to index chemical substances. In this scheme each chemical substance is identifiable by a number known as its CAS registry number.

Molecule

 

A ball-and-stick representation of the caffeine molecule (C₈H₁₀N₄O₂).

A molecule is the smallest indivisible portion of a pure chemical substance that has its unique set of chemical properties, that is, its potential to undergo a certain set of chemical reactions with other substances. However, this definition only works well for substances that are composed of molecules, which is not true of many substances (see below). Molecules are typically a set of atoms bound together by covalent bonds, such that the structure is electrically neutral and all valence electrons are paired with other electrons either in bonds or in lone pairs.

Thus, molecules exist as electrically neutral units, unlike ions. When this rule is broken, giving the "molecule" a charge, the result is sometimes named a molecular ion or a polyatomic ion. However, the discrete and separate nature of the molecular concept usually requires that molecular ions be present only in well-separated form, such as a directed beam in a vacuum in a mass spectrometer. Charged polyatomic collections residing in solids (for example, common sulfate or nitrate ions) are generally not considered "molecules" in chemistry.

A 2-D skeletal model of a benzene molecule (C₆H₆)

The "inert" or noble gas elements (helium, neon, argon, krypton, xenon and radon) are composed of lone atoms as their smallest discrete unit, but the other isolated chemical elements consist of either molecules or networks of atoms bonded to each other in some way. Identifiable molecules compose familiar substances such as water, air, and many organic compounds like alcohol, sugar, gasoline, and the various pharmaceuticals.

However, not all substances or chemical compounds consist of discrete molecules, and indeed most of the solid substances that make up the solid crust, mantle, and core of the Earth are chemical compounds without molecules. These other types of substances, such as ionic compounds and network solids, are organized in such a way as to lack the existence of identifiable molecules per se.
Instead, these substances are discussed in terms of formula units or unit cells as the smallest repeating structure within the substance. Examples of such substances are mineral salts (such as table salt), solids like carbon and diamond, metals, and familiar silica and silicate minerals such as quartz and granite.

One of the main characteristics of a molecule is its geometry often called its structure. While the structure of diatomic, triatomic or tetra atomic molecules may be trivial, (linear, angular pyramidal etc.) the structure of polyatomic molecules, that are constituted of more than six atoms (of several elements) can be crucial for its chemical nature.

Substance and mixture

Examples of pure chemical substances. From left to right: the elements tin (Sn) and sulfur (S), diamond (an allotrope of carbon), sucrose (pure sugar), and sodium chloride (salt) and sodium bicarbonate (baking soda), which are both ionic compounds.

A chemical substance is a kind of matter with a definite composition and set of properties.^[46] A collection of substances is called a mixture. Examples of mixtures are air and alloys.^{[citation needed]}

Mole and amount of substance

The mole is a unit of measurement that denotes an amount of substance (also called chemical amount). The mole is defined as the number of atoms found in exactly 0.012 kilogram (or 12 grams) of carbon-12, where the carbon-12 atoms are unbound, at rest and in their ground state.^[47] The number of entities per mole is known as the Avogadro constant, and is determined empirically to be approximately 6.022×10²³ mol⁻¹.^[48] Molar concentration is the amount of a particular substance per volume of solution, and is commonly reported in moldm⁻³.^[49]

Phase

Example of phase changes

 

In addition to the specific chemical properties that distinguish different chemical classifications, chemicals can exist in several phases. For the most part, the chemical classifications are independent of these bulk phase classifications; however, some more exotic phases are incompatible with certain chemical properties. A phase is a set of states of a chemical system that have similar bulk structural properties, over a range of conditions, such as pressure or temperature.

Physical properties, such as density and refractive index tend to fall within values characteristic of the phase. The phase of matter is defined by the phase transition, which is when energy put into or taken out of the system goes into rearranging the structure of the system, instead of changing the bulk conditions.

Sometimes the distinction between phases can be continuous instead of having a discrete boundary, in this case the matter is considered to be in a supercritical state. When three states meet based on the conditions, it is known as a triple point and since this is invariant, it is a convenient way to define a set of conditions.

The most familiar examples of phases are solids, liquids, and gases. Many substances exhibit multiple solid phases. For example, there are three phases of solid iron (alpha, gamma, and delta) that vary based on temperature and pressure. A principal difference between solid phases is the crystal structure, or arrangement, of the atoms. Another phase commonly encountered in the study of chemistry is the aqueous phase, which is the state of substances dissolved in aqueous solution (that is, in water).

Less familiar phases include plasmas, Bose–Einstein condensates and fermionic condensates and the paramagnetic and ferromagnetic phases of magnetic materials. While most familiar phases deal with three-dimensional systems, it is also possible to define analogs in two-dimensional systems, which has received attention for its relevance to systems in biology.

Bonding

 

An animation of the process of ionic bonding between sodium (Na) and chlorine (Cl) to form sodium chloride, or common table salt. Ionic bonding involves one atom taking valence electrons from another (as opposed to sharing, which occurs in covalent bonding)

Atoms sticking together in molecules or crystals are said to be bonded with one another. A chemical bond may be visualized as the multipole balance between the positive charges in the nuclei and the negative charges oscillating about them.^[50] More than simple attraction and repulsion, the energies and distributions characterize the availability of an electron to bond to another atom.

A chemical bond can be a covalent bond, an ionic bond, a hydrogen bond or just because of Van der Waals force. Each of these kinds of bonds is ascribed to some potential. These potentials create the interactions which hold atoms together in molecules or crystals. In many simple compounds, Valence Bond Theory, the Valence Shell Electron Pair Repulsion model (VSEPR), and the concept of oxidation number can be used to explain molecular structure and composition.

An ionic bond is formed when a metal loses one or more of its electrons, becoming a positively charged cation, and the electrons are then gained by the non-metal atom, becoming a negatively charged anion. The two oppositely charged ions attract one another, and the ionic bond is the electrostatic force of attraction between them. For example, sodium (Na), a metal, loses one electron to become an Na⁺ cation while chlorine (Cl), a non-metal, gains this electron to become Cl^-. The ions are held together due to electrostatic attraction, and that compound sodium chloride (NaCl), or common table salt, is formed.

In the methane molecule (CH₄), the carbon atom shares a pair of valence electrons with each of the four hydrogen atoms. Thus, the octet rule is satisfied for C-atom (it has eight electrons in its valence shell) and the duet rule is satisfied for the H-atoms (they have two electrons in their valence shells).

In a covalent bond, one or more pairs of valence electrons are shared by two atoms: the resulting electrically neutral group of bonded atoms is termed a molecule. Atoms will share valence electrons in such a way as to create a noble gas electron configuration (eight electrons in their outermost shell) for each atom. Atoms that tend to combine in such a way that they each have eight electrons in their valence shell are said to follow the octet rule. However, some elements like hydrogen and lithium need only two electrons in their outermost shell to attain this stable configuration; these atoms are said to follow the duet rule, and in this way they are reaching the electron configuration of the noble gas helium, which has two electrons in its outer shell.

Similarly, theories from classical physics can be used to predict many ionic structures. With more complicated compounds, such as metal complexes, valence bond theory is less applicable and alternative approaches, such as the molecular orbital theory, are generally used. See diagram on electronic orbitals.

Energy

In the context of chemistry, energy is an attribute of a substance as a consequence of its atomic, molecular or aggregate structure. Since a chemical transformation is accompanied by a change in one or more of these kinds of structures, it is invariably accompanied by an increase or decrease of energy of the substances involved. Some energy is transferred between the surroundings and the reactants of the reaction in the form of heat or light; thus the products of a reaction may have more or less energy than the reactants.

A reaction is said to be exergonic if the final state is lower on the energy scale than the initial state; in the case of endergonic reactions the situation is the reverse. A reaction is said to be exothermic if the reaction releases heat to the surroundings; in the case of endothermic reactions, the reaction absorbs heat from the surroundings.

Chemical reactions are invariably not possible unless the reactants surmount an energy barrier known as the activation energy. The speed of a chemical reaction (at given temperature T) is related to the activation energy E, by the Boltzmann's population factor - that is the probability of a molecule to have energy greater than or equal to E at the given temperature T. This exponential dependence of a reaction rate on temperature is known as the Arrhenius equation. The activation energy necessary for a chemical reaction to occur can be in the form of heat, light, electricity or mechanical force in the form of ultrasound.^[51]

A related concept free energy, which also incorporates entropy considerations, is a very useful means for predicting the feasibility of a reaction and determining the state of equilibrium of a chemical reaction, in chemical thermodynamics. A reaction is feasible only if the total change in the Gibbs free energy is negative, ; if it is equal to zero the chemical reaction is said to be at equilibrium.
There exist only limited possible states of energy for electrons, atoms and molecules. These are determined by the rules of quantum mechanics, which require quantization of energy of a bound system. The atoms/molecules in a higher energy state are said to be excited. The molecules/atoms of substance in an excited energy state are often much more reactive; that is, more amenable to chemical reactions.

The phase of a substance is invariably determined by its energy and the energy of its surroundings. When the intermolecular forces of a substance are such that the energy of the surroundings is not sufficient to overcome them, it occurs in a more ordered phase like liquid or solid as is the case with water (H₂O); a liquid at room temperature because its molecules are bound by hydrogen bonds.^[52] Whereas hydrogen sulfide (H₂S) is a gas at room temperature and standard pressure, as its molecules are bound by weaker dipole-dipole interactions.

The transfer of energy from one chemical substance to another depends on the size of energy quanta emitted from one substance. However, heat energy is often transferred more easily from almost any substance to another because the phonons responsible for vibrational and rotational energy levels in a substance have much less energy than photons invoked for the electronic energy transfer. Thus, because vibrational and rotational energy levels are more closely spaced than electronic energy levels, heat is more easily transferred between substances relative to light or other forms of electronic energy. For example, ultraviolet electromagnetic radiation is not transferred with as much efficacy from one substance to another as thermal or electrical energy.

The existence of characteristic energy levels for different chemical substances is useful for their identification by the analysis of spectral lines. Different kinds of spectra are often used in chemical spectroscopy, e.g. IR, microwave, NMR, ESR, etc. Spectroscopy is also used to identify the composition of remote objects - like stars and distant galaxies - by analyzing their radiation spectra.

Emission spectrum of iron

The term chemical energy is often used to indicate the potential of a chemical substance to undergo a transformation through a chemical reaction or to transform other chemical substances.

Reaction

 

During chemical reactions, bonds between atoms break and form, resulting in different substances with different properties. In a blast furnace, iron oxide, a compound, reacts with carbon monoxide to form iron, one of the chemical elements, and carbon dioxide.

When a chemical substance is transformed as a result of its interaction with another substance or with energy, a chemical reaction is said to have occurred. A chemical reaction is therefore a concept related to the 'reaction' of a substance when it comes in close contact with another, whether as a mixture or a solution; exposure to some form of energy, or both. It results in some energy exchange between the constituents of the reaction as well with the system environment which may be designed vessels which are often laboratory glassware.

Chemical reactions can result in the formation or dissociation of molecules, that is, molecules breaking apart to form two or more smaller molecules, or rearrangement of atoms within or across molecules. Chemical reactions usually involve the making or breaking of chemical bonds. Oxidation, reduction, dissociation, acid-base neutralization and molecular rearrangement are some of the commonly used kinds of chemical reactions.

A chemical reaction can be symbolically depicted through a chemical equation. While in a non-nuclear chemical reaction the number and kind of atoms on both sides of the equation are equal, for a nuclear reaction this holds true only for the nuclear particles viz. protons and neutrons.^[53]

The sequence of steps in which the reorganization of chemical bonds may be taking place in the course of a chemical reaction is called its mechanism. A chemical reaction can be envisioned to take place in a number of steps, each of which may have a different speed. Many reaction intermediates with variable stability can thus be envisaged during the course of a reaction. Reaction mechanisms are proposed to explain the kinetics and the relative product mix of a reaction. Many physical chemists specialize in exploring and proposing the mechanisms of various chemical reactions.
Several empirical rules, like the Woodward–Hoffmann rules often come in handy while proposing a mechanism for a chemical reaction.

According to the IUPAC gold book, a chemical reaction is "a process that results in the interconversion of chemical species."^[54] Accordingly, a chemical reaction may be an elementary reaction or a stepwise reaction. An additional caveat is made, in that this definition includes cases where the interconversion of conformers is experimentally observable. Such detectable chemical reactions normally involve sets of molecular entities as indicated by this definition, but it is often conceptually convenient to use the term also for changes involving single molecular entities (i.e. 'microscopic chemical events').

Ions and salts

The crystal lattice structure of potassium chloride (KCl), a salt which is formed due to the attraction of K⁺ cations and Cl^- anions. Note how the overall charge of the ionic compound is zero.

An ion is a charged species, an atom or a molecule, that has lost or gained one or more electrons. When an atom loses an electron and thus has more protons than electrons, the atom is a positively-charged ion or cation. When an atom gains an electron and thus has more electrons than protons, the atom is a negatively-charged ion or anion. Cations and anions can form a crystalline lattice of neutral salts, such as the Na⁺ and Cl^- ions forming sodium chloride, or NaCl. Examples of polyatomic ions that do not split up during acid-base reactions are hydroxide (OH⁻) and phosphate (PO₄³⁻).
Plasma is composed of gaseous matter that has been completely ionized, usually through high temperature.

Acidity and basicity

When hydrogen bromide (HBr), pictured, is dissolved in water, it forms the strong acid hydrobromic acid

A substance can often be classified as an acid or a base. There are several different theories which explain acid-base behavior. The simplest is Arrhenius theory, which states than an acid is a substance that produces hydronium ions when it is dissolved in water, and a base is one that produces hydroxide ions when dissolved in water. According to Brønsted–Lowry acid–base theory, acids are substances that donate a positive hydrogen ion to another substance in a chemical reaction; by extension, a base is the substance which receives that hydrogen ion.

A third common theory is Lewis acid-base theory, which is based on the formation of new chemical bonds. Lewis theory explains that an acid is a substance which is capable of accepting a pair of electrons from another substance during the process of bond formation, while a base is a substance which can provide a pair of electrons to form a new bond. According to this theory, the crucial things being exchanged are charges.^{[55][unreliable source?]} There are several other ways in which a substance may be classified as an acid or a base, as is evident in the history of this concept^[56]

Acid strength is commonly measured by two methods. One measurement, based on the Arrhenius definition of acidity, is pH, which is a measurement of the hydronium ion concentration in a solution, as expressed on a negative logarithmic scale. Thus, solutions that have a low pH have a high hydronium ion concentration, and can be said to be more acidic. The other measurement, based on the Brønsted–Lowry definition, is the acid dissociation constant (K_a), which measures the relative
ability of a substance to act as an acid under the Brønsted–Lowry definition of an acid. That is, substances with a higher K_a are more likely to donate hydrogen ions in chemical reactions than those with lower K_a values.

Redox

Redox (reduction-oxidation) reactions include all chemical reactions in which atoms have their oxidation state changed by either gaining electrons (reduction) or losing electrons (oxidation). Substances that have the ability to oxidize other substances are said to be oxidative and are known as oxidizing agents, oxidants or oxidizers. An oxidant removes electrons from another substance. Similarly, substances that have the ability to reduce other substances are said to be reductive and are known as reducing agents, reductants, or reducers.

A reductant transfers electrons to another substance, and is thus oxidized itself. And because it "donates" electrons it is also called an electron donor. Oxidation and reduction properly refer to a change in oxidation number—the actual transfer of electrons may never occur. Thus, oxidation is better defined as an increase in oxidation number, and reduction as a decrease in oxidation number.

Equilibrium

Although the concept of equilibrium is widely used across sciences, in the context of chemistry, it arises whenever a number of different states of the chemical composition are possible, as for example, in a mixture of several chemical compounds that can react with one another, or when a substance can be present in more than one kind of phase.

A system of chemical substances at equilibrium, even though having an unchanging composition, is most often not static; molecules of the substances continue to react with one another thus giving rise to a dynamic equilibrium. Thus the concept describes the state in which the parameters such as chemical composition remain unchanged over time.

Chemical laws

Chemical reactions are governed by certain laws, which have become fundamental concepts in chemistry. Some of them are:

• Avogadro's law
• Beer–Lambert law
• Boyle's law (1662, relating pressure and volume)
• Charles's law (1787, relating volume and temperature)
• Fick's laws of diffusion
• Gay-Lussac's law (1809, relating pressure and temperature)
• Le Chatelier's principle
• Henry's law
• Hess's law
• Law of conservation of energy leads to the important concepts of equilibrium, thermodynamics, and kinetics.
• Law of conservation of mass continues to be conserved in isolated systems, even in modern physics. However, special relativity shows that due to mass–energy equivalence, whenever non-material "energy" (heat, light, kinetic energy) is removed from a non-isolated system, some mass will be lost with it. High energy losses result in loss of weighable amounts of mass, an important topic in nuclear chemistry.
• Law of definite composition, although in many systems (notably biomacromolecules and minerals) the ratios tend to require large numbers, and are frequently represented as a fraction.
• Law of multiple proportions
• Raoult's law

Practice

Subdisciplines

Chemistry is typically divided into several major sub-disciplines. There are also several main cross-disciplinary and more specialized fields of chemistry.^[57]

• Analytical chemistry is the analysis of material samples to gain an understanding of their chemical composition and structure. Analytical chemistry incorporates standardized experimental methods in chemistry. These methods may be used in all subdisciplines of chemistry, excluding purely theoretical chemistry.
• Biochemistry is the study of the chemicals, chemical reactions and chemical interactions that take place in living organisms. Biochemistry and organic chemistry are closely related, as in medicinal chemistry or neurochemistry. Biochemistry is also associated with molecular biology and genetics.
• Inorganic chemistry is the study of the properties and reactions of inorganic compounds. The distinction between organic and inorganic disciplines is not absolute and there is much overlap, most importantly in the sub-discipline of organometallic chemistry.
• Materials chemistry is the preparation, characterization, and understanding of substances with a useful function. The field is a new breadth of study in graduate programs, and it integrates elements from all classical areas of chemistry with a focus on fundamental issues that are unique to materials. Primary systems of study include the chemistry of condensed phases (solids, liquids, polymers) and interfaces between different phases.
• Neurochemistry is the study of neurochemicals; including transmitters, peptides, proteins, lipids, sugars, and nucleic acids; their interactions, and the roles they play in forming, maintaining, and modifying the nervous system.
• Nuclear chemistry is the study of how subatomic particles come together and make nuclei. Modern Transmutation is a large component of nuclear chemistry, and the table of nuclides is an important result and tool for this field.
• Organic chemistry is the study of the structure, properties, composition, mechanisms, and reactions of organic compounds. An organic compound is defined as any compound based on a carbon skeleton.
• Physical chemistry is the study of the physical and fundamental basis of chemical systems and processes. In particular, the energetics and dynamics of such systems and processes are of interest to physical chemists. Important areas of study include chemical thermodynamics, chemical kinetics, electrochemistry, statistical mechanics, spectroscopy, and more recently, astrochemistry.^[58] Physical chemistry has large overlap with molecular physics. Physical chemistry involves the use of infinitesimal calculus in deriving equations. It is usually associated with quantum chemistry and theoretical chemistry. Physical chemistry is a distinct discipline from chemical physics, but again, there is very strong overlap.
• Theoretical chemistry is the study of chemistry via fundamental theoretical reasoning (usually within mathematics or physics). In particular the application of quantum mechanics to chemistry is called quantum chemistry. Since the end of the Second World War, the development of computers has allowed a systematic development of computational chemistry, which is the art of developing and applying computer programs for solving chemical problems. Theoretical chemistry has large overlap with (theoretical and experimental) condensed matter physics and molecular physics.

Other disciplines within chemistry are traditionally grouped by the type of matter being studied or the kind of study. These include inorganic chemistry, the study of inorganic matter; organic chemistry, the study of organic (carbon based) matter; biochemistry, the study of substances found in biological organisms; physical chemistry, the study of chemical processes using physical concepts such as thermodynamics and quantum mechanics; and analytical chemistry, the analysis of material samples to gain an understanding of their chemical composition and structure. Many more specialized disciplines have emerged in recent years, e.g. neurochemistry the chemical study of the nervous system (see subdisciplines).

Other fields include agrochemistry, astrochemistry (and cosmochemistry), atmospheric chemistry, chemical engineering, chemical biology, chemo-informatics, electrochemistry, environmental chemistry, femtochemistry, flavor chemistry, flow chemistry, geochemistry, green chemistry, histochemistry, history of chemistry, hydrogenation chemistry, immunochemistry, marine chemistry, materials science, mathematical chemistry, mechanochemistry, medicinal chemistry, molecular biology, molecular mechanics, nanotechnology, natural product chemistry, oenology, organometallic chemistry, petrochemistry, pharmacology, photochemistry, physical organic chemistry, phytochemistry, polymer chemistry, radiochemistry, solid-state chemistry, sonochemistry, supramolecular chemistry, surface chemistry, synthetic chemistry, thermochemistry, and many others.

Chemical industry

The chemical industry represents an important economic activity. The global top 50 chemical producers in 2004 had sales of 587 billion US dollars with a profit margin of 8.1% and research and development spending of 2.1% of total chemical sales.^[59]

Professional societies

• American Chemical Society
• American Society for Neurochemistry
• Chemical Institute of Canada
• Chemical Society of Peru
• International Union of Pure and Applied Chemistry
• Royal Australian Chemical Institute
• Royal Netherlands Chemical Society
• Royal Society of Chemistry
• Society of Chemical Industry
• World Association of Theoretical and Computational Chemists
• List of chemistry societies

Biology

From Wikipedia, the free encyclopedia

 

Biology deals with the study of the many varieties of living organisms. Clockwise from top left: Salmonella typhimurium (a type of bacteria), Phascolarctos cinereus (koala), Athyrium filix-femina (common lady-fern), Amanita muscaria (fly agaric, a toxic toadstool), Agalychnis callidryas (red-eyed tree frog) and Brachypelma smithi (Mexican Red-kneed Tarantula)

Biology is a natural science concerned with the study of life and living organisms, including their structure, function, growth, evolution, distribution, and taxonomy.^[1] Modern biology is a vast and eclectic field, composed of many branches and subdisciplines. However, despite the broad scope of biology, there are certain general and unifying concepts within it that govern all study and research, consolidating it into single, coherent fields. In general, biology recognizes the cell as the basic unit of life, genes as the basic unit of heredity, and evolution as the engine that propels the synthesis and creation of new species. It is also understood today that all organisms survive by consuming and transforming energy and by regulating their internal environment to maintain a stable and vital condition.

Subdisciplines of biology are defined by the scale at which organisms are studied, the kinds of organisms studied, and the methods used to study them: Biochemistry examines the rudimentary chemistry of life; molecular biology studies the complex interactions among biological molecules; botany studies the biology of plants; cellular biology examines the basic building-block of all life, the cell; physiology examines the physical and chemical functions of tissues, organs, and organ systems of an organism; evolutionary biology examines the processes that produced the diversity of life; and ecology examines how organisms interact in their environment.^[2]

History

 

Ernst Haeckel's Tree of Life (1879)

The term biology is derived from the Greek word βίος, bios, "life" and the suffix -λογία, -logia, "study of."^[3][4] The Latin form of the term first appeared in 1736 when Linnaeus (Carl von Linné) used biologi in his Bibliotheca botanica. It was used again in 1766 in a work entitled Philosophiae naturalis sive physicae: tomus III, continens geologian, biologian, phytologian generalis, by Michael Christoph Hanov, a disciple of Christian Wolff. The first German use, Biologie, was used in a 1771 translation of Linnaeus' work. In 1797, Theodor Georg August Roose used the term in a book, Grundzüge der Lehre van der Lebenskraft, in the preface. Karl Friedrich Burdach used the term in 1800 in a more restricted sense of the study of human beings from a morphological, physiological and psychological perspective (Propädeutik zum Studien der gesammten Heilkunst). The term came into its modern usage with the six-volume treatise Biologie, oder Philosophie der lebenden Natur (1802–22) by Gottfried Reinhold Treviranus, who announced:^[5]

The objects of our research will be the different forms and manifestations of life, the conditions and laws under which these phenomena occur, and the causes through which they have been effected. The science that concerns itself with these objects we will indicate by the name biology [Biologie] or the doctrine of life [Lebenslehre].

Although modern biology is a relatively recent development, sciences related to and included within it have been studied since ancient times. Natural philosophy was studied as early as the ancient civilizations of Mesopotamia, Egypt, the Indian subcontinent, and China. However, the origins of modern biology and its approach to the study of nature are most often traced back to ancient Greece.^[6] While the formal study of medicine dates back to Hippocrates (ca. 460 BC – ca. 370 BC), it was Aristotle (384 BC – 322 BC) who contributed most extensively to the development of biology.
Especially important are his History of Animals and other works where he showed naturalist leanings, and later more empirical works that focused on biological causation and the diversity of life. Aristotle's successor at the Lyceum, Theophrastus, wrote a series of books on botany that survived as the most important contribution of antiquity to the plant sciences, even into the Middle Ages.^[7]

Scholars of the medieval Islamic world who wrote on biology included al-Jahiz (781–869), Al-Dinawari (828–896), who wrote on botany,^[8] and Rhazes (865–925) who wrote on anatomy and physiology. Medicine was especially well studied by Islamic scholars working in Greek philosopher traditions, while natural history drew heavily on Aristotelian thought, especially in upholding a fixed hierarchy of life.

Biology began to quickly develop and grow with Anton van Leeuwenhoek's dramatic improvement of the microscope. It was then that scholars discovered spermatozoa, bacteria, infusoria and the diversity of microscopic life. Investigations by Jan Swammerdam led to new interest in entomology and helped to develop the basic techniques of microscopic dissection and staining.^[9]

Advances in microscopy also had a profound impact on biological thinking. In the early 19th century, a number of biologists pointed to the central importance of the cell. Then, in 1838, Schleiden and Schwann began promoting the now universal ideas that (1) the basic unit of organisms is the cell and (2) that individual cells have all the characteristics of life, although they opposed the idea that (3) all cells come from the division of other cells. Thanks to the work of Robert Remak and Rudolf Virchow, however, by the 1860s most biologists accepted all three tenets of what came to be known as cell theory.^[10][11]

Meanwhile, taxonomy and classification became the focus of natural historians. Carl Linnaeus published a basic taxonomy for the natural world in 1735 (variations of which have been in use ever since), and in the 1750s introduced scientific names for all his species.^[12] Georges-Louis Leclerc, Comte de Buffon, treated species as artificial categories and living forms as malleable—even suggesting the possibility of common descent. Though he was opposed to evolution, Buffon is a key figure in the history of evolutionary thought; his work influenced the evolutionary theories of both Lamarck and Darwin.^[13]

Serious evolutionary thinking originated with the works of Jean-Baptiste Lamarck, who was the first to present a coherent theory of evolution.^[14] He posited that evolution was the result of environmental stress on properties of animals, meaning that the more frequently and rigorously an organ was used, the more complex and efficient it would become, thus adapting the animal to its environment. Lamarck believed that these acquired traits could then be passed on to the animal's offspring, who would further develop and perfect them.^[15] However, it was the British naturalist Charles Darwin, combining the biogeographical approach of Humboldt, the uniformitarian geology of Lyell, Malthus's writings on population growth, and his own morphological expertise and extensive natural observations, who forged a more successful evolutionary theory based on natural selection; similar reasoning and evidence led Alfred Russel Wallace to independently reach the same conclusions.^[16][17] Although it was the subject of controversy (which continues to this day), Darwin's theory quickly spread through the scientific community and soon became a central axiom of the rapidly developing science of biology.

The discovery of the physical representation of heredity came along with evolutionary principles and population genetics. In the 1940s and early 1950s, experiments pointed to DNA as the component of chromosomes that held the trait-carrying units that had become known as genes. A focus on new kinds of model organisms such as viruses and bacteria, along with the discovery of the double helical structure of DNA in 1953, marked the transition to the era of molecular genetics. From the 1950s to present times, biology has been vastly extended in the molecular domain. The genetic code was cracked by Har Gobind Khorana, Robert W. Holley and Marshall Warren Nirenberg after DNA was understood to contain codons. Finally, the Human Genome Project was launched in 1990 with the goal of mapping the general human genome. This project was essentially completed in 2003,^[18] with further analysis still being published. The Human Genome Project was the first step in a globalized effort to incorporate accumulated knowledge of biology into a functional, molecular definition of the human body and the bodies of other organisms.

Foundations of modern biology

Cell theory

 

Cell theory states that the cell is the fundamental unit of life, and that all living things are composed of one or more cells or the secreted products of those cells (e.g. shells). All cells arise from other cells through cell division. In multicellular organisms, every cell in the organism's body derives ultimately from a single cell in a fertilized egg. The cell is also considered to be the basic unit in many pathological processes.^[19] In addition, the phenomenon of energy flow occurs in cells in processes that are part of the function known as metabolism. Finally, cells contain hereditary information (DNA), which is passed from cell to cell during cell division.

Evolution

Natural selection of a population for dark coloration.

A central organizing concept in biology is that life changes and develops through evolution, and that all life-forms known have a common origin. The theory of evolution postulates that all organisms on the Earth, both living and extinct, have descended from a common ancestor or an ancestral gene pool. This last universal common ancestor of all organisms is believed to have appeared about 3.5 billion years ago.^[20] Biologists generally regard the universality and ubiquity of the genetic code as definitive evidence in favor of the theory of universal common descent for all bacteria, archaea, and eukaryotes (see: origin of life).^[21]

Introduced into the scientific lexicon by Jean-Baptiste de Lamarck in 1809,^[22] evolution was established by Charles Darwin fifty years later as a viable scientific model when he articulated its driving force: natural selection.^[23][24][25] (Alfred Russel Wallace is recognized as the co-discoverer of this concept as he helped research and experiment with the concept of evolution.)^[26] Evolution is now used to explain the great variations of life found on Earth.

Darwin theorized that species and breeds developed through the processes of natural selection and artificial selection or selective breeding.^[27] Genetic drift was embraced as an additional mechanism of evolutionary development in the modern synthesis of the theory.^[28]

The evolutionary history of the species—which describes the characteristics of the various species from which it descended—together with its genealogical relationship to every other species is known as its phylogeny. Widely varied approaches to biology generate information about phylogeny. These include the comparisons of DNA sequences conducted within molecular biology or genomics, and comparisons of fossils or other records of ancient organisms in paleontology.^[29] Biologists organize and analyze evolutionary relationships through various methods, including phylogenetics, phenetics, and cladistics. (For a summary of major events in the evolution of life as currently understood by biologists, see evolutionary timeline.)

A Punnett square depicting a cross between two pea plants heterozygous for purple (B) and white (b) blossoms

Genetics

Genes are the primary units of inheritance in all organisms. A gene is a unit of heredity and corresponds to a region of DNA that influences the form or function of an organism in specific ways. All organisms, from bacteria to animals, share the same basic machinery that copies and translates DNA into proteins. Cells transcribe a DNA gene into an RNA version of the gene, and a ribosome then translates the RNA into a protein, a sequence of amino acids. The translation code from RNA codon to amino acid is the same for most organisms, but slightly different for some. For example, a sequence of DNA that codes for insulin in humans also codes for insulin when inserted into other organisms, such as plants.^[30]

DNA usually occurs as linear chromosomes in eukaryotes, and circular chromosomes in prokaryotes. A chromosome is an organized structure consisting of DNA and histones. The set of chromosomes in a cell and any other hereditary information found in the mitochondria, chloroplasts, or other locations is collectively known as its genome. In eukaryotes, genomic DNA is located in the cell nucleus, along with small amounts in mitochondria and chloroplasts. In prokaryotes, the DNA is held within an irregularly shaped body in the cytoplasm called the nucleoid.^[31] The genetic information in a genome is held within genes, and the complete assemblage of this information in an organism is called its genotype.^[32]

Homeostasis

 

The hypothalamus secretes CRH, which directs the pituitary gland to secrete ACTH. In turn, ACTH directs the adrenal cortex to secrete glucocorticoids, such as cortisol. The GCs then reduce the rate of secretion by the hypothalamus and the pituitary gland once a sufficient amount of GCs has been released.^[33]

Homeostasis is the ability of an open system to regulate its internal environment to maintain stable conditions by means of multiple dynamic equilibrium adjustments controlled by interrelated regulation mechanisms. All living organisms, whether unicellular or multicellular, exhibit homeostasis.^[34]

To maintain dynamic equilibrium and effectively carry out certain functions, a system must detect and respond to perturbations. After the detection of a perturbation, a biological system normally responds through negative feedback. This means stabilizing conditions by either reducing or increasing the activity of an organ or system. One example is the release of glucagon when sugar levels are too low.

Basic overview of energy and human life.

Energy

The survival of a living organism depends on the continuous input of energy. Chemical reactions that are responsible for its structure and function are tuned to extract energy from substances that act as its food and transform them to help form new cells and sustain them. In this process, molecules of chemical substances that constitute food play two roles; first, they contain energy that can be transformed for biological chemical reactions; second, they develop new molecular structures made up of biomolecules.

The organisms responsible for the introduction of energy into an ecosystem are known as producers or autotrophs. Nearly all of these organisms originally draw energy from the sun.^[35] Plants and other phototrophs use solar energy via a process known as photosynthesis to convert raw materials into organic molecules, such as ATP, whose bonds can be broken to release energy.^[36] A few ecosystems, however, depend entirely on energy extracted by chemotrophs from methane, sulfides, or other non-luminal energy sources.^[37]

Some of the captured energy is used to produce biomass to sustain life and provide energy for growth and development. The majority of the rest of this energy is lost as heat and waste molecules. The most important processes for converting the energy trapped in chemical substances into energy useful to sustain life are metabolism^[38] and cellular respiration.^[39]

Study and research

Structural

 

Schematic of typical animal cell depicting the various organelles and structures.

Molecular biology is the study of biology at a molecular level.^[40] This field overlaps with other areas of biology, particularly with genetics and biochemistry. Molecular biology chiefly concerns itself with understanding the interactions between the various systems of a cell, including the interrelationship of DNA, RNA, and protein synthesis and learning how these interactions are regulated.

Cell biology studies the structural and physiological properties of cells, including their behaviors, interactions, and environment. This is done on both the microscopic and molecular levels, for unicellular organisms such as bacteria, as well as the specialized cells in multicellular organisms such as humans. Understanding the structure and function of cells is fundamental to all of the biological sciences. The similarities and differences between cell types are particularly relevant to molecular biology.

Anatomy considers the forms of macroscopic structures such as organs and organ systems.^[41]
Genetics is the science of genes, heredity, and the variation of organisms.^[42][43] Genes encode the information necessary for synthesizing proteins, which in turn play a central role in influencing the final phenotype of the organism. In modern research, genetics provides important tools in the investigation of the function of a particular gene, or the analysis of genetic interactions. Within organisms, genetic information generally is carried in chromosomes, where it is represented in the chemical structure of particular DNA molecules.

Developmental biology studies the process by which organisms grow and develop. Originating in embryology, modern developmental biology studies the genetic control of cell growth, differentiation, and "morphogenesis," which is the process that progressively gives rise to tissues, organs, and anatomy. Model organisms for developmental biology include the round worm Caenorhabditis elegans,^[44] the fruit fly Drosophila melanogaster,^[45] the zebrafish Danio rerio,^[46] the mouse Mus musculus,^[47] and the weed Arabidopsis thaliana.^[48][49] (A model organism is a species that is extensively studied to understand particular biological phenomena, with the expectation that discoveries made in that organism provide insight into the workings of other organisms.)^[50]

Physiological

Physiology studies the mechanical, physical, and biochemical processes of living organisms by attempting to understand how all of the structures function as a whole. The theme of "structure to function" is central to biology. Physiological studies have traditionally been divided into plant physiology and animal physiology, but some principles of physiology are universal, no matter what particular organism is being studied. For example, what is learned about the physiology of yeast cells can also apply to human cells. The field of animal physiology extends the tools and methods of human physiology to non-human species. Plant physiology borrows techniques from both research fields.

Physiology studies how for example nervous, immune, endocrine, respiratory, and circulatory systems, function and interact. The study of these systems is shared with medically oriented disciplines such as neurology and immunology.

Evolutionary

Evolutionary research is concerned with the origin and descent of species, as well as their change over time, and includes scientists from many taxonomically oriented disciplines. For example, it generally involves scientists who have special training in particular organisms such as mammalogy, ornithology, botany, or herpetology, but use those organisms as systems to answer general questions about evolution.

Evolutionary biology is partly based on paleontology, which uses the fossil record to answer questions about the mode and tempo of evolution,^[51] and partly on the developments in areas such as population genetics.^[52] In the 1980s, developmental biology re-entered evolutionary biology from its initial exclusion from the modern synthesis through the study of evolutionary developmental biology.^[53] Related fields often considered part of evolutionary biology are phylogenetics, systematics, and taxonomy.

Systematic

A phylogenetic tree of all living things, based on rRNA gene data, showing the separation of the three domains bacteria, archaea, and eukaryotes as described initially by Carl Woese. Trees constructed with other genes are generally similar, although they may place some early-branching groups very differently, presumably owing to rapid rRNA evolution. The exact relationships of the three domains are still being debated.

The hierarchy of biological classification's eight major taxonomic ranks. Intermediate minor rankings are not shown. This diagram uses a 3 Domains / 6 Kingdoms format

 

Multiple speciation events create a tree structured system of relationships between species. The role of systematics is to study these relationships and thus the differences and similarities between species and groups of species.^[54] However, systematics was an active field of research long before evolutionary thinking was common.^[55]

Traditionally, living things have been divided into five kingdoms: Monera; Protista; Fungi; Plantae; Animalia.^[56] However, many scientists now consider this five-kingdom system outdated. Modern alternative classification systems generally begin with the three-domain system: Archaea (originally Archaebacteria); Bacteria (originally Eubacteria) and Eukaryota (including protists, fungi, plants, and animals)^[57] These domains reflect whether the cells have nuclei or not, as well as differences in the chemical composition of key biomolecules such as ribosomes.^[57]

Further, each kingdom is broken down recursively until each species is separately classified. The order is: Domain; Kingdom; Phylum; Class; Order; Family; Genus; Species.
Outside of these categories, there are obligate intracellular parasites that are "on the edge of life"^[58] in terms of metabolic activity, meaning that many scientists do not actually classify these structures as alive, due to their lack of at least one or more of the fundamental functions or characteristics that define life. They are classified as viruses, viroids, prions, or satellites.

The scientific name of an organism is generated from its genus and species. For example, humans are listed as Homo sapiens. Homo is the genus, and sapiens the species. When writing the scientific name of an organism, it is proper to capitalize the first letter in the genus and put all of the species in lowercase.^[59] Additionally, the entire term may be italicized or underlined.^[60]

The dominant classification system is called the Linnaean taxonomy. It includes ranks and binomial nomenclature. How organisms are named is governed by international agreements such as the International Code of Nomenclature for algae, fungi, and plants (ICN), the International Code of Zoological Nomenclature (ICZN), and the International Code of Nomenclature of Bacteria (ICNB).
The classification of viruses, viroids, prions, and all other sub-viral agents that demonstrate biological characteristics is conducted by the International Committee on Taxonomy of Viruses (ICTV) and is known as the International Code of Viral Classification and Nomenclature (ICVCN).^{[61][62][63][64]} However, several other viral classification systems do exist.

A merging draft, BioCode, was published in 1997 in an attempt to standardize nomenclature in these three areas, but has yet to be formally adopted.^[65] The BioCode draft has received little attention since 1997; its originally planned implementation date of January 1, 2000, has passed unnoticed. A revised BioCode that, instead of replacing the existing codes, would provide a unified context for them, was proposed in 2011.^[66][67][68] However, the International Botanical Congress of 2011 declined to consider the BioCode proposal. The ICVCN remains outside the BioCode, which does not include viral classification.

Ecological and environmental

Mutual symbiosis between clownfish of the genus Amphiprion that dwell among the tentacles of tropical sea anemones. The territorial fish protects the anemone from anemone-eating fish, and in turn the stinging tentacles of the anemone protects the clown fish from its predators.

Ecology studies the distribution and abundance of living organisms, and the interactions between organisms and their environment.^[69] The habitat of an organism can be described as the local abiotic factors such as climate and ecology, in addition to the other organisms and biotic factors that share its environment.^[70] One reason that biological systems can be difficult to study is that so many different interactions with other organisms and the environment are possible, even on small scales. A microscopic bacterium in a local sugar gradient is responding to its environment as much as a lion searching for food in the African savanna. For any species, behaviors can be co-operative, competitive, parasitic, or symbiotic. Matters become more complex when two or more species interact in an ecosystem.

Ecological systems are studied at several different levels, from individuals and populations to ecosystems and the biosphere. The term population biology is often used interchangeably with population ecology, although population biology is more frequently used when studying diseases, viruses, and microbes, while population ecology is more commonly used when studying plants and animals. Ecology draws on many subdisciplines.

Ethology studies animal behavior (particularly that of social animals such as primates and canids), and is sometimes considered a branch of zoology. Ethologists have been particularly concerned with the evolution of behavior and the understanding of behavior in terms of the theory of natural selection. In one sense, the first modern ethologist was Charles Darwin, whose book, The Expression of the Emotions in Man and Animals, influenced many ethologists to come.^[71]

Biogeography studies the spatial distribution of organisms on the Earth, focusing on topics like plate tectonics, climate change, dispersal and migration, and cladistics.

Basic unresolved problems in biology

Despite the profound advances made over recent decades in our understanding of life’s fundamental processes, some basic problems have remained unresolved. For example, one of the major unresolved problems in biology is the primary adaptive function of sex, and particularly its key processes in eukaryotes, meiosis and homologous recombination. One view is that sex evolved primarily as an adaptation for increasing genetic diversity (see references e.g.^[72][73]). An alternative view is that sex is an adaptation for promoting accurate DNA repair in germ-line DNA, and that increased genetic diversity is primarily a byproduct that may be useful in the long run.^[74][75] (See also Evolution of sexual reproduction).

Another basic unresolved problem in biology is the biologic basis of aging. At present, there is no consensus view on the underlying cause of aging. Various competing theories are outlined in Ageing#Theories.

Branches

These are the main branches of biology:^[76][77]

• Aerobiology – the study of airborne organic particles
• Agriculture – the study of producing crops and raising livestock, with an emphasis on practical applications
• Anatomy – the study of form and function, in plants, animals, and other organisms, or specifically in humans
  • Histology – the study of cells and tissues, a microscopic branch of anatomy
• Astrobiology (also known as exobiology, exopaleontology, and bioastronomy) – the study of evolution, distribution, and future of life in the universe
• Biochemistry – the study of the chemical reactions required for life to exist and function, usually a focus on the cellular level
• Bioengineering – the study of biology through the means of engineering with an emphasis on applied knowledge and especially related to biotechnology
• Biogeography – the study of the distribution of species spatially and temporally
• Bioinformatics – the use of information technology for the study, collection, and storage of genomic and other biological data
• Biomathematics (or Mathematical biology) – the quantitative or mathematical study of biological processes, with an emphasis on modeling
• Biomechanics – often considered a branch of medicine, the study of the mechanics of living beings, with an emphasis on applied use through prosthetics or orthotics
• Biomedical research – the study of health and disease
  • Pharmacology – the study and practical application of preparation, use, and effects of drugs and synthetic medicines
• Biomusicology – the study of music from a biological point of view.
• Biophysics – the study of biological processes through physics, by applying the theories and methods traditionally used in the physical sciences
• Biotechnology – the study of the manipulation of living matter, including genetic modification and synthetic biology
  • Synthetic Biology – research integrating biology and engineering; construction of biological functions not found in nature
• Building biology – the study of the indoor living environment
• Botany – the study of plants
• Cell biology – the study of the cell as a complete unit, and the molecular and chemical interactions that occur within a living cell
• Cognitive biology – the study of cognition as a biological function
• Conservation biology – the study of the preservation, protection, or restoration of the natural environment, natural ecosystems, vegetation, and wildlife
• Cryobiology – the study of the effects of lower than normally preferred temperatures on living beings
• Developmental biology – the study of the processes through which an organism forms, from zygote to full structure
  • Embryology – the study of the development of embryo (from fecundation to birth)
• Ecology – the study of the interactions of living organisms with one another and with the non-living elements of their environment
• Environmental biology – the study of the natural world, as a whole or in a particular area, especially as affected by human activity
• Epidemiology – a major component of public health research, studying factors affecting the health of populations
• Evolutionary biology – the study of the origin and descent of species over time
• Genetics – the study of genes and heredity.
  • Epigenetics – the study of heritable changes in gene expression or cellular phenotype caused by mechanisms other than changes in the underlying DNA sequence
• Hematology (also known as Haematology) – the study of blood and blood-forming organs.
• Integrative biology – the study of whole organisms
• Limnology – the study of inland waters
• Marine biology (or Biological oceanography) – the study of ocean ecosystems, plants, animals, and other living beings
• Microbiology – the study of microscopic organisms (microorganisms) and their interactions with other living things
  • Parasitology – the study of parasites and parasitism
  • Virology – the study of viruses and some other virus-like agents
• Molecular biology – the study of biology and biological functions at the molecular level, some cross over with biochemistry
• Mycology – the study of fungi
• Neurobiology – the study of the nervous system, including anatomy, physiology and pathology
• Population biology – the study of groups of conspecific organisms, including
  • Population ecology – the study of how population dynamics and extinction
  • Population genetics – the study of changes in gene frequencies in populations of organisms
• Paleontology – the study of fossils and sometimes geographic evidence of prehistoric life
• Pathobiology or pathology – the study of diseases, and the causes, processes, nature, and development of disease
• Physiology – the study of the functioning of living organisms and the organs and parts of living organisms
• Phytopathology – the study of plant diseases (also called Plant Pathology)
• Psychobiology – the study of the biological bases of psychology
• Sociobiology – the study of the biological bases of sociology
• Structural biology – a branch of molecular biology, biochemistry, and biophysics concerned with the molecular structure of biological macromolecules
• Zoology – the study of animals, including classification, physiology, development, and behavior. Subbranches include: Ethology(animal behavior), Entomology(insects), Herpetology(reptiles and amphibians), Ichthyology(fish), Mammalogy(mammals), and Ornithology(birds)