Glossary of cellular and molecular biology (M–Z) (this page) lists terms beginning with the letters M through Z.
This glossary is intended as introductory material for novices (for more specific and technical detail, see the article corresponding to each term). It has been designed as a companion toGlossary of genetics and evolutionary biology, which contains many overlapping and related terms; other related glossaries includeGlossary of virology andGlossary of chemistry.
Any very largemolecule composed of dozens, hundreds, or thousands ofcovalently bonded atoms, especially one with biological significance. Many importantbiomolecules, such asnucleic acids andproteins, arepolymers consisting of a repeated series of smallermonomers; others such aslipids andcarbohydrates may not be polymeric but are nevertheless large and complex molecules.
Any of a class of relatively long-livedphagocytic cells of the mammalianimmune system which are activated in response to the presence of foreign materials in certain tissues and subsequently play important roles inantigen presentation, stimulating other types of immune cells, and killing orengulfing parasitic microorganisms, diseased cells, or tumor cells.[3]
The branch of medicine and medical science that involves the study, diagnosis, and management ofhereditary disorders, and more broadly the application of knowledge about humangenetics to medical care.
A supramolecular aggregate ofamphipathiclipid molecules which when suspended in a polar solvent tend to arrange themselves into structures which minimize the exposure of theirhydrophobic tails by sheltering them within a ball created by their ownhydrophilic heads (i.e. amicelle). Certain types of lipids, specificallyphospholipids and othermembrane lipids, commonly occur asdouble-layered sheets of molecules when immersed in an aqueous environment, which can themselves assume approximately spherical shapes, acting as semipermeable barriers surrounding a water-filled interior space. This is the basic structure of the biological membranes enclosing allcells,vesicles, andmembrane-bound organelles.
The structure of a typical mature protein-codingmessenger RNA ormRNA, drawn approximately to scale. The coding sequence (green) is bounded byuntranslated regions at both the5'-end (yellow) and the3'-end (pink). Prior to export from the nucleus, a5' cap (red) and a3' poly(A) tail (black) are added to help stabilize the mRNA and prevent its degradation by ribonucleases.
A stepwise series of biochemical reactions occurring within a cell, often but not necessarilycatalyzed by specificenzymes, that fulfills some activity or process related tometabolism. The reactions are linked by the sharing of reactants, products, or intermediate compounds in consecutive steps, such that the product of one reaction is used as a reactant in a subsequent reaction. Byproducts are often removed from the cell asmetabolic waste. The overall pathway may beanabolic,catabolic, oramphibolic in nature.[5] In any actively metabolizing cell, an elaborate network of interconnected metabolic pathways is required to maintainhomeostasis, with degradative catabolic processes providing the energy necessary to conduct anabolic biosynthesis; for example,glycolysis, theelectron transport chain, andoxidative phosphorylation provide theATP used infatty acid synthesis. The flux ofmetabolites through each pathway is regulated by the needs of the cell and the availability ofsubstrates.
The complete set of chemical reactions which sustain and account for the basic processes of life in all living cells,[2] especially those involving: 1) the conversion of energy from food into energy available for cellular activities; 2) the breakdown of food into simpler compounds which can then be used assubstrates to build complexbiomolecules such asproteins,lipids, andnucleic acids; and 3) the degradation and excretion of toxins, byproducts, and other unusable compounds known asmetabolic wastes. In a broader sense the term may includeall chemical reactions occurring in living organisms, even those which are not strictly necessary for life but instead serve accessory functions. Many specific cellular activities are accomplished bymetabolic pathways in which one chemical is ultimately transformed through a stepwise series of reactions into another chemical, with each reactioncatalyzed by a specificenzyme. Most metabolic reactions can be subclassified ascatabolic oranabolic.
An intermediate or end product ofmetabolism, especially degradative metabolism (catabolism);[2] or any substance produced by or taking part in a metabolic reaction. Metabolites include a huge variety of small molecules generated by cells from variouspathways and having various functions, including as inputs to other pathways and reactions, assignaling molecules, and as stimulators, inhibitors, andcofactors ofenzymes. Metabolites may result from the degradation and elimination of naturally occurring compounds as well as of synthetic compounds such as pharmaceuticals.
(of a linearchromosome or chromosome fragment) Having acentromere positioned in the middle of the chromosome, resulting inchromatid arms of approximately equal length.[6]
Any of a class oftransferaseenzymes which catalyze the covalent bonding of amethyl group (–CH 3) to another compound, protein, or biomolecule, a process known asmethylation.
A group that "aims to provide a standard for the representation ofDNA microarraygene expression data that would facilitate the exchange of microarray information between different data systems".[7]
Any of a diverse class of smallmembrane-bound organelles orvesicles found in the cells of many eukaryotes, especially plants and animals, usually having some specific metabolic function and occurring in great numbers in certain specialized cell types.Peroxisomes,glyoxysomes,glycosomes, andhydrogenosomes are often considered microbodies.
Achromosomaldeletion that is too short to cause any apparent change in morphology under a light microscope, though it may still be detectable with other methods such assequencing.
A long, thin, flexible, rod-like structure composed of polymeric strands of proteins, usuallyactins, that occurs in abundance in thecytoplasm of eukaryotic cells, forming part of thecytoskeleton. Microfilaments comprise the cell's structural framework. They are modified by and interact with numerous other cytoplasmic proteins, playing important roles in cell stability, motility, contractility, and facilitating changes in cell shape, as well as incytokinesis.
The smaller of the two types ofnuclei that occur in pairs in the cells of some ciliatedprotozoa. Whereas the largermacronucleus ispolyploid, the micronucleus isdiploid and generally transcriptionally inactive except for the purpose of sexual reproduction, where it has important functions duringconjugation.[2]
Alsoshort tandem repeat (STR) orsimple sequence repeat (SSR).
A type ofsatellite DNA consisting of a relatively shortsequence oftandem repeats, in which certainmotifs (ranging in length from one to six or morebases) are repeated, typically 5–50 times. Microsatellites are widespread throughout most organisms' genomes and tend to have higher mutation rates than other regions. They are classified asvariable number tandem repeat (VNTR) DNA, along with longerminisatellites.
An instrument used to cut extremely thin slices of material, known asmicrosections or simplysections, preparatory to observation under a microscope.[5] Sections of tissues and cells are usually 50 nanometres (nm) to 100 micrometres (μm) in width. The process of cutting them is known asmicrotomy.
microtrabecula
(pl.)microtrabeculae
A fine protein filament of the cytoskeleton. Multiple filaments form the microtrabecular network.[2]
Any of the long, generally straight, hollow tubes, about 24 nanometers in diameter and composed of interwoven polymeric filaments of the proteintubulin, found in the cytoplasm of many eukaryotic cells, where they are involved in maintaining the cell's shape and structural integrity as well as in force generation for cellular ororganellar locomotion (as withcilia andflagella). They also comprise thespindle apparatus critical tomitosis andmeiosis. Microtubules are rigid but transient all-purpose structural members which can be rapidly assembled and disassembled at the cell's needs. Many differentmicrotubule-associated proteins interact with them.[5] See alsomicrofilament.
A region near the center of a eukaryotic cell typically consisting of twocentrioles oriented at right angles to each other and surrounded by acomplex of associated proteins, which functions as the site of initiation for the assembly ofmicrotubules.[5]
A type ofextracellular vesicle released when an evagination of thecell membrane "buds off" into the extracellular space. Microvesicles vary in size from 30–1,000 nanometres in diameter and are thought to play roles in many physiological processes, includingintercellular communication by shuttling molecules such as RNA and proteins between cells.[8]
A small, slender, tubular cytoplasmic projection, generally 0.2–4 micrometres long and 0.1 micrometres in diameter,[9] protruding from the surface of some animal cells and supported by a central core ofmicrofilaments. When present in large numbers, such as onepithelial cells lining the respiratory and alimentary tracts, they form a densebrush border which presumably serves to increase each cell's absorptive surface area.[2][3]
mid body
The centrally constricted region that forms across the central axis of a cell duringcytokinesis, constricted by the closing of thecontractile ring until thedaughter cells are finally separated,[2] but occasionally persisting as a tether between the two cells for as long as a completecell cycle.[9]
In plant cells, the outermost layer of thecell wall; a continuous, unified layer of extracellularpectins which is the first layer deposited by the cell duringcytokinesis and which serves to cement together the primary cell walls of adjacent cells.[4]
An incorrectpairing ofnucleobases oncomplementarystrands ofDNA orRNA; i.e. the presence in one strand of a duplex molecule of a base that is not complementary (by Watson–Crick pairing rules) to the base occupying the corresponding position in the other strand, which prevents normalhydrogen bonding between the bases. For example, aguanine paired with athymine would be a mismatch, as guanine normally pairs withcytosine.[13]
The insertion of an incorrectamino acid in a growingpeptide chain duringtranslation, i.e. the inclusion of any amino acid that is not the one specified by a particularcodon in anmRNA transcript. Mistranslation may originate from amischargedtransfer RNA or from a malfunctioningribosome.[13]
The set of DNA molecules contained withinmitochondria, usually one or more circularplasmids representing a semi-autonomousgenome which is physically separate from and functionally independent of thechromosomal DNA in the cell's nucleus. The mitochondrial genome encodes many unique enzymes found only in mitochondria.
The selective degradation ofmitochondria by means ofautophagy; i.e. the mitochondrion initiates its own degradation. Mitophagy is a regular process in healthy populations of cells by which defective or damaged mitochondria are recycled, preventing their accumulation. It may also occur in response to the changingmetabolic needs of the cell, e.g. during certain developmental stages.
Ineukaryotic cells, the part of thecell cycle during which thedivision of thenucleus takes place and replicatedchromosomes are separated into two distinct nuclei. Mitosis is generally preceded by theS phase ofinterphase, when the cell'sDNA is replicated, and either occurs simultaneously with or is followed bycytokinesis, when thecytoplasm andplasma membrane are divided into two newdaughter cells. Colloquially, the term "mitosis" is often used to refer to the entire process of cell division, not just the division of the nucleus.
The proportion of cells within a sample which are undergoingmitosis at the time of observation, typically expressed as a percentage or as a value between 0 and 1. The number of cells dividing by mitosis at any given time can vary widely depending on organism,tissue, developmental stage, andculture media, among other factors.[2]
The abnormalexchange of genetic material betweenhomologous chromosomes duringmitosis (as opposed tomeiosis, where it occurs normally).Homologous recombination during mitosis is relatively uncommon; in the laboratory, it can be induced by exposing dividing cells to high-energy electromagnetic radiation such as X rays. As in meiosis, it can separateheterozygous alleles and thereby propagate potentially significant changes in zygosity todaughter cells, though unless it occurs very early in development this often has little or no phenotypic effect, since any phenotypic variance shown by mutant lineages arising in terminally differentiated cells is generally masked or compensated for by neighboringwild-type cells.[2]
The process by which most animal cells undergo an overall change in shape during or precedingmitosis, abandoning the various complex or elongated shapes characteristic ofinterphase and rapidly contracting into a rounded or spherical morphology that is more conducive tocell division. This phenomenon has been observed bothin vivo andin vitro.
The presence of more than one differentploidy level, i.e. more than one number of sets ofchromosomes, in different cells of the same cellular population.[13]
The branch of biology that studies biological activity at themolecular level, in particular the various mechanisms underlying the biological processes that occur in and betweencells, including the structures, properties, synthesis, and modification ofbiomolecules such asproteins andnucleic acids, their interactions with the chemical environment and with other biomolecules, and how these interactions explain the observations of classical biology (which in contrast studies biological systems at much larger scales).[14] Molecular biology relies largely on laboratory techniques of physics and chemistry to manipulate and measure microscopic phenomena. It is closely related to and overlaps with the fields ofcell biology,biochemistry, andmolecular genetics.
Any of variousmolecular biology methods designed toreplicate a particular molecule, usually aDNAsequence or aprotein, many times inside the cells of a natural host. Commonly, arecombinant DNA fragment containing agene of interest isligated into aplasmidvector, whichcompetent bacterial cells are then induced to uptake in a process known astransformation. The bacteria, carrying the recombinant plasmid, are then allowed to proliferate naturally incell culture, so that each time the bacterial cells divide, the plasmids are replicated along with the rest of the bacterial genome. Any functioning gene of interest within the plasmid will beexpressed by the bacterial cells, and thereby itsgene products will also be cloned. The plasmids or gene products, which now exist in many copies, may then be extracted from the bacteria and purified. Molecular cloning is a fundamental tool ofgenetic engineering employed for a wide variety of purposes, often to studygene expression, to amplify a specific gene product, or to generate aselectable phenotype.
Describing cells, proteins, or molecules descended or derived from a singleclone (i.e. from the same genome or genetic lineage) or made in response to a single unique compound. Monoclonalantibodies are raised against only oneantigen or can only recognize one uniqueepitope on the same antigen. Similarly, the cells of sometissues andneoplasms may be described as monoclonal if they are all the asexual progeny of one originalparent cell.[2] Contrastpolyclonal.
A type of largeleukocyte of the mononuclear phagocyte system in mammals, characterized by pale-staining cytoplasm and a kidney-shaped or horseshoe-shaped nucleus. Monocytes are derived frompluripotentstem cells in bone marrow and becomemacrophages in other tissues.[5]
Amolecule orcompound which can exist individually or serve as a building block orsubunit of a largermacromolecular aggregate known as apolymer.[4] Polymers form when multiple monomers of the same or similar molecular species are connected to each other bychemical bonds, either in a linear chain or a non-linear conglomeration. Examples include the individualnucleotides which formnucleic acid polymers, the individualamino acids which formpolypeptides, and the individual proteins which formprotein complexes.
A syntheticnucleic acid analogue connecting a short sequence ofnucleobases into an artificialantisenseoligomer, used ingenetic engineering toknockdowngene expression bypairing withcomplementary sequences in naturally occurring RNA or DNA molecules, especiallymRNA transcripts, thereby inhibiting interactions with other biomolecules such as proteins andribosomes. Morpholino oligomers are not themselvestranslated, and neither they nor their hybrid duplexes with RNA are attacked bynucleases; also, unlike the negatively chargedphosphates of normal nucleic acids, the synthetic backbones of Morpholinos are electrically neutral, making them less likely to interact non-selectively with a host cell's charged proteins. These properties make them useful and reliable tools for artificially generatingmutant phenotypes in living cells.[13]
The presence of two or more populations of cells with differentgenotypes in an individual organism which has developed from a single fertilizedegg. A mosaic organism can result from many kinds of genetic phenomena, includingnondisjunction of chromosomes,endoreduplication, or mutations in individualstem cell lineages during the early development of the embryo. Mosaicism is similar to but distinct fromchimerism.
Anyprotein which converts chemical energy derived from the hydrolysis ofnucleoside triphosphates such asATP andGTP into mechanical work in order to effect its own locomotion, by propelling itself along a filament or through thecytoplasm.[4]
Composed of more than onecell. The term is used especially to describe organisms or tissues consisting of many cells descendant from the same originalparent cell which work together in an organized way, but may also describe groups of nominally single-celled organisms such as protists and bacteria which live symbiotically with each other in large colonies. Contrastunicellular.
The integration of data from multiple "omics" technologies (e.g. data from thegenome,epigenome,transcriptome,proteome,metabolome, etc.) in order to study complex biological relationships, discover novel associations between biological entities, pinpoint relevantbiomarkers, or build elaborate models of physiology and disease.
A locus or sequence within aplasmidvector which contains multiple uniquerestriction sites recognized by variousrestriction endonucleases, which makes it possible for scientists to target theinsertion of a DNA fragment (often agene cassette) specifically to that locus and in the desired orientation, bydigesting the insert and the vector with the same endonuclease(s) and thenligating them together via compatible restriction ends, a technique known asrestriction cloning.[5] Commercial plasmids designed for cloning commonly incorporate one or more multiple cloning sites.
Any physical or chemical agent thatchanges the genetic material (usuallyDNA) of an organism and thereby increases the frequency ofmutations above natural background levels.
1. The process by which the genetic information of an organism is changed, resulting in amutation. Mutagenesis may occur spontaneously or as a result of exposure to amutagen.
2. Inmolecular biology, any laboratory technique by which one or more genetic mutations are deliberatelyengineered in order to produce amutant gene, regulatory element, gene product, orgenetically modified organism so that the functions of a genetic locus, process, or product can be studied in detail.
Any permanent change in thenucleotide sequence of a strand ofDNA orRNA, or in theamino acid sequence of apeptide. Mutations play a role in both normal and abnormal biological processes; their natural occurrence is integral to the process ofevolution. They can result from errors inreplication, chemical damage, exposure to high-energy radiation, or manipulations bymobile genetic elements.Repair mechanisms have evolved in many organisms to correct them. By understanding the effect that a mutation has onphenotype, it is possible to establish the function of thegene or sequence in which it occurs.
One of two possible orientations by which a linear DNA fragment can be inserted into avector, specifically the one in which thegene maps of both fragment and vector have the same orientation.[13] Contrastu orientation.
A laboratory technique involving the use of a microscopic lance ornanopipette (typically about 100nanometres in diameter) in the presence of an electric field in order to deliver DNA or RNA directly into a cell, often azygote or earlyembryo, via anelectrophoretic mechanism. While submerged in a pH-buffered solution, a positive electric charge is applied to the lance, attracting negatively charged nucleic acids to its surface; the lance then penetrates the cell membrane and the electric field is reversed, applying a negative charge which repels the accumulated nucleic acids away from the lance and thus into the cell. Comparemicroinjection.
The inhibition or deactivation of some biological process caused by the presence of a specific molecular entity (e.g. arepressor), in the absence of which the process is not inhibited and thus can proceed normally.[5] Ingene regulation, for example, a repressor may bind to anoperator upstream from a coding sequence and prevent access bytranscription factors and/orRNA polymerase, thereby blocking the gene'stranscription. This is contrasted withpositive control, in which the presence of aninducer is necessary to switch on transcription.[9]
Another name for anicking enzyme, especially one that has been artificially engineered to create single-stranded breaks (i.e.nicks) by altering the cleavage activity of an endonuclease that normally creates double-stranded breaks, e.g.Cas9 nickase (nCas9).[15]
Anyamino acid, natural or artificial, that is not one of the 20 or 21proteinogenic amino acids encoded by thestandard genetic code. There are hundreds of such amino acids, many of which have biological functions and are specified by alternative codes or incorporated into proteins accidentally byerrors in translation. Many of the best known naturally occurring ncAAs occur as intermediates in the metabolic pathways leading to the standard amino acids, while others have been made synthetically in the laboratory.[16]
Any segment ofDNA that does notencode a sequence that may ultimately betranscribed andtranslated into aprotein. In most organisms, only a small fraction of the genome consists of protein-coding DNA, though the proportion varies greatly between species. Some non-coding DNA may still be transcribed into functionalnon-coding RNA (as withtransfer RNAs) or may serve important developmental orregulatory purposes; other regions (as with so-called "junk DNA") appear to have no known biological function.
Any molecule ofRNA that is not ultimatelytranslated into aprotein. TheDNA sequence from which a functional non-coding RNA istranscribed is often referred to as an "RNA gene". Numerous types of non-coding RNAs essential to normal genome function are produced constitutively, includingtransfer RNA (tRNA),ribosomal RNA (rRNA),microRNA (miRNA), andsmall interfering RNA (siRNA); other non-coding RNAs (sometimes described as "junk RNA") have no known function and are likely the product of spurious transcription.
A factor which can inhibit the effects of anonsense mutation (i.e. a premature stop codon) by any mechanism, usually either a mutatedtransfer RNA which can bind the mutated stop codon or some kind ofribosomal mutation.[17]
A type ofmutation in which thesubstitution of onenucleotide base for another results, aftertranscription andtranslation, in an amino acid sequence that is different from that produced by the original unmutated gene. Because nonsynonymous mutations always result in a biological change in the organism, they are often subject to strongselection pressure. Contrastsynonymous mutation.
The end of a linear chain ofamino acids (i.e. apeptide) that is terminated by the freeamine group (–NH 2) of the first amino acid added to the chain duringtranslation. This amino acid is said to beN-terminal. By convention, sequences, domains, active sites, or any other structure positioned nearer to the N-terminus of thepolypeptide or the foldedprotein it forms relative to others are described asupstream. ContrastC-terminus.
AnyDNA molecule contained within thenucleus of a eukaryotic cell, most prominently the DNA inchromosomes. It is sometimes used interchangeably withgenomic DNA.
A sub-cellular barrier consisting of two concentriclipid bilayermembranes that surrounds thenucleus ineukaryotic cells. The nuclear envelope is sometimes simply called the "nuclear membrane", though the structure is actually composed of two distinct membranes, aninner membrane and anouter membrane.
The principle that the nuclei of essentially alldifferentiated cells of a mature multicellular organism are genetically identical to each other and to the nucleus of thezygote from which they descended; i.e. they all contain the same genetic information on the same chromosomes, having been replicated from the original zygotic set with extremely high fidelity. Even though all adultsomatic cells have the same set of genes, cells can nonetheless differentiate into distinctcell types byexpressing different subsets of these genes. Though this principle generally holds true, the reality is slightly more complex, as mutations such asinsertions,deletions,duplications, andtranslocations as well aschimerism,mosaicism, and various types ofgenetic recombination can all cause different somatic lineages within the same organism to be genetically non-identical.
Anamino acid sequence within aprotein which serves as a molecular signal marking the protein fortransport into thenucleus, typically consisting of one or more short motifs containing positively charged amino acid residues exposed on the mature protein's surface (especiallylysines andarginines). Though all proteins aretranslated in the cytoplasm, many whose primary biological activities occur inside the nucleus (e.g.transcription factors) require nuclear localization signals identifiable bymolecular chaperones in order to cross thenuclear envelope. Contrastnuclear export signal.
A mesh-like latticework of protein polymers andmicrofilaments suspended in thenucleoplasm in thenuclei of eukaryotic cells, akin to thecytoskeleton in thecytoplasm. The nuclear matrix functions as a scaffold and an anchor for large DNA molecules such aschromosomes and for the macromolecular complexes that perform essential nuclear activities such astranscription andDNA replication.[3]
Acomplex ofmembrane proteins that creates an opening in thenuclear envelope through which certain molecules and ions arepermitted to pass and thereby enter or exit thenucleus (analogous to thechannel proteins in thecell membrane). The nuclear envelope typically has thousands of pores to selectively regulate the exchange of specific materials between thenucleoplasm and thecytoplasm, includingmessenger RNAs, which are transcribed in the nucleus but must be translated in the cytoplasm, as well asnuclear proteins, which are synthesized in the cytoplasm but must return to the nucleus to serve their functions.[4][3]
AnyRNA molecule located within a cell'snucleus, whether associated with chromosomes or existing freely in the nucleoplasm, includingsmall nuclear RNA (snRNA),enhancer RNA (eRNA), and all newly transcribedimmature RNAs,coding ornon-coding, prior to their export to the cytosol (hnRNA).
The mechanisms by which molecules cross thenuclear envelope surrounding a cell's nucleus. Though small molecules and ions can cross the membrane freely, the entry and exit of larger molecules is tightly regulated bynuclear pores, so that mostmacromolecules such as RNAs and proteins require association with transport factors in order to bechaperoned across.
Any of a class ofenzymes capable of cleavingphosphodiester bonds connecting adjacentnucleotides in a nucleic acid molecule (the opposite of aligase). Nucleases maynick onestrand orcut both strands of a duplex molecule, and may cleave randomly or at specific recognition sequences. They are ubiquitous and imperative for normal cellular function, and are also widely employed in laboratory techniques.
A long,polymericmacromolecule made up of smallermonomers callednucleotides which are chemically linked to one another in a chain. Two specific types of nucleic acid,DNA andRNA, are common to all living organisms, serving to encode the genetic information governing the construction, development, and ordinary processes of all biological systems. This information, contained within the order orsequence of the nucleotides, istranslated intoproteins, which direct all of the chemical reactions necessary for life.
The precise order of consecutively linkednucleotides in anucleic acid molecule such asDNA orRNA. Long sequences of nucleotides are the principal means by which biological systems store genetic information, and therefore the accuratereplication,transcription, andtranslation of such sequences is of the utmost importance, lest the information be lost or corrupted. Nucleic acid sequences may be equivalently referred to as sequences of nucleotides,nitrogenous bases,nucleobases, or, induplex molecules,base pairs, and they correspond directly to sequences ofcodons andamino acids.
Sometimes used interchangeably withnitrogenous base or simplybase.
Any of the five primary or canonicalnitrogenous bases –adenine (A),guanine (G),cytosine (C),thymine (T), anduracil (U) – that formnucleosides andnucleotides, the latter of which are the fundamental building blocks ofnucleic acids. The ability of these bases to formbase pairs viahydrogen bonding, as well as their flat, compact three-dimensional profiles, allows them to "stack" one upon another and leads directly to the long-chain structures ofDNA andRNA. When writing sequences in shorthand notation, the letterN is often used to represent a nucleotide containing a generic or unidentified nucleobase.
An irregularly shaped region which contains most or all of the genetic material in prokaryotic cells such as bacteria, but is not enclosed by anuclear membrane as in eukaryotes.
The basic structural subunit ofchromatin used inpackaging nuclear DNA such as chromosomes, consisting of acore particle of eighthistone proteins around whichdouble-stranded DNA is wrapped in a manner akin to thread wound around a spool. The technical definition of a nucleosome includes a segment of DNA about 146 base pairs in length which makes 1.67 left-handed turns as it coils around the histone core, as well as a stretch oflinker DNA (generally 38–80 bp) connecting it to an adjacent core particle, though the term is often used to refer to the core particle alone. Long series of nucleosomes are further condensed by association withhistone H1 into higher-order structures such as30-nm fibers and ultimatelysupercoiledchromatids. Because the histone–DNA interaction limits access to the DNA molecule by other proteins and RNAs, the precise positioning of nucleosomes along the DNA sequence plays a fundamental role in controlling whether or not genes aretranscribed andexpressed, and hence mechanisms for moving and ejecting nucleosomes have evolved as a means ofregulating the expression of particular loci.
nucleosome-depleted region (NDR)
A region of a genome or chromosome in which long segments of DNA are bound by few or nonucleosomes, and thus exposed to manipulation by other proteins and molecules, especially implying that the region istranscriptionally active.
Thenucleobases (blue) are the five specificnitrogenous bases canonically used in DNA and RNA. A nucleobase bonded to apentose sugar (eitherribose ordeoxyribose; yellow) is known as anucleoside (yellow + blue). A nucleoside bonded to a singlephosphate group (red) is known as a nucleoside monophosphate (NMP) or anucleotide (red + yellow + blue). When not incorporated into a nucleic acid chain, free nucleosides can bind multiple phosphate groups: two phosphates yields anucleoside diphosphate (NDP), and three yields anucleoside triphosphate (NTP).
A large spherical or lobularorganelle surrounded by adedicated membrane which functions as the main storage compartment for the genetic material of eukaryotic cells, including the DNA comprisingchromosomes, as well as the site of RNA synthesis duringtranscription. The vast majority of eukaryotic cells have a single nucleus, though some cells may havemore than one nucleus, either temporarily or permanently, and in some organisms there exist certain cell types (e.g. mammalianerythrocytes) which lose their nuclei upon reaching maturity, effectively becominganucleate. The nucleus is one of the defining features of eukaryotes; the cells of prokaryotes such as bacteria lack nuclei entirely.[2]
A suffix used to describe any of the diverse fields of study that conduct rigorous, systematic analyses of any of the "omes", e.g. thegenome,transcriptome,proteome,metabolome, etc.,[5] each of which represents the totality of a specific class of biological content that has been or could hypothetically be isolated from an individual cell, population of cells, organism, species, or some other particular context. Thusgenomics is the field of study which analyzes the totality of genes in a genome,proteomics studies the complete set of all of the proteins in a proteome, etc. The term may also be used to refer to all of these fields collectively.
Agene that has the potential to causecancer. Intumor cells, such genes are oftenmutated and/orexpressed at abnormally high levels.
one gene–one polypeptide
Alsoone gene–one protein orone gene–one enzyme.
The hypothesis that there exists a large class ofgenes in which each particular gene directs the synthesis of one particularpolypeptide orprotein.[13] Historically it was thought that all genes and proteins might follow this rule by definition, but it is now known that many proteins are composites of different polypeptides and therefore the product of multiple genes, and also that some genes do not encode polypeptides at all but instead producenon-coding RNAs, which are never translated.
A functional unit ofgene expression consisting of a cluster of neighboringstructural genes which are collectively under the control of a singlepromoter, along with one or more adjacentregulatory sequences such asoperators. The set of genes istranscribed together, resulting in a singlepolycistronicmessenger RNA molecule encoding multiple distinct polypeptides which may then betranslated together or undergosplicing to create multiple mRNAs which are translated independently; the result is that the genes contained in the operon are either expressed together or not at all. Regulatory proteins, includingrepressors andactivators, usually bind specifically to the regulatory sequences of a given operon; by some definitions, the genes that code for these regulatory proteins are also considered part of the operon.
Any substance, especially certain blood-serum proteins such asimmunoglobulins, that in binding to the surface of foreign cells or particulate matter increases the susceptibility of the foreign material tophagocytosis byphagocytes.[3] Opsonins work by linking foreign particles to specificreceptors on the surface of phagocytic cells in a process known asopsonization.[5]
A spatially distinct compartment or subunit within acell which has a specialized function. Organelles occur in both prokaryotic and eukaryotic cells. In the latter they are often separated from thecytoplasm by being enclosed with their ownmembranebilayer (whence the termmembrane-bound organelles), though organelles may also be functionally specific areas or structures without a surrounding membrane; some cellular structures which exist partially or entirely outside of the cell membrane, such ascilia andflagella, are also referred to as organelles. There are numerous types of organelles with a wide variety of functions, including the various compartments of theendomembrane system (e.g. thenuclear envelope,endoplasmic reticulum, andGolgi apparatus),mitochondria,chloroplasts,lysosomes,endosomes, andvacuoles, among others. Many organelles are unique to particular cell types or species.
A particular location within a DNA molecule at whichDNA replication is initiated. Origins are usually defined by the presence of a particular replicator sequence or by specific chromatin patterns.
Physiological dysfunction caused by a sudden change in the concentration of dissolved solutes in theextracellular environment surrounding a cell, which provokes the rapid movement of water across thecell membrane byosmosis, either into or out of the cell. In a severelyhypertonic environment, where extracellular solute concentrations are extremely high, osmotic pressure may force large quantities of water to move out of the cell (plasmolysis), leading to its desiccation; this may also have the effect of inhibiting transport of solutes into the cell, thus denying it the substrates necessary to sustain normal cellular activities. In a severelyhypotonic environment, where extracellular solute concentrations are much lower than intracellular concentrations, water is forced to move into the cell (turgescence), causing it to swell in size and potentially burst, or triggeringapoptosis.
An abnormally high level ofgene expression which results in an excessive number of copies of one or moregene products. Overexpression produces a pronounced gene-relatedphenotype.[19][20]
The process by which cells use chemical energy obtained by the oxidation of nutrients to power the production ofadenosine triphosphate (ATP). Oxidative phosphorylation couples two related processes: in theelectron transport chain, a series of enzyme-catalyzedredox reactions transfers electrons from energetic donors such asNADH andFADH through various intermediates and ultimately to a terminal electron acceptor such as molecular oxygen (O 2); the energy liberated by these reactions is simultaneously used inchemiosmosis to move protons (H+ ) across a membrane and against their concentration gradient, generating an electrochemical potential which powersATP synthase, an enzyme that catalyzes thephosphorylation ofADP into ATP. In eukaryotes, both of these processes are carried out by proteins embedded in the membranes ofmitochondria andchloroplasts; in prokaryotes, they occur in the cell membrane.
The flow ofoxygen from environmental sources (e.g. the air in the atmosphere) to themitochondria of a cell, where oxygen atoms participate in biochemical reactions that result in theoxidation of energy-rich substrates such ascarbohydrates in a process known asaerobic respiration.
AlsoTumor protein P53 (TP53),transformation-related protein 53 (TRP53), andcellular tumor antigen p53.
A class of regulatory proteins encoded by theTP53 gene in vertebrates whichbind DNA andregulate gene expression in order to protect the genome from mutation and block progression through thecell cycle if DNA damage does occur.[4] It is mutated in more than 50% of human cancers, indicating it plays a crucial role in preventing cancer formation.
Describing or relating to a class ofagonistsignaling molecules produced and secreted by regulatory cells into the extracellular environment and then transported by passive diffusion to target cells other than those which produced them. The term may refer to the molecules themselves, sometimes calledparamones, to the cells that produce them, or to signaling pathways which rely on them.[5] Compareautocrine,endocrine, andjuxtacrine.
Anidiotope, i.e. the specific site or region within anantibody that recognizes and binds to a particularantigen orepitope.[21] The uniqueness of a paratope allows it to bind to only one epitope with very high affinity. At the end of each arm of the Y-shaped antibody is an identical paratope, and each paratope comprises a total of sixcomplementarity-determining regions (three from each of thelight andheavy chains) which protrude from a series of antiparallelbeta sheets in the antibody's higher structure.[22] The term is also sometimes used to refer to the specific site on aligand molecule which defines the ligand's specificity for other molecules such ascell-surface receptors.[3]
parent cell
The original or ancestral cell from which a given set of descendant cells, known asdaughter cells, have divided bymitosis ormeiosis.
The movement of asolute across amembrane by traveling down an electrochemical or concentration gradient, using only the energy stored in the gradient and not any energy from external sources.[3] Contrastactive transport.
A phenomenon observed infacultatively anaerobic cells, including animal tissues and many microorganisms such asyeast, whereby the presence of oxygen in the environment inhibits the cell's use of ethanolfermentation pathways to generate energy, and drives the cell to instead make use of the available oxygen inaerobic respiration;[23] or more generally the observed decrease in the rate ofglycolysis or oflactate production in cells exposed to oxygenated air.[5]
Aglycoconjugate complex of interwoven peptides and polysaccharides that is a primary constituent of thecell wall in all bacteria and archaea, consisting of strands ofglycosaminoglycanscrosslinked by shortoligopeptides (usually 4–10 residues[3]) to form a rigid lattice of indefinite size.[5] The proportion of the cell wall that is peptidoglycan varies widely by strain and is often used to aid strain identification: the higher peptidoglycan content of the cell walls ofGram-positive bacteria causes them tostain a darker color thanGram-negative bacteria.
Any of a class ofmembrane proteins which attach only temporarily to thecell membrane, either by penetrating thelipid bilayer or by attaching toother proteins which are permanently embedded within the membrane.[24] The ability to reversibly interact with membranes makes peripheral membrane proteins important in many different roles, commonly as regulatorysubunits ofchannel proteins andcell surface receptors. Theirdomains often undergo rearrangement, dissociation, orconformational changes when they interact with the membrane, resulting in the activation of their biological activity.[25] Inprotein purification, peripheral membrane proteins are typically more water-soluble and much easier to isolate from the membrane thanintegral membrane proteins.
1. The tendency of amoving cell to continue moving in the same direction as previously; that is, even in isotropic environments, there inevitably still exists an inherent bias by which, from instant to instant, cells are more likely not to change direction than to change direction. Averaged over long periods of time, however, this bias is less obvious and cell movements are better described as arandom walk.[3]
2. The ability of some viruses to remain present and viable in cells, organisms, or populations for very long periods of time by any of a variety of strategies, including retroviral integration and immune suppression, often in a latent form which replicates very slowly or not at all.[3]
A shallow, transparent plastic or glass dish, usually circular and covered with a lid, which is widely used in biology laboratories to hold solid or liquidgrowth media for the purpose ofculturing cells. They are particularly useful foradherent cultures, where they provide a flat, sterile surface conducive to colony formation from which scientists can easily isolate and identify individual colonies.
Abacteriophage with a genome encoding a mobileplasmid that can beexcised by co-infection of the host cell with ahelper phage. Phagemids are useful as vectors for library production.[3]
Any cell capable ofphagocytosis, especially any of various cell types of the immune system which engulf and ingest harmful foreign molecules, bacteria, and dead or dying cells, includingneutrophils andmacrophages.[3]
The process by which foreign cells, molecules, and small particulate matter are engulfed and ingested viaendocytosis by specialized cells known asphagocytes (a class which includesmacrophages andneutrophils).[4]
A large, intracellular, membrane-boundvesicle formed as a result ofphagocytosis and containing whatever previously extracellular material was engulfed during that process.[4]
The complete set ofphenotypes that are or can be expressed by agenome, cell, tissue, organism, or species; the sum of all of its manifest chemical, morphological, and behavioral characteristics or traits.
phenomic lag
A delay in thephenotypicexpression of a geneticmutation owing to the time required for the manifestation of changes in the affected biochemical pathways.[9]
The composite of the observable morphological, physiological, and behavioraltraits of anorganism that result from theexpression of the organism'sgenotype as well as the influence of environmental factors and the interactions between the two.
A type ofphenotypic plasticity in which a cell rapidly undergoes major changes to its morphology and/or function, usually viaepigenetic modifications, allowing it to quickly switch back and forth between disparate phenotypes in response to changes in the local microenvironment.
Any chemical species or functional group derived fromphosphoric acid (H 3PO 4) by the removal of one or more protons (H+ ); the completely ionized form,[PO 4]3− , consists of a single, centralphosphorus atom covalently bonded to fouroxygen atoms via three single bonds and one double bond. Phosphates are abundant and ubiquitous in biological systems, where they occur either as free anions in solution, known asinorganic phosphates and symbolizedPi, or bonded to organic molecules viaester bonds. The huge diversity oforganophosphate compounds includes allnucleotides, whose phosphate groups are linked byphosphodiester bonds to form thestructural backbones oflong nucleotide chains such asDNA andRNA, and the high-energy diphosphate and triphosphate substituents of individual nucleotides such asADP andATP serve as essential energy carriers in all cells.Phospholipids are major components of mostmembranes. Enzymes known askinases andphosphatases catalyze theaddition andremoval of phosphate groups to and from these and other biomolecules.
The linear chain of alternatingphosphate and sugar compounds that results from the linking of consecutivenucleotides in the samestrand of anucleic acid molecule, and which serves as the structural framework of the nucleic acid. Each individual strand is held together by a repeating series ofphosphodiester bonds connecting eachphosphate group to theribose ordeoxyribose sugars of two adjacent nucleotides. These bonds are created byligases and broken bynucleases.
A defining element of nucleic acid structure is the linear chain of alternatingsugars (orange) andphosphates (yellow) known as thephosphate backbone, which acts as a scaffold to whichnucleobases are attached. The phosphorus atom of each phosphate group forms twoester bonds to specific carbon atoms within the pentose sugars—ribose in RNA anddeoxyribose in DNA—of two adjacent nucleosides.
A pair ofester bonds linking aphosphate molecule with the twopentose rings of consecutivenucleosides on the same strand of anucleic acid. Each phosphate forms a covalent bond with the3' carbon of one pentose and the5' carbon of the adjacent pentose; the repeated series of such bonds that holds together the long chain of nucleotides comprisingDNA andRNA molecules is known as thephosphate or phosphodiester backbone.
Any of a subclass oflipids consisting of a central alcohol (usuallyglycerol) covalently bonded to three functional groups: a negatively chargedphosphate group, and two longfatty acid chains. This arrangement results in a highlyamphipathic molecule which in aqueous solutions tends to aggregate with similar molecules in a lamellar or micellar conformation with thehydrophilic phosphate "heads" oriented outward, exposing them to the solution, and thehydrophobic fatty acid "tails" oriented inward, minimizing their interactions with water and other polar compounds. Phospholipids are the major structuralmembrane lipid in almost all biologicalmembranes except the membranes of some plant cells andchloroplasts, whereglycolipids dominate instead.[3]
A form ofendocytosis in which liquid and suspended solids from theextracellular environment are captured in inwardinvaginations of thecell membrane which then "bud off" into enclosedvesicles in thecytoplasm. The contents of these vesicles are then passed to organelles such asendosomes by fusion of the vesicular and organellar membranes. Pinocytosis is the predominant form of endocytosis occurring in most cells, such that the term is often used interchangeably with endocytosis as a whole.[5]
The number ofbase pairs contained within a single complete turn of theDNAdouble helix,[13] used as a measure of the "tightness" or density of the helix's spiral.
Any of a class ofmembrane-bound organelles found in the cells of some eukaryotes such as plants and algae which are hypothesized to have evolved fromendosymbioticcyanobacteria; examples includechloroplasts,chromoplasts, andleucoplasts. Plastids retain their owncircular chromosomes which replicate independently of the host cell's genome. Many contain photosynthetic pigments which allow them to performphotosynthesis, while others have been retained for their ability to synthesize unique chemical compounds.
1. Variability in the size, shape, orstaining of cells and/or their nuclei, particularly as observed inhistology andcytopathology, where morphological variation is frequentlyan indicator of a cellular abnormality such as disease ortumor formation.
2. Inmicrobiology, the ability of some microorganisms such as certain bacteria and viruses to alter their morphology, metabolism, or mode of reproduction in response to changes in their environment.
The tendency of cells within amonolayer to migrate in the direction of the local highest tension or maximal principal stress, exerting minimal shear stress on neighboring cells and thereby propagating the tension across many intercellular junctions and causing the cells to exhibit a sort of collective migration.[27]
The number of complete sets ofchromosomes in a cell, and hence the number of possiblealleles present within the cell at any givenautosomal locus.
A cell'sploidy level is defined by the number of copies it has of each specific chromosome: if the cell has two copies of each of three distinct chromosomes, it is said to bediploid (2N).
The addition of a series of multipleadenosineribonucleotides, known as apoly(A) tail, to the3'-end of aprimary RNA transcript, typically amessenger RNA. Primary transcripts are first cleaved 10–30 nucleotides downstream of a highly conservedAAUAAA sequence, then the poly(A) tail is generated from the chaining of multipleATP molecules through the action ofpolynucleotide adenylyltransferase.[5] A class ofpost-transcriptional modification, polyadenylation serves different purposes in different cell types and organisms. In eukaryotes, the addition of a poly(A) tail is an important step in the processing of a raw transcript into a mature mRNA, ready for export to the cytoplasm wheretranslation occurs; in many bacteria, polyadenylation has the opposite function, instead promoting the RNA's degradation.
Describing cells, proteins, or molecules descended or derived from more than oneclone (i.e. from more than one genome or genetic lineage) or made in response to more than one unique stimulus.Antibodies are often described as polyclonal if they have been produced or raised against multiple distinctantigens or multiple variants of the same antigen, such that they can recognize more than one uniqueepitope.[2] Contrastmonoclonal.
Amacromolecule composed of multiple repeatingsubunits ormonomers; a chain or aggregation of many individual molecules of the same compound or class of compound.[2] The formation of polymers is known aspolymerization and generally only occurs whennucleation sites are present and the concentration of monomers is sufficiently high.[3] Many of the major classes ofbiomolecules are polymers, includingnucleic acids andpolypeptides.
Any of a wide variety of molecular biology methods involving the rapid production of millions or billions of copies of a specificDNA sequence, allowing scientists to selectivelyamplify fragments of a very small sample to a quantity large enough to study in detail. In its simplest form, PCR generally involves the incubation of a target DNA sample of known or unknown sequence with a reaction mixture consisting ofoligonucleotideprimers, a heat-stableDNA polymerase, and freedeoxyribonucleotide triphosphates (dNTPs), all of which are supplied in excess. This mixture is then alternately heated and cooled to pre-determined temperatures for pre-determined lengths of time according to a specified pattern which is repeated for many cycles, typically in athermal cycler which automatically controls the required temperature variations. In each cycle, the most basic of which includes adenaturation phase,annealing phase, andelongation phase, the copies synthesized in the previous cycle are used astemplates for synthesis in the next cycle, causing achain reaction that results in the exponential growth of the total number of copies in the reaction mixture. Amplification by PCR has become a standard technique in virtually all molecular biology laboratories.
A diagram of the exponential amplification of a specific DNA sequence via thepolymerase chain reaction (PCR)
The formation of apolymer from its constituentmonomers; the chemical reaction or series of reactions by which monomericsubunits are covalently linked together into a polymeric chain or branching aggregate; e.g. the polymerization of anucleic acid chain by linking consecutivenucleotides, a reaction catalyzed by apolymerase enzyme.
polymorphism
1. In genetics, the regular and simultaneous existence of two or more discontinuousalleles or genotypes in the same population where the frequency of each allele is greater than can be explained by recurrent mutation alone, typically occurring in more than 1 percent of the population's individuals.[3] An example is the differenthuman blood types (A, B, AB, and O).[5]
2. In chemistry, the existence of the same substance in two or more different crystalline forms.[5]
(of a cell or organism) Having more than two homologous copies of eachchromosome; i.e. anyploidy level that is greater thandiploid. Polyploidy may occur as a normal condition of chromosomes in certain cells or even entire organisms, or it may result from errors incell division or mutations causing the duplication of the entire chromosome set.
The condition of a cell or organism having at least one more copy of a particularchromosome than is normal for itsploidy level, e.g. adiploid organism with three copies of a given chromosome is said to showtrisomy. Every polysomy is a type ofaneuploidy.
Any effect on theexpression or functionality of agene or sequence that is a consequence of its location or position within achromosome or other DNA molecule. A sequence's precise location relative to other sequences and structures tends to strongly influence its activity and other properties, because differentloci on the same molecule can have substantially differentgenetic backgrounds and physical/chemical environments, which may also change over time. For example, thetranscription of a gene located very close to anucleosome,centromere, ortelomere is oftenrepressed or entirely prevented because the proteins that make up these structures block access to the DNA bytranscription factors, while the same gene is transcribed at a much higher rate when located ineuchromatin. Proximity topromoters,enhancers, and otherregulatory elements, as well as to regions of frequenttransposition bymobile elements, can also directly affect expression; being located near the end of a chromosomal arm or to commoncrossover points may affect whenreplication occurs and the likelihood ofrecombination. Position effects are a major focus of research in the field ofepigenetic inheritance.
A strategy for identifying andcloning acandidate gene based on knowledge of itslocus or position alone and with little or no information about itsproducts or function, in contrast tofunctional cloning. This method usually begins by comparing the genomes of individuals expressing aphenotype of unknown provenance (often ahereditary disease) and identifyinggenetic markers shared between them. Regions defined by markers flanking one or moregenes of interest are cloned, and the genes located between the markers can then be identified by any of a variety of means, e.g. bysequencing the region and looking foropen reading frames, by comparing the sequence and expression patterns of the region inmutant andwild-type individuals, or by testing the ability of the putative gene torescue a mutant phenotype.[13]
The initiation, activation, or enhancement of some biological process by the presence of a specific molecular entity (e.g. anactivator orinducer), in the absence of which the process cannot proceed or is otherwise diminished.[5] Ingene regulation, for example, the binding of an activating molecule such as atranscription factor to apromoter may recruitRNA polymerase to a coding sequence, thereby causing it to betranscribed. Contrastnegative control.
A partially differentiated or intermediatestem cell with the ability to further differentiate into only onecell type; i.e. aunipotent stem cell that is the immediate parent cell from which fully differentiated cell types divide. The term "precursor cell" is sometimes used interchangeably withprogenitor cell, though this term may also be considered technically distinct.
A short,single-strandedoligonucleotide, typically 5–100 bases in length, which "primes" or initiates nucleic acid synthesis byhybridizing to a complementary sequence on atemplate strand and thereby providing an existing3'-end from which apolymerase canextend the new strand. Natural systems exclusively useRNA primers to initiateDNA replication and some forms of prokaryotictranscription, whereas thein vitro syntheses performed in many laboratory techniques such asPCR often useDNA primers. In modern laboratories, primers are carefully designed, often in "forward" and "reverse" pairs, to complement specific and unique sequences in target DNA molecules, with consideration given to theirmelting andannealing temperatures, and then purchased from commercial suppliers which create oligonucleotides on demand byde novo synthesis.
An inactive precursor of aprotein orpolypeptide that is converted into the active form by somepost-translational modification, such as by cleaving a specific peptide sequence from the precursor or by attaching other molecules to specific amino acid residues. The names of protein precursors are often prefixed withpro-, as inproinsulin. Enzyme precursors may be calledpro-enzymes or zymogens.
probe
Anyreagent used to make a single measurement in a biochemical assay such as a gene expression experiment. Molecules which have a specific affinity for one or more other molecules may be used to probe for the presence of those other molecules in samples of unknown composition. Probes are oftenlabelled or otherwise used asreporters to indicate whether or not a specific chemical reaction is taking place. See alsohybridization probe.
probe-set
A collection of two or moreprobes designed to measure a single molecular species, such as a collection ofoligonucleotides designed tohybridize to various parts of themRNA transcripts generated from a single gene.
An alternative definition of agene which emphasizes the contribution of non-DNA factors to the process by which the information encoded in aDNA sequence results in the synthesis of apolypeptide.
Any of a class ofenzymes which catalyzeproteolysis, i.e. the decomposition of proteins into smaller polypeptides or individual amino acids, by cleavingpeptide bonds viahydrolysis. Proteases are ubiquitous components of numerousbiological pathways, and therefore it is often necessary toinhibit them in order for laboratory techniques involving protein activity to be effective.
A largecomplex ofprotease enzymes that selectively degrades intracellular proteins which have beentagged for degradation byubiquitination. Proteasomes play important roles in the timing and onset of cellular processes through the signal-mediatedproteolysis of certain enzymes and regulatory proteins; they also contribute to the stress response by removing abnormal proteins and to the immune response by generatingantigenic peptides.[5]
Apolymericmacromolecule composed of one or morelong chains ofamino acids linked bypeptide bonds. Proteins are the three-dimensional structures created when these chainsfold into specific higher-order arrangements followingtranslation, and it is this folded structure which determines a protein's chemical activity and hence its biological function. Ubiquitous and fundamental in all living organisms, proteins are the primary means by which the activities of life are performed, participating in the vast majority of thebiochemical reactions that occur inside and outside of cells. They are often classified according to the type(s) of reaction(s) they facilitate or catalyze, by the chemical substrate(s) they act upon, or by their functional role in cellular activity; e.g. asstructural proteins,motor proteins,enzymes,transcription factors, or links withinbiochemical pathways.
An assembly or aggregate of multipleproteins held together by intermolecular forces, especially one with a particular biological function. Complexes may include many of the same protein or all different proteins. Numerous cellular activities, includingDNA replication,transcription, andtranslation, rely on protein complexes.[4]
The physical process by which the linear chains of amino acids (i.e.polypeptides) synthesized duringtranslation are changed from random coils into stable, orderly, three-dimensional shapes (i.e.proteins) by assuming a higher-order structure orconformation which permits the protein to be biologically functional, known as itsnative state. Folding is the consequence of amino acid residues participating in intermolecular electrostatic interactions with each other and with their surroundings, including other molecules, and so is strongly influenced by the particularities of the local chemical environment. The time it takes to properly fold a protein can vary greatly, but the process often begins while chain synthesis is still ongoing. Some chains may havemotifs ordomains whichlack intrinsic order and remain unfolded across a wide range of chemical conditions. Having the correct three-dimensional structure is essential for proper protein function, and misfolded proteins are generally biologically inactive, though mutant folds can occasionally modify functionality in useful ways.
Any of a class of enzymes whichphosphorylate proteins by catalyzing the transfer of aphosphate fromATP to an amino acid residue and often causing a functionally relevantconformational change as a result. The great majority of protein kinases phosphorylate the hydroxyl side chains of eitherserine,threonine, ortyrosine, though other types also exist.[3] Separate classes ofkinases phosphorylate non-protein molecules such as lipids and carbohydrates.
The set of biological mechanisms by whichproteins are directed and transported to appropriate destinations within or outside of the cell. Proteins must often be routed into the interior oforganelles, embeddedwithin a membrane, orsecreted into the extracellular environment in order to serve their functions, and information contained in the protein itself instructs this delivery process.[28] In eukaryotic cells, an expansive network of organelles andpathways is specialized to facilitate protein sorting, including theendoplasmic reticulum and theGolgi apparatus.
Agene containing acoding sequence which can be transcribed and translated to produce aprotein, as opposed to anRNA gene, which producesnon-coding RNA transcripts that are not translated into proteins but instead have functions in and of themselves.
Any of the 20 canonicalamino acids which are encoded by thestandard genetic code and incorporated intopeptides and ultimatelyproteins duringtranslation. The term may also be inclusive of an additional two amino acids encoded by non-standardcodes which can be incorporated by special translation mechanisms.
Any heavilyglycosylatedprotein, i.e. a core polypeptide with one or more covalently attachedglycosaminoglycan chains. Proteoglycans are therefore considered a subclass ofglycoproteins in which the carbohydrate units are long, linearpolysaccharide polymers containing amino sugars[29] and generally bearing a net negative charge under physiological conditions due to the presence of sulfates and uronic acid groups. They are a major component of theextracellular matrix between animal cells, where they form large hydrated complexes commonly employed in connective tissues such ascartilage.
The decomposition ofproteins into their componentpolypeptides or individualamino acids bycleaving thepeptide bonds linking the amino acids together viahydrolysis. Proteolysis is an important reaction used not only for degrading and inactivating proteins but sometimes also to activate them by removing amino acid residues which inhibit their activity.[3] It is usually catalyzed byenzymes known asproteases.
The entire set ofproteins that is or can beexpressed by a particulargenome, cell, tissue, or species at a particular time (such as during a single lifespan or during a specific developmental stage) or under particular conditions (such as when compromised by a certain disease).
The study of theproteome of a particular genome, cell, or organism, i.e. the sum total of all of theproteins produced from it bytranslation. Proteomics technologies allow scientists topurify and identify proteins andpolypeptides and determine which ones are most and least abundant at a given time or under a given experimental condition.
Any molecular subunit from which a largerpolymericmacromolecule is built, including those subunits which are not strictlymonomers and can themselves be divided into subunits. For example, aheterodimer of tubulin proteins is the protomer formicrotubule assembly.[3]
The biological contents enclosed within amembrane-bound space, variously referring to thecytoplasm, or the cytoplasm andnucleoplasm considered collectively, and sometimes exclusive ofvacuoles.
A plant, fungal, or bacterial cell which has had itscell wall removed by mechanical, chemical, or enzymatic means; or the complete contents (theprotoplasm) of an intact cell excluding the cell wall.
A double-ringedheterocyclic organic compound which, along withpyrimidine, is one of two molecules from which allnitrogenous bases (including thenucleobases used inDNA andRNA) are derived.Adenine (A) andguanine (G) are classified as purines. The letterR is sometimes used to indicate a generic purine; e.g. in a nucleotide sequence read,R may be used to indicate that either purine nucleobase,A orG, can be substituted at the indicated position.
putative gene
A specificnucleotide sequence suspected to be a functionalgene based on the identification of itsopen reading frame. The gene is said to be "putative" in the sense that no function has yet been described for itsproducts.
The irreversible condensation ofchromatin inside thenucleus as the cell undergoesnecrosis orapoptosis, resulting in a compact mass whichstains strongly and is conspicuous under a microscope.[13] It is followed bykaryorrhexis.
A single-ringedheterocyclic organic compound which, along withpurine, is one of two molecules from which allnitrogenous bases (including thenucleobases used inDNA andRNA) are derived.Cytosine (C),thymine (T), anduracil (U) are classified as pyrimidines. The letterY is sometimes used to indicate a generic pyrimidine; e.g. in a nucleotide sequence read,Y may be used to indicate that either pyrimidine nucleobase –C,T, orU – can be substituted at the indicated position.
Acell culture in which there is little or no active cell growth or replication but in which the cells nonetheless continue to survive, as observed with someconfluent cultures.[2]
A popular description of the path followed by alocomotive cell or particle when there is no bias in movement, i.e. when the direction of movement at any given instant is not influenced by the direction of movement in the preceding instant. The essential randomness of cell movement in a uniform environment is only apparent over long periods of time, however; in the short term, cells can and do exhibita tendency to continue moving in the same direction.[3]
A way of dividing thenucleotide sequence in aDNA orRNA molecule into a series of consecutive, non-overlapping groups of three nucleotides, known astriplets, which is how the sequence is interpreted or "read" byribosomes duringtranslation. Incoding DNA, each triplet is referred to as acodon and corresponds to a particularamino acid to be added to the nascent peptide chain during translation. In general, only one reading frame (the so-calledopen reading frame) in a given sequence encodes a functional protein, though there are exceptions. Aframeshift mutation results in a shift in the normal reading frame which affects all downstream codons and usually results in a completely different and senseless amino acid sequence.
The measurement and manipulation of the rate ofreannealing ofcomplementary strands ofDNA, generally by heating and denaturing adouble-stranded molecule intosingle strands and then observing their rehybridization at a cooler temperature. Because thebase pairG+C requires more energy to anneal than the base pairA+T, the rate of reannealing between two strands depends partly on theirnucleotide sequence, and it is therefore possible to predict or estimate the sequence of the duplex molecule by the time it takes to fully hybridize. Reassociation kinetics is studied withC0t analysis: fragments reannealing at low C0t values tend to have highlyrepetitive sequences, while higher C0t values imply more unique sequences.[13]
Aprotein which initiates a cellular response to an external stimulus orpropagates a molecular signal by binding a specificligand, often a dedicated signaling molecule. Numerous types of receptors exist which serve an enormous variety of functions.Cell-surface receptors, such as those that bindacetylcholine andinsulin, are embedded within thecell membrane with theirbinding sites exposed to the extracellular space;intracellular receptors, including manyhormone receptors, are located in the cytoplasm, where they bind ligands that have diffused across the membrane and into the cell.[4]
A type ofchromosomal translocation by which there is a reciprocal exchange of chromosome segments between two or more non-homologouschromosomes. When the exchange of material is evenly balanced, reciprocal translocations are usually harmless.
A specificmotif orsequence, either of nucleotides in a nucleic acid molecule or of amino acids in a protein, that is "recognized" or identified by another protein in order to direct the protein's activity to a specific molecule or location. Recognition motifs may consist of a simple consecutive sequence within a single molecule or may involve multiple non-consecutive motifs, e.g. amino acids in separate parts of the same polypeptide which are brought into juxtaposition by thequaternary structure created duringprotein folding. Recognition sites often help to distinguish the nucleic acid or protein bearing the motif from other similar molecules and thereby identify it as a valid target for some biochemical activity, or to specify a locus or subregion within the larger macromolecule at which the activity is to occur. In this sense recognition sites are critical for properly localizing proteins to their biochemical targets. A protein's recognition site is often but not necessarily the same as itsbinding site ortarget site.[5]
AnyDNA molecule in which laboratory methods ofgenetic recombination have brought together genetic material from multiple sources, thereby creating asequence that would not otherwise be found in a naturally occurring genome. Because DNA molecules from all organisms share the same basic chemical structure and properties, DNA sequences from any species, or even sequences createdde novo byartificial gene synthesis, may be incorporated into recombinant DNA molecules. Recombinant DNA technology is widely used ingenetic engineering.
The smallest unit of a DNA molecule capable of undergoinghomologous recombination, i.e. a pair of consecutive nucleotides, adjacent to each other incis.[13]
A group of non-contiguousgenes which areregulated as a unit, generally by virtue of having theirexpression controlled by the same regulatory element or set of elements, e.g. the samerepressor oractivator. The term is most commonly used with prokaryotes, where a regulon may consist of genes from multipleoperons.
Any pattern ofnucleobases within anucleic acid sequence which occurs in multiple copies in the same nucleic acid molecule such as a chromosome or within a genome. Repeated sequences are classified according to their length, structure, location, mode of replication, or evolutionary origin. They may be any length, but are often shortmotifs of less than 100 bases; they may bedirect orinverted, and may occur intandem arrays with the copies immediately adjacent to each other orinterspersed with non-repeated sequences. Significant fractions of most eukaryotic genomes consist ofrepetitive DNA, much of itretroviral in origin, though repeats may also result from errors in normal cellular processes, as withduplications duringDNA replication orcell division. Because so many genetic mechanisms depend on thebinding orcomplementing of locally unique sequences, sequences containing or adjacent to repeats are particularly prone to errors in replication and transcription bystrand slippage, or to forming problematicsecondary structures, and thus repeats are often unstable in the sense that the number of copies tends to expand or diminish stochastically with each round of replication, causing greatvariation in copy number even between different cells in the same organism. When repeats occur withingenes orregulatory elements, these properties often result in aberrant expression and lead to disease. Repeats are also essential for normal genome function in other contexts, as withtelomeres andcentromeres, which consist largely of repetitive sequences.
1. The process by which certain biological molecules, notably thenucleic acidsDNA andRNA, produce copies of themselves.
2. A technique used to estimate technical and biological variation in experiments forstatistical analysis ofmicroarray data. Replicates may betechnical replicates, such asdye swaps or repeated arrayhybridizations, orbiological replicates, biological samples from separate experiments which are used to test the effects of the same experimental treatment.
The eye-shaped structure that forms when a pair ofreplication forks, each growing away from theorigin, separates the strands of the double helix duringDNA replication.
The point at which the paired strands of adouble-stranded DNA molecule are separated byhelicase duringDNA replication, breaking the hydrogen bonds between the complementary strands and thereby forming a structure with two branching single strands of DNA. Once unpaired, these strands serve astemplates from whichDNA polymerase synthesizes theleading strand andlagging strand. As replication proceeds, helicase moves along the DNA and continues to separate the strands, causing the replication fork to move as well.[3] A pair of replication forks forms when helicases work in opposite directions from a singleorigin of replication, creating areplication eye.
replication rate
The speed at whichdeoxyribonucleotides are incorporated into an elongating chain byDNA polymerases duringDNA replication; or more generally the speed at which any chromosome, genome, cell, or organism makes a complete, independently functional copy of itself.
The entire complex of molecular machinery that carries out the process ofDNA replication, including all proteins, nucleic acids, and other molecules which participate at an activereplication fork.
Ingenetic engineering, a gene which when properly expressed encodes a gene product that is easily detected or visualized with biochemical assays (e.g.green fluorescent protein,β-galactosidase,chloramphenicol O-acetyltransferase, etc.), allowing researchers to use its expression in order to study the functions and properties of associatedregulatory sequences. Reporters are commonlycloned into plasmidvectors in proximity to putativepromoters,enhancers, orresponse elements, which are then mutated in order to precisely identify the specificrecognition motifs within these sequences that are necessary for expression. In the broadest sense, reporters may also include things like moleculartags, fluorescentlabels, andhybridization probes which render their conjugated molecules conspicuous or able to be purified; or they may be used similarly toselectable markers, to distinguish cells that express a given product from those that do not, so that researchers can easily identify mutants of interest or verify the success of an experimental treatment or laboratory procedure.[5]
The restoration of a defective cell or tissue to a healthy or normal condition,[13] or thereversion or recovery of a mutant gene to its normal functionality, especially in the context of experimental genetics, where an experiment (e.g. a drug,cross, or gene transfer) resulting in such a restoration is said torescue the normalphenotype.
Any short sequence of DNA that serves some function related to the activity of a protein or other biomolecule, especially a sequence within apromoter region that is able to bind specifictranscription factors in order toregulatetranscription of specific genes.
restitution
The spontaneous rejoining of an experimentally brokenchromosome which restores the original configuration.
restitution nucleus
Anucleus containing twice the expected number of chromosomes owing to an error in cell division, especially an unreduced,diploid product ofmeiosis resulting from the failure of the first or second meiotic division.
Anendonuclease orexonucleaseenzyme that recognizes and cleaves a nucleic acid molecule intofragments at or near specific recognition sequences known asrestriction sites by breaking thephosphodiester bonds of the nucleic acidbackbone. Restriction enzymes are naturally occurring in many organisms, but are also routinely used for artificial modification of DNA in laboratory techniques such asrestriction cloning.
Variability within a population of organisms observed in the size of therestriction fragments produced whengenomic DNA (or any particular DNA molecule) isdigested by one or morerestriction endonucleases. This variability results from a correspondingpolymorphism in the locations of restriction sites within the molecule(s) due to slight differences in nucleotide sequence between individuals. RFLP is frequently exploited in the laboratory to construct physicalmaps of the genome, to identify the specificlocus occupied by a particular gene, and to detect genetic differences between closely related individuals or determine that different samples originated from the same individual. Analysis of restriction fragments can also reveal the presence of a mutation that may itself cause disease or be closely linked to one that does.[5]
The use of type IIrestriction endonucleases to cleave DNA molecules at specificrestriction sites in order to produce characteristic patterns offragments which can be resolved by size usinggel electrophoresis.Digesting DNA molecules such asgenomic DNA orplasmids with one or multiple restriction enzymes makes it possible to deduce from the sizes of the resulting fragments the order or arrangement of the restriction sites within the molecule and the distances between them, and thus to construct reliablemaps with restriction sites effectively serving asgenetic markers.[5]
A short, specificsequence of nucleotides (typically 4 to 8 bases in length) that is reliably recognized by a particularrestriction enzyme. Because restriction enzymes usually bind ashomodimers, restriction sites are generallypalindromic sequences spanning both strands of adouble-stranded DNA molecule. Restrictionendonucleases cleave thephosphate backbone between two nucleotides within the recognized sequence itself, while other types of restriction enzymes make their cuts at one end of the sequence or at a nearby sequence.
A double-stranded DNA molecule containing the sequenceGAATTC and its palindromic complement functions as arestriction site for the bacterial enzymeEcoRI, which recognizes andcuts or "digests" it in the manner shown here, by breaking phosphodiester bonds in the backbones of both strands and leaving behindsingle-stranded overhangs at the ends of each of the now separate molecules.
Agene or other DNA sequence which has arisen in a genome by the stableintegration of the genetic material of aretrovirus, e.g. by thereverse transcription of viral RNA and the subsequentinsertion of the resulting DNA fragments into the host cell'sgenomic DNA.[5] Theseendogenous viral elements can then be replicated along with the host's own genes and thus persist indefinitely in the host genome, and in many cases retain the ability to produce functional viral proteins from this latent state, by which they may continue to copy,excise, and/ortranspose themselves.
An experimental approach inmolecular genetics in which a researcher starts with a knowngene and attempts to determine its function or its effect on phenotype by any of a variety of laboratory techniques, commonly by deliberately mutating the gene's DNA sequence or byrepressing orsilencing itsexpression and thenscreening the mutant organisms for changes in phenotype. When the gene of interest is the only one in the genome whose expression has been manipulated, any observed phenotypic changes are assumed to be influenced by it. This is the opposite offorward genetics, in which a known phenotype is linked to one or more unknown genes.
A polymericnucleic acid molecule composed of a series ofribonucleotides which incorporate a set of fournucleobases:adenine (A),guanine (G),cytosine (C), anduracil (U). UnlikeDNA, RNA is more often found as asingle strand folded onto itself, rather than a paired double strand. Various types of RNA molecules serve in a wide variety of essential biological roles, includingcoding,decoding,regulating, andexpressinggenes, as well as functioning as signaling molecules and, in certainviral genomes, as the primary genetic material itself.
Amonosaccharide sugar which, as D-ribose in itspentose ring form, is one of three primary components of theribonucleotides from whichribonucleic acid (RNA) molecules are built. Ribose differs from its structural analogdeoxyribose only at the 2' carbon, where ribose has an attachedhydroxyl group that deoxyribose lacks.
A DNA sequence that codes forribosomal RNA (rRNA). In many eukaryotic genomes, rDNA occupies large, highly conserved regions of multiple chromosomes and is rich in bothgenes andrepeats.
A type ofnon-coding RNA which is the primary constituent ofribosomes, binding to ribosomal proteins to form thesmall andlarge subunits. It is ribosomal RNA which enables ribosomes to perform protein synthesis by working as aribozyme that catalyzes the set of reactions comprisingtranslation. Ribosomal RNA is transcribed from the correspondingribosomal DNA (rDNA) and is the most abundant class of RNA in most cells, bearing responsibility for the translation of all encoded proteins despite never being translated itself.
A macromolecular complex made of both RNA and protein which serves as the site of protein synthesis bytranslation. Ribosomes have twosubunits, each of which consists of one or more strands ofribosomal RNA bound to variousribosomal proteins: thesmall subunit, which reads the messages encoded inmessenger RNA molecules, and thelarge subunit, which linksamino acids in sequence to form apolypeptide chain. Ribosomes are essential and ubiquitous in all cell types and are used by all known forms of life.
AnRNA molecule with enzymatic activity,[4] i.e. one that is capable of catalyzing one or more specific biochemical reactions, similar toproteinenzymes. Ribozymes function in numerous capacities, including inribosomes as part of thelarge subunitribosomal RNA.
Any of a class ofpolymeraseenzymes that synthesizeRNA molecules from aDNA template. RNA polymerases are essential fortranscription and are found in all living organisms and many viruses. They build long single-stranded polymers calledtranscripts by addingribonucleotides one at a time in the5'-to-3' direction, relying on thetemplate provided by thecomplementary strand to transcribe the nucleotide sequence faithfully. UnlikeDNA polymerases, RNA polymerases notably do not require oligonucleotideprimers to initiate synthesis; i.e. they are capable of synthesizing RNA moleculesde novo.
Aribonucleoprotein complex which works tosilence endogenous and exogenous genes by participating in variousRNA interference pathways at the transcriptional and translational levels. RISC can bind bothsingle-stranded anddouble-stranded RNA fragments and then cleave them or use them as guides to target complementary mRNAs for degradation.
A type ofchromosomal translocation by whichdouble-strand breaks at or near thecentromeres of twoacrocentricchromosomes cause a reciprocal exchange of segments that gives rise to one largemetacentric chromosome (composed of thelong arms) and one extremely small chromosome (composed of theshort arms), the latter of which is often subsequently lost from the cell with little effect because it contains very few genes. The resultingkaryotype shows one fewer than the expected total number of chromosomes, because two previously distinct chromosomes have essentially fused together.Carriers of Robertsonian translocations are generally not associated with any phenotypic abnormalities, but do have an increased risk of generating meiotically unbalancedgametes.
A type of membrane in theendoplasmic reticulum with numerousribosomes conspicuously attached to its surface, in contrast to the"smooth" endoplasmic reticulum which lacks ribosomes. The rough ER serves as the site of protein synthesis for the majority of the cell's secreted and transmembrane proteins, as well as the site of synthesis of membrane lipids. It may be continuous with the smooth ER or exist separately.[3]
A method ofDNA sequencing based on thein vitroreplication of a DNAtemplate sequence, during whichfluorochrome-labeled, chain-terminatingdideoxynucleotides are randomly incorporated in the elongating strand; the resulting fragments are then sorted by size withelectrophoresis, and the particular fluorochrome terminating each of the size-sorted fragments is detected by laser chromatography, thus revealing thesequence of the original DNA template through the order of the fluorochrome labels as one reads from small-sized fragments to large-sized fragments. Though Sanger sequencing has been replaced in some contexts bynext-generation methods, it remains widely used for its ability to produce relatively long sequence reads (500+nucleotides) and its very low error rate.
Anin vitro nucleic acidhybridization reaction in which one polynucleotide component (eitherDNA orRNA) is supplied in great excess relative to the other, causing all complementary sequences in the other polynucleotide to pair with the excess sequences and form hybridduplex molecules.[13]
Agene or other genetic material whoseexpression in cultured cells confers a selective advantage in the culture environment, causing cells expressing the gene to have one or more traits suitable forartificial selection. Selectable markers are widely used in the laboratory as a type ofreporter, usually to indicate the success of a procedure meant to introduce exogenous DNA into a host cell such astransfection ortransformation. A common example is anantibiotic resistance gene which is transformed into competent bacterial cells cultured on a medium containing the particular antibiotic, such that only those cells which have successfully taken up and expressed the gene are able to survive and grow into colonies.
Any genetic material (e.g. agene or any other DNA sequence) which can enhance its ownreplication and/or transmission into subsequent generations at the expense of other genes in the genome, even if doing so has no positive effect or even a net negative effect on thefitness of the genome as a whole. Selfish elements usually work by producing self-actinggene products which repeatedlycopy and paste their owncoding sequences into other parts of the genome, independently of normalDNA replication (as withtransposable elements); by facilitating the uneven swapping of chromosome segments duringgenetic recombination events (as withunequal crossing over); or by disrupting the normally equal redistribution of replicated material duringmitosis ormeiosis such that the probability that the selfish element is present in a givendaughter cell is greater than the normal 50 percent (as withgene drives).
The standard mode ofDNA replication that occurs in all living cells, in which each of the two parentalstrands of the originaldouble-stranded DNA molecule are used astemplate strands, withDNA polymerases replicating each strand separately and simultaneously inantiparallel directions. The result is that each of the two double-stranded daughter molecules is composed of one of the original parental strands and one newly synthesized complementary strand, such that each daughter molecule conserves the precise sequence of information (indeed the very same atoms) from one-half of the original molecule. Contrastconservative replication anddispersive replication.
Three different modes ofDNA replication. Insemiconservative replication, each of the two daughter molecules is built from one of the original parental strands and one newly synthesized strand. Inconservative replication, the original parent molecule remains intact while the replicated molecule is composed of two newly synthesized strands. Indispersive replication, each of the daughter molecules is an uneven mix of old and new, with some segments consisting of the two parental strands and others consisting of two newly synthesized strands. Only semiconservative replication occurs naturally.
A distinction made between the individualstrands of adouble-stranded DNA molecule in order to easily and specifically identify each strand. The twocomplementary strands are distinguished assense andantisense or, equivalently, thecoding strand and thetemplate strand. It is the antisense/template strand which is actually used as the template fortranscription; the sense/coding strand merely resembles the sequence ofcodons on the RNA transcript, which makes it possible to determine from the DNA sequence alone the expected amino acid sequence of any proteintranslated from the RNA transcript. Which strand is which is relative only to a particular RNA transcript and not to the entire DNA molecule; that is, either strand can function as the sense/coding or antisense/template strand.
Anycodon that specifies anamino acid, as opposed to astop codon, which does not specify any particular amino acid but instead signals the end of translation.
Asequence logo depicts the statistical frequency with which each nucleobase (or amino acid) occurs within a givensequence. Each position in the sequence is represented by a vertical stack of letters; the total height of the stack indicates the degree ofconsensus at that position between all of the aligned sequences, and the height of each individual letter in the stack indicates the proportion of the aligned sequences having that nucleobase at that position. A single very large letter filling most of the stack indicates that most or all of the aligned sequences have that particular nucleobase at that position.
The determination of the order orsequence ofnucleotides in anucleic acid molecule, or ofamino acids in apeptide, by any means. Sequences are usually written as a linear string of letters which conveniently summarizes much of the atomic-level structure of the molecule.
The presence of a particulargene or DNA sequence on asex chromosome (in mammals either theX chromosome or theY chromosome) rather than on anautosome; these genes are said to besex-linked. Expression of sex-linked genes varies by organism depending on the mechanism ofsex determination and the types of sex chromosomes present, but the associatedphenotypes often exclusively appear in either the homogametic or heterogametic sex.[2]
In condensedchromosomes where the positioning of thecentromere creates two segments or "arms" of unequal length, the shorter of the two arms of achromatid. Contrastlong arm.
Any sequence ofamino acids, usually 15–30 residues in length, that functions as a molecular signal directing thesorting and transport of thepolypeptide bearing it to aspecific location within a cell or organelle. Signal peptides are commonly located close to either theN-terminal orC-terminal ends ofnascent or recently synthesized polypeptides, especially those destined for secretion from the cell or integration into a membrane, and are typically cleaved off by a dedicatedsignal peptidase when their polypeptide reaches theendoplasmic reticulum.[5] Similar but distinct varieties of protein targeting are accomplished withnuclear localization signals andpost-translationalprotein tags.
The process by which a chemical, electrical, or mechanical signal is converted into a cellular response, or the transmission or propagation of such a signal through a cell as a series of molecular events known as asignaling pathway. For example, the extracellular interaction of ahormone, growth factor, or some other chemical agonist with a specificcell surface receptor can trigger acascade of sequential biochemical reactions which propagate through the cell membrane and into the cytoplasm, provoking the synthesis ofsecond messengers and leading to amplification of the signal or activation of other pathways. Other modes of transduction involve agonists which diffuse across the membrane freely, eliciting intracellular changes without amplification, or rapid shifts incell polarity which transmit electrical impulses, such as those that cause the axons of neural cells to releaseneurotransmitters at synapses.[5]
The total or near-total loss ofexpression of a particulargene or DNA sequence by any mechanism, natural or artificial, whether before, during, or aftertranscription ortranslation, which completely prevents the normalgene product from being produced and thereby deprives the cell of its ordinary function. Gene silencing may occur via naturalregulatory mechanisms such as condensation of the relevant segment of DNA into a transcriptionally inactive,heterochromatic state, in which case the term is more or less equivalent torepression; genes are also commonly silenced artificially for research purposes by using techniques such asknockdown (e.g. byRNA interference) orknockout (bydeleting the gene from the genome entirely). See alsodownregulation.
A type ofneutral mutation which does not have an observable effect on the organism'sphenotype. Though the term "silent mutation" is often used interchangeably withsynonymous mutation, synonymous mutations are not always silent, nor vice versa.Missense mutations which result in a differentamino acid but one with similar functionality (e.g.leucine instead ofisoleucine) are also often classified as silent, since such mutations usually do not significantly affect protein function.
Anysubstitution of a singlenucleotide which occurs at a specific position within agenome and with measurable frequency within a population; for example, at a specific base position in a DNA sequence, the majority of the individuals in a population may have acytosine (C), while in a minority of individuals, the same position may be occupied by anadenine (A). SNPs are usually defined with respect to a "standard" reference genome; an individual human genome differs from the reference human genome at an average of 4 to 5 million positions, most of which consist of SNPs and shortindels. See alsopolymorphism.
AnyDNA molecule that consists of a single nucleotide polymer orstrand, as opposed to a pair of complementary strands held together by hydrogen bonds (double-stranded DNA). In most circumstances, DNA is more stable and more common in double-stranded form, but high temperatures, low concentrations of dissolved salts, and very high or low pH can cause double-stranded molecules to decompose into two single-stranded molecules in adenaturation process known asmelting; this reaction is exploited by naturally occurring enzymes such as those involved inDNA replication as well as by laboratory techniques such aspolymerase chain reaction.
A pair of identical copies (chromatids) produced as the result of theDNA replication of achromosome, particularly when both copies are joined together by a commoncentromere; the pair of sister chromatids is called adyad. The two sister chromatids are ultimately separated from each other into two different cells duringmitosis ormeiosis.
A class of smallRNA molecules engineered so as to change conformation conditionally in response to cognate molecular inputs, often with the goal of controllingsignal transduction pathwaysin vitro orin vivo.
A class of smallnon-coding RNA molecules, approximately 100–300 nucleotides in length and rich inuridine residues, found in association with specific proteins as part ofribonucleoprotein complexes known assnRNPs withinnuclear speckles andCajal bodies of the eukaryotic nucleus.[5] SnRNPs assemble into larger complexes known asspliceosomes which play important roles in thesplicing ofpre-mRNA transcripts (hnRNAs) before they are exported to the cytoplasm.
A subclass ofmicroRNAs, originally described innematodes, which regulate the timing of developmental events by binding to complementary sequences in the3' untranslated regions ofmessenger RNAs and inhibiting theirtranslation. In contrast tosiRNAs, which serve similar purposes, stRNAs bind to their target mRNAs after the initiation of translation and without affecting mRNA stability, which makes it possible for the target mRNAs to resume translation at a later time.
A type of membrane in theendoplasmic reticulum that lacksribosomes on its surface, thus visibly contrasting with the"rough" endoplasmic reticulum. Smooth ER tends to be tubular rather than sheet-like, and may form an extension of the rough ER or exist separately. It is especially abundant in cells concerned withlipid metabolism.[3]
Any biologicalcell forming the body of an organism, or, in multicellular organisms, any cell other than agamete,germ cell, or undifferentiatedstem cell. Somatic cells are theoretically distinct from cells of thegerm line, meaning themutations they have undergone can never be transmitted to the organism's descendants, though in practice exceptions do exist.
The application ofsound energy atultrasonic frequencies in order to agitate particles in a chemical or biological sample. Intense acoustic vibrations produce pressure waves and cavitations that propagate through a liquid medium, thereby converting the sound energy to mechanical energy which can disperse solutes, disrupt intermolecular interactions, and break covalent bonds. At various amplitudes sonication can be used to increase the permeability of cell or nuclearmembranes, a technique known assonoporation, or tocompletely destroy them and release their contents for isolation and extraction. It has a wide variety of applications in industry and research, including creatingnanoparticles such asliposomes, shearing DNA and proteins into smaller fragments,degassing liquids, andultrasonic cleaning.
Theexpression of one or more genes only within a specific anatomical region or tissue, often in response to aparacrine signal. The boundary between the jurisdictions of two spatially restricted genes may generate a sharpphenotypic gradient there, as with striping patterns.
Thecytoskeletal structure that forms duringcell division in eukaryotic cells, consisting of a network of long, flexiblemicrotubules extending from each pole of theparent cell and attaching tokinetochores at the centromeres ofhomologous chromosomes orsister chromatids near the cell equator. As the microtubules shorten, they pull the chromosomes apart, separating them into differentdaughter cells. Proper formation of this apparatus is critical in bothmitosis andmeiosis, where it is respectively referred to as themitotic spindle andmeiotic spindle.
Any natural or artificial process involving theexcision of oligonucleotide sequences from nucleic acid molecules (either DNA or RNA) or of peptide sequences from proteins and the subsequentre-ligation of the flanking fragments into a single continuous molecule lacking the excised sequence.RNA splicing in particular is an important form ofpost-transcriptional processing wherebyintrons are removed fromprimary mRNA transcripts and theexons rejoined (and sometimesrearranged) to create mature mRNAs; asimilar process also occurs with the removal ofinteins and the rejoining ofexteins in thepost-translational modification of certain proteins. The term may also refer more generally to artificial techniques for creatingrecombinant sequences ingenetic engineering.[5]
Thegenetic code used by the vast majority of living organisms fortranslatingnucleic acid sequences intoproteins. In this system, of the 64 possible permutations ofthree-letter codons that can be made from the fournucleotides, 61 code for one of the 20amino acids, and the remaining three code forstop signals. For example, the codonCAG codes for the amino acidglutamine and the codonUAA is a stop codon. The standard genetic code is described asdegenerate or redundant because some amino acids can be coded for by more than one different codon.
Thestandard genetic code specifies a set of 20 differentamino acids from triplet arrangements of the four differentRNAnucleobases (A,G,C, andU). To read this chart, choose one of the four letters in the innermost ring and then move outward, adding two more letters to complete acodon triplet: a total of 64 unique codons can be made this way, 61 of which signal the addition of one of the 20 amino acids (identified by single-letter abbreviation as well as by full name and chemical structure) to a nascentpeptide chain, while the remaining three codons arestop codons signalling the termination of translation. Also indicated are some of the chemical properties of the amino acids and the various ways in which they can be modified.
Any biological cell which has not yetdifferentiated into a specialized cell type and which can divide throughmitosis to produce more undifferentiated stem cells.
A term used to describe the end of adouble-stranded DNA molecule where onestrand is longer than the other by one or morenucleobases, creating a single-stranded "overhang" of unpaired bases, in contrast to a so-calledblunt end, where no such overhang exists because the terminal nucleobases on each strand arebase-paired with each other. Blunt ends and sticky ends are relevant whenligating linear DNA molecules, e.g. inrestriction cloning, because manyrestriction enzymes cleave the phosphate backbone in a way that leaves behind terminal overhangs in the digested fragments. These sticky-ended molecules ligate much more readily with other sticky-ended molecules havingcomplementary overhangs, allowing scientists to ensure that specific DNA fragments are ligated together in specific places.
Acodon that signals the termination of protein synthesis duringtranslation of amessenger RNA transcript. In thestandard genetic code, three different stop codons are used to dissociateribosomes from the growing amino acid chain, thereby ending translation:UAG (nicknamed "amber"),UAA ("ochre"), andUGA ("opal"). Contraststart codon.
The effect of conditions such as temperature and pH upon the degree ofcomplementarity that is required for ahybridization reaction to occur between two single-stranded nucleic acid molecules. In the most stringent conditions, only exact complements can successfully hybridize; as stringency decreases, an increasing number ofmismatches can be tolerated between the two hybridizing strands.[18]
Anyprotein which contributes to the mechanical shape and structure ofcells,organelles, ortissues (e.g.collagen andactin), as distinguished from proteins which serve some other purpose, such asenzymes. This distinction is not well-defined, however, as many proteins have both structural and non-structural roles.[2]
1. The subdivision of the interior of a cell into functionally distinct spaces orcompartments (e.g.membrane-bound organelles) and the delegation of particular cellular functions and activities to these particular spaces.
2. The determination by any of various laboratory methods (e.g. fluorescentlabelling) of the precise location(s) within a cell where a specific molecule has occupancy, or at which a specific activity occurs.
(of a linearchromosome or chromosome fragment) Having acentromere positioned close to but not exactly in the middle of the chromosome, resulting inchromatid arms of slightly different lengths.[6] Comparemetacentric.
1. A chemical compound or molecule upon which a particularenzyme directly acts, often but not necessarily binding the molecule by forming one or more chemical bonds.[2] See alsoligand.
2. The substance, biotic or abiotic, upon which an organism grows or lives, or by which it is supported; e.g. a particulargrowth medium used incell culture. See alsosubstratum.
substratum
A solid surface to which a cell or organism adheres or by which it is supported, or over which it moves.[3] See alsosubstrate.
subunit
A single unit of a multi-unit compound or molecular aggregate; e.g. amonomer from which a largerpolymer is composed (as withnucleotides innucleic acids), or an individualpolypeptide chain in a multi-chainprotein, or an entire protein which participates alongside other proteins as part of aprotein complex.[2][4]
A type ofpost-translational modification in which aSUMO protein is conjugated to a polar residue of another protein (usually alysine) via a covalentisopeptide bond. This effectivelytags the second protein, making it distinguishable to other biomolecules and in many cases allowing it to participate in specific reactions or to interact with specificprotein complexes. SUMOlyation is closely related toubiquitination, relying on the sameE1/E2/E3 enzymes to transfer SUMO to specific recognition motifs in the target protein, though detaching SUMO depends on SUMO-specificproteases. It plays important roles in numerous cellular processes, includingprotein localization, transcriptional regulation, stress-response pathways, andcell cycle checkpoints, among others. SUMOlyation is also used in the laboratory as a molecularlabel and to help solubilize proteins which are difficult topurify.
A type ofcell culture in which individualcells or aggregates of cells are suspended in a liquidgrowth medium, and usually prevented from settling by continuous gentle agitation. Many prokaryotic and eukaryotic cell types readily proliferate in suspension cultures, but they are particularly useful for culturing non-adherent cell lines such ashematopoietic cells, plant cells, and insect cells. Compareadherent culture.
Any of a class oftransmembranetransporter proteins which facilitate the transport of two or more different molecules across the membrane at the same time and in the same direction; e.g. glucose and sodium ions. Contrastantiporter anduniporter.
Amultinucleate cell, i.e. a cell containing more than onenucleus or, in the broadest sense, more than onenuclear genome (a meaning which is equated withpolyploidy). Syncytia may form as a result ofcell fusion between uninucleate cells, migration of a nucleus from one cell to another, or multiple nuclear divisions without accompanyingcytokinesis (forming acoenocyte).[9] The term may also refer to cells which are interconnected by specialized membranes withgap junctions as in some neuromuscular cell types.
A type ofmutation in which thesubstitution of onenucleotide base for another results, aftertranscription andtranslation, in an amino acid sequence which is identical to the original unmutated sequence. This is possible because of thedegeneracy of thegenetic code, which allows differentcodons to code for the same amino acid. Though synonymous mutations are often consideredsilent, this is not always the case; a synonymous mutation may affect the efficiency or accuracy oftranscription,splicing,translation, or any other process by which genes areexpressed, and thus become effectively non-silent. Contrastnonsynonymous mutation.
A pattern within anucleic acid sequence in which one or morenucleobases are repeated and the repetitions are directly adjacent (i.e. tandem) to each other. An example isATGACATGACATGAC, in which the sequenceATGAC is repeated three times.
target site
The site or locus upon another molecule at which a protein performs a particular biochemical activity; e.g. the nucleotidemotif at which arestriction endonuclease cleaves a DNA molecule, often but not necessarily the same as the enzyme'srecognition site (i.e. a restriction enzyme may recognize one motif, known as arestriction site, and cleave at another).[5]
A directional response by a cell or a population of cells to a specific stimulus; a movement or other activity occurring in a non-random direction and dependent on the direction from which the stimulus originated.[3] This contrasts withkinesis, a response without directional bias.
The transmission of three‐dimensional structural stability from a stable part of a macromolecule to a distal part of the same molecule, especially an inherently less stable part.[5] Instability may also be transmitted in this way, e.g. destabilization of the DNAdouble helix may occur at alocus that is relatively distant from thebinding site of aDNA-binding protein.[13]
(of a linearchromosome or chromosome fragment) Having acentromere positioned at the terminal end of the chromosome (near or within thetelomere), resulting in only a single arm.[6] Compareacrocentric.
A region ofrepetitivenucleotide sequences at each end of a linearchromosome which protects the end of the chromosome from deterioration and from fusion with other chromosomes. Since each round ofreplication results in the shortening of the chromosome, telomeres act as disposable buffers which are sacrificed to perpetual truncation instead of nearby genes; telomeres can also be lengthened by the enzymetelomerase.
A DNAsequence or its RNAcomplement which signals the termination oftranscription by triggering processes that ultimately arrest the activity ofRNA polymerase or otherwise cause the release of the RNAtranscript from the transcriptional complex. Terminator sequences are usually found near the3'-ends of thecoding sequences ofgenes oroperons. They generally function after being themselves transcribed into the nascent RNA strand, whereupon the part of the strand containing the sequence either directly interacts with the transcriptional complex or forms asecondary structure such as ahairpin loop which signals the recruitment of enzymes that promote its disassembly.[13]
One of the four standardnucleosides used inDNA molecules, consisting of athyminebase with its N9 nitrogenbonded to the C1 carbon of adeoxyribose sugar. The prefixdeoxy- is commonly omitted, since there are no ribonucleoside analogs of thymidine used in RNA, where it is replaced withuridine instead.
Apyrimidinenucleobase used as one of the four standard nucleobases inDNA molecules. Thymine forms abase pair withadenine. InRNA, thymine is not used at all, and is instead replaced withuracil.
A type of specialized intercellular junction characterized by very close contact between the plasma membranes of adjacent cells, which are held together by largemultiprotein complexes that completely or nearly completely occlude the passage of water and solutes through theintercellular space between cells. Tight junctions occur in many vertebrate tissues, especially between theepithelial andendothelial cells that line the surfaces of most organs and vessels. These cells are completely encircled by tight junctions which create a gasket-like seal that separates each cell's plasma membrane into apical and basolateral domains and prevents the exchange of extracellular materials between them.[5][3]
In a multicellular organism, a contiguous aggregation ofcells held together by a commonextracellular matrix and specialized to perform a particular function. Some tissues are composed primarily of a single cell type; others are a heterogeneous mixture of many cell types.[2] Tissues represent a level of multicellular organization between that of individual cells and that oforgans, which may be composed of one or more distinct types of tissue.[3]
The growth and maintenance, or "culturing", of multicellulartissues, or of cells harvested from tissues, under carefully controlled conditionsin vitro, in the strictest sense by taking a piece of explanted tissue directly from a living plant or animal and maintaining it outside of the body of the source organism. In common usage, the term may also refer tocell culture in general, especially when growing certain cell types which have been harvested from tissues but dispersed from their original tissue-specific organization into a population of more or less independently growing cells.[3]
tissue-specific gene expression
Gene function andexpression which is restricted to a particulartissue or cell type. Tissue-specific expression is usually the result of anenhancer which is activated only in the proper cell type.
A measure of the effectiveosmotic pressure gradient of one solution relative to another solution, used especially to describe thewater potential that exists between two aqueous solutions separated by a semipermeable membrane (as with acell, where the intracellularcytosol is separated from theextracellular fluid by theplasma membrane). Tonicity depends on the relative concentrations of solutes on either side of the membrane, which determine the direction and extent to which solvent molecules move across the membrane byosmosis; it is affected only by those solutes which cannot cross the membrane, as those which can cross freely can achieve equilibrium without any net movement of solute. The extracellular environment is commonly described ashypotonic,hypertonic, orisotonic with respect to the intracellular environment.
Tonicity describes the pressure to restoreosmotic equilibrium between the inside and outside of cells by moving water across the cell membrane. Red blood cells tend to lose water and shrivel up in a severelyhypertonic environment (left) or gain water and swell to bursting in a severelyhypotonic environment (right), but the water potential is balanced in anisotonic environment (center).
Any of a class ofDNA-binding enzymes which catalyze changes in the topological state of adouble-stranded DNA molecule bynicking orcutting thesugar-phosphate backbone of one or both strands, relaxing the torsional stress inherent in thedouble helix and unwinding or untangling the paired strands beforere-ligating the nicks. This process is usually necessary prior toreplication andtranscription. Topoisomerases thereby convert DNA between itsrelaxed andsupercoiled,linked and unlinked, andknotted and unknotted forms without changing the sequence or overall chemical composition, such that the substrate and product molecules are structural isomers, differing only in their shape and theirtwisting,linking, and/orwrithing numbers.
A state ofcell potency in which a cell or nucleus fully retains the ability todifferentiate into all of thecell types represented in the adult organism, or to give rise to all of these cell types upontransplantation into an appropriate cytoplasm (as innuclear transfer). Such cells or nuclei are said to betotipotent. Thezygote that serves as the progenitor cell for sexually reproducing multicellular organisms is the archetypal totipotent cell; almost all of the cells into which it ultimately differentiates are not totipotent, though some cells such asstem cells remain totipotent orpluripotent throughout the organism's life.[2]
tracer
A molecule or a specific atom within a molecule that has been chemically or radioactivelylabelled so that it can be easily tracked or followed through a biochemical process or located in a cell or tissue.[4]
Affecting agene or sequence on a different nucleic acid molecule orstrand. Alocus or sequence within a particular DNA molecule such as achromosome is said to betrans-acting if it or itsproducts influence or act upon other sequences located relatively far away or on an entirely different molecule or chromosome. For example, aDNA-binding protein acts "intrans" if it binds to or interacts with a sequence located on any strand or molecule different from the one on which it is encoded. Contrastcis-acting.
A form ofRNA splicing in which different RNAtranscripts, synthesized in separatetranscription events, are spliced together into a single, continuous transcript. This contrasts with the more conventional "cis-splicing", where segments of the same transcript are excised or re-arranged.[3]
An experimental approach to artificially controlgene expression by introducing a transactivator gene under the control of an induciblepromoter into a genome. The transactivator encodes atranscription factor capable ofacting intrans upon one or more other genes by recognizing and specifically binding their promoters; thus by inducing the transactivator gene, the expression of many other genes can be experimentally manipulated.[3]
A product oftranscription; that is, anyRNA molecule which has been synthesized byRNA polymerase using a complementaryDNA molecule as atemplate. When transcription is completed, transcripts separate from the DNA and become independentprimary transcripts. Particularly in eukaryotes, multiplepost-transcriptional modifications are usually necessary for raw transcripts to be converted into stable and persistent molecules, which are then described asmature, though not all transcribed RNAs undergo maturation. Many transcripts are accidental, spurious, incomplete, or defective; others are able to perform their functions immediately and without modification, such as certainnon-coding RNAs.
Any RNAtranscript whose function is unclear. Such transcripts may include functionalnon-coding RNAs which have not yet been studied in detail as well as spurious transcripts without any definite function. The DNA sequences from which TUFs are transcribed are generally located inintergenic orintronic regions of the genome. See alsojunk RNA.
The first step in the process ofgene expression, in which anRNA molecule, known as atranscript, is synthesized by enzymes calledRNA polymerases using agene or otherDNA sequence as atemplate. Transcription is a critical and fundamental process in all living organisms and is necessary in order to make use of the information encoded within agenome. All classes of RNA must be transcribed before they can exert their effects upon a cell, though onlymessenger RNA (mRNA) proceeds totranslation to produce a functionalprotein, whereas the many types ofnon-coding RNA fulfill their duties without being translated. Transcription is also not always beneficial for a cell: when it occurs at the wrong time or at afunctionless locus, or whenmobile elements or infectious pathogens utilize the host's transcription machinery, the resulting transcripts (not to mention the waste of valuable energy and resources) are often harmful to the host cell or genome.
A simplified diagram oftranscription. RNA polymerase (RNAP) synthesizes an RNA transcript (blue) in the 5'-to-3' direction, using one of the DNA strands as atemplate, while a complex of multipletranscription factors binds to apromoter upstream of the gene.
Anyprotein that controls the rate oftranscription of genetic information fromDNA toRNA by binding to a specificDNA sequence andpromoting orblocking the recruitment ofRNA polymerase to nearbygenes. Transcription factors can effectively turn "on" and "off" specific genes in order to make sure they areexpressed at the right times and in the right places; for this reason, they are a fundamental and ubiquitous mechanism ofgene regulation.
The specific location within agene at whichRNA polymerase beginstranscription, defined by the specific nucleotide or codon corresponding to the first ribonucleotide(s) to be assembled in thenascent transcript (which is not necessarily the same as thefirst codon to betranslated). This site is usually considered the beginning of thecoding sequence and is the reference point for numbering the individual nucleotides within a gene. Nucleotidesupstream of the start site are assigned negative numbers and thosedownstream are assigned positive numbers, which are used to indicate the positions of nearby sequences or structures relative to the TSS. For example, thebinding site for RNA polymerase might be a short sequence immediately upstream of the TSS, from approximately -80 to -5, whereas anintron within the coding region might be defined as the sequence starting at nucleotide +207 and ending at nucleotide +793.
transcription unit
The segment of DNA between theinitiation site and the termination site oftranscription, containing thecoding sequences for one or moregenes. All genes within a transcription unit are transcribed together into a single transcript during a single transcription event; the resultingpolycistronic RNA may subsequently be cleaved into separate RNAs, or may betranslated as a unit and then cleaved into separate polypeptides.[13]
The intermittent nature oftranscription andtranslation mechanisms. Both processes occur in "bursts" or "pulses", with periods of gene activity separated by irregular intervals.
The entire set ofRNA molecules (often referring to all types of RNA but sometimes exclusively tomessenger RNA) that is or can beexpressed by a particulargenome, cell, population of cells, or species at a particular time or under particular conditions. The transcriptome is distinct from theexome and thetranslatome.
The study of thetranscriptome of a particular genome, cell, or organism, i.e. the sum total of all of the RNAtranscripts produced from it bytranscription. Transcriptomics technologies allow scientists to isolate and sequence transcriptomes, which can then be mapped to the genome to determine which genes are being expressed or which cellular processes are active and which are dormant at a given time.
The transport of molecules across the interior of a cell, i.e. through thecytoplasm, especially apolarized cell such as anepithelial cell with contrastingapical andbasal surfaces, thereby providing a spatially oriented transport system. Molecules undergoing transcytosis are usually contained withinvesicles.[5]
transductant
A cell which has undergonetransduction and been successfully transduced.
The deliberate experimental introduction of exogenousnucleic acids into a cell or embryo. In the broadest sense the term may refer to any such transfer and is sometimes used interchangeably withtransformation, though some applications restrict the usage of transfection to the introduction of naked or purified non-viralDNA orRNA into cultured eukaryotic cells (especially animal cells) resulting in the subsequent incorporation of the foreign DNA into the hostgenome or the non-hereditary modification ofgene expression by the foreign RNA. As a contrast to both standard non-viral transformation andtransduction, transfection has also occasionally been used to refer to the uptake of purified viral nucleic acids by bacteria or plant cells without the aid of a viral vector.[13]
A special class ofRNA molecule, typically 76 to 90nucleotides in length, that serves as a physical adapter allowingmRNA transcripts to betranslated into sequences ofamino acids during protein synthesis. Each tRNA contains a specificanticodon triplet corresponding to an amino acid that is covalently attached to the tRNA's opposite end; as translation proceeds, tRNAs are recruited to theribosome, where each mRNAcodon is paired with a tRNA containing the complementary anticodon. Depending on the organism, cells may employ as many as 41 distinct tRNAs with unique anticodons; because ofcodon degeneracy within thegenetic code, several tRNAs containing different anticodons carry the same amino acid.
A type of RNA molecule in some bacteria which has dualtRNA-like andmRNA-like properties, allowing it to simultaneously perform a number of different functions duringtranslation.
Anygene or other segment of genetic material that has been isolated from one organism and then transferred either naturally or by any of a variety ofgenetic engineering techniques into another organism, especially one of a different species. Transgenes are usually introduced into the second organism'sgerm line. They are commonly used to study gene function or to confer an advantage not otherwise available in the unaltered organism.
The entire set ofmessenger RNA molecules that aretranslated by a particulargenome, cell, tissue, or species at a particular time or under particular conditions. Like thetranscriptome, it is often used as a proxy for quantifying levels ofgene expression, though the transcriptome also includes many RNA molecules that are never translated.
Any of a diverse variety ofselfishmobile genetic elements consisting of self-acting DNA sequences capable ofreplicating themselves semi-autonomously andinserting into random or specific sites within a host genome, a process known astransposition. Transposons contain one or more genes which encode enzymes known astransposases capable of recognizing sequences within a flanking pair ofinverted repeats, such that the enzymes effectively catalyze their own replication,excision, and/or re-insertion into other DNA molecules by any of various mechanisms.[3]
Any of a class of self-actingenzymes capable ofbinding to the flanking sequences of thetransposable element which encodes them and catalyzing its movement to another part of the genome, typically by anexcision/insertion mechanism or a replicative mechanism, in a process known astransposition.
The process by which a nucleic acid sequence known as atransposable element changes its position within agenome, either byexcising and re-inserting itself at a differentlocus (cut-and-paste) or byduplicating itself and inserting into another locus without moving the original element from its original locus (copy-paste). These reactions are catalyzed by an enzyme known as atransposase which is encoded by a gene within the transposable element itself; thus the element's products are self-acting and can autonomously direct their own replication. Transposed sequences may re-insert at random loci or at sequence-specific targets, either on the same DNA molecule or on different molecules.
Any of a class of chemical compounds which areester derivatives ofglycerol, consisting of a glycerol backbone connected to any threefatty acid substituents via ester bonds. Triglycerides are one of three major classes of esters formed by fatty acids in biological systems, along withphospholipids andcholesteryl esters. They are the primary constituent ofadipose tissue in vertebrates.
Any sequence in which an individual nucleotidetriplet isrepeated many timesin tandem, whether in a gene or non-coding sequence. At mostloci some degree of repetition is normal and harmless, but mutations which cause specific triplets (especially those of the formCnG) to increase incopy number above the normal range are highly unstable and responsible for a variety ofgenetic disorders.
triplet
A unit of three successivenucleotides in aDNA orRNA molecule.[13] A triplet within a coding sequence that codes for a specific amino acid is known as acodon.
The directional growth or movement of a cell or organism in response to a stimulus, e.g.light,heat, the pull ofgravity, or the presence of a particularchemical, such that the response is dependent on the direction of the stimulus (as opposed to a non-directionalnastic response).Positive tropism is growth or movement toward the stimulus;negative tropism is away from the stimulus.[2] See alsotaxis andkinesis.
The force within a cell which pushes theplasma membrane against thecell wall,[32] a type ofhydrostatic pressure influenced by theosmotic flow of water into and out of the cell. Turgidity is observed in plants, fungi, bacteria, and some protists with cell walls, but generally not in animal cells.
Inenzymology, a measure of therate at which a particularenzymecatalyzes a particular biochemical reaction, usually expressed as the average number ofsubstrate molecules it is capable of converting into reaction products per unit time at a given concentration of enzyme.[33]
Thelabelling of a biomolecule (often another protein) by covalently attaching aubiquitin protein to it—generally via the formation of anamide bond between the ubiquitin's C-terminalglycine and positively charged side chains (oftenlysine orarginine residues) of the labelled molecule, anATP-dependent reaction catalyzed byubiquitin-conjugating enzymes[3]—thus making it identifiable to molecules capable of recognizing ubiquitinepitopes. Ubiquitination is a widely usedpost-translational modification by which proteins aretagged; the attachment of a single ubiquitin molecule (monoubiquitination) can variously activate or inhibit a protein's activity, while the attachment of a chain of multiple consecutively linked ubiquitin molecules (polyubiquitination) commonly targets the protein for degradation byproteasomes.
A type oftransport protein which catalyzes the movement of a single, specific solute or chemical species across a lipid membrane in either direction.[4] Contrastantiporter andsymporter.
A class of DNAsequences determined byC0t analysis to be present only once in the analyzed genome, as opposed torepetitive sequences. Most structural genes and their introns are unique.[13]
Anynon-coding sequence which is transcribed along with aprotein-coding sequence, and thus included within amessenger RNA, but which is not ultimatelytranslated during protein synthesis. A typical mRNA transcript includes two such regions: one immediately upstream of the coding sequence, known as the5' untranslated region (5'-UTR), and one downstream of the coding sequence, known as the3' untranslated region (3'-UTR). These regions are not removed duringpost-transcriptional processing (unlikeintrons) and are usually considered distinct from the5' cap and the3' polyadenylated tail (both of which are later additions to a primary transcript and not themselves products of transcription). UTRs are a consequence of the fact that transcription usually begins considerably upstream of thestart codon of the coding sequence and terminates long after thestop codon has been transcribed, whereas translation is more precise. They often include motifs with regulatory functions.
upregulation
Alsopromotion.
Any process, natural or artificial, which increases the level ofgene expression of a certaingene. A gene which is observed to be expressed at relatively high levels (such as by detecting higher levels of itsmRNA transcripts) in one sample compared to another sample is said to beupregulated. Contrastdownregulation.
Any of a class ofenclosed, fluid-filledcompartments present in many eukaryotic cells as well as bacteria, often large and conspicuous under the microscope and serving any of a huge variety of functions, including acting as a resizable reservoir for the storage of water,metabolic waste, toxins, or foreign material; maintaining cellularhomeostasis andhydrostatic pressure; supporting immune functions; housing symbiotic bacteria; and assisting in thedegradation and recycling of old cellular components.[2]
Any of a class oftandem repeats for which thecopy number of therepeated sequence at a particular locus tends to vary between individuals of the same species. VNTRs may occur throughout the genome, both within and outside ofcoding DNA, and if the copy number is stably inherited may be used inDNA fingerprinting to uniquely identify individuals or to determine their genealogical relatedness to other individuals.
Variation or irregularity in a particularphenotype, especially a conspicuous visibletrait such as color or pigmentation, occurring simultaneously in different parts of the same individual organism due to any of a variety of causes, such asX-inactivation,mitotic recombination,transposable element activity,position effects, or infection by pathogens.
Anymembrane-bound space completely enclosed by its ownmembrane, which is separate though usually derived from other membranes (often thecell membrane) either bybudding or by mechanical disruption such assonication.[3] The term is applied to many different structures but especially to the small, roughly sphericalcompartments created duringendocytosis andexocytosis, as well as tolysosomes and various other small intracellular or extracellular organelles.[2]
The process ofdetermining the entirety or near-entirety of the DNA sequences comprising an organism'sgenome with a single procedure or experiment, generally inclusive of allchromosomal andextrachromosomal (e.g.mitochondrial) DNA.
Thephenotype of the typical form of aspecies as it occurs in nature; a product of the standard "normal"allele at a givenlocus, as opposed to that produced by a non-standardmutant allele.
An index of thesuperhelical coiling of a DNA molecule. The writhing number does not have a precise quantitative definition but instead represents the degree of supercoiling. Together, the writhing number and thetwisting number determine thelinking number.[5]
One of twosex chromosomes present in organisms which use theXY sex-determination system, and the only sex chromosome in theX0 system. The X chromosome is found in both males and females and typically contains much moregene content than its counterpart, theY chromosome.
The process by which one of the two copies of theX chromosome is silenced by being irreversibly condensed into transcriptionally inactiveheterochromatin in the cells of female therian mammals. A form ofdosage compensation, X-inactivation prevents females from producing twice as manygene products from genes on the X chromosome as males, who only have one copy of the X chromosome. Which X chromosome is inactivated is randomly determined in the early embryo, making it possible for cell lineages with different inactive Xs to exist in the same organism.
Asupersecondarypolypeptide structural motif andDNA-binding domain occurring in manyDNA-binding proteins, characterized by a series of non-adjacent amino acidresidues whichfold into a three-dimensional arrangement capable ofcoordinating one or more zinc ions (Zn2+ ) between them, thus stabilizing the fold into a definite structure that can interact specifically with other biomolecules such as nucleic acids or other polypeptides. There are many distinct classes of zinc fingers using different ligands and spatial arrangements to achieve coordination; in perhaps the most common variant, a shortalpha helix is oriented antiparallel to aβ sheet, with twohistidine residues in the former and twocysteines in the latter forming the coordination complex. Zinc fingers bind DNA as the primary functional domain of manytranscription factors.
The degree to which multiple copies of agene,chromosome, orgenome have the same genetic sequence; e.g. in a diploid organism with two complete copies of its genome (one maternal and one paternal), the degree of similarity of thealleles present in each copy. Individuals carrying two different alleles for a particular gene are said to beheterozygous for that gene; individuals carrying two identical alleles are said to behomozygous for that gene. Zygosity may also be considered collectively for a group of genes, or for the entire set of genes and geneticloci comprising the genome.
A type ofeukaryotic cell formed as the direct result of afertilization event between twogametes. In multicellular organisms, the zygote is the earliest developmental stage.
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