DNA

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The ångström or angstrom (symbol Å) (pronounced /ˈɔːŋstrəm/; Swedish: IPA: [ˈɔŋstrˈøm]) is an internationally recognized unit of length equal to 0.1 nanometre or 1 × 10⁻¹⁰ metres. It is named after Anders Jonas Ångström. Although accepted for use, it is not formally defined within the International System of Units (SI).

5-Methylcytosine

5-Methylcytosine is a methylated form of cytosine in which a methyl group is attached to carbon 5, altering its structure without altering its base-pairing properties.

5-hydroxymethylcytosine

5-Hydroxymethylcytosine is a DNA nitrogen base that was first seen in bacteriophages in 1952.^[1][2] However, it was recently found to be abundant in human and mouse brains,^[3] as well as in embryonic stem cells.^[4] In mammals, it can be generated by oxidation of 5-methylcytosine, a reaction mediated by the Tet family of enzymes. It is a hydroxylated and methylated form of cytosine. Its molecular formula is C₅H₇N₃O₂.^[5]

A-DNA

A-DNA is one of the many possible double helical structures of DNA. A-DNA is thought to be one of three biologically active double helical structures along with B- and Z-DNA. It is a right-handed double helix fairly similar to the more common and well-known B-DNA form, but with a shorter more compact helical structure. It appears likely that it occurs only in dehydrated samples of DNA, such as those used in crystallographic experiments, and possibly is also assumed by DNA-RNA hybrid helices and by regions of double-stranded RNA.

Acetylation

Acetylation (or in IUPAC nomenclature ethanoylation) describes a reaction that introduces an acetyl functional group into an organic compound. Deacetylation is the removal of the acetyl group.

Active site

The active site is usually a big pocket or cleft surrounded by amino acid- and other side chains at the surface of the enzyme that contains residues responsible for the substrate specificity (charge, hydrophobicity, steric hindrance) and catalytic residues which often act as proton donors or acceptors or are responsible for binding a cofactor such as PLP, TPP or NAD. The active site is also the site of inhibition of enzymes (see Enzyme inhibitor article). The active site of an enzyme contains the catalytic and binding sites. The structure and chemical properties of the active site allow the recognition and binding of the substrate.

Adduct

An adduct (from the Latin adductus, "drawn toward") is a product of a direct addition of two or more distinct molecules, resulting in a single reaction product containing all atoms of all components, with formation of two chemical bonds and a net reduction in bond multiplicity in at least one of the reactants.^[1] The resultant is considered a distinct molecular species. Examples include the adduct between hydrogen peroxide and sodium carbonate to give sodium percarbonate, and the addition of sodium bisulfite to an aldehyde to give a sulfonate.

Adenosine monophosphate

Adenosine monophosphate (AMP), also known as 5'-adenylic acid, is a nucleotide that is found in RNA. It is an ester of phosphoric acid and the nucleoside adenosine. AMP consists of a phosphate group, the sugar ribose, and the nucleobase adenine.

Adenosine triphosphate

Adenosine-5'-triphosphate (ATP) is a multifunctional nucleotide used in cells as a coenzyme. It is often called the "molecular unit of currency" of intracellular energy transfer.^[1] ATP transports chemical energy within cells for metabolism. It is produced during photosynthesis and cellular respiration and used by enzymes and structural proteins in many cellular processes, including biosynthetic reactions, motility, and cell division.^[2] One molecule of ATP contains three phosphate groups, and it is produced by ATP synthase from inorganic phosphate and adenosine diphosphate (ADP) or adenosine monophosphate (AMP). Metabolic processes that use ATP as an energy source convert it back into its precursors. ATP is therefore continuously recycled in organisms, with the human body turning over its own weight in ATP each day.^[3]

Aflatoxin

Aflatoxins are naturally occurring mycotoxins that are produced by many species of Aspergillus, a fungus, most notably Aspergillus flavus and Aspergillus parasiticus. Aflatoxins are toxic and among the most carcinogenic substances known.^[1] After entering the body, aflatoxins are metabolized by the liver to a reactive intermediate, aflatoxin M₁, an epoxide.

Agriculture

Agriculture is the production of food and goods through farming and forestry. Agriculture was the key development that led to the rise of human civilization, with the husbandry of domesticated animals and plants (i.e. crops) creating food surpluses that enabled the development of more densely populated and stratified societies. The study of agriculture is known as agricultural science.

Alec Jeffreys

Sir Alec John Jeffreys, FRS (born 9 January 1950 at Oxford in Oxfordshire) is a British geneticist, who developed techniques for DNA fingerprinting and DNA profiling which are now used all over the world in forensic science to assist police detective work, and also to resolve paternity and immigration disputes.^[1] He is a professor of genetics at the University of Leicester,^[2] and he became an honorary freeman of the City of Leicester on 26 November 1992.^[3] In 1994, he was knighted by her Majesty Queen Elizabeth II of the United Kingdom, for Services to Science and Technology .

Alkaloid

Alkaloids are naturally occurring chemical compounds containing basic nitrogen atoms.^[1] The name derives from the word alkaline and is used to describe any nitrogen-containing base and organic compounds with one or more of the following features: a heterocyclic compound containing nitrogen, with an alkaline pH and a marked physiological action on animal physiology.^{[citation needed]} However, There are exceptions to each of these criteria. Alkaloids are produced by a large variety of organisms, including bacteria, fungi, plants, and animals and are part of the group of natural products (also called secondary metabolites). Many alkaloids can be purified from crude extracts by acid-base extraction. Many alkaloids are toxic to other organisms. They often have pharmacological effects and are used as medications, as recreational drugs, or in entheogenic rituals. Examples are the local anesthetic and stimulant cocaine, the stimulant caffeine, nicotine, the analgesic morphine, or the antimalarial drug quinine. Most alkaloids have a bitter taste.

Alkylation

Alkylation is the transfer of an alkyl group from one molecule to another. The alkyl group may be transferred as an alkyl carbocation, a free radical, a carbanion or a carbene (or their equivalents) ^[1]. Alkylating agents are widely used in chemistry because the alkyl group is probably the most common group encountered in organic molecules. Many biological target molecules or their synthetic precursors are composed of an alkyl chain with specific functional groups in a specific order. Selective alkylation, or adding parts to the chain with the desired functional groups, is used, especially if there is no commonly available biological precursor. Alkylation with only one carbon is termed methylation.

Alternative splicing

Alternative splicing is a process by which the exons of the RNA produced by transcription of a gene (a primary gene transcript or pre-mRNA) are reconnected in multiple ways during RNA splicing. The resulting different mRNAs may be translated into different protein isoforms; thus, a single gene may code for multiple proteins^[1].

Amino acid

Amino acids are molecules containing an amine group, a carboxylic acid group and a side chain that varies between different amino acids. These molecules are particularly important in biochemistry, where this term refers to alpha-amino acids with the general formula H₂NCHRCOOH, where R is an organic substituent.^[1] In the alpha amino acids, the amino and carboxylate groups are attached to the same carbon atom, which is called the α–carbon. The various alpha amino acids differ in which side chain (R group) is attached to their alpha carbon. These side chains can vary in size from just a hydrogen atom in glycine, to a methyl group in alanine, through to a large heterocyclic group in tryptophan.

Animal

Animals are a major group of mostly multicellular, eukaryotic organisms of the kingdom Animalia or Metazoa. Their body plan eventually becomes fixed as they develop, although some undergo a process of metamorphosis later on in their life. Most animals are motile, meaning they can move spontaneously and independently. All animals are also heterotrophs, meaning they must ingest other organisms for sustenance.

Antisense RNA

Antisense RNA is a single-stranded RNA that is complementary to a messenger RNA (mRNA) strand transcribed within a cell. Antisense RNA may be introduced into a cell to inhibit translation of a complementary mRNA by base pairing to it and physically obstructing the translation machinery.^[1] This effect is therefore stoichiometric. An example of naturally occurring mRNA antisense mechanism is the hok/sok system of the E.coli R1 plasmid. Antisense RNA has long been thought of as a promising technique for disease therapy; the only such case to have reached the market is the drug fomivirsen. One commentator has characterized antisense RNA as one of "dozens of technologies that are gorgeous in concept, but exasperating in [commercialization]".^[2] Generally, antisense RNA still lack effective design, biological activity, and efficient route of administration.^[3]

Aromaticity

In organic chemistry, the structures of some rings of atoms are unexpectedly stable. Aromaticity is a chemical property in which a conjugated ring of unsaturated bonds, lone pairs, or empty orbitals exhibit a stabilization stronger than would be expected by the stabilization of conjugation alone. It can also be considered a manifestation of cyclic delocalization and of resonance.^[1][2][3]

Atom

The atom is a basic unit of matter consisting of a dense, central nucleus surrounded by a cloud of negatively charged electrons. The atomic nucleus contains a mix of positively charged protons and electrically neutral neutrons (except in the case of hydrogen-1, which is the only stable nuclide with no neutron). The electrons of an atom are bound to the nucleus by the electromagnetic force. Likewise, a group of atoms can remain bound to each other, forming a molecule. An atom containing an equal number of protons and electrons is electrically neutral, otherwise it has a positive or negative charge and is an ion. An atom is classified according to the number of protons and neutrons in its nucleus: the number of protons determines the chemical element, and the number of neutrons determine the isotope of the element.^[1]

Atomic force microscope

The atomic force microscope (AFM) or scanning force microscope (SFM) is a very high-resolution type of scanning probe microscopy, with demonstrated resolution of fractions of a nanometer, more than 1000 times better than the optical diffraction limit. The precursor to the AFM, the scanning tunneling microscope, was developed by Gerd Binnig and Heinrich Rohrer in the early 1980s, a development that earned them the Nobel Prize for Physics in 1986. Binnig, Quate and Gerber invented the first AFM in 1986. The AFM is one of the foremost tools for imaging, measuring, and manipulating matter at the nanoscale. The information is gathered by "feeling" the surface with a mechanical probe. Piezoelectric elements that facilitate tiny but accurate and precise movements on (electronic) command enable the very precise scanning.

Avery-MacLeod-McCarty experiment

The Avery-MacLeod-McCarty experiment was an experimental demonstration, reported in 1944 by Oswald Avery, Colin MacLeod, and Maclyn McCarty, that DNA is the substance that causes bacterial transformation. It was the culmination of research in the 1930s and early 1940s at the Rockefeller Institute for Medical Research to purify and characterize the "transforming principle" responsible for the transformation phenomenon first described in Griffith's experiment of 1928: killed Streptococcus pneumoniae of the virulent strain type III-S, when injected along with living but non-virulent type II-R pneumococci, resulted in a deadly infection of type III-S pneumococci. In their paper "Studies on the Chemical Nature of the Substance Inducing Transformation of Pneumococcal Types: Induction of Transformation by a Desoxyribonucleic Acid Fraction Isolated from Pneumococcus Type III", published in the February 1944 issue of the Journal of Experimental Medicine, Avery and his colleagues suggest that DNA, rather than protein as widely believed at the time, may be the hereditary material of bacteria, and could be analogous to genes and/or viruses in higher organisms.^[1][2]

Bacterial artificial chromosome

A bacterial artificial chromosome (BAC) is a DNA construct, based on a functional fertility plasmid (or F-plasmid), used for transforming and cloning in bacteria, usually E. coli.^[1][2] F-plasmids play a crucial role because they contain partition genes that promote the even distribution of plasmids after bacterial cell division. The bacterial artificial chromosome's usual insert size is 150-350 kbp, but can be greater than 700 kbp.^[3] A similar cloning vector called a PAC has also been produced from the bacterial P1-plasmid.

Bacteriophage

A bacteriophage (from 'bacteria' and Greek φᾰγεῖν phagein "to eat") is any one of a number of viruses that infect bacteria. Bacteriophages are among the most common organisms on Earth.^[1] The term is commonly used in its shortened form, phage.

Base pair

In molecular biology, two nucleotides on opposite complementary DNA or RNA strands that are connected via hydrogen bonds are called a base pair (often abbreviated bp). In the canonical Watson-Crick base pairing, adenine (A) forms a base pair with thymine (T), as does guanine (G) with cytosine (C) in DNA. In RNA, thymine is replaced by uracil (U). Non-Watson-Crick base pairing with alternate hydrogen bonding patterns also occur, especially in RNA; common such patterns are Hoogsteen base pairs. Pairing is also the mechanism by which codons on messenger RNA molecules are recognized by anticodons on transfer RNA during protein translation. Some DNA- or RNA-binding enzymes can recognize specific base pairing patterns that identify particular regulatory regions of genes.

Bessel function

In mathematics, Bessel functions, first defined by the mathematician Daniel Bernoulli and generalized by Friedrich Bessel, are canonical solutions y(x) of Bessel's differential equation:

Binding site

In biochemistry, a binding site is a region on a protein, DNA, or RNA to which specific other molecules and ions—in this context collectively called ligands, or more specifically, protein ligands—form a chemical bond.

Bioinformatics

Bioinformatics is the application of information technology and computer science to the field of molecular biology. The term bioinformatics was coined by Paulien Hogeweg in 1979 for the study of informatic processes in biotic systems. Its primary use since at least the late 1980s has been in genomics and genetics, particularly in those areas of genomics involving large-scale DNA sequencing. Bioinformatics now entails the creation and advancement of databases, algorithms, computational and statistical techniques, and theory to solve formal and practical problems arising from the management and analysis of biological data. Over the past few decades rapid developments in genomic and other molecular research technologies and developments in information technologies have combined to produce a tremendous amount of information related to molecular biology. It is the name given to these mathematical and computing approaches used to glean understanding of biological processes. Common activities in bioinformatics include mapping and analyzing DNA and protein sequences, aligning different DNA and protein sequences to compare them and creating and viewing 3-D models of protein structures.

Biology

Biology (from Greek βιολογία - βίος, bios, "life"; -λογία, -logia, study of) is the natural science concerned with the study of life and living organisms, including their structure, function, growth, origin, evolution, distribution, and taxonomy.^[1] The term biology in its modern sense appears to have been introduced independently by Karl Friedrich Burdach (1800), Gottfried Reinhold Treviranus (Biologie oder Philosophie der lebenden Natur, 1802), and Jean-Baptiste Lamarck (Hydrogéologie, 1802).^[2][3]

Blood

Blood is a specialized bodily fluid that delivers necessary substances to the body's cells – such as nutrients and oxygen – and transports waste products away from those same cells.

Blueprint

A blueprint is a type of paper-based reproduction usually of a technical drawing, documenting an architecture or an engineering design. More generally, the term "blueprint" has come to be used to refer to any detailed plan.

Brain

The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals.^[1] Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell.

Branched DNA

In biology, a branched DNA assay is a test for specific nucleic acid chains, and is typically used to detect retroviruses such as HIV.^[1] However, the assay can be used to detect and quantitate other types of RNA or DNA target. In the assay, branched DNA is mixed with a sample to be tested. The detection is done using a non-radioactive method and does not require preamplification of the nucleic acid to be detected. The assay entirely relies on hybridization. Enzymes are used to indicate the extent of hybridization but are not used to manipulate the nucleic acids. Thus, small amounts of a nucleic acid can be detected and quantified without a reverse transcription step (in the case of RNA) and/or PCR. The assay can be run as a "high throughput assay", unlike quantitative Northern-blotting or the RNAse-protection assay, which are labor-intensive and thus difficult to perform on a large number of samples. The other major high throughput technique employed in the quantitation of specific RNA molecules is quantitative PCR, after reverse transcription of the RNA to cDNA.

C-value

The term C-value refers to the amount of DNA contained within a haploid nucleus (e.g., in a gamete or one half the amount in a diploid somatic cell) of a eukaryotic organism. In some cases (notably among diploid organisms), the terms C-value and genome size are used interchangeably, however in polyploids the C-value may represent two genomes contained within the same nucleus. Greilhuber et al.^[1] have suggested some new layers of terminology and associated abbreviations to clarify this issue, but these somewhat complex additions have yet to be used by other authors. C-values are reported in picograms.

C-value enigma

The C-value enigma or C-value paradox is a term used to describe the complex puzzle surrounding the extensive variation in nuclear genome size among eukaryotic species. At the center of the C-value enigma is the observation that genome size does not correlate with organismal complexity; for example, some single-celled protists have genomes much larger than that of humans.

Caenorhabditis elegans

Caenorhabditis elegans (pronounced /ˌsiːnɵræbˈdaɪtɪs ˈɛlɪɡænz/) is a free-living, transparent nematode (roundworm), about 1 mm in length,^[2] which lives in temperate soil environments. Research into the molecular and developmental biology of C. elegans was begun in 1974 by Sydney Brenner and it has since been used extensively as a model organism.^[3]

Cambridge University Press

Cambridge University Press is the publishing business of the University of Cambridge. Granted a Royal Letters Patent by Henry VIII in 1534, it is the world's oldest continually operating book publisher. Cambridge is both an academic and educational publishing house, with a regional structure operating in Europe, the Middle East and Africa (EMEA); the Americas; and Asia-Pacific.

Cancer

Cancer /ˈkænsə(r)/  ( listen) (medical term: malignant neoplasm) is a class of diseases in which a group of cells display uncontrolled growth (division beyond the normal limits), invasion (intrusion on and destruction of adjacent tissues), and sometimes metastasis (spread to other locations in the body via lymph or blood). These three malignant properties of cancers differentiate them from benign tumors, which are self-limited, and do not invade or metastasize. Most cancers form a tumor but some, like leukemia, do not. The branch of medicine concerned with the study, diagnosis, treatment, and prevention of cancer is oncology.

Carbohydrate

A carbohydrate is an organic compound with general formula C_m(H₂O)_n, that is, consisting only of carbon, hydrogen and oxygen, the last two in the 2:1 atom ratio. Carbohydrates can be viewed as hydrates of carbon, hence their name.

Carcinogen

A carcinogen is any substance, radionuclide or radiation that is an agent directly involved in the exacerbation of cancer or in the increase of its propagation. This may be due to the ability to damage the genome or to the disruption of cellular metabolic processes. Several radioactive substances are considered carcinogens, but their carcinogenic activity is attributed to the radiation, for example gamma rays and alpha particles, which they emit. Common examples of carcinogens are inhaled asbestos, certain dioxins, and tobacco smoke.

Carotenoid

Carotenoids are organic pigments that are naturally occurring in the chloroplasts and chromoplasts of plants and some other photosynthetic organisms like algae, some types of fungus and some bacteria.

Catalysis

Catalysis is the process in which the rate of a chemical reaction is either increased or decreased by means of a chemical substance known as a catalyst. Unlike other reagents that participate in the chemical reaction, a catalyst is not consumed by the reaction itself. The catalyst may participate in multiple chemical transformations. Catalysts that speed the reaction are called positive catalysts. Catalysts that slow down the reaction are called negative catalysts or inhibitors. Substances that increase the activity of catalysts are called promoters and substances that deactivate catalysts are called catalytic poisons.

Cell (biology)

The cell is the basic structural and functional unit of all known living organisms. It is the smallest unit of life that is classified as a living thing, and is often called the building block of life.^[1] Some organisms, such as most bacteria, are unicellular (consist of a single cell). Other organisms, such as humans, are multicellular. (Humans have an estimated 100 trillion or 10¹⁴ cells; a typical cell size is 10 µm; a typical cell mass is 1 nanogram.) The largest known cell is an unfertilized ostrich egg cell.^[2]

Cell division

Cell division is the process by which a parent cell divides into two or more daughter cells. Cell division is usually a small segment of a larger cell cycle. This type of cell division in eukaryotes is known as mitosis, and leaves the daughter cell capable of dividing again. The corresponding sort of cell division in prokaryotes is known as binary fission. In another type of cell division present only in eukaryotes, called meiosis, a cell is permanently transformed into a gamete and cannot divide again until fertilization. For simple unicellular organisms^{[nb 1]} such as the amoeba, one cell division is equivalent to reproduction-- an entire new organism is created. On a larger scale, mitotic cell division can create progeny from multicellular organisms, such as plants that grow from cuttings. Cell division also enables asexually reproducing organisms to develop from the one-celled zygote, which itself was produced by cell division from gametes. And after growth, cell division allows for continual construction and repair of the organism.^[1] A human being's body experiences about 10,000 trillion cell divisions in a lifetime.^[2]

Cell metabolism

Metabolism is the set of chemical reactions that happen in living organisms to maintain life. These processes allow organisms to grow and reproduce, maintain their structures, and respond to their environments. Metabolism is usually divided into two categories. Catabolism breaks down organic matter, for example to harvest energy in cellular respiration. Anabolism, uses energy to construct components of cells such as proteins and nucleic acids.

Cell nucleus

In cell biology, the nucleus (pl. nuclei; from Latin nucleus or nuculeus, meaning kernel), also sometimes referred to as the "control center", is a membrane-enclosed organelle found in eukaryotic cells. It contains most of the cell's genetic material, organized as multiple long linear DNA molecules in complex with a large variety of proteins, such as histones, to form chromosomes. The genes within these chromosomes are the cell's nuclear genome. The function of the nucleus is to maintain the integrity of these genes and to control the activities of the cell by regulating gene expression — the nucleus is therefore the control center of the cell.

Cellular differentiation

In developmental biology, cellular differentiation is the process by which a less specialized cell becomes a more specialized cell type. Differentiation occurs numerous times during the development of a multicellular organism as the organism changes from a single zygote to a complex system of tissues and cell types. Differentiation is a common process in adults as well: adult stem cells divide and create fully-differentiated daughter cells during tissue repair and during normal cell turnover. Differentiation dramatically changes a cell's size, shape, membrane potential, metabolic activity, and responsiveness to signals. These changes are largely due to highly-controlled modifications in gene expression. With a few exceptions, cellular differentiation almost never involves a change in the DNA sequence itself. Thus, different cells can have very different physical characteristics despite having the same genome.

Centromere

A centromere is a region of DNA typically found near the middle of a chromosome where two identical sister chromatids come in contact. It is involved in cell division as the point of mitotic spindle.

Chargaff's rules

Chargaff's rules state that DNA from any cell of all organisms should have a 1:1 ratio of pyrimidine and purine bases and, more specifically, that the amount of guanine is equal to cytosine and the amount of adenine is equal to thymine. This pattern is found in both strands of the DNA. They were discovered by Austrian chemist Erwin Chargaff.^{[1][2][3][4][5][6]}

Chelation

Chelation (pronounced /kiːˈleɪʃən/) is the formation or presence of two or more separate bindings between a polydentate (multiple bonded) ligand and a single central atom. ^[1] Usually these ligands are organic compounds, and are called chelants, chelators, chelating agents, or sequestering agents.

Chemotherapy

Chemotherapy, in its most general sense, is the treatment of disease by chemicals^[1] especially by killing micro-organisms or cancerous cells. In popular usage, it refers to antineoplastic drugs used to treat cancer or the combination of these drugs into a cytotoxic standardized treatment regimen. In its non-oncological use, the term may also refer to antibiotics (antibacterial chemotherapy). In that sense, the first modern chemotherapeutic agent was Paul Ehrlich's arsphenamine, an arsenic compound discovered in 1909 and used to treat syphilis. This was later followed by sulfonamides discovered by Domagk and penicillin discovered by Alexander Fleming.

Chloroplast

Chloroplasts are organelles found in plant cells and other eukaryotic organisms that conduct photosynthesis. Chloroplasts capture light energy to conserve free energy in the form of ATP and reduce NADP to NADPH through a complex set of processes called photosynthesis.^[1]

Chloroplasts

Chloroplasts are organelles found in plant cells and other eukaryotic organisms that conduct photosynthesis. Chloroplasts capture light energy to conserve free energy in the form of ATP and reduce NADP to NADPH through a complex set of processes called photosynthesis.^[1]

Chromatin

Chromatin is the complex combination of DNA and protein that makes up chromosomes. It is found inside the nuclei of eukaryotic cells. It is divided between heterochromatin (condensed) and euchromatin (extended) forms.^{[1] [2]} The major components of chromatin are DNA (Genetic Formula) and histone proteins, although many other chromosomal proteins have prominent roles too. The functions of chromatin are to package DNA into a smaller volume to fit in the cell, to strengthen the DNA to allow mitosis and meiosis, and to serve as a mechanism to control expression and DNA replication. Chromatin contains genetic material-instructions to direct cell functions. Changes in chromatin structure are affected by chemical modifications of histone proteins such as methylation (DNA and proteins) and acetylation (proteins), and by non-histone, DNA-binding proteins.