Thisglossary of cellular and molecular biology is a list of definitions of terms and concepts commonly used in the study ofcell biology,molecular biology, and related disciplines, includinggenetics,biochemistry, andmicrobiology.[1] It is split across two articles:
This page,Glossary of cellular and molecular biology (0–L), lists terms beginning with numbers and with the letters A through L.
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.
One of two ends of a single linear strand ofDNA orRNA, specifically the end at which the chain ofnucleotides terminates at the third carbon atom in thefuranose ring ofdeoxyribose orribose (i.e. the terminus at which the 3' carbon is not attached to another nucleotide via aphosphodiester bond;in vivo, the 3' carbon is often still bonded to ahydroxyl group). By convention, sequences and structures positioned nearer to the 3'-end relative to others are referred to asdownstream. Contrast5'-end.
Aribose ring with the carbon atoms numbered 1' through 5' according to chemical convention. The5' carbon is said to beupstream; the3'carbon is said to bedownstream. Bonds to a genericbase and aphosphate group are also shown.
A specially alterednucleotide attached to the5'-end of someprimary RNA transcripts as part of the set ofpost-transcriptional modifications which convert raw transcripts into mature RNA products. The precise structure of the 5' cap varies widely by organism; ineukaryotes, the most basic cap consists of amethylatedguaninenucleoside bonded to the triphosphate group that terminates the 5'-end of an RNA sequence. Among other functions, capping helps to regulate the export of mature RNAs from thenucleus, prevent their degradation byexonucleases, and promotetranslation in the cytoplasm. MaturemRNAs can also bedecapped.
One of two ends of a single linear strand ofDNA orRNA, specifically the end at which the chain ofnucleotides terminates at the fifth carbon atom in thefuranose ring ofdeoxyribose orribose (i.e. the terminus at which the 5' carbon is not attached to another nucleotide via aphosphodiester bond;in vivo, the 5' carbon is often still bonded to aphosphate group). By convention, sequences and structures positioned nearer to the 5'-end relative to others are referred to asupstream. Contrast3'-end.
Any of a class oftransferaseenzymes which catalyze the covalent bonding of anacetyl group (–COCH 3) to another compound, protein, or biomolecule, a process known asacetylation.
The region of anenzyme to which one or moresubstrate molecules bind, causing the substrate or another molecule to undergo a chemical reaction. This region usually consists of one or moreamino acid residues (commonly three or four) which, when the enzyme isfolded properly, are able to form temporary chemical bonds with the atoms of the substrate molecule; it may also include one or more additional residues which, by interacting with the substrate, are able to catalyze a specific reaction involving the substrate. Though the active site constitutes only a small fraction of all the residues comprising the enzyme, its specificity for particular substrates and reactions is responsible for the enzyme's biological function.
The covalent attachment of anyacyl group (e.g.acetyl orbenzoyl) to a chemical compound, protein, or other biomolecule via the substitution of the acyl group for a hydrogen atom, either spontaneously or by enzymatic catalysis.[3]Acetylation is a type of acylation.
Anucleoside diphosphate consisting ofadenosine attached to two consecutivephosphate groups via high-energy ester bonds. ADP can bephosphorylated to produceATP and thus is a precursor for its synthesis; it can also be dephosphorylated intoAMP.
Anucleoside consisting ofadenosine attached to a singlephosphate group via a high-energy ester bond. Additional phosphate groups can be added to AMP to produceADP andATP; thecyclic ester of AMP serves as a second messenger in some signaling pathways.
Anucleoside triphosphate consisting ofadenosine attached to three consecutivephosphate groups via high-energy ester bonds. The conversion of ATP intoADP orAMP viahydrolysis of these phosphates releases energy which is used to drive the majority of energy-consuming chemical reactions in all living cells, and hence ATP functions as a universal and ubiquitous energy carrier which is often referred to as the "molecular currency" of intracellularmetabolism. It is continuously regenerated viaphosphorylation of ADP and AMP by enzymes such asATP synthase. Like other nucleoside triphosphates, it also serves as a precursor fornucleic acid synthesis.
Adenosine triphosphate (ATP) is continuously decomposed intoadenosine diphosphate (ADP) and regenerated by the loss and gain, respectively, of one or more phosphate groups.
One of three main biologically activestructural conformations of theDNAdouble helix, along withB-DNA andZ-DNA. The A-form helix has a right-handed twist with 11base pairs per full turn, only slightly more compact than B-DNA, but its bases are sharply tilted with respect to the helical axis. It is often favored in dehydrated conditions and within sequences of consecutivepurine nucleotides (e.g.GAAGGGGA); it is also the primary conformation adopted bydouble-stranded RNA andRNA-DNA hybrids.[5]
Any pair of organisms which are related genetically and both affected by the sametrait. For example, two cousins who both have blue eyes are an affected relative pair since they are both affected by theallele that codes for blue eyes.
One of multiple alternative versions of an individualgene, each of which is a viableDNA sequence occupying a given position, orlocus, on achromosome. For example, in humans, one allele of the eye-color gene produces blue eyes and another allele of the same gene produces brown eyes.
Anychromosome that differs from an ordinaryautosome in size, form, or behavior and which is responsible for determining thesex of an organism. In humans, theX chromosome and theY chromosome are sex chromosomes.
A common structuralmotif in the secondary structures ofproteins consisting of a right-handed helix conformation resulting fromhydrogen bonding betweenamino acid residues which are not immediately adjacent to each other.
Any of a class of organic compounds whose basic structural formula includes a central carbon atom bonded toamine andcarboxylfunctional groups and to a variableside chain. Out of nearly 500 known amino acids, a set of 20 are coded for by thestandard genetic code and incorporated into long polymeric chains as the building blocks ofpeptides and hence ofpolypeptides andproteins. The specific sequences of amino acids in the polypeptide chains that form a protein are ultimately responsible for determining the protein's structure and function.
Everyamino acid has the same basic structural formula, consisting of a central carbon atom (α) bonded to three major substituents: oneamino group (blue), onecarboxyl group (red), and one variableside chain (green). The side chain, which can range from a simplemethyl group (alanine) to more complex functional groups such as a double-ringedindole (tryptophan), gives each particular amino acid its unique identity. Duringtranslation, amino acids are joined into a linear chain by condensation reactions which createpeptide bonds between the carboxyl group of one amino acid and the amino group of an adjacent amino acid. The first and last amino acids in the chain are said to beN-terminal andC-terminal, respectively, in reference to the unbonded amino group of the first amino acid and the unbonded carboxyl group of the last.
Any of a set of enzymes which catalyze thetransesterification reaction that results in the attachment of a specificamino acid (or a precursor) to one of its cognatetransfer RNA molecules, forming anaminoacyl-tRNA. Each of the 20 different amino acids used in thegenetic code is recognized and attached by its own specific synthetase enzyme, and most synthetases are cognate to several different tRNAs according to their specificanticodons.
Any DNA or RNA sequence or fragment that is the source and/or product of anamplification reaction. The term is most frequently used to describe the numerous copied fragments that are the products of thepolymerase chain reaction orligase chain reaction, though it may also refer to sequences that are amplified naturally within a genome, e.g. bygene duplication.
amplification
Thereplication of a biomolecule, in particular the production of one or more copies of anucleic acid sequence, known as anamplicon, either naturally (e.g. by spontaneousduplications) or artificially (e.g. byPCR), and especially implying many repeated replication events resulting in thousands, millions, or billions of copies of the target sequence, which is then said to beamplified.
Anymetabolic reaction or process in which energy is expended in order to build complex substances such as macromolecules from simpler compounds, including aspects of growth and biosynthesis. Anabolic processes andpathways tend to involvereductive steps that create high-enthalpy, low-entropy compounds such as proteins and nucleic acid polymers.[3] Contrastcatabolism.
1. Describing conditions in whichdiatomic oxygen is entirely absent, as opposed toaerobic conditions.[3]
2. Describing an organism that is able to survive and grow in the absence of diatomic oxygen, or a pathway or process characterized by the absence of diatomic oxygen; e.g.anaerobic respiration.[3]
The condition of a cell or organism having an abnormal number of one or more particularchromosomes (but excluding abnormal numbers of complete sets of chromosomes, which instead is known aseuploidy).
A gene that confers resistance to one or more specificantibiotic compounds. In molecular cloning,plasmidvectors are often designed to carry antibiotic resistance genes asselectable markers alongside other genes of interest, because it permits the artificial selection of successfullytransformed cell populations when the cells are cultured in the presence of the antibiotic.
Any of a diverse family ofglycoproteins known asimmunoglobulins capable of binding specifically but reversibly via non-covalent interactions to a particularantigen orimmunogen. Antibodies are generated as part of an organism's immune response to the introduction of a specific antigen into a host organism, and their binding of the antigen frequently (though not always) counteracts or inhibits any biological activity the antigen may have.[3] Antibodies have a characteristic Y-shaped structure consisting of aheavy chain andlight chain held together bydisulfide bonds.
Aseries of three consecutivenucleotides within atransfer RNA whichcomplement the three nucleotides of acodon within anmRNA transcript. Duringtranslation, each tRNA recruited to theribosome contains a single anticodon triplet that pairs with its complementary codon from the mRNA sequence, allowing each codon to specify a particularamino acid to be added to the growing peptide chain. Anticodons containinginosine in the first position are capable of pairing with more than one codon due to a phenomenon known aswobble base pairing.
Anyexogenous agent that, upon introduction into an immunocompetent organism, stimulates a response from the organism's immune system that results in the production of one or moreantibodies which can bind to it specifically; in this sense the term is synonymous withimmunogen. Antigens may be pure substances, mixtures of substances, or particulate matter such as cells or cell fragments. Broader definitions may include substances that can bind to a specific antibody but are not themselves immunogenic, i.e. those which are only able to stimulate antibody production when combined with acarrier.[3]
Agene which helps to regulate cell growth and suppress tumors when functioning correctly, such that its absence or malfunction can result in uncontrolled cell growth and possibly cancer.[7] Compareoncogene.
The contrasting orientations of the twostrands of adouble-strandednucleic acid (and more generally any pair ofbiopolymers) which are parallel to each other but with oppositedirectionality. For example, the twocomplementary strands of aDNA molecule run side-by-side but in opposite directions with respect to chemical numbering conventions, with one strand oriented5'-to-3' and the other 3'-to-5'.
Atransport protein which works by exchanging two different ions or small molecules across amembrane in opposite directions, either at the same time or consecutively.[8]
(of a cell or organism) Lacking anucleus, i.e. a discrete, membrane-bound organelle enclosing the cell'sgenomic DNA, used especially of cells which normally have a nucleus but from which the nucleushas been removed (e.g. in artificialnuclear transfer), and also of specialized cell types that develop without nuclei despite that the cells of other tissues comprising the same organism ordinarily do have nuclei (e.g. mammalianerythrocytes).
The process by which contraction of theapical side of a cell (and often a corresponding expansion of the opposingbasal side) causes the cell to assume a wedge-shaped morphology. The process is common during early development, where it is often coordinated across many adjacent cells of anepithelial layer simultaneously in order to generate bends or folds in developingtissues.
Theapical constriction of specific groups of cells during developmental morphogenesis allows bends and turns to form in higher-order tissues.
Any artificialDNA,RNA, orXNAoligonucleotide molecule,single-stranded ordouble-stranded, which functions as aligand by binding selectively to one or more specific target molecules, usually other nucleic acids orproteins, and often a family of such molecules. The term is used in particular to describe short nucleic acid fragments which have been randomly generated and then artificially selectedin vitro by procedures such asSELEX. Aptamers are useful in the laboratory asantibody mimetics, particularly in applications where conventional proteinantibodies are not appropriate.
Any process by which chemical compounds containing biologically relevant elements (e.g. carbon, hydrogen, oxygen, nitrogen, phosphorus, sulfur, selenium, iron, cobalt, nickel, copper, zinc, molybdenum, etc.) are uptaken bymicroorganisms and incorporated into complexbiomolecules in order to synthesize various cellular components. In contrast, adissimilatory process uses the energy released by decomposing exogenous molecules to power the cell'smetabolism andexcretesresidual or toxic compounds out of the cell, instead of reusing them to build new molecules.
A singlemonocentricchromosome containing two or more physically attached copies of the normalX chromosome as a result of either a natural internalduplication or any of a variety ofgenetic engineering methods. The resulting compound chromosome effectively carries two or more doses of all genes and sequences included on the X, yet functions in all other respects as a single chromosome, meaning that haploid 'XX'gametes (rather than the ordinary 'X' gametes) will be produced bymeiosis and inherited by progeny. In mechanisms such asgenic balance in which the sex of an organism is determined by the total dosage of X-linked genes, an abnormal 'XXY'zygote, fertilized by one XX gamete and one Y gamete, will develop into a female.
The orderlyautolytic degradation and recycling of dysfunctional or unnecessary cellular components by the cell's own enzymes as part of a carefully regulated,lysosome-dependent pathway. Autophagic programs play important roles in nutrient-deprived andsenescent cells but also help maintainhomeostasis in healthy cells.
Anychromosome that is not anallosome and hence is not involved in the determination of thesex of an organism. Unlike the sex chromosomes, the autosomes in adiploid cell exist in pairs, with the members of each pair having the same structure, morphology, and geneticloci.
A cell or organism that ishomozygous for alocus at which the two homologousalleles are identical by descent, both having been derived from a single gene in a common ancestor.[6] Contrastallozygote.
Describing acell culture in which only a single species, variety, or strain is present, and which is therefore entirely free of contaminating organisms including symbiotes and parasites.
Any supernumerarynuclear DNA molecule which is not a duplicate of norhomologous to any of the standard complement of normal "A" chromosomes comprising a genome. Typically very small and devoid of structural genes, B chromosomes are by definition not necessary for life. Though they occur naturally in many eukaryotic species, they arenot stably inherited and thusvary widely in copy number even between closely related individuals.[6]
A pair of twonucleobases oncomplementaryDNA orRNA strands which are loosely attracted to each other viahydrogen bonding, a type of non-covalent electrostatic interaction between individual atoms in the purine or pyrimidine rings of the complementing bases. This phenomenon, known asbase pairing, is the mechanism underlying thehybridization that commonly occurs between nucleic acid polymers, allowing twosingle-stranded molecules to combine into a more energetically stabledouble-stranded molecule, as well as enabling certain individual strands tocomplement themselves. The ability of consecutive base pairs to stack one upon another contributes to the long-chaindouble helix structures observed in bothdouble-stranded DNA anddouble-stranded RNA molecules.
baseline
A measure of thegene expression level of agene or genes prior to a perturbation in an experiment, as in anegative control.Baseline expression may also refer to the expected or historical measure of expression for a gene.
A computer algorithm widely used inbioinformatics foraligning and comparing primary biological sequence information such as thenucleotide sequences of DNA or RNA or theamino acid sequences of proteins. BLAST programs enable scientists to quickly check for homology between two or more sequences by directly comparing the nucleotides or amino acids present at each position within each sequence; a common use is to search for matches between a specific query sequence and a digital sequence database such as agenome library, with the program returning a list of sequences from the database which resemble the query sequence above a specified threshold of similarity. Such comparisons can permit the identification of an organism from an unknown sample or the inference of evolutionary relationships between genes, proteins, or species.
The "standard" or classicalstructural conformation of theDNAdouble helixin vivo, thought to represent an average of the various distinct conformations assumed by very long DNA molecules under physiological conditions.[5] The B-form double helix has a right-handed twist with a diameter of 23.7ångströms and apitch of 35.7 ångströms or about 10.5base pairs per full turn, such that each nucleotide pair is rotated 36° around the helical axis with respect to its neighboring pairs. See alsoA-DNA andZ-DNA.
The three principal biologically active conformations ofDNA molecules:A-DNA,B-DNA, andZ-DNA (left to right), as viewed from the side and down the axis of thedouble helix.
Themetabolic pathway by whichfatty acid molecules arebroken down into simpler molecules, generatingacetyl-CoA in the process. This occurs via a series of enzyme-catalyzed reactions whichoxidize thebeta carbon of the fatty acid chain and ultimately convert it into acarbonyl group, which is then susceptible to nucleophilic attack by another molecule ofcoenzyme A, causingthiolysis of the bond between the alpha and beta carbons; this process can be repeated to sequentially digest long chains of hydrocarbons into shorter chains, generating an additional molecule of acetyl-CoA with every cycle. In prokaryotes, beta oxidation occurs in the cytosol, while in eukaryotes it primarily takes place in the innermitochondrial membrane or inperoxisomes.
The separation of a single entity (e.g. acell) into exactly two discrete entities closely resembling the original. The term refers in particular to a type ofcell division used byprokaryotes such as bacteria, whereby a singleparent cell divides evenly into twodaughter cells which are genetically identical to each other and to the parent. Binary fission is preceded byreplication of the parent cell's DNA, rapid growth of thecell wall, and various other processes which ensure even distribution of the cell's contents between the two progeny, but is generally a quicker and simpler process than themitosis andcytokinesis that occur ineukaryotes.
A region of a macromolecule such as a nucleic acid or a protein that directly participates in chemical interactions with another molecule. A wide variety of chemical interactions of varying strength and specificity can be described as "binding"; they may be long-term or transient, reversible or irreversible, and may rely upon relatively weakintermolecular forces or much strongercovalent bonds. Binding sites are defined by the spatial proximity of one or moreresidues havingfunctional groups with particular chemical properties. For example, thefolding of polypeptides in such a way that particular amino acids are positioned near each other in the protein'squaternary structure may confer chemical properties that permit the interaction of those residues with a particularligand. Similarly, a specific sequence of nucleobases in a DNA molecule may function as arecognition site for aDNA-binding protein. Whether and how the binding site functions depends on the precise spatial arrangement of the interacting residues and their physical accessibility to potential binding partners; thus mutations or changes in the chemical environment such asconformational changes can dramatically alter functionality. See alsoactive site.
Any analytical method that measures or qualifies the presence, effect, or potency of a substance within or upon a biological system, either directly or indirectly, e.g. by quantifying the concentration of a particular chemical compound within a sample obtained from living organisms, cells, or tissues, and ideally under controlled conditions that compare a sample subjected to an experimental treatment with an unmanipulated sample, so as to permit inferences about the effect of the treatment upon some measured variable.[10]
A subdiscipline of both biology and chemistry which studies the chemical basis of biological phenomena, focusing on understanding the chemical reactions and interactions that occur betweenbiomolecules and give rise to the processes that define and characterize living systems. It is closely related to and largely overlaps withmolecular biology.
The branch ofbiochemistry andcell biology that studies the flow ofenergy through living systems, in particular how organisms acquire, produce, transform, and utilize energy in order to perform biochemicalwork such asmetabolic reactions.
A community of symbiotic microorganisms, especially bacteria, where cells produce and embed themselves within a slimy, stickyextracellular matrix composed ofvarious high-molecular weight biopolymers,adhering to each other and sometimes also to asubstratum, which may be a biotic or abiotic surface.[11] Many bacteria can exist either as independent single cells or switch to a physiologically distinct biofilm phenotype; those that create biofilms often do so in order to shelter themselves from harmful environments. Cells residing within biofilms can easily share nutrients andcommunicate, and subpopulations of cells maydifferentiate to perform specialized functions supporting the whole biofilm.[12]
A measurable indicator of some biological state, especially a compound orbiomolecule whose presence or absence in a biological system is a reliable sign of a normal or abnormal process, condition, or disease.[13] Things that may serve as biomarkers include direct measurements of the concentration of a particular compound or molecule in a tissue or fluid sample, or any other characteristic physiological, histological, or radiographic signal (e.g. a change in heart rate, or a distinctmorphology under a microscope). They are regularly used as predictive or diagnostic tools in clinical medicine and laboratory research.
Any metallic element found naturally in small but measurable amounts in biological contexts. Metal ions play important roles in many biochemical processes and some are essential for normal function in living organisms, especiallyiron (Fe),zinc (Zn),copper (Cu),manganese (Mn),magnesium (Mg),potassium (K),sodium (Na), andcalcium (Ca).
Any difference in the concentration ofbiomolecules between two spaces within a biological system, whetherintracellular,extracellular, across amembrane, or between different cells or different parts of a tissue or organ system. Gradients of one kind or another drive virtually all biochemical processes occurring within and between cells, as natural systems tend to move toward athermodynamic equilibrium where concentrations are uniformly distributed in all spaces and no gradients exist. Gradients thus cause chemical reactions to occur in particular directions, which can be used by cells to accomplish essential biological functions, includingmetabolic energy transfer,signal transduction, and movement of ions and solutes into and out of cells and organelles. It is often necessary for cells to continuously regenerate gradients such asmembrane potentials in order to permit these processes to continue.
A term used to describe the end of adouble-stranded DNA molecule where the terminal nucleobases on eachstrand arebase-paired with each other, such that neither strand has a single-stranded "overhang" of unpaired bases. This is in contrast to a so-called "sticky end", where an overhang is created by one strand being one or more bases longer than the other. Blunt ends and sticky ends are relevant whenligating multiple DNA molecules, e.g. inrestriction cloning, because sticky-ended molecules will not readilyanneal to each other unless they have matching overhangs; blunt-ended molecules do not anneal in this way, so special procedures must be used to ensure that fragments with blunt ends are joined in the correct places.
Any of a class oftransmembrane proteins which are dependent on calcium ions (Ca2+) and whose extracellulardomains function as mediators of cell–cell adhesion atadherens junctions in eukaryotic tissues.
An unorganized mass ofparenchymal cells that forms naturally at the site of wounds in plant tissues, and which is commonly artificially induced to form in planttissue culture as a means of initiatingsomatic embryogenesis.[10]
Agene whose location on a chromosome isassociated with a particularphenotype (often a disease-related phenotype), and which is therefore suspected of causing or contributing to the phenotype. Candidate genes are often selected for study based ona priori knowledge or speculation about their functional relevance to the trait or disease being researched.
Any of a class of organic compounds having the generic chemical formula(CH 2O) n, and one of several major classes ofbiomolecules found universally in biological systems. Carbohydrates include individualmonosaccharides as well as largerpolymericoligosaccharides andpolysaccharides, in which multiple monosaccharide monomers are joined byglycosidic bonds.[10] Abundant and ubiquitous, these compounds are involved in numerous essential biochemical processes andpathways; they are widely used as an energy source for cellularmetabolism, as a form of energy storage, assignaling molecules, and asbiomarkers tolabel or modify the activity of other molecules. Carbohydrates are often colloquially described as "sugars"; the prefixglyco- indicates a compound or process containing or involving carbohydrates, and the suffix-ose usually signifies that a compound is a carbohydrate or a derivative.
2. A protein to which a specificligand orhapten has been conjugated and which thereby carries anantigen capable of eliciting anantibody response.[4]
3. A protein which is included in anassay at high concentrations in order to prevent non-specific interactions of the assay's reagents with vessel surfaces, sample components, or other reagents.[4] For example, in manyblotting techniques,albumin is intentionally allowed to bind non-specifically to the blotted membrane prior tofluorescent labelling, so as to "block" potential off-target binding of thefluorophore to the membrane, which might otherwise cause background fluorescence that obscures genuine signal from the target.
A pre-existing nucleic acid sequence or construct, especially a DNAvector with an annotated sequence and precisely positionedregulatory elements, into which one or morefragments can be readilyinserted or recombined by variousgenetic engineering methods. Recombinantplasmid vectors containing reliablepromoters,origins of replication, and antibiotic resistance genes are commercially manufactured as cassettes to allow scientists to easily swapgenes of interest into and out of an active "slot" or locus within the plasmid. See alsomultiple cloning site.
Anymetabolic reaction or process involving the decomposition of large or complex substances into smaller, simpler compounds, especially the breakdown of organic compounds in order to liberate energy.[3] Catabolic processes andpathways are usually exergonic and tend to involve oxidative steps that break chemical bonds, generating low-enthalpy, high-entropy products.[4] Contrastanabolism.
An increase in thereaction rate of a chemical reaction due to the presence of acatalyst.[3] A reaction whose rate is increased in this manner is said to becatalyzed.Enzyme-directed catalysis is the primary means by which many otherwise energetically unfavorable biochemical reactions occur.
Any chemical species or substance whose presenceincreases the reaction rate of one or more particular chemical reactions but which is itself unchanged by the reaction, being neither a reactant nor a product of the reaction. Catalysts often need only be present in very low concentrations relative to the reactants in order for catalysis to occur.[3] They may be simple molecules which catalyze reactions spontaneously, though most biochemical reactions are catalyzed by specifically evolvedenzymes which allow them to proceed at rates millions or billions of times faster than they otherwise would.
The basic structural and functional unit of which all living organisms are composed, essentially a self-replicating ball ofprotoplasm surrounded by asurface membrane which separates the interior from the external environment, thus providing a protected space in which the carefully controlled chemical reactions necessary to sustain biological processes can be carried out unperturbed.Unicellular organisms are composed of a single autonomous cell, whereasmulticellular organisms consist of numerous cells cooperating together, with individual cells more or less specialized ordifferentiated to serve particular functions.[4] Cells vary widely in size, shape, and substructure, particularly betweenprokaryotes andeukaryotes. The typical cell is microscopic, averaging 1 to 20micrometres (μm) in diameter, though they may range in size from 0.1 μm to more than 20 centimetres in diameter for the eggs laid by some birds and reptiles, which are highly specialized single-celledova.[10]
The branch ofbiology that studies the structures, functions, processes, and properties of biologicalcells, the self-contained units of life common to all living organisms.
A specialized layer ofcytoplasmic proteins lining the inner face of thecell membrane in most eukaryotic cells, composed primarily ofactinmicrofilaments andmyosinmotor proteins and usually 100–1000 nanometres thick, which functions as a modulator of membrane behavior and cell surface properties.
The process of determining the number ofcells within a biological sample orculture by any of a variety of methods. Counting cells is an important aspect ofcytometry used widely in research and clinical medicine. It is generally achieved by using a manual or digitalcytometer to count the number of cells present in small fractions of a sample, and then extrapolating to estimate the total number present in the entire sample. The resulting quantification is typically expressed as a density or concentration, i.e. the number of cells per unit area or volume.
The process by which living cells are grown and maintained, or "cultured", under carefully controlled conditions, generally outside of their natural environment. Optimal growth conditions vary widely for different cell types but usually consist of a suitable vessel (e.g. aculture tube orPetri dish) containing a specifically formulatedsubstrate orgrowth medium that supplies all of the nutrients essential for life (amino acids,carbohydrates,vitamins, minerals, etc.) plus any desirable growth factors andhormones, permits gas exchange (if necessary), and regulates the environment by maintaining consistent physico-chemical properties (temperature,pH, osmotic pressure, etc.). Some cell types require a solid surface to which they canadhere in order to reproduce, whereas others can be grown while floating freely in a liquid or gelatinoussuspension. Most cells have a genetically determined reproduction limit, butimmortalized cells will divide indefinitely if provided with optimal conditions.
The separation of an individualparent cell into twodaughter cells by any process. Cell division generally occurs by a complex, carefully structured sequence of events involving the reorganization of the parent cell's internal contents, the physicalcleavage of thecytoplasm andplasma membrane, and the even distribution of contents between the two resulting cells, so that each ultimately contains approximately half of the original cell's starting material. It usually impliesreproduction via thereplication of the parent cell's genetic material prior to division, though cells may also divide without replicating their DNA. In prokaryotic cells,binary fission is the primary form of cell division. In eukaryotic cells, asexual division occurs bymitosis andcytokinesis, while specific cell types reserved for sexual reproduction can additionally divide bymeiosis.[8]
The merging or coalescence of two or more cells into a single cell, as occurs in the fusion ofgametes to form azygote. Generally this occurs by the destabilization of each cell'splasma membrane and the formation ofcytoplasmic bridges between them which then expand until the two cytoplasms are completely mixed; intercellular structures ororganelles such asnuclei may or may not fuse as well. Some cells can be artificially induced to fuse with each other by treating them with a fusogen such aspolyethylene glycol or by passing an electric current through them.[10]
A population ofcellsculturedin vitro that is descended from a single primary culture through one or more generations or subcultures. All of the cells of an established cell line are (hypothetically) genetically identical both within and across generations, and tend to share the same patterns ofgene expression when cultured in similar conditions. Established lines that are alsoimmortalized can be propagated indefinitely with little or nocellular senescence.[3]
The selectively permeablemembrane surrounding all prokaryotic and eukaryotic cells, defining the outermost boundary of the cell and physically separating thecytoplasm from theextracellular environment.[14] Like all membranes, the cell membrane is a flexible, fluid, sheet-likephospholipid bilayer withmembrane proteins,carbohydrates, and numerous other molecules embedded within or interacting with it from both sides. Embedded molecules often havefreedom to move laterally alongside the membrane's lipids. Though the cell membrane can be freely crossed by many ions, small organic molecules, and water, most other substances requireactive transport through special pores orchannels or byendocytosis orexocytosis in order to enter or exit the cell, especially very large or electrically charged molecules such as proteins and nucleic acids. Besides regulating the transport of substances into and out of the cell, the cell membrane creates an organized interior space in which to perform life-sustaining activities and plays fundamental roles in all of the cell's interactions with its environment, making it important incell signaling,motility, defense, anddivision, among numerous other processes.
Cross-sectional diagram of a typical eukaryoticcell membrane
The study of the various biological activities and biochemical processes which sustain life insidecells, particularly (but not necessarily limited to) those related tometabolism and energy transfer, growth andreproduction, and the ordinary processes of thecell cycle.
The spatial variation within acell, i.e. the existence of differences in shape, structure, or function between different parts of the same cell. Almost allcell types exhibit some form of polarity, often along an invisible axis which defines opposing sides or poles where the variation is most extreme. Having internal polarity permits cells to accomplish specialized functions such assignal transduction or to serve asepithelial cells which must perform different tasks on different sides, or facilitatescell migration ordivision.
The diverse set of processes by which cells transmit information to and receive information from themselves, from other cells, or from their surroundings.Signal transduction occurs in all cell types, prokaryotic and eukaryotic, and is of critical importance to the cell's ability to navigate and survive its physical environment. Countless mechanisms of signaling have evolved in different organisms and are often categorized according to the proximity between sender and recipient (autocrine,intracrine,juxtacrine,paracrine, orendocrine).
Any of a class ofreceptor proteins embedded within or attached to the external surface of thecell membrane, with one or morebinding sites facing theextracellular environment and one or moreeffector sites that couple the binding of a particularligand to anintracellular event or process. Cell surface receptors are a primary means by which environmental signals are received by the cell andtransmitted across the membrane into the cell interior. Some may also bind exogenous ligands and transport them into the cell in a process known asreceptor-mediated endocytosis.[15]
A tough, variously flexible or rigid layer ofpolysaccharide orglycoprotein polymers surrounding some cell types immediately outside of thecell membrane, including plant cells and mostprokaryotes, which functions as an additional protective and selective barrier and gives the cell a definite shape and structural support. The chemical composition of the cell wall varies widely between taxonomic groups, and even between different stages of thecell cycle: in land plants it consists primarily ofcellulose,hemicellulose, andpectin, while algae make use ofcarrageenan andagar, fungi usechitin, and bacterial cell walls containpeptidoglycan.
A unit for measuringgenetic linkage defined as the distance between chromosomalloci for which the expected average number of interveningchromosomal crossovers in a single generation is 0.01. Though not an actual measure of physical distance, it is used to infer the actual distance between two loci based on the apparent likelihood of a crossover occurring between them in any givenmeiotic division.
A generalized framework for understanding the flow of genetic information between macromolecules within biological systems. The central dogma outlines the fundamental principle that the sequence information encoded in the three major classes ofbiopolymer—DNA,RNA, andprotein—can only be transferred between these three classes in certain ways, and not in others: specifically, information transfer between thenucleic acids and from nucleic acid to protein is possible, but transfer from protein to protein, or from protein back to either type of nucleic acid, is impossible and does not occur naturally.
Possible types of information transfer according to thecentral dogma of molecular biology. Three general transfers, in red, occur routinely in all living cells: DNA-to-DNA (DNA replication), DNA-to-RNA (transcription), and RNA-to-protein (translation). Three special transfers, in blue, are known to occur only in viruses or in the laboratory: RNA-to-RNA (RNA replication), RNA-to-DNA (reverse transcription), and DNA-to-protein (direct translation without an mRNA intermediate). An additional three transfers are believed not to be possible at all: protein-to-protein, protein-to-RNA, and protein-to-DNA—though it has been argued that there are exceptions by which all three can occur.
A cylindricalorganelle composed ofmicrotubules, present only in certain eukaryotes. A pair of centrioles migrate to and define the two opposite poles of adividing cell where, as part of acentrosome, they initiate the growth of thespindle apparatus.
A specialized DNA sequence within achromosome that links a pair ofsister chromatids. The primary function of the centromere is to act as the site of assembly forkinetochores, protein complexes which direct the attachment ofspindle fibers to the centromere and facilitatesegregation of the chromatids duringmitosis ormeiosis.
centromeric index
The proportion of the total length of achromosome encompassed by itsshort arm, typically expressed as a percentage; e.g. a chromosome with a centromeric index of 15 isacrocentric, with a short arm comprising only 15% of its overall length.[6]
A type oftransmembrane protein whose shape forms an aqueous pore in amembrane, permitting the passage of specific solutes, often small ions, across the membrane in either or both directions.[8]
A set of axioms which state that, in theDNA of any chromosome, species, or organism, the total number ofadenine (A)residues will be approximately equal to the total number ofthymine (T) residues, and the number ofguanine (G) residues will be equal to the number ofcytosine (C) residues; accordingly, the total number ofpurines (A +G) will equal the total number ofpyrimidines (T +C). These observations illustrate the highly specific nature of thecomplementarybase-pairing that occurs in allduplex DNA molecules: even though non-standard pairings are technically possible, they are exceptionally rare because the standard ones are strongly favored in most conditions. Still, the 1:1 equivalence is seldom exact, since at any given time nucleobase ratios are inevitably distorted to some small degree byunrepairedmismatches, missing bases, and non-canonical bases. The presence ofsingle-stranded DNA polymers also alters the proportions, as an individualstrand may contain any number of any of the bases.
A non-directional, random change in the movement of a molecule, cell, or organism in response to a chemical stimulus, e.g. a change in speed resulting from exposure to a particular chemical compound.
A directed, non-random change in the movement of a molecule, cell, or organism in response to a chemical stimulus, e.g. towards or away from an area with a high concentration of a particular chemical compound.[8]
A cross-shaped junction that forms the physical point of contact between two non-sisterchromatids belonging tohomologous chromosomes duringsynapsis. As well as ensuring propersegregation of the chromosomes, these junctions are also thebreakpoints at whichchromosomal crossover may occur duringmitosis ormeiosis, which results in the reciprocal exchange of DNA between the synapsed chromatids.
The presence of two or more populations of cells with distinctgenotypes in an individual organism, known as achimera, which has developed from the fusion of cells originating from separatezygotes; each population of cells retains its own genome, such that the organism as a whole is a mixture of genetically non-identical tissues. Genetic chimerism may be inherited (e.g. by the fusion of multiple embryos during pregnancy) or acquired after birth (e.g. byallogeneic transplantation of cells, tissues, or organs from a genetically non-identical donor); in plants, it can result fromgrafting or errors in cell division. It is similar to but distinct frommosaicism.
A type of small, lens-shapedplastidorganelle found in the cells of green algae and plants which contains light-sensitivephotosynthetic pigments and in which the series of biochemical reactions that comprisephotosynthesis takes place. Likemitochondria, chloroplasts are bound by a double membrane, contain their owninternal circular DNA molecules from which they direct transcription of a unique set of genes, and replicate independently of the nuclear genome.[10][4]
The set ofDNA molecules contained withinchloroplasts, a type of photosyntheticplastidorganelle located within the cells of some eukaryotes such as plants and algae, representing a semi-autonomousgenome separate from that within the cell's nucleus. Like other types of plastid DNA, cpDNA usually exists in the form of small circularplasmids.
A chemical compound that is the principalsterol biosynthesized by animal cells and an essential component ofcell membranes, in which it serves to buffer the membrane'sfluidity and plays roles insignal transduction. It is produced primarily in tissues of the liver and the nervous system, and is transported in an esterified form bylipoproteins in the blood plasma.[4]
One copy of a newly copiedchromosome, which is joined to the original chromosome by acentromere. Paired copies of the same individual chromosome are known assister chromatids.
A complex ofDNA,RNA, andprotein found ineukaryotic cells that is the primary substance comprisingchromosomes. Chromatin functions as a means ofpackaging very long DNA molecules into highly organized and densely compacted shapes, which prevents the strands from becoming tangled, reinforces the DNA duringcell division, helps to prevent DNA damage, and plays an important role in regulatinggene expression andDNA replication.
A central amorphous mass ofpolytene chromosomes found in the nuclei of cells of the salivary glands inDrosophila larvae and resulting from the fusion ofheterochromatic regions surrounding thecentromeres of the somatically paired chromosomes, with the distaleuchromatic arms radiating outward.[6]
A region of achromosome that has been locally compacted orcoiled intochromatin, conspicuous under a microscope as a "bead", node, or dark-staining band, especially when contrasted with nearby uncompacted strings of DNA.
AnuclearDNA molecule containing part or all of the genetic material of an organism. Chromosomes may be considered a sort of molecular "package" for carrying DNA within thenucleus of cells and, in mosteukaryotes, are composed of long strands of DNA coiled withpackaging proteins which bind to andcondense the strands to prevent them from becoming an unmanageable tangle. Chromosomes are most easily distinguished and studied in their completely condensed forms, which only occur duringcell division. Some simple organisms have only one chromosome made of circular DNA, while most eukaryotes have multiple chromosomes made of linear DNA.
chromosome condensation
The process by which eukaryotic chromosomes become shorter, thicker, denser, and more conspicuous under a microscope duringprophase due to systemic coiling andsupercoiling ofchromatic strands of DNA in preparation forcell division.
A slender, thread-like,membrane-bound projection extending from the surface of a eukaryotic cell, longer than amicrovillus but shorter than aflagellum. Most eukaryotic cells have at least oneprimary cilium serving sensory or signaling functions; some cells employ thousands ofmotile cilia covering their entire surface in order to achieve locomotion or to move extracellular material past the cell.
Anyextracellular DNA fragments derived from tumor cells which are circulating freely in the bloodstream.
cis
On the same side; adjacent to;acting from the same molecule. Contrasttrans.
cis-acting
Affecting agene or sequence on the same nucleic acid molecule. Alocus or sequence within a particular DNA molecule such as achromosome is said to becis-acting if it influences or acts upon other sequences located within short distances (i.e. physically nearby, usually but not necessarilydownstream) on the same molecule or chromosome; or, in the broadest sense, if it influences or acts upon other sequences located anywhere (not necessarily within a short distance) on the same chromosome of ahomologous pair.Cis-acting factors are often involved in theregulation ofgene expression by acting to inhibit or to facilitatetranscription. Contrasttrans-acting.
cis-dominant mutation
Amutation occurring within acis-regulatory element (such as anoperator) which alters the functioning of a nearbygene or genes on the samechromosome.Cis-dominant mutations affect theexpression of genes because they occur at sites that control transcription rather than within the genes themselves.
Any of a class of flattened, membrane-boundvesicles orsaccules of thesmooth androughendoplasmic reticulum and theGolgi apparatus. By traveling through one or more cisternae, each of which contains a distinct set of enzymes, newly created proteins and polysaccharides undergo chemical modifications such asphosphorylation andglycosylation, which are used as packaging signals to direct their transport to specific destinations within the cell.[18]
The branch ofgenetics based solely on observation of the visible results of reproductive acts, as opposed to that made possible by the modern techniques and methodologies ofmolecular biology. Contrastmolecular genetics.
2. Inembryology, the series ofmitotic divisions by which afertilized ovum is divided, without an accompanying overall change in size, into a ball of smaller cells constituting the earlyembryo.[3]
The process of producing, either naturally or artificially, individual organisms or cells which are genetically identical to each other. Clones are the result of all forms ofasexual reproduction, and cells that undergomitosis produce daughter cells that are clones of the parent cell and of each other. Cloning may also refer to biotechnology methods which artificially create copies of organisms or cells, or, inmolecular cloning, copies of DNA fragments or other molecules.
Alsosense strand,positive (+) sense strand, andnontemplate strand.
The strand of a double-stranded DNA molecule whose nucleotide sequence corresponds directly to that of the RNA transcript produced duringtranscription (except thatthymine bases are substituted withuracil bases in the RNA molecule). Though it is not itself transcribed, the coding strand is by convention the strand used when displaying a DNA sequence because of the direct analogy between its sequence and thecodons of the RNA product. Contrasttemplate strand; see alsosense.
A series of three consecutivenucleotides in a coding region of anucleic acid sequence. Each of these triplets codes for a particularamino acid orstop signal duringprotein synthesis.DNA andRNA molecules are each written in a language using four "letters" (four differentnucleobases), but the language used to construct proteins includes 20 "letters" (20 different amino acids). Codons provide the key that allows these two languages to betranslated into each other. In general, each codon corresponds to a single amino acid (or stop signal). The full set of codons is called thegenetic code.
The preferential use of a particularcodon to code for a particularamino acid rather than alternative codons that are synonymous for the same amino acid, as evidenced by differences between organisms in the frequencies of the synonymous codons occurring in their coding DNA. Because thegenetic code isdegenerate, most amino acids can be specified by multiple codons. Nevertheless, certain codons tend to be overrepresented (and others underrepresented) in different species.
A relatively small, independentcofactor which associates with a specificenzyme and participates in the reaction(s) catalyzed by the enzyme, often by forming a covalent bond with thesubstrate. Examples includebiotin,NAD+, andcoenzyme A.[8]
A property ofnucleic acidbiopolymers whereby two polymeric chains or "strands" alignedantiparallel to each other will tend to formbase pairs consisting ofhydrogen bonds between the individualnucleobases comprising each chain, with each type of nucleobase pairing almost exclusively with one other type of nucleobase; e.g. indouble-strandedDNA molecules,A pairs only withT andC pairs only withG. Strands that are paired in such a way, and the bases themselves, are said to becomplementary. The degree of complementarity between two strands strongly influences the stability of theduplex molecule; certain sequences may also be internally complementary, which can result in a single strandbinding to itself. Complementarity is fundamental to the mechanisms governingDNA replication,transcription, andDNA repair.
DNA that is synthesized from a single-strandedRNA template (typicallymRNA ormiRNA) in a reaction catalyzed by the enzymereverse transcriptase. cDNA is produced both naturally byretroviruses and artificially in certain laboratory techniques, particularlymolecular cloning. Inbioinformatics, the term may also be used to refer to the sequence of an mRNA transcript expressed as its DNAcoding strand counterpart (i.e. withthymine replacinguracil).
Incell culture, a measure of the proportion of the surface area of aculture vessel that is covered byadherent cells, commonly expressed as a percentage. A culture in which the entire surface is completely covered by a continuousmonolayer, such that all cells are immediately adjacent to and in direct physical contact with other cells, with no gaps or voids, is said to be 100-percent confluent. Differentcell lines may exhibit differences in morphology, growth rate, orgene expression depending on the degree of confluence. Because ofcontact inhibition, most show a significant reduction in the rate ofcell division as they approach complete confluence, though someimmortalized cells may continue to divide, expanding vertically rather than horizontally by stacking themselves on top of theparent cells, until all available nutrients are depleted.[10][4]
conformation
The three-dimensional spatial configuration of the atoms comprising a molecule ormacromolecular structure.[10] The conformation of aprotein is the physical shape into which itspolypeptide chains arrange themselves duringprotein folding, which is not necessarily rigid and maychange with the protein's particular chemical environment.
A change in the spatialconformation or physical shape of a molecule or macromolecule such as a protein or nucleic acid, rarely spontaneously but more commonly as a result of some alteration in the molecule's chemical environment (e.g. temperature, pH, salt concentration, etc.) or an interaction with another molecule. Changes in thetertiary structures of proteins can affect whether or how strongly they bindligands orsubstrates; inducing these changes is a common means (both naturally and artificially) of activating, inactivating, or otherwise controlling the function of many enzymes and receptor proteins.[4]
A calculated order of the most frequentresidues (of eithernucleotides oramino acids) found at each position in a commonsequence alignment and obtained by comparing multiple closely related sequence alignments.
conservative replication
A hypothetical mode ofDNA replication in which the two parentalstrands of the originaldouble-stranded DNA molecule ultimately remain hybridized to each other at the end of the replication process, with the two daughter strands forming their own separate molecule; hence one molecule is composed of both of the starting strands while the other is composed of the two newly synthesized strands. This is in contrast tosemiconservative replication, in which each molecule is a hybrid of one old and one new strand. See alsodispersive replication.
Anucleic acid orprotein sequence that is highly similar or identical across many species or within agenome, indicating that it has remained relatively unchanged through a long period of evolutionary time.
constitutive expression
1. The continuoustranscription of agene, as opposed tofacultative expression, in which a gene is only transcribed as needed. A gene that is transcribed continuously is called aconstitutive gene.
Alsocontact inhibition of growth ordensity-dependent inhibition.
Incell culture, the phenomenon by which most normal eukaryotic cellsadhering to a planar substratum cease to grow anddivide upon reaching a critical cell density, usually as they approach fullconfluence or come into physical contact with other cells. As a result, many types of cells cultured on plates or inPetri dishes will continue to proliferate until they cover the whole surface of the culture vessel, at which point the rate of cell division abruptly decreases or is arrested entirely, thus forming a confluentmonolayer with minimal overlap between neighboring cells, even if the nutrient medium remains plentiful, rather than stacking themselves on top of each other.[15]Transformed orneoplastic cells tend not to respond to cell density in the same way and may continue to proliferate at high densities.[10] This type of density-dependent inhibition of growth is similar to and may occur simultaneously with, but is nonetheless distinct from, the related phenomenon of contact inhibition of movement,[4] whereby moving cells respond to physical contact by temporarily stopping and then reversing their direction of locomotion away from the point of contact.
A phenomenon observed in someenzymes,receptor proteins, andprotein complexes which have multiplebinding sites, whereby the binding of aligand to one or more sites apparently increases or decreases the affinity of one or more other binding sites for other ligands. This concept highlights the sensitive nature of the chemistry that governs interactions between biomolecules: the strength and specificity of interactions between protein and ligand are influenced, sometimes substantially, by nearby interactions (oftenconformational changes) and by the local chemical environment in general. Cooperativity is frequently invoked to account for the non-linearity of data resulting from attempts to measure theassociation/dissociation constants of particularprotein–protein interactions.[4]
A phenomenon in which sections of agenome are repeated and the number ofrepeats varies between individuals in the population, usually as a result ofduplication ordeletion events that affect entire genes or sections of chromosomes. Copy-number variations play an important role in generatinggenetic variation within a population.
A sequence of DNA in which acytosine nucleotide is immediately followed by aguanine nucleotide on the samestrand in the 5'-to-3'direction; the "p" in CpG refers simply to the interveningphosphate group linking the two consecutive nucleotides.
Any chemical bond or series of bonds, normal or abnormal, natural or artificial, that connects two or morepolymeric molecules to each other, creating an even larger, often structurally rigid and mechanically durablemacromolecular complex. Crosslinks may consist ofcovalent,ionic, orintermolecular interactions, or even extensive physical entanglements of molecules, and may be reversible or irreversible; inpolymer chemistry the term is often used to describe macrostructures that form predictably in the presence of a specific catalyst. Inmolecular biology the usage generally implies abnormal bonding (whether naturally occurring or experimentally induced) between differentbiomolecules (or different parts of the same biomolecule) which are ordinarily separate, especiallynucleic acids andproteins.Crosslinking of DNA may occur betweennucleobases on oppositestrands of adouble-stranded DNA molecule (interstrand), or between bases on the same strand (intrastrand), via the formation of covalent bonds that are stronger than the hydrogen bonds of normalbase pairing; these are common targets ofDNA repair pathways. Proteins are also susceptible to becoming crosslinked to DNA or to other proteins through bonds to specific surface residues, a process which is deliberately induced in many laboratory methods such asfixation and which can be useful for studyinginteractions between proteins in theirnative states. Crosslinks are generated by a variety ofexogenous andendogenous agents, including chemical compounds and high-energy radiation, and tend to interfere with normal cellular processes such asDNA replication andtranscription, meaning their persistence usually compromises cell health.
DNA (black) and protein (blue) can undergocrosslinking in the presence of sufficiently concentratedformaldehyde (red).
The end of a linear chain ofamino acids (i.e. apeptide) that is terminated by the freecarboxyl group (–COOH) of the last amino acid to be added to the chain duringtranslation. This amino acid is said to beC-terminal. By convention, sequences, domains, active sites, or any other structure positioned nearer to the C-terminus of thepolypeptide or the foldedprotein it forms relative to others are described asdownstream. ContrastN-terminus.
The total amount ofDNA contained within ahaploidnucleus (e.g. agamete) of a particular organism or species, expressed in number ofbase pairs or in units of mass (typicallypicograms); or, equivalently, one-half the amount in adiploidsomatic cell. For simple diploideukaryotes the term is often used interchangeably withgenome size, but in certain cases, e.g. in hybridpolyploids descended from parents of different species, the C-value may actually represent two or more distinctgenomes contained within the same nucleus. C-values apply only togenomic DNA, and notably excludeextranuclear DNA.
A term used to describe a diverse variety of questions regarding the immense variation in nuclearC-value orgenome size among eukaryotic species, in particular the observation that genome size does not correlate with the perceived complexity of organisms, nor necessarily with the number ofgenes they possess; for example, many single-celledprotists have genomes containing thousands of times more DNA than thehuman genome. This was considered paradoxical until the discovery that eukaryotic genomes consist mostly ofnon-coding DNA, which lacks genes by definition. The focus of the enigma has since shifted to understanding why and how eukaryotic genomes came to be filled with so much non-coding DNA, and why some genomes have a higher gene content than others.
The study of the morphology, processes, and life history of livingcells, particularly by means of light and electron microscopy.[10] The term is also sometimes used as a synonym for the broader field ofcell biology.
The interdisciplinary field that studiescell biology,cytology, andbiochemistry at the level of an individual cell by making use of single-cell molecular techniques and advanced microscopy to visualize the interactions of cellular componentsin vivo.[19]
All of the material contained within acell excluding (in eukaryotes) thenucleus;[8][4] i.e. that part of theprotoplasm which is enclosed by theplasma membrane but separated from thenucleoplasm by thenuclear envelope, consisting of the fluidcytosol and the totality of its contents, including all of the cell's internalcompartments,organelles, and substructures such asmitochondria,lysosomes, theendoplasmic reticulum,vesicles andinclusions, and a network of filamentousmicrotubules known as thecytoskeleton.[10] Some definitions of cytoplasm exclude certain organelles such asvacuoles andplastids. Composed of about 80 percent water, the numerous small molecules and macromolecular complexes dissolved or suspended within the cytoplasm give it characteristicviscoelastic andthixotropic properties, allowing it to behave variously as a gel or a liquid solution.[15] Though continuous throughout the intracellular space, the cytoplasm can often be resolved into distinct phases of different density and composition, such as anendoplasm andectoplasm.[15] Most of the metabolic and biosynthetic activities of the cell take place in the cytoplasm, includingprotein synthesis byribosomes. Despite their physical separation, the cytoplasm and the nucleus are mutually dependent upon each other, such that an isolated nucleus without cytoplasm is as incapable of surviving for long periods as is thecytoplasm without a nucleus.[15]
The flow of thecytoplasm inside a cell, driven by forces exerted upon cytoplasmic fluids by thecytoskeleton. This flow functions partly to speed up the transport of molecules andorganelles suspended in the cytoplasm to different parts of the cell, which would otherwise have to rely on passivediffusion for movement. It is most commonly observed in very large eukaryotic cells, for which there is a greater need for transport efficiency.
Anenucleated eukaryotic cell; or all other cellular components besides the nucleus (i.e. the cell membrane, cytoplasm, organelles, etc.) considered collectively. The term is most often used in the context ofnuclear transfer experiments, during which the cytoplast can sometimes remain viable in the absence of a nucleus for up to 48 hours.[15]
A spontaneousmutation in the genome of an individual organism that is new to that organism's lineage, having first appeared in agerm cell of one of the organism's parents or in the fertilized egg that develops into the organism; i.e. a mutation that was not present in either parent's genome.[6]
The assembly of a syntheticnucleic acid sequence from freenucleotides without relying on an existingtemplate strand, i.e.de novo, by any of a variety of laboratory methods.De novo synthesis makes it theoretically possible to construct completelyartificial molecules with no naturally occurring equivalent, and no restrictions on size or sequence. It is performed routinely in the commercial production of customized, made-to-orderoligonucleotide sequences such asprimers.
The removal of anacetyl group (–COCH 3) from a chemical compound, protein, or other biomolecule via hydrolysis of the covalentester bond adhering it, either spontaneously or byenzymatic catalysis. Deacetylation is the opposite ofacetylation.
The redundancy of thegenetic code, exhibited as the multiplicity of differentcodons that specify the sameamino acid. For example, in thestandard genetic code, the amino acidserine is specified by six unique codons (UCA,UCG,UCC,UCU,AGU, andAGC). Codon degeneracy accounts for the existence ofsynonymous mutations.
The removal of amethyl group (–CH 3) from a chemical compound, protein, or other biomolecule, either spontaneously or byenzymatic catalysis. Demethylation is the opposite ofmethylation; both reactions play important roles in numerous biochemical processes, including inregulating gene expression, as the methylation state of particular residues within particular proteins or nucleic acids can affect their structuralconformation in a way that alters their affinity for other molecules, making transcription at nearby genetic loci more or less likely.
The process by whichnucleic acids orproteins lose theirquaternary,tertiary, and/orsecondary structures, either reversibly or irreversibly, through the application of some external chemical or mechanical stress, e.g. by heating, agitation, or exposure to a strong acid or base, all of which can disrupt intermolecular forces such ashydrogen bonding and thereby change or destroy chemical activity. Denatured proteins may be both a cause and a consequence of cell death. Denaturation may also be a normal process; the denaturation ofdouble-stranded DNA molecules, for example, which breaks the hydrogen bonds betweenbase pairs and causes the separation of the duplex molecule into twosingle strands, is a necessary step inDNA replication andtranscription and hence is routinely performed by enzymes such ashelicases. The same mechanism is also fundamental to laboratory methods such asPCR.
Any of multiple freely branchingprotoplasmic processes extending from a vertebratenerve cell that receive electrical signals from other nerve cells or sensory receptors and integrate them in order to generate electrical impulses known asaction potentials. These pulse-like changes in electrical polarity are then propagated along anaxon and transmitted to other cells.[3]
Apolymericnucleic acid molecule composed of a series of covalently linkeddeoxyribonucleotides, each of which incorporates one of fournucleobases:adenine (A),guanine (G),cytosine (C), andthymine (T). DNA is most often found indouble-stranded form, which consists of twocomplementary,antiparallel nucleotide chains in which each of the nucleobases on each individualstrand ispaired viahydrogen bonding with one on the opposite strand; this structure commonly assumes the shape of adouble helix. DNA can also exist insingle-stranded form. By storing and encoding genetic information in thesequence of these nucleobases, DNA serves as the universal molecular basis of biological inheritance and the fundamental template from which all proteins, cells, and living organisms are constructed.
Amonosaccharidepentose sugar derived fromribose by the replacement of the hydroxyl group attached to the C2 carbon with a single hydrogen atom. D-deoxyribose, in its cyclic ring form, is one of three main functional groups ofdeoxyribonucleotides and hence ofdeoxyribonucleic acid (DNA) molecules.
Deoxyribose differs fromribose only at the 2' carbon, where ribose has an oxygen atom that deoxyribose lacks (hence its name).
The removal of aphosphate group,PO3− 4, from a chemical compound, protein, or other biomolecule, either spontaneously or byenzymatic catalysis. Dephosphorylation is the opposite ofphosphorylation; both reactions are common molecular modifications involved in numerous biochemical pathways and processes, including in metabolism, where high-energy bonds to phosphate groups are used to transfer energy between molecules, and in thepost-translational modification of proteins, where the phosphorylation state of particular residues can affect the protein's affinity for other molecules or function as amolecular signal.
The artificial modification of a molecule or protein with the intent of altering its solubility or other chemical properties so as to enable analysis (e.g. bymass spectroscopy orchromatography), or oflabelling it by attaching a detectable chemical moiety (e.g. a fluorescent tag) to make it easier to identify and trackin vivo. Molecules modified in this way are described as derivatives of their naturally occurring counterparts and are said to have beenderivatized.[4]
A specialized cell junction between neighboringepithelial cells consisting of a network ofkeratin filaments and structural proteins bridging the gap between the plasma membranes.[4]
Inmeiosis, the fifth and final substage ofprophase I, followingdiplonema and precedingmetaphase I. During diakinesis, the chromosomes are further condensed, the twocentrosomes reach opposite poles of the cell, and thespindle apparatus begins to extend from the poles to the equator.[6]
dicentric
(of a linearchromosome or chromosome fragment) Having twocentromeres instead of the normal one.[2]
The process by which a eukaryotic cell changes from onecell type to another, in particular from a non-specializedstem cell to a more specialized cell type which is then said to bedifferentiated. This usually occurs by a carefully regulated series ofepigenetic modifications which change the specific set ofgenesexpressed by the cell, turning certain genes "off" and others "on". These modifications result in a cascade ofphenotypic changes which can dramatically alter the cell's size, shape,metabolism,membrane properties, and rate ofdivision, and therefore its functions, behaviors, and responsiveness to signals, permitting multicellular organisms to create a huge variety of functionally distinct cell types from a singlegenome. Differentiation occurs repeatedly during an organism's development from a single-celledzygote into a complex multicellular system oftissues and cell types, and continues to some extent after the organism reaches maturity in order to repair and replace damaged and dying cells. In most cases differentiation is irreversible, though some cells may also undergodedifferentiation in specific circumstances.
A moleculardimer consisting of exactly two covalently linkednucleotides; or any two nucleotides which are immediately adjacent to each other on the samestrand of a longernucleic acid polymer.
Any two or morerepetitions of a specificsequence of nucleotides occurring in the same orientation (i.e. in precisely the same order and notinverted) and on the samestrand, either separated by intervening nucleotides or not. An example is the sequenceTACCGnnnnnnTACCG, in whichTACCG occurs twice, though separated by six nucleotides that are not part of the repeated sequence. A direct repeat in which the repeats are immediately adjacent to each other is known as atandem repeat.
The end-to-end orientation of a linearstrand orsequence of anucleic acid polymer or apolypeptide. The nomenclature used to indicate nucleic acid directionality is based on the chemical convention of identifying individual carbon atoms in theribose ordeoxyribose sugars of nucleotides, specifically the5' carbon and3' carbon of thepentose ring. The sequence of nucleotides in a polymeric chain may be read or interpreted in the 5'-to-3' direction (i.e. starting from the terminal nucleotide in which the 5' carbon is not connected to another nucleotide, and proceeding to the other terminal nucleotide, in which the 3' carbon is not connected to another nucleotide) or in the opposite 3'-to-5' direction. Most types of nucleic acid synthesis, includingDNA replication andtranscription, build chains of nucleotides exclusively in the 5'-to-3' direction, because thepolymerases involved can only catalyze the addition of free nucleotides to the open 3'-end of the previous nucleotide in the chain. Because of this, the convention when writing any nucleic acid sequence is to present it in the 5'-to-3' direction from left to right. Indouble-stranded nucleic acids, the two paired strands must beoriented in opposite directions in order tobase-pair with each other. Polypeptide directionality is similarly based on identifying the functional groups ofamino acids, specifically the amino group, which forms theN-terminus, and the carboxyl group, which forms theC-terminus; amino acid sequences are assembled in the N-to-C direction duringtranslation, and by convention are written in the same direction.
A hypothetical mode ofDNA replication in which the pairing oftemplate strands and newly synthesized strands is not consistent within the same daughter molecule; i.e. each of the replicated daughter molecules is a heterogeneous mixture, with some segments composed of the original template strands and others composed of the newly synthesized strands. This process implies that the pairing of strands does not occur uniformly at allreplication forks. Only thesemiconservative mode of replication occurs naturally. See alsoconservative replication.
dissimilatory process
Anyexergonic process of microbialcatabolism by whichredox-active chemical species participate inoxidation-reduction reactions (exchange of electrons) to provide the cell with energy needed for sustainingmetabolic activities.Exogenous substances are absorbed by the cell from its environment and then decomposed to release energy, with thebyproducts subsequentlyexcreted out of the cell. This is in contrast to anassimilatory process, in which the atoms of the exogenous substances are reused in the synthesis of biomolecules or the fabrication of cellular components.
distance measure
Any quantity used to measure the dissimilarity between thegene expression levels of differentgenes.[21]
A method of taxonomic identification in which short DNA sequences from one or more specific genes are isolated from unidentified samples and thenaligned with a genomicreference library in order to uniquely identify the species or other taxon from which the samples originated. The sequences used in the comparison are chosen carefully from genes that are both widelyconserved and that show greatervariation between species than within species, e.g. thecytochrome c oxidase gene for eukaryotes or certainribosomal RNA genes for prokaryotes. These genes are present in nearly all living organisms but tend to evolve different mutations in different species, such that a unique sequence variant can often be linked to one particular species, effectively creating a unique identifier akin to a retailbarcode. DNA barcoding allows unknown specimens to be identified from otherwise indistinct tissues or body parts, where identification by morphology would be difficult or impossible, and the library of organismal barcodes is now comprehensive enough that even organisms previously unknown to science can often bephylogenetically classified with confidence. The simultaneous identification of multiple different species from a mixed sample is known asmetabarcoding.
Ahigh-throughput technology used to measureexpression levels ofmRNA transcripts or to detect certain changes innucleotide sequence. It consists of an array of thousands of microscopic spots ofDNAoligonucleotides, calledfeatures, each containing picomoles of a specific DNA sequence. This can be a short section of agene or any other DNA element, and is used as aprobe to hybridize acDNA, cRNA, orgenomic DNA sample (called atarget) underhigh-stringency conditions. Probe-targethybridization is usually detected and quantified by fluorescence-based detection offluorophore-labeled targets.
Any of a class ofenzymes which synthesizeDNA molecules from individualdeoxyribonucleotides. DNA polymerases are essential forDNA replication and usually work in pairs to create identical copies of the twostrands of an original double-stranded molecule. They build long chains of DNA by adding nucleotides one at a time to the3'-end of a DNA strand, usually relying on thetemplate provided by thecomplementary strand to copy the nucleotide sequence faithfully.
The set of processes by which a cell identifies and corrects structural damage ormutations in theDNA molecules that encode itsgenome. The ability of a cell to repair its DNA is vital to the integrity of the genome and the normal functionality of the organism.
The process by which aDNA molecule copies itself, producing two identical copies of one original DNA molecule. This occurs by asemiconservative mechanism involving the separation of a double-stranded molecule into two individual strands, each of which then serves as a template for the synthesis of a new strand of complementary nucleotides. Replication ofchromosomes takes place during theS phase ofinterphase, thoughextrachromosomal DNA molecules such asmitochondrial DNA andplasmids may replicate independently at other times. DNA replication is the chief process by which genetic information is propagated in all living organisms and the central mechanism underlying biological inheritance.
The process of determining, by any of a variety of different methods and technologies, the order of thebases in the long chain of nucleotides that constitutes asequence ofDNA.
A proteindomain containing at least one structural motif capable of recognizing and interacting with thenucleotides of adouble-stranded orsingle-strandedDNA molecule. DNA-binding domains may bind to specific sequences or have a non-specific affinity for DNA. They are the primary functional components ofDNA-binding proteins, including manytranscription factors and regulatory proteins.
The molecular structures of several common classes ofDNA-binding domains (grey), showing how they interact with the DNA double helix (blue)
Anypolypeptide orprotein containing one or moredomains capable of interacting chemically with one or more parts of aDNA molecule, and consequently having a specific or general affinity forsingle- and/ordouble-stranded DNA. DNA-binding activity often depends on the presence and physical accessibility of a specific nucleobase sequence, and mostly occurs at themajor groove, since it exposes more of the functional groups which uniquely identify the bases. Binding is also influenced by the spatial conformation of the DNA chain and the occupancy of other proteins near the binding site; many proteins cannot bind to DNA without first undergoingconformational changes induced by interactions with other molecules.
A discrete, usually contiguous region of aprotein (or the correspondingamino acid sequence of apolypeptide) which serves a particular function or is defined by particular physico-chemical properties (e.g.hydrophobic, polar, non-polar,globular, etc.),[4] and especially one which folds independently of the rest of the polypeptide into a characteristic, self-stabilizing spatialconformation as part of the protein'ssupersecondary structure and which contributes to or defines its biological activity. Large proteins are generally composed of multiple domains linked by short, intervening non-domain sequences.[8] Domains are commonly grouped into classes with similar properties or functions, e.g.DNA-binding domains. More broadly, the term may also be used to refer to a discrete structural entity within any biomolecule, including functionally or compositionally distinct subregions ofnucleic acid sequences andchromosomes.[15]
Any mechanism by which organisms neutralize the large difference ingene dosage caused by the presence of differing numbers ofsex chromosomes in the different sexes, thereby equalizing theexpression of sex-linked genes so that the members of each sex receive the same or similar amounts of theproducts of such genes. An example isX-inactivation in female mammals.
The shape most commonly assumed bydouble-strandednucleic acid molecules, resembling a ladder that has been twisted upon its long axis, with the rungs of the ladder consisting ofpairednucleobases. Thissecondary structure is the most energetically stable conformation of the double-stranded forms of bothDNA andRNA under most naturally occurring conditions, arising as a consequence of theprimary structure of thephosphodiester backbone and the stacking of thenucleotides bonded to it. InB-DNA, the most common DNA variant found in nature, the double helix has a right-handed twist with about 10 base pairs per full turn, and the molecular geometry results in an alternating pattern of "grooves" of differing widths (amajor groove and aminor groove) between the parallel backbones.
Double-stranded DNA most commonly exists in the shape of adouble helix.
The loss of continuity of thephosphate-sugar backbone in both strands of adouble-stranded DNA molecule, in particular when the two breaks occur at sites that are directly across from or very close to each other on the complementary strands.[15] Contrastsingle-strand break.
Any process, natural or artificial, which decreases the level ofgene expression of a certaingene. A gene which is observed to be expressed at relatively low levels (such as by detecting lower levels of itsmRNA transcripts) in one sample compared to another sample is said to bedownregulated. Contrastupregulation.
The abnormal growth or development of atissue or organ; a change in the growth, behavior, or organization of cells within a tissue, or the presence of cells of an abnormal type, such that the tissue becomes disordered,[8] an event which often precedes the development ofcancer.
Occurring or developing in an abnormal place or position or in an unusual form or manner; displaced, malpositioned, or produced in an unnatural context. For example, ectopic expression refers to the expression of a particular gene product in a cell or tissue where it is not normally expressed.[3] Contrastentopic.
Any small molecule orligand which by interacting with a particularenzyme changes its catalytic activity but is not itself changed. Apositive effector enhances the enzyme's activity while anegative effector reduces it.[3]
The process by whichelectrons are transferred fromelectron donors toelectron acceptors via a stepwise series ofredox reactions carried out by dedicatedenzymes andprotein complexes, especially as a component ofmetabolic pathways which convert chemical energy from food into a form that is readily accessible by the cell. Most electron transport chains begin by oxidizing molecules derived fromglycolysis such asNADH andFADH, converting them into a series of intermediate compounds via a specific sequence of independently catalyzed reactions, with the products of the previous reaction used as reactants in the next reaction until ultimately reaching a terminal electron acceptor. The particular compounds used as donors, intermediates, and acceptors vary widely between organisms and cell types; inaerobic respiration, the terminal acceptor is diatomic oxygen (O 2), whereasanaerobic respiration uses other acceptors. In all variants, the free energy released by these reactions is coupled to thechemiosmotic pumping ofprotons (H+ ) across a membrane in order to generate anelectrochemical gradient which is then used to drive the production ofATP, a process known asoxidative phosphorylation. In eukaryotes, electron transport chains are conducted by proteins embedded within the membranes ofmitochondria andchloroplasts, while in prokaryotes the relevant proteins are embedded within thecell membrane.
A schematic layout of theelectron transport chain as it occurs in most animal mitochondria:NADH andFADH supplied by thecitric acid cycle donate their electrons to an enzyme embedded within the inner mitochondrial membrane, from which the electrons are then transferred through a series of other embedded enzymes, all of which use the free energy gained to pump protons into the intermembrane space, against their concentration gradient. The pressure to restore electrochemical equilibrium bymoving protons back across the membrane is exploited byATP synthase, which uses the free energy to catalyze the addition of a phosphate group toADP, converting it toATP.
The physical separation of molecules, e.g.nucleic acids orproteins, according to their movement through a fluid medium to which an electric field is applied, where the distance they travel is proportional to their size. Because of their negatively chargedphosphate backbones, nucleic acids are repelled by the negative electrode at one end of the medium and attracted to the positive electrode at the other end, which causes them to be pulled toward the latter over time;denatured proteins and even whole cells may migrate through the medium in a similar manner. The speed at which the molecules migrate depends on their netelectric charge and is inversely proportional to their overall size (i.e. the number of atoms they contain), such that very small molecules tend to move faster through the medium than very large molecules. Thus electrophoretic techniques, particularlygel electrophoresis withagarose orpolyacrylamide-based gels as the supporting medium, are widely used in molecular biology laboratories to quickly and conveniently isolate molecules of interest from heterogeneous mixtures and/or identify them based on their expectedmolecular weight. Reference markers containing molecules of known weight are commonly run alongside unknown samples to aid size-based identification. Electrophoresis is often combined with other techniques such asimmunolabelling and radiolabelling.[10]
A molecular biology technique in which a strong electric field is applied to living cells in order to temporarily increase the permeability of their cell membranes, allowing exogenous nucleic acids, proteins, or chemical compounds to easily pass through the membrane and thereby enter the cells. It is a common method of achievingtransformation andtransfection.
The developing organism that represents the earliest stages ofdevelopment in all sexually reproducingmulticellular organisms, traditionally encompassing the period afterfertilization of anegg cell and formation of thezygote but prior to birth, hatching, or metamorphosis. During this period, known asembryonic development, the single-cell zygote is transformed by repeatedcell divisions and rearrangements into a series of increasingly complex multicellular structures. For humans, the term "embryo" is only used until the ninth week after conception, after which time the embryo is known as afoetus; for most other organisms, including plants, "embryo" can be used more broadly to describe any early stage of the life cycle.
Any process by which a substance isactively uptaken by or brought inside of acell, crossing theplasma membrane from anextracellular space into anintracellular space, which includes the subclasses ofpinocytosis,phagocytosis, andreceptor-mediated processes. All of these involve surrounding an extracellular molecule, protein, or even another cell or organism with an extension orinvagination of the cell membrane, which then "buds off" or separates from the rest of the membrane on the cytoplasmic side, forming a membrane-enclosedvesicle containing the ingested materials. By this mechanism the material can cross thelipid bilayer without being exposed to the hydrophobic space in between, instead remaining suspended in the fluid of the extracellular space. Many large, polar macromolecules which cannot simply diffuse across the membrane, such asmetabolites andhormones, are transported into the cell by endocytosis. It is distinguished from alternative routes such as passing throughprotein channels or being chaperoned bytransport proteins. The reverse process is calledexocytosis.
Originating or arising inside of an organism or cell; produced by the organism or cell itself, rather than sourced from the external environment; of or pertaining to native or internal factors or processes, to be distinguished from foreign orexogenous factors or processes.[3]
Anyenzyme whose activity is to cleavephosphodiester bonds within a chain ofnucleotides, including those that cleave relatively nonspecifically (without regard tosequence) and those that cleave only at very specific sequences (so-calledrestriction endonucleases). When recognition of a specific sequence is required, endonucleases make their cuts in the middle of the sequence. Contrastexonuclease.
The irregular network of unit membranes, continuous with theouter nuclear membrane, that extends from thenucleus into thecytoplasm in most eukaryotic cells, where it serves important packaging and transport functions for newly synthesized macromolecules. The membranes interweave to form a mesh of tubular channels and flattened sacs calledcisternae which house a variety of enzymes that performpost-translational modifications includingtagging proteins forsorting. The outer surfaces of so-calledrough endoplasmic reticulum are studded with attachedribosomes that serve as sites of protein synthesis, whereassmooth endoplasmic reticulum, lacking ribosomes, functions in the synthesis oflipids and steroid hormones and in the detoxification of metabolic wastes.[3] Generally both types of ER occur together, though some cell types are characterized by different proportions of rough and smooth ER, depending on the activities of the cell.
Any of a class of intracellularmembrane-bound organelles which serve transportation and sorting functions in eukaryotic cells as part of theendocytic cycle. They are formed when proteins or other macromolecules enter the cytoplasm insidevesicles invaginated from thecell membrane or thetrans-Golgi network byendocytosis, after which they are shuttled across the cell to various destinations; e.g. endosomes carrying foreign molecules often fuse withlysosomes, where the contents are then degraded.
A subclass oflong non-coding RNAs transcribed from regions of DNA containingenhancer sequences. The expression of a given eRNA generally correlates with the activity of the corresponding enhancer in enhancing transcription of its target genes, suggesting that eRNAs play an active role in gene regulationincis orintrans.
Occurring or developing in the normal or natural place or position, as opposed toectopic.[3]
enucleate
To artificially remove thenucleus from acell, e.g. by micromanipulation in the laboratory or by destroying it through irradiation with ultraviolet light, rendering the cellanucleate.[10]
Aprotein which acts as acatalyst for a biological process by accelerating a specificchemical reaction, typically by binding one or moresubstrate molecules and decreasing theactivation energy necessary for the initiation of a particular reaction involving the substrate(s). Enzymatic catalysis often results in the chemical conversion of the substrate(s) into one or more products, which then inhibit or permit subsequent reactions. Allmetabolic pathways consist of a series of individual reactions which each depend upon one or more specific enzymes to drive them forward at rates fast enough to sustain life.
Abiochemical assay designed to detect the presence of a particularantigen orligand in a liquid sample usingenzymes conjugated toantibodies capable of specifically binding the antigen. The antigen of interest is usually first immobilized by adhering to a solid support (e.g. a polystyrenemicrotiter plate), then one or more antigen-specific antibodies covalently bonded to a particular enzyme are added and any unbound antibody is washed away; when the attached enzyme'ssubstrate is subsequently added, the reaction between enzyme and substrate produces a detectable, quantifiable change in some measurablebiomarker (often a color change), thus reporting the presence of the targeted antigen in the sample. ELISA techniques are widely used as diagnostic tools in clinical medicine and academic research, as well as a form of quality control in many biotechnology industries.
1. Another name for aplasmid, especially one that is capable of integrating into achromosome.
2. Ineukaryotes, any non-integratedextrachromosomal circularDNA molecule that is stably maintained and replicated in thenucleus simultaneously with the rest of the host cell. Such molecules may include viral genomes, bacterial plasmids, and aberrant chromosomal fragments.
The collective action of multiple genes interacting duringgene expression. A form of gene action, epistasis can be either additive or multiplicative in its effects on specificphenotypic traits.
The specific site or region within anantigenicmacromolecule such as aprotein orcarbohydrate which is recognized byB orT cells of the immune system, against which a specificantibody is produced, and with which the antibody'sparatope specifically interacts or binds. In proteins, epitopes are typicallymotifs of 4–5 amino acid residues, sequential or discontiguous, which by virtue of the distinct spatialconformation they adopt uponprotein folding are able to uniquely interact with a particular paratope. In this sense they may be consideredbinding sites, though they do not necessarily overlap with ligand binding sites and need not be in any way relevant to the protein's normal function. Very large molecules may have multiple epitopes, each of which is recognized by a different antibody.
A relatively open, lightly compacted form ofchromatin in whichDNA is only sporadically bound innucleosomes and thus broadly accessible to binding and manipulation byproteins and other molecules. Euchromatic regions of a genome are often enriched ingenes and actively undergoingtranscription, in contrast toheterochromatin, which is relatively gene-poor, nucleosome-rich, and less accessible to transcription machinery.
The condition of a cell or organism having an abnormal number of complete sets ofchromosomes, possibly excluding thesex chromosomes. Euploidy differs fromaneuploidy, in which a cell or organism has an abnormal number of one or more specific individual chromosomes.
The change in theheritable characteristics of biological populations over successive generations. In the most traditional sense, it occurs by changes in the frequencies ofalleles in a population'sgene pool.
Occurring outside of a cell or organism, as with observations made or experiments performed in or on cells ortissues which have been isolated or removed from their natural context to an external environment (usually a carefully controlled environment with minimal alteration of natural conditions, such as acell culture being grown in a laboratory). This is in contrast toin vivo observations, which are made in an entirely natural context.
excision
The enzymatic removal of a polynucleotide sequence from one or more strands of anucleic acid, or of a polypeptide sequence from aprotein, typically implying both the breaking of the polymeric molecule in two locations and the subsequent rejoining of the two breakpoints after the sequence between them has been removed. The term may be used to describe a wide variety of processes performed by distinct enzymes, including mostsplicing andDNA repair pathways.[6]
Anyactive transport process by which a substance is secreted from or transported out of acell, crossing theplasma membrane from theinterior of the cell into theextracellular space, especially that which occurs by the fusion of the membrane surrounding a secretoryvesicle with the larger cell membrane. This fusion causes the intra-vesicular space to merge with the extracellular fluid, releasing the vesicle's contents on the exterior side of the cell without exposing them to the hydrophobic space between thelipid bilayer. More narrowly the term may refer in particular to the bulk transport of a large amount of molecules out of the cell all at once, oftenmetabolites orhormones which are too large and polar to passively diffuse across the membrane themselves. The reverse process, whereby materials are invaginated into the cell, is known asendocytosis.
Originating outside of an organism or cell; of or pertaining to foreign or external factors or processes, to be distinguished from native orendogenous factors or processes.[3]
Any part of agene that encodes a part of the final maturemessenger RNA produced by that gene afterintrons have been removed byalternative splicing. The term refers to both the sequence as it exists within a DNA molecule and to the corresponding sequence in RNA transcripts.
1. (protein complex) An intracellular multi-protein complex which serves the function of degrading various types ofRNA molecules.
2. (vesicle) A type of membrane-boundextracellular vesicle produced in many eukaryotic cells by the inward budding of anendosome and the subsequent fusion of the endosome with theplasma membrane, causing the release of the vesicle into various extracellular spaces, including biological fluids such as blood and saliva, where they may serve any of a wide variety of physiological functions, from waste management to intercellular signaling.
The network of interactingmacromolecules and minerals secreted by and existing outside of and between cells inmulticellular structures such astissues andbiofilms, forming a hydrated, mesh-like, semi-solid suspension which not only holds the cells together in an organized fashion but also provides structural and biochemical support, acting as an elastic, compressible buffer against external stresses as well as both regulating and influencing numerous aspects of cell behavior, among themcell adhesion,motility,metabolism,division, andcell-to-cell communication. The composition and properties of the ECM vary enormously between organisms and tissue types, but generally it takes the form of apolysaccharide gel in which various fibrous proteins (especiallycollagen andelastin), enzymes, andglycoproteins are embedded. Cells themselves both produce the matrix components and respond constantly to local matrix composition, a source of environmental feedback which is critical fordifferentiation, tissue organization, and development.[10][22]
AnyDNA that is not found inchromosomes or in thenucleus of a cell and hence is notgenomic DNA. This may include the DNA contained inplasmids ororganelles such asmitochondria orchloroplasts, or, in the broadest sense, DNA introduced byviral infection. Extrachromosomal DNA usually shows significant structural differences from nuclear DNA in the same organism.
A type ofpassive transport by which substances are conveyed acrossmembranes more quickly than would be possible by ordinary passivediffusion alone, generally becauseproteins embedded within the membrane act as shuttles or pores, being arranged in such a way as to provide ahydrophilic environment that is favorable for the movement of small polar molecules, which would otherwise be repulsed by thehydrophobic interior of thelipid bilayer.[4]
facultative expression
Thetranscription of agene only as needed, as opposed toconstitutive expression, in which a gene is transcribed continuously. A gene that is transcribed as needed is called afacultative gene.
Any of a subclass oflipid compounds consisting of acarboxylic acid bonded to analiphatic chain of hydrocarbons, usually 4 to 28 carbon atoms in length, which may be either saturated (containing only single bonds between the carbon atoms) or unsaturated (containing one or more double bonds). In biological systems, fatty acid chains are commonly linked to other compounds viaester bonds, primarily intriglycerides,phospholipids, and derivatives ofcholesterol, all of which serve a wide variety of important cellular functions including as structural components of membranes and as energy sources in metabolic pathways.
Anyanaerobicmetabolic pathway in which organic molecules such asglucose or other carbohydrates arecatabolized in the absence of oxygen in order to produceATP; or, in the broadest sense, any catabolic process in which organic compounds serve as both electron donors and acceptors.[23] This definition distinguishes fermentation fromaerobic respiration, where inorganic diatomic oxygen (O 2) is the terminal electron acceptor, and from some types ofanaerobic respiration. Fermentation encompasses hundreds of different redox pathways which start and end with a huge variety of reactants and end-products, often branching from various steps inglycolysis, with the most common fermentation products beinglactate,acetate,ethanol,succinate,propionate,butyrate, carbon dioxide (CO 2), and diatomic hydrogen (H 2). It occurs in both prokaryotes and eukaryotes in conditions where exogenously supplied electron acceptors are unavailable, especially in oxygen-poor environments. Fermentation yields the equivalent of just 2 to 5 ATP per molecule of glucose, making it much less efficient than aerobic respiration, which can yield as much as 32 ATP per molecule of glucose. In multicellular organisms that primarily rely on aerobic respiration, such as animals, it is often employed as a contingency pathway; the termanaerobic glycolysis refers to the diversion of glycolysis intermediates to fermentation pathways when tissues cannot keep up with the demand for ATP due to insufficient oxygen supply.
1. (histology) The preservation of biological material by treating it with a chemicalfixative that prevents or delays the natural postmortem processes of decay (e.g.autolysis andputrefaction) which would otherwise eventually cause cells, tissues, and biomolecules to lose their characteristic structures and properties. Biological specimens are usually fixed with the broad objective of arresting or slowing biochemical reactions for long enough to study them in detail, essentially 'freezing' cellular processes in their natural state at a specific point in time, while minimizing disruption to existing structures and arrangements, all of which can improve subsequentstaining and microscopy of the fixed samples. Though fixation tends to irreversibly terminate any ongoing reactions, thus killing the fixed cells, it makes it possible to study molecular details that occur too rapidly or transiently to observe in living samples. Common fixatives such asformaldehyde work by disablingproteolytic enzymes, coagulating, insolubilizing, and/ordenaturing macromolecules, creatingcrosslinks between them, and protecting specimens from decomposition by bacteria and fungi.
2. (population genetics) The process by which a singleallele for a particulargene with multiple different alleles increases infrequency in a given population such that it becomes permanently established as the only allele at thatlocus within the population'sgene pool.
fixative
Any chemical compound or solution that causes thefixation of cells, tissues, or other microscopic structures by any mechanism, thus preserving them for long-term, detailed study by methods such as embedding,staining, and microscopy. Common fixatives include dilute solutions ofethanol,acetic acid,formaldehyde, andosmium tetroxide, among others.[10]
A long, thin, hair-like appendage protruding from the surface of some cells, which serves locomotory functions by undulating in a way that propels the cell through its environment or by effecting the movement ofextracellular fluids and solutes past the cell surface. Many unicellular organisms, including some bacteria, protozoa, and algae, bear one or more flagella, and certain cell types in multicellular organisms, namely sperm cells, also have flagella. Eukaryotic flagella are essentially just longer versions ofcilia, often up to 150micrometres (μm) in length, while bacterial flagella are typically smaller and completely different in structure and mechanism of action.[8][10]
The prevailing scientific model of the structure and properties ofcell membranes, according to which the typical membrane consists ofback-to-back layers of amphipathicmembrane lipids (generallyphospholipids orglycolipids) interspersed with a dynamic variety of embeddedproteins,carbohydrates, and (especially in animal cells)cholesterol, all of which behave as if suspended in a "two-dimensional liquid", constantly moving laterally between the lipids and interacting with each other and with thecytoplasm and theextracellular space. The membrane as a whole thus retains a fluidity and elasticity which allow it to change shape and adapt to the cell's environment.[24]
An experimental approach inmolecular genetics in which a researcher starts with a specific knownphenotype and attempts to determine the genetic basis of that phenotype by any of a variety of laboratory techniques, commonly byinducing randommutations in the organism's genome and thenscreening for changes in the phenotype of interest. Observed phenotypic changes are assumed to have resulted from the mutation(s) present in the screened sample, which can then bemapped to specific genomicloci and ultimately to one or more specificcandidate genes. This methodology contrasts withreverse genetics, in which a specific gene or its gene product is individually manipulated in order to identify the gene's function.
A type ofmutation in anucleic acid sequence caused by theinsertion ordeletion of a number ofnucleotides that is not divisible by three. Because of the triplet nature by which nucleotides code for amino acids, a mutation of this sort causes a shift in thereading frame of the nucleotide sequence, resulting in the sequence ofcodons downstream of the mutation site being completely different from the original.
An organization that works with others "to develop standards for biological research data quality, annotation and exchange" as well as software tools that facilitate their use.[25]
A technique used incytogenetics to produce a visiblekaryotype bystaining the condensed chromosomes withGiemsa stain. The staining produces consistent and identifiable patterns of dark and light "bands" in regions ofchromatin, which allows specific chromosomes to be easily distinguished.
Ahaploid cell that is themeiotic product of a progenitorgerm cell and the final product of thegerm line insexually reproducing multicellular organisms. Gametes are the means by which an organism passes its genetic information to its offspring; during fertilization, two gametes (one from each parent) are fused into a singlediploidzygote.
Any segment or set of segments of anucleic acid molecule that contains the information necessary to produce a functionalRNA transcript in a controlled manner. In living organisms, genes are often considered the fundamental units ofheredity and are typically encoded inDNA. A particular gene can have multiple different versions, oralleles, and a single gene can result in agene product that influences many differentphenotypes.
The number of copies of a particulargene present in agenome. Gene dosage directly influences the amount ofgene product a cell is able to express, though a variety of controls have evolved which tightlyregulategene expression. Changes in gene dosage caused by mutations includecopy-number variations.
The set of processes by which the information encoded in agene is used in the synthesis of agene product, such as a protein or anon-coding RNA, or otherwise made available to influence one or morephenotypes; both the product and the gene encoding it are then said to beexpressed. Canonically, the first step istranscription, which produces amessenger RNA molecule complementary to theDNA molecule in which the gene is encoded. For protein-coding genes, the second step istranslation, in which the messenger RNA is read by aribosome to produce apolypeptide and ultimately a protein. The information contained within a DNA sequence need not necessarily be transcribed and translated to exert an influence on molecular events, however: broader definitions encompass a huge variety of other ways in which genetic information can be expressed.
In the typical model ofgene expression, genetic information (red) encoded in a DNA molecule istranscribed with help from nearbyregulatory elements into a rawmessenger RNA, then processed into a mature form by the removal ofintrons and the addition of a5' cap and apoly-A tail, then finallytranslated into a polypeptide sequence which is folded into a functional protein.
The union, either by natural mutation or byrecombinant laboratory techniques, of two or more previously independent genes that code for different gene products such that they become subject to control by the sameregulatory systems. The resulting hybrid sequence is known as afusion gene.[6]
Any of a variety of methods used to precisely identify thelocation of a particulargene within a DNA molecule (such as a chromosome) and/or the physical orlinkage distances between it and other genes.
gene of interest (GOI)
Agene being studied in a scientific experiment, especially one that is the focus of agenetic engineering technique such ascloning.
Any of the biochemical material resulting from theexpression of agene, most commonly interpreted as the functionalmRNA transcript produced bytranscription of the gene or the fully constructedprotein produced bytranslation of the transcript, thoughnon-coding RNA molecules such astransfer RNAs may also be considered gene products. A measurement of the quantity of a given gene product that is detectable in a cell or tissue is sometimes used to infer how active the corresponding gene is.
The broad range of mechanisms used by cells to control the activity of their genes, especially to allow, prohibit, increase, or decrease the production orexpression of specificgene products, such asRNA orproteins. Gene regulation increases an organism's versatility and adaptability by allowing its cells to express different gene products when required by changes in its environment. In multicellular organisms, the regulation of gene expression also drivescellular differentiation andmorphogenesis in theembryo, enabling the creation of a diverse array ofcell types from the samegenome.
Any mechanism ofgene regulation which drastically reduces or completely prevents theexpression of a particular gene. Gene silencing may occur naturally during eithertranscription ortranslation. Laboratory techniques often exploit natural silencing mechanisms to achievegene knockdown.
The insertion of a functional orwild-type gene or part of a gene into an organism (especially a patient) with the intention of correcting agenetic defect, either by direct substitution of the defective gene or by supplementation with a second, functional version.[15]
1. In any given organism, a singlereproductive cycle, or the phase between two consecutive reproductive events, i.e. between an individual organism's reproduction and that of the progeny of that reproduction; or the actual or average length of time required to complete a single reproductive cycle, either for a particularlineage or for a population or species as a whole.
2. In a given population, those individuals (often but not necessarily living contemporaneously) who are equally removed from a givencommon ancestor by virtue of the same number of reproductive events having occurred between them and the ancestor.[15]
Any illness, disease, or other health problem directly caused by one or more abnormalities in an organism'sgenome which arecongenital (present at birth) and not acquired later in life. Causes may include amutation to one or moregenes, or achromosomal abnormality such as ananeuploidy of a particular chromosome. The mutation responsiblemay occur spontaneously during embryonic development or may beinherited from one or both parents, in which case the genetic disorder is also classified as ahereditary disorder. Though the abnormality itself is present before birth, the actual disease it causes may not develop until much later in life; some genetic disorders do not necessarily guarantee eventual disease but simplyincrease the risk of developing it.
A measure of the genetic divergence between species, populations within a species, or individuals, used especially inphylogenetics to express either the time elapsed since the existence of acommon ancestor or the degree of differentiation in theDNA sequences comprising thegenomes of each population or individual.
The direct, deliberate manipulation of an organism's genetic material using any of a variety of biotechnology methods, including theinsertion orremoval ofgenes, the transfer of genes within and between species, themutation of existing sequences, and the construction of novel sequences usingartificial gene synthesis. Genetic engineering encompasses a broad set of technologies by which the genetic composition of individual cells, tissues, or entire organisms may be altered for various purposes, commonly in order to study the functions andexpression of individual genes, to produce hormones, vaccines, and other drugs, and to creategenetically modified organisms for use in research and agriculture.
A specific, easily identifiable, and usually highlypolymorphicgene or otherDNAsequence with a known location on achromosome that can be used to identify the individual or species possessing it.
The redundant encoding of two or more distinctgene products that ultimately perform the same biochemical function.Mutations in one of these genes may have a smaller effect on fitness than might be expected, since the redundant genes often compensate for anyloss of function and obviate anygain of function.
Agraph that represents the regulatory complexity ofgene expression. The vertices (nodes) are represented by various regulatory elements andgene products while the edges (links) are represented by their interactions. These network structures also represent functional relationships by approximating the rate at which genes aretranscribed.
A broad class of various procedures used to identify features of an individual's particular chromosomes, genes, or proteins in order to determine parentage orancestry, diagnose vulnerabilities to heritable diseases, or detectmutant alleles associated with increased risks of developinggenetic disorders. Genetic testing is widely used in human medicine, agriculture, and biological research.
Any organism whose genetic material has been altered usinggenetic engineering techniques, particularly in a way that does not occur naturally by mating or by naturalgenetic recombination.
1. The entire complement of genetic material contained within thechromosomes of an organism,organelle, orvirus.
2. The collective set ofgenes or geneticloci shared by every member of a population or species, regardless of the differentalleles that may be present at these loci in different individuals.
The total amount ofDNA contained within one copy of agenome, typically measured bymass (in picograms ordaltons) or by the total number ofbase pairs (inkilobases ormegabases). Fordiploid organisms, genome size is often used interchangeably withC-value.
A method ofwhole-genome sequencing in which thesequences ofgenomic DNA fragments in alibrary sample are assembled into a longer sequence, such as that of a full chromosome or the entire genome, by placing fragments with overlapping ends, known ascontigs, adjacent to each other. By repeating this procedure, one can hypothetically determine the correct arrangement of contigs for the entire sequence.[3]
Anepigenetic phenomenon that causesgenes to beexpressed in a manner dependent upon the particular parent from which the gene was inherited. It occurs when epigenetic marks such asDNA orhistone methylation are established or "imprinted" in thegerm cells of a parent organism and subsequently maintained through cell divisions in thesomatic cells of the organism's progeny; as a result, a gene in the progeny that was inherited from the father may be expressed differently than another copy of the same gene that was inherited from the mother.
A region of agenome that shows evidence ofhorizontal transfer from another organism. The term is used especially in describing microbial genomes such as those of bacteria, where genomic islands having the same or similar sequences commonly occur in species or strains that are otherwise only distantly related, implying that they were not passed on through vertical descent from a common ancestor but through some form of lateral transfer such asconjugation. These islands often contain functional genes which confer adaptive traits such asantibiotic resistance.
The ability of certain chemical agents to cause damage to genetic material within a living cell (e.g. through single- or double-stranded breaks,crosslinking, orpoint mutations), which may or may not result in a permanentmutation. Though allmutagens are genotoxic, not all genotoxic compounds are mutagenic.
The process of determining differences in thegenotype of an individual by examining theDNA sequences in the individual'sgenome usingbioassays and comparing them to another individual's sequences or a reference sequence.
Anycell that gives rise to thegametes of asexually reproducing organism. Germ cells are the vessels for the genetic material which will ultimately be passed on to the organism's descendants and are usually distinguished fromsomatic cells, which are entirely separate from thegerm line.
1. In multicellular organisms, the subpopulation of cells which are capable of passing on their genetic material to the organism's progeny and are therefore (at least theoretically) distinct fromsomatic cells, which cannot pass on their genetic material except to their own immediatemitotic daughter cells. Cells of the germ line are calledgerm cells.
2. Thelineage of germ cells, spanning many generations, that contains the genetic material which has been passed on to an individual from its ancestors.
The chain ofmetabolic reactions that results in the generation ofglucose from some non-carbohydrate carbon substrates, including theglucogenic amino acids. It is one of two primarypathways used by most animals to maintain blood sugar levels (the other beingglycogenolysis), especially during periods of fasting, starvation, and intense exercise.
A simple sugar with the molecular formulaC 6H 12O 6 and the most abundantmonosaccharide in nature, being the primary product ofphotosynthesis, where it is made in a sunlight-powered reaction of water with carbon dioxide. All living organisms are capable of metabolizing glucose viaglycolysis, an exergonic pathway which for most organisms is the primary means of obtaining chemical energy to power cellular activities.[10] Metabolic glucose is usually stored in the form of large polymeric aggregates such asamylose in plants andglycogen in animals, and is released by the breakdown of these polymers viaglycogenolysis.
A branchedpolysaccharide composed of as many as 30,000 covalently bonded units of themonosaccharideglucose which functions as the primary form of short-term energy storage in most animal cells.[10][4] Glycogen reserves are especially abundant in muscle and liver cells,[8] where they can be metabolized at-need into their component glucoses as a means of buffering blood sugar levels, a process known asglycogenolysis.
Ametabolic pathway in which polymericglycogen molecules are broken down into individualglucose monomers by the sequential removal of glucose units viaphosphorolysis, a reaction catalyzed by the enzymeglycogen phosphorylase. Glycogenolysis is one of two primary pathways used in animal tissues to generate free glucose for the maintenance of blood sugar levels, the other beinggluconeogenesis.
Themetabolic pathway in whichcarbohydrate sugars such asglucose are broken down into simpler molecules, releasing chemical energy which can then be used for various cellular functions. In a series of ten enzyme-catalyzed reactions, each molecule of glucose is converted into two molecules ofpyruvate, with the free energy liberated in this process simultaneously being used to form high-energy bonds in two molecules of reducednicotinamide adenine dinucleotide (NADH) and two molecules ofadenosine triphosphate (ATP). Inaerobic conditions pyruvate and NADH are further oxidized in themitochondria; inanaerobic conditions NADH itself subsequently reduces pyruvate tolactate.
Glycolysis convertsglucose topyruvate via a series of 10 steps, each catalyzed by a different enzyme and producing different intermediate metabolites. Steps 1 and 3 consumeATP (blue arrows) and steps 7 and 10 produce ATP (yellow arrows); steps 6 through 10 occur twice per molecule of glucose.
Aprotein with one or morecarbohydrate molecules, typically shortoligosaccharide chains, covalently attached to one or more of its amino acid side chains.[8] Proteins exposed on the outer surface of theplasma membrane or secreted into the extracellular space are commonly modified in this way, after which they are said to beglycosylated.
Any chemical compound consisting of acarbohydrate molecule covalently bonded to another molecule containing ahydroxyl group (including other carbohydrates) via one or moreC–Oglycosidic bonds. When all of the compound's substituents are carbohydrates, the glycoside is apolysaccharide.[10]
A covalentether bond that connects a carbon atom within acarbohydrate molecule (e.g. amonosaccharide) or a carbohydrate derivative to another substituent or functional group, which may or may not be another carbohydrate; such bonds form as the result of adehydration reaction between hydroxyl groups on each molecule. A substance containing a glycosidic bond is known as aglycoside.
The proportion ofnitrogenous bases in anucleic acid that are eitherguanine (G) orcytosine (C), typically expressed as a percentage. DNA and RNA molecules with higher GC-content are generally morethermostable than those with lower GC-content due to molecular interactions that occur during base stacking.[30]
A shortsingle-stranded RNAoligonucleotide which complexes with Casendonucleases and, by annealing to a specific complementary sequence in aDNA molecule, serves to "guide" these proteins to viral DNA introduced by foreign pathogens, which can then be digested and degraded as part of an adaptive immune defense employed by bacteria and archaea. Custom-made guide RNAs are designed by scientists to target specific genomic loci in CRISPR-Casgene editing.
A characteristicsecondary structure that commonly forms in self-complementarynucleic acid sequences by intramolecularbase pairing between different parts of the same linear,single-stranded molecule. The resulting conformation resembles ahairpin, where non-adjacent lengths of nucleotides form hydrogen bonds with each other, creating a local double-strandedduplex (the "stem") which ends in a circle of unpaired nucleotides (the "loop"). Hairpin loops form readily in single-stranded DNA molecules containinginverted repeats[3] and are especially common in large RNA molecules, where they play various roles in promoting or inhibiting the formation of other secondary structures, stabilizingmessenger RNAs, providing recognition sites forRNA-binding proteins, or serving assubstrates for enzymes.[31]
The structure of a basichairpin loop in a single-stranded RNA molecule
In adiploid organism, having just oneallele at a givengenetic locus (where there would ordinarily be two). Hemizygosity may be observed when only one copy of achromosome is present in a normally diploid cell or organism, or when a segment of a chromosome containing one copy of an allele isdeleted, or when a gene is located on asex chromosome in theheterogametic sex (in which the sex chromosomes do not exist in matching pairs); for example, in human males with normal chromosomes, almost allX-linked genes are said to be hemizygous because there is only oneX chromosome and few of the same genes exist on theY chromosome.
The storage, transfer, and expression of molecular information in biological organisms,[15] as manifested by the passing on ofphenotypic traits from parents to theiroffspring, either throughsexual orasexual reproduction. Offspring cells or organisms are said toinherit the genetic information of their parents.
A compact, highly condensed form ofchromatin characterized chiefly by the close spatial proximity of adjacentnucleosomes and the consequent inaccessibility of intervening DNA sequences toDNA-binding proteins, which contrasts with the more open and accessible form known aseuchromatin. The transcription of genes located within heterochromatic regions of chromosomes is therefore relatively limited, and so the formation of heterochromatin at specific loci is an important means of regulatinggene expression. Establishment of heterochromatin is associated with themodification of specific residues within specifichistones, such asmethylation of the ninthlysine residue ofhistone H3 (H3K9); the presence of these modifications at a specific locus signals the recruitment of other proteins which cause local DNA condensation. Many repetitive and structurally important regions of chromosomes are nearly always compacted in so-calledconstitutive heterochromatin, while the compaction offacultative heterochromatin is more temporary.
Theexpression of a foreigngene or any other foreign DNA sequence within a host organism which does not naturally contain the same gene. Insertion of foreigntransgenes into heterologous hosts usingrecombinantvectors is a common biotechnology method for studying gene structure and function.
high-throughput
Describing a method or system capable ofassaying very large numbers of samples or of processing very large quantities of data extremely rapidly, generally by utilizing automation and miniaturization to greatly increase speed and efficiency. For example,high-throughput sequencing refers to modernDNA sequencing technologies that can produce sequence reads for hundreds of millions of DNA fragments simultaneously, allowing scientists tosequence entire genomes quickly and inexpensively.[32]
The study or analysis of the microscopic anatomy of biologicaltissues or ofcells within tissues, particularly by making use of specialized techniques to distinguish structures and functions based on visual morphology and differential staining. In practice the term is sometimes used more broadly to includecytology.
The complex of eighthistone proteins around which double-stranded DNA wraps within anucleosome. The canonical histone octamer consists of two each of histonesH2A,H2B,H3, andH4, which pair with each other symmetrically to form a ball-shaped cluster around which DNA winds through interactions with the histones' surfacedomains, thoughvariant histones may replace their analogues in certain contexts.
Thepost-translational modification ofhistone proteins by the chemical attachment of various molecules or functional groups to specific amino acid residues. Because histones form thecore ofnucleosomes, the modification of exposed parts of their polypeptide chains is used to regulate gene expression by marking them withmolecular labels that signal the recruitment of other proteins to induce conformational changes that variously widen or condense the spacing of nucleosomes along strands of DNA, thereby changing the accessibility of nearby DNA sequences to transcriptional machinery. Histones are modified by many different labels, most commonlymethylation,acetylation,ubiquitination,phosphorylation, andcitrullination.
(of a linearchromosome or chromosome fragment) Having no singlecentromere but rather multiplekinetochore assembly sites dispersed along the entire length of the chromosome. During cell division, thechromatids of holocentric chromosomes move apart in parallel and do not form the classical V-shaped structures typical ofmonocentric chromosomes.
Any of a class of DNAsequences approximately 180 base pairs in length occurring near the3'‐end of certain eukaryotic genes and encoding a 60-amino acid domain, known as ahomeodomain, which is capable ofbinding to DNA or RNA via a characteristic helix-turn-helix motif. Homeobox-containing genes are translated into homeodomain-containing proteins, which commonlyregulate transcription or translation by binding to other genes or messenger RNAs containinghomeobox responsive elements. The products of many homeotic genes, exemplified by theHox genes, are of critical importance in developmental pathways.[6]
homeobox responsive element (HRE)
Alsohomeodomain responsive element.
Any DNA or RNAsequence that is specificallyrecognized and bound by thehomeodomain of a homeodomain-containing protein.
A set of two matchingchromosomes, one maternal and one paternal, which pair up with each other inside the nucleus duringmeiosis. They have the samegenes at the sameloci, but may have differentalleles.
Any process by which genetic material is transferred between unicellular and/or multicellular organisms other than by vertical transmission from parent to offspring, e.g.bacterial conjugation.
Anyconstitutive gene that istranscribed at a relatively constant level across many or all known conditions and cell types. Theproducts of housekeeping genes typically play critical roles in the maintenance of cellular integrity and basic metabolic function. It is generally assumed that their expression is unaffected by experimental or pathological conditions.
A subset of highlyconservedhomeobox-containinggenes whose protein products function astranscription factors essential for the proper organization of thebody plan in developing animalembryos, ensuring that the correct structures are formed in the correct places. Hox genes are usually arranged on a chromosome intandem arrays and areexpressed sequentially during development, with the sequence of gene activation corresponding to their physical arrangement within the genome and/or the physical layout of the tissues in which they are expressed along the organism's anterior–posterior axis.[6]
A collaborative international scientific research project with the goal ofsequencing all of thechromosomal DNA and identifying andmapping all of thegenes within human cells, and ultimately of assembling a completereference genome for the human species. The project was launched in 1990 by a consortium of federal agencies, universities, and research institutions and was declared complete in 2003. Because each individual human being has a unique genome, the finished reference genome is amosaic of sequences obtained by sampling DNA from thousands of individuals across the world and does not represent any one individual.
Theoffspring that results from combining the qualities of two organisms of differentgenera,species,breeds, or varieties throughsexual reproduction. Hybrids may occur naturally or artificially, as duringselective breeding of domesticated animals and plants. Reproductive barriers typically prevent hybridization between distantly related organisms, or at least ensure that hybrid offspring are sterile, but fertile hybrids may result inspeciation.
3. A step in some experimental assays in which a single-stranded DNA or RNA preparation is added to an array surface and anneals to acomplementaryhybridization probe.
Asingle-strandedDNA orRNA fragment (or anucleic acid analogue) which is artificiallylabelled with a radioactive or fluorescent compound or some other detectable marker and then allowed tohybridize withcomplementary DNA or RNA sequences in order to detect the presence of those complements in a heterogeneous sample or their specificin situlocalization; or anassay in which this procedure is performed. As with antibodies inimmunostaining, nucleic acid probes bind with high specificity to their target sequences, permitting visualization of the targets, if present, against a non-specific background, whether in amembrane blot ormicroarray or evenin vivo. A unique advantage of hybridization probes is that thestringency of the hybridization reaction is easily modifiable by changing the temperature and salt concentration, making it possible for the same probe to bind to sequences with differing degrees of complementarity. Hybridization probes are employed inSouthern blotting andnorthern blotting and as part of many other laboratory methods. See alsoprobe.
Soluble in or having an affinity for water or otherpolar compounds; describing a polar molecule, or a moiety or functional group within a molecule, which participates in intermolecular interactions such ashydrogen bonding with other polar molecules and therefore readily dissolves in polar solvents such as water oraqueous solutions.[8] Unlikehydrophobic compounds, hydrophilic compounds can form energetically favorable contacts with the aqueous phase of biological fluids and so can often be suspended directly in thecytosol or exposed to extracellular spaces.[4] Together, the contrasting properties of hydrophilicity and hydrophobicity play major roles in determining the structuralconformations and functions of mostbiomolecules.
Having a lowsolubility in or affinity for water or otherpolar solvents; describing anon-polar molecule, or a moiety or functional group within a molecule, which cannot form energetically favorable interactions with polar compounds and which therefore tends to "avoid" or be repulsed by such compounds, insteadclustering together with other hydrophobic molecules or arranging itself in a way that minimizes its exposure to its polar surroundings. This phenomenon is not so much due to the affinity of the hydrophobic molecules for each other as it is a consequence of the strong intermolecular forces that allow polar compounds such as water molecules to bond with each other; hydrophobic species are unable to form alternative bonds of equivalent strength with the polar compounds, hence they tend to be excluded fromaqueous solutions by the tendency of the polar solvent to maximize interactions with itself. Hydrophobicity is a major determinant of countless chemical interactions in biological systems, including the spatialconformations assumed bymacromolecules such asproteins andlipids, the binding ofligands andsubstrates to proteins, and the structure and properties of lipidmembranes.[10][8] Contrasthydrophilic.
Describing a solution containing a high concentration of dissolved solutes relative to another solution, i.e. having positiveosmotic pressure, such that solvent will tend to move byosmosis across a semipermeable membrane from the solution of lower solute concentration to the solution of higher concentration until both solutions have equal concentrations. In a cell where the intracellularcytosol is hypertonic relative to the surroundingextracellular fluid (which by definition ishypotonic relative to the cytosol), the solvent (water) will flow across theplasma membrane into the cytosol, filling the cell with extra water and diluting its contents until both sides of the membrane areisotonic. Cells placed in severely hypotonic environments may be at risk of bursting due to the sudden inflow.
A mutantallele that permits a subnormal expression of the gene's normal phenotype, e.g. by encoding an unstable enzyme which degrades too quickly to fully serve its function but which nevertheless is functional in some limited capacity, being generated in quantities sufficient for its reaction to proceed slowly or at low levels.[6]
Describing a solution containing a low concentration of dissolved solutes relative to another solution, i.e. having negativeosmotic pressure, such that solvent will tend to move byosmosis across a semipermeable membrane from the solution of lower solute concentration to the solution of higher concentration until both solutions have equal concentrations. In a cell where the intracellularcytosol is hypotonic relative to the surroundingextracellular fluid (which by definition ishypertonic relative to the cytosol), the solvent (water) will flow across theplasma membrane out of the cytosol, causing the cell to lose water until both sides of the membrane areisotonic. Cells placed in severely hypertonic environments may be at risk of shriveling and desiccating due to the sudden outflow.
A naturally occurring, non-canonicalpurinenucleobase that is used in someRNA molecules and pairs with standard nucleobases in a phenomenon known aswobble base pairing. Itsnucleoside form is known asinosine, which is the reason it is commonly abbreviated with the letterI in sequence reads.
A diagrammatic or schematickaryotype of the entire set ofchromosomes within a cell or genome, in which annotated illustrations depict each chromosome in its most idealized form (e.g. with straight lines and obviouscentromeres) so as to facilitate the easy identification of sequences, structural features, and physical distances, which may be less apparent in photomicrographs of the actual chromosomes.
The natural or artificial changing of acell population with a normally finite lifespan into one with a hypothetically infinite lifespan, capable of dividing indefinitely withoutcellular senescence as long as essential nutrients are available and conditions are conducive forcell division. Cells that undergo such a change are said to beimmortalized. Mutations that cause immortalization occur naturally in theneoplasms that cause cancer but can also be induced artificially, which makes it possible toculture certain cell linesin vitro for prolonged periods. Immortalized cell lines are thus broadly useful for experimental purposes and in many biotechnology applications. Immortalized eukaryotic cells are commonly obtained by isolating them from a naturally occurring neoplasm (as with the humanHeLa cell line), or may be generated from normal cells by introducing viral genes (as withHEK 293 cells), by artificiallyoverexpressing proteins required for immortality such astelomerase, or byfusing normal cells with cancer cells (as in thehybridoma technologies used in the commercial production ofantibodies).[3] Thoughstem cells are also capable of continuous self-renewal and are thus technically 'immortal', their immortalization is not abnormal because they are an ordinary part of the development of multicellular organisms.
A family of laboratory techniques in which a particularantigen orantibody is conjugated to a fluorescent dye and then allowed to bind specifically to its complementary antibody or antigen, if any exists, in aculture vessel, tissue section or smear,hybridization probe, membraneblot, or any other context. The presence or absence of the complement and its specific location(s) can be visualized by illuminating the sample with ultraviolet light and observing the fluorescence from the conjugated fluorophore, often under a microscope.[3]
The use of anantibodyconjugated to achromophore orfluorophore to bind a specificantigen within a target substance (e.g. a protein) and thereby make the substance visible amidst a background of non-specific substances, allowing for detection of the target in a biological sample. The term originally referred to antibody-based staining of tissue sections with strong dyes or colorants, known asimmunohistochemistry, but in modern usage encompasses a much broader range of laboratory methods united by their use of antibodies tolabel specific biomolecules with visually conspicuous compounds.
(of a scientific experiment or research) Conducted, produced, or analyzed by means of computer modeling or simulation, as opposed to a real-world trial.
(of a scientific experiment or biological process) Occurring or made to occur in a natural, uncontrolled setting, or in the natural or original position or place, as opposed to in a foreign cell or tissue type orin an artificial environment.
Ahybridization probe assay in which alabeled, single-stranded DNA or RNA molecule ornucleic acid analogue containing a sequence that iscomplementary to a particular DNA or RNA sequence is allowed tohybridize with its complementin situ, i.e. in its natural context, such as within cells or tissue sections (as opposed to within homogeneous samples extracted from cells or tissues, where cellular or histological structure has been lost in the process of obtaining the sample), in order toreveal the precise location of the complementary sequence within this context. The label may be a radioactive compound,fluorescent molecule, orhapten, permitting detection by a variety of visualization techniques.In situ hybridization is commonly used to identify the physical locations of specific DNA sequences such as genes and regulatory elements onchromosomes, which can provide insight into chromosomal structure and integrity; to determine the subcellular locations where various types of RNA accumulate and interact with other molecules; and to visualize the tissues and organs within an organism where specific genes areexpressed at various developmental stages (by probing for the genes' RNA transcripts).
(of a scientific experiment or biological process) Occurring or made to occur in a laboratory vessel or other controlled artificial environment, e.g. in a test tube or a petri dish, as opposed toinside a living organism orin a natural setting.
(of a scientific experiment or biological process) Occurring or made to occur inside the cells or tissues of a living organism; or, in the broadest sense, in any natural, unmanipulated setting. Contrastex vivo andin vitro.
1. (of a gene or sequence) Read or transcribed in the samereading frame as another gene or sequence; not requiring a shift in reading frame to be intelligible or to result in a functionalpeptide.
Any nucleotide sequence that isinserted naturally or artificially into another sequence. The term is used in particular to refer to the part of atransposable element that codes for those proteins directly involved in the transposition process, e.g. thetransposase enzyme. The coding region in a transposable insertion sequence is usually flanked by shortinverted repeats, and the structure of larger transposable elements may include a pair of flanking insertion sequences which are themselves inverted.
The alteration of a DNA sequence by theinsertion of one or more nucleotides into the sequence, either naturally or artificially. Depending on the precise location of the insertion within the target sequence, insertions may partially or totally inactivate or even upregulate agene product or biochemical pathway, or they may beneutral, leading to no substantive changes at all. Manygenetic engineering techniques rely on the insertion of exogenous genetic material into host cells in order to study gene function and expression.[6]
Any of a class ofintegral membrane proteins which span the entirety of thecell membrane, extending from the interior orcytosolic side of the membrane to the exterior orextracellular side. Transmembrane proteins typically have hydrophilicdomains exposed to each side as well as one or more hydrophobic domains crossing the nonpolar space inside thelipid bilayer, by which they are further classified assingle-pass ormultipass membrane proteins. As such many transmembrane proteins function asgated channels ortransporters to permit or prohibit the movement of specific molecules or ions across the membrane, often undergoing conformational changes in the process, or asreceptors incell signaling pathways. Contrastintegral monotopic protein.
Amobile genetic element consisting of agene cassette containing the gene for asite-specific recombinase,integrase-specific recognition sites, and apromoter that governs the expression of one or more genes conferring adaptive traits on the host cell. Integrons usually exist in the form of circularepisomal DNA fragments, through which they facilitate the rapid adaptation of bacteria by enablinghorizontal gene transfer of antibiotic resistance genes between different bacterial species.[6]
The insertion, naturally or artificially, of chemical compounds between the planarbases of aDNA molecule, which generally disrupts thehydrogen bonding necessary forbase pairing.
Two molecules of the chemotherapeutic drugdoxorubicinintercalated between the bases of a DNA molecule
The abbreviated pause in activities related to cell division that occurs duringmeiosis in some species, between the first and second meiotic divisions (i.e. meiosis I and meiosis II). NoDNA replication occurs during interkinesis, unlike during the normalinterphase that precedes meiosis I andmitosis.[6]
A sequence present in somemessenger RNAs that permits recognition by theribosome and thus the initiation oftranslation even in the absence of a5' cap, which in eukaryotes is otherwise required for assembly of the initiation complex. IRES elements are often located in the5' untranslated region, but may also be found in other positions.
An international non-governmental organization devoted to promoting scientific research and education in the disciplines ofbiochemistry andmolecular biology, primarily by standardizing biochemical nomenclature, developing and publishing laboratory methods, and awarding grants and fellowships to students and researchers.
Aprotein (or a region ordomain within a protein) that lacks any distinct, fixed three-dimensional structure or organization under physiological conditions, instead changing continuously and randomly between multiple transientconformational states rather than folding into any one stable conformation, especially in the absence of specific macromolecular interaction partners. The majority of eukaryotic proteins contain domains with intrinsic structure alongside unstructured domains.Peptide sequences lacking intrinsic order are generally characterized by high proportions of charged and hydrophilic amino acids and low proportions of hydrophobic amino acids, making them inherently flexible, accessible, and modifiable, which allows the same peptide sequence to have distinct functions across a wide variety of biochemical circumstances. They are frequently enriched inbinding motifs and are common targets ofpost-translational modifications, giving them important roles incell signaling pathways and as hubs inprotein complexes.[33]
The infolding of amembrane toward the interior of a cell or organelle, or of a sheet of cells toward the interior of a developingembryo,tissue, or organ, forming a distinct membrane-lined pocket. In the case of individual cells, the invaginated pocket may proceed to separate from the source membrane entirely, creating a membrane-boundvesicle within the cell, as inendocytosis.[10]
Anucleotide sequence followeddownstream on the samestrand by its ownreverse complement. The initial sequence and the reverse complement may be separated by any number of nucleotides, or may be immediately adjacent to each other; in the latter case, the composite sequence is also called apalindromic sequence. Inverted repeats areself-complementary by definition, a property which involves them in many biological functions and dysfunctions. Contrastdirect repeat.
Any chemical compound or macromolecule that facilitates the movement ofions across biological membranes, or more specifically, any chemical species that reversibly binds electrically charged atoms or molecules. Many ionophores are lipid-solubleproteins that catalyze the transport of monovalent and divalent cations across the hydrophobiclipid bilayers surrounding cells and vesicles.[10]
A large region ofgenomic DNA with a relatively homogeneous composition ofbase pairs, distinguished from other regions by the proportion of pairs that areG-C orA-T. The genomes of most plants and vertebrates are composed of different classes of GC-rich and AT-rich isochores.[6]
A type ofabnormalchromosome in which the arms of the chromosome are mirror images of each other. Isochromosome formation is equivalent to simultaneousduplication anddeletion events such that two copies of either thelong arm or theshort arm comprise the resulting chromosome.
The pH at which a particular molecule, often aprotein, carries no net electrical charge, i.e. at which it is electrically neutral in the statistical mean. The concentration ofprotons (H+) in the surrounding environment affects how readily molecules gain or lose protons and thus their electrical properties. When the environmental pH is greater than the molecule's pI, the molecule is negatively charged, and when the pH is less than the pI, it is positively charged. Isoelectric point is therefore important for determining the behavior of molecules exposed to electric fields, as inelectrophoresis andion chromatography. Proteins are least soluble at their isoelectric points because electrically neutral species do not repulse each other with electrostatic forces, such that they tend to aggregate andprecipitate out of solution.[10]
Any of a class ofenzymes which catalyze the conversion of a molecule from oneisomer to another, such that the product of the reaction has the same molecular formula as the original substrate but differs in the connectivity or spatial arrangement of its atoms.
isomeric genes
Two or moregenes that are equivalent and redundant in the sense that, despite coding for distinctgene products, they each result in the samephenotype when set within the samegenetic background. If several isomeric genes are present in a singlegenotype they may be either cumulative or non-cumulative in their contributions to the phenotype.[15]
Describing a solution containing the same concentration of dissolved solutes as another solution, such that the two solutions have equalosmotic pressure. Isotonic solutions separated from each other by a semipermeable membrane (as with a cell, where the intracellularcytosol is separated from theextracellular fluid by theplasma membrane) have noconcentration gradient and thus will not exchange solvent byosmosis. Contrasthypertonic andhypotonic.
Any DNA sequence that appears to have no known biological function, or which acts in a way that has no positive or a net negative effect on the fitness of thegenome in which it is located. The term was once more broadly used to refer to allnon-coding DNA, though much of this was later discovered to have a function; in modern usage it typically refers to broken or vestigial sequences andselfish genetic elements, includingintrons,pseudogenes,intergenic DNA, and fragments oftransposons andretroviruses, which together constitute a large proportion of the genomes of most eukaryotes. Despite not contributing productively to the host organism, these sequences are able to persist indefinitely inside genomes because the disadvantages of continuing to copy them are too small to be acted upon bynatural selection.
junk RNA
Any RNA-encoded sequence, especially atranscript, that appears to have no known biological function, or whose function has no positive or a net negative effect on the fitness of the genome from which it is transcribed. Despite remaininguntranslated, manynon-coding RNAs still serve important functions, whereas junk RNAs are truly useless: often they are the product of accidental transcription of ajunk DNA sequence, or they may result frompost-transcriptional processing ofprimary transcripts, as withspliced-outintrons. Junk RNA is usually quickly degraded byribonucleases and other cytoplasmic enzymes.
Akaryotype which depicts the entire set ofchromosomes in a cell or organism by using photomicrographs of the actual chromosomes as they appearin vivo (usually duringmetaphase, in their most condensed forms), as opposed to the idealized illustrations of chromosomes used inidiograms. The photomicrographs are often still arranged in pairs and by size for easier identification of particular chromosomes, whereas in the actual nucleus there is seldom any apparent organization.
The fragmentation and degeneration of thenucleus of a dying cell, during which thenuclear envelope is destroyed and the contents of the nucleus, includingchromatin, are dispersed throughout thecytoplasm and degraded by enzymes. Karyorrhexis is usually preceded bypyknosis and may occur as a result ofapoptosis,cellular senescence, ornecrosis.
The number and appearance ofchromosomes within thenucleus of a eukaryotic cell, especially as depicted in an organizedkaryogram oridiogram (in pairs and arranged by size and by position of thecentromere). The term is also used to refer to the complete set of chromosomes in a species or individual organism or to any test that detects this complement or measures the chromosome number.
A non-specific, non-directional movement or change in activity by a cell or a population of cells in response to a stimulus, such that the rate of the movement or activity is dependent on the intensity of the stimulus but not on the direction from which the stimulus occurs. Kinesis refers particularly to cellular locomotion without directional bias, in contrast totaxis andtropism.
Incytogenetics, an enlarged, heavily stainingchromomere that can be used as a visual marker, allowing specific chromosomes to be easily identified in the nucleus.[6]
Agenetic engineering method by which the normal rate ofexpression of one or more of an organism'sgenes is reduced or suppressed (though not necessarily completely turned off, as inknockout), either through direct modification of a DNA sequence or through treatment with areagent such as a short DNA or RNAoligonucleotide with a sequencecomplementary to either anmRNA transcript or a gene.
Agenetic engineering method in which one or more novelgenes areinserted into an organism's genome, particularly when targeted to a specificlocus, or in which one or more existing genes are replaced by orsubstituted with novel genes.[35] This is in contrast to aknockout, in which a gene is deleted or completely inactivated.
Agenetic engineering method in which one or more specificgenes are inactivated or entirelyremoved from an organism's genome, by any of a variety of mechanisms which disrupt theirexpression at some point in the pathway that produces theirgene products, such that no functional gene products are produced. This allows researchers to study the function of a genein vivo, by observing how the organism'sphenotype changes when deprived of the gene's normal effects. Acomplete knockout permanently inactivates the gene; aconditional knockout allows the gene to be turned on or off at will, e.g. at specific times or in specific tissues, by linking the expression of the gene to some easily modifiable biochemical state or condition. In aheterozygous knockout, only one of a diploid organism's two alleles is knocked out; in ahomozygous knockout, both copies are knocked out. Contrastknockin.
The chemical attachment of a highly selective substance, known as alabel,tag, orprobe, to a particular cell, protein, amino acid, or other molecule of interest, either naturally or artificially,in vivo orin vitro. Natural labelling is a primary mechanism by which biomolecules specifically identify and interact with other biomolecules; important examples includemethylation,acetylation,phosphorylation, andglycosylation. Labelling is also a common laboratory technique, where the label is typically a reactive derivative of a naturallyfluorescent compound (e.g.green fluorescent protein), dye, enzyme,antibody, radioactive molecule, or any other substance that makes its target distinguishable in some way. The labelled targets are thereby rendered distinct from their unlabelled surroundings, allowing them to be detected, identified, quantified, or isolated for further study.
InDNA replication, the nascentstrand for whichDNA polymerase's direction of synthesis is away from thereplication fork, which necessitates a complex and discontinuous process in contrast to the streamlined, continuous synthesis of the other nascent strand, known as theleading strand, which occurs simultaneously. Because DNA polymerase works only in the5' to3' direction, but the lagging strand's overall direction of chain elongation must ultimately be the opposite (i.e. 3' to 5', toward the replication fork), elongation must occur by an indirect mechanism in which aprimase enzyme synthesizes shortRNAprimers complementary to the template DNA, and DNA polymerase then extends the primed segments into short chains of nucleotides known asOkazaki fragments. The RNA primers are then removed and replaced with DNA, and the Okazaki fragments are joined byDNA ligase.
1. Any thin layer, membrane, or plate of tissue, occurring in a wide variety of structures of various scales and with various functions; e.g. a lamella made of a sheet of lipids forms a component of theextracellular matrix between the cells of some tissues.
2. The leading edge of a motile cell, of which thelamellipodia is the most forward portion.
A transcriptionally active, highly de-condensed morphology assumed by certainchromosomes during thediplotene stage ofmeioticprophase I in theprogenitor cells ofoocytes in female insects, amphibians, birds, and some other animals. Lampbrush chromosomes are conspicuous under the microscope because thepost-synaptichomologs, still attached atchiasmata, are gigantically elongated into large loops of unpackagedeuchromatin extending laterally from a series ofchromomeres. Large numbers ofmessenger RNAs andnon-coding RNAs are transcribed from the lateral loops, generating a rich pool oftranscripts to be used in the immature oocyte and after fertilization, with functions in bothoogenesis andembryogenesis. Because they allow individualtranscription units to be directly visualized, lampbrush chromosomes are useful models for studying chromosome organization and genome structure and for constructing high-resolution chromosome maps.[37]
Alampbrush chromosome magnified 11,000 times with an electron microscope, showing the characteristic lateral loops containing transcriptionally active segments of DNA
InDNA replication, the nascentstrand for which both the direction of synthesis byDNA polymerase and the direction of overall chain elongation are toward thereplication fork; i.e. both occur in the5' to3' direction, resulting in a single, continuous elongation process with few or no interruptions. By contrast, the other nascent strand, known as thelagging strand, is assembled in a discontinuous process involving the ligation of shortDNA fragments synthesized in the opposite direction, away from the replication fork.[6]
Inmeiosis, the first of five substages ofprophase I, followinginterphase and precedingzygonema. During leptonema, the replicated chromosomes condense from diffusechromatin into long, thin strands that are much more visible within thenucleus.
A common structuralmotif inDNA-bindingtranscription factors and some other types of proteins, approximately 35 amino acids in length, characterized chiefly by the recurrence of the amino acidleucine every seven residues. When modeled in an idealizedalpha-helical conformation, the leucine residues are positioned in such a way that they can interdigitate with the same or similar motifs in an alpha helix belonging to another similar polypeptide, facilitatingdimerization and the formation of a complex resembling a zipper.[4]
In biochemistry, any molecule that binds to or interacts with aspecific site on aprotein or otherbiomolecule, usually reversibly via intermolecular forces;[8] or any substance that forms a complex with a biomolecule as part of a biological process. The binding of specific ligands to DNA or proteins is important in manybiochemical pathways; for example, protein–ligand binding may result in the protein undergoing aconformational change which alters its function or affinity for other molecules.
A class ofenzymes which catalyze the synthesis of large molecules such asnucleic acids by forming one or more chemical bonds between them, typicallyC–C,C–O,C–S, orC–N bonds viacondensation reactions. An example isDNA ligase, which catalyzes the formation ofphosphodiester bonds between adjacentnucleotides on the same strand of a DNA molecule, a reaction known asligation.
The tendency of DNA sequences which are physically near to each other on the same chromosome to beinherited together duringmeiosis. Because the physical distance between them is relatively small, the chance that any two nearby parts of a DNA sequence (oftenloci orgenetic markers) will be separated on to differentchromatids duringchromosomal crossover is statistically very low; such loci are then said to be morelinked than loci that are farther apart. Loci that exist on entirely different chromosomes are said to be perfectlyunlinked. The standard unit for measuring genetic linkage is thecentimorgan (cM).
1. A short, synthetic DNA duplex containing therecognition sequence for a particularrestriction enzyme.[6] Inmolecular cloning, linkers are often deliberately included inrecombinant molecules in order to make them easily modifiable by permitting cleavage andinsertion of foreign sequences at precise locations. A segment of an engineeredplasmid containing many such restriction sites is sometimes called apolylinker.
The number of times that the two strands of a circulardouble-helicalDNA molecule cross each other, equivalent to thetwisting number (which measures the torsion of the double helix) plus thewrithing number (which measures the degree of supercoiling). The linking number of a closed molecule cannot be changed without breaking and rejoining the strands. DNA molecules which are identical except for their linking numbers are known astopological isomers.[6]
Any of a heterogeneous class of organic compounds, includingglycerides (fats),waxes,sterols, and some vitamins, united only by theiramphipathic orhydrophobic nature and consequently their very low solubility in water.[4] Some lipids such asphospholipids tend to form lamellar structures ormicelles in aqueous environments, where they serve as the primary constituents of biologicalmembranes. Others such asfatty acids can bemetabolized for energy, have important functions in energy storage, or serve assignaling molecules. Colloquially, the term "lipids" is sometimes used as a synonym for fats, though fats are more correctly considered a subclass of lipids.
A lamellar structure composed of numerous amphipathiclipid molecules packed together in two back-to-back sheets or layers, with theirhydrophobicfatty acid "tails" directed inward and theirhydrophilic "heads" exposed on the outer surface. This is the basic structural motif for all biologicalmembranes, including theplasma membrane surrounding all cells as well as the membranes surroundingorganelles andvesicles. Though bilayers are sometimes colloquially described asphospholipid bilayers,phospholipids are just one of several classes ofmembrane lipids which form bilayers; most membranes are actually afluid, heterogeneous mixture of phospholipids,glycolipids, andcholesterols, interspersed and studded with various other molecules such asintegral proteins.[4]
Any water-solubleprotein to which one or more lipid molecules are attached by covalent bonding to amino acid residues. Many classes of lipids can be conjugated to proteins, includingtriacylglycerols,cholesterols, andphospholipids.[3] Compareproteolipid.
1. Any small, naturallipid globule, such as amicelle, occurring naturally in the cytoplasm;[3] they are commonly formed by budding off from larger membrane-bound vesicles.
2. A small, spherical, artificialvesicle having at least one continuousbilayer of lipid molecules enclosing some of the medium in which it is suspended.[38] Liposomes can be created in the laboratory by disrupting existing biological membranes and allowing complex lipids to form bilayer-bound vesicles in aqueous solution, usually with the aid ofsonication. They are used experimentally as models of natural membranes and also therapeutically for the encapsulation and delivery of pharmaceutical compounds, enzymes, nutrients, nucleic acids,lipid-based nanoparticles (as in some vaccines), and many other agents between or inside of cells.[3]
In condensedchromosomes where the positioning of thecentromere creates two segments or "arms" of unequal length, the longer of the two arms of achromatid. Contrastshort arm.
Any of a large family of non-LTRretrotransposons which together comprises one of the most widespreadmobile genetic elements in eukaryotic genomes. Each LINEinsertion is on average about 7,000 base pairs in length.
The disruption and decomposition of theplasma membrane surrounding a cell, or more generally of any membrane-boundorganelle orvesicle, especially byosmotic,enzymatic, or other chemical or mechanical processes which compromise the membrane's integrity and thereby cause the unobstructed interchange of the contents ofintracellular andextracellular spaces. Lysis generally implies the complete and irreversible loss of intracellular organization as a result of the release of the cell's internal components and the dilution of thecytosol, and therefore the death of the cell. Such a cell is said to belysed, and a fluid containing the contents of lysed cells (usually includingnucleic acids,proteins, and many other organic molecules) is called alysate. Lysis may occur both naturally and artificially, and is a normal part of the cellular life cycle.
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^abLewin, Benjamin (2003).Genes VIII. Upper Saddle River, NJ: Pearson Prentice Hall.ISBN0-13-143981-2.
^Maheshri N, O'Shea EK (2007). "Living with noisy genes: how cells function reliably with inherent variability in gene expression".Annu. Rev. Biophys. Biomol. Struct.36:413–434.doi:10.1146/annurev.biophys.36.040306.132705.PMID17477840.
^Singer, S. J.; Nicolson, Garth L. (18 February 1972). "The Fluid Mosaic Model of the Structure of Cell Membranes: Cell membranes are viewed as two-dimensional solutions of oriented globular proteins and lipids".Science.175 (4023):720–731.doi:10.1126/science.175.4023.720.PMID4333397.
^Reitsma, Sietze. "The endothelial glycocalyx: composition, functions, and visualization." European Journal of Physiology. 2007. Vol. 454. Num. 3. p. 345–359
^Bogolyubov DS (2018-01-01). Galluzzi L (ed.). "Karyosphere (Karyosome): A Peculiar Structure of the Oocyte Nucleus".International Review of Cell and Molecular Biology.337. Academic Press:1–48.doi:10.1016/bs.ircmb.2017.12.001.ISBN978-0-12-815195-2.PMID29551157.
^Gibson, Greg (2009).A Primer Of Genome Science 3rd ed. Sunderland, Massachusetts: Sinauer. pp. 301–302.ISBN978-0-87893-236-8.
^Morgan, G.T. (2002) "Lampbrush chromosomes and associated bodies: new insights into principles of nuclear structure and function."Chromosome Research. 10: 177–200.
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