Glossary of cellular and molecular biology (0–L)

This glossary of cellular and molecular biology is a list of definitions of terms and concepts commonly used in the study of cell biology, molecular biology, and related disciplines, including genetics, biochemistry, and microbiology.^[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.
Glossary of cellular and molecular biology (M–Z) lists terms beginning with the letters M through Z.

The glossary is intended as introductory material for novices; for more specific and technical detail, see the article corresponding to each term. Overlapping and related glossaries include Glossary of evolutionary biology, Glossary of virology, and Glossary of chemistry.

0–9[edit]

3' untranslated region (3'-UTR)
3'-end: One of two ends of a single linear strand of DNA or RNA, specifically the end at which the chain of nucleotides terminates at the third carbon atom in the furanose ring of deoxyribose or ribose (i.e. the terminus at which the 3' carbon is not attached to another nucleotide via a phosphodiester bond; in vivo, the 3' carbon is often still bonded to a hydroxyl group). By convention, sequences and structures positioned nearer to the 3'-end relative to others are referred to as downstream. Contrast 5'-end.
5' cap: A specially altered nucleotide attached to the 5'-end of some primary RNA transcripts as part of the set of post-transcriptional modifications which convert raw transcripts into mature RNA products. The precise structure of the 5' cap varies widely by organism; in eukaryotes, the most basic cap consists of a methylated guanine nucleoside 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 the nucleus, prevent their degradation by exonucleases, and promote translation in the cytoplasm. Mature mRNAs can also be decapped.
5' untranslated region (5'-UTR)
5-bromodeoxyuridine: See bromodeoxyuridine.
5'-end: One of two ends of a single linear strand of DNA or RNA, specifically the end at which the chain of nucleotides terminates at the fifth carbon atom in the furanose ring of deoxyribose or ribose (i.e. the terminus at which the 5' carbon is not attached to another nucleotide via a phosphodiester bond; in vivo, the 5' carbon is often still bonded to a phosphate group). By convention, sequences and structures positioned nearer to the 5'-end relative to others are referred to as upstream. Contrast 3'-end.
5-methyluracil: See thymine.

A[edit]

acentric: (of a linear chromosome or chromosome fragment) Having no centromere.^[2]
acetyl coenzyme A (acetyl-CoA): A biochemical compound consisting of a coenzyme A molecule to which an acetyl group (–COCH
₃) is attached via a high-energy thioester bond. Acetylation of coenzyme A occurs as part of the metabolism of proteins, carbohydrates (glycolysis), and fatty acids (beta oxidation), after which it participates as an energy carrier in several important biochemical pathways, notably the citric acid cycle, in which hydrolysis of the acetyl group releases energy which is ultimately captured in 11 ATP and one GTP.
acetylation: The covalent attachment of an acetyl group (–COCH
₃) to a chemical compound, protein, or other biomolecule via an esterification reaction with acetic acid, either spontaneously or by enzymatic catalysis. Acetylation plays important roles in several metabolic pathways and in histone modification. Contrast deacetylation.
acetyltransferase: Any of a class of transferase enzymes which catalyze the covalent bonding of an acetyl group (–COCH
₃) to another compound, protein, or biomolecule, a process known as acetylation.
acrocentric: (of a linear chromosome or chromosome fragment) Having a centromere positioned very close to one end of the chromosome, as opposed to at the end or in the middle.^[2]
action potential: The local change in voltage that occurs when the membrane potential of a specific location along the membrane of a cell rapidly depolarizes, such as when a nerve impulse is transmitted between neurons.
activation: See upregulation.
activator: A type of transcription factor that increases the transcription of a gene or set of genes. Most activators work by binding to a specific sequence located within or near an enhancer or promoter and facilitating the binding of RNA polymerase and other transcription machinery in the same region. See also coactivator; contrast repressor.
active site: The region of an enzyme to which one or more substrate molecules bind, causing the substrate or another molecule to undergo a chemical reaction. This region usually consists of one or more amino acid residues (commonly three or four) which, when the enzyme is folded 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.
active transport: Transport of a substance (such as a protein or drug) across a membrane against a concentration gradient. Unlike passive transport, active transport requires an expenditure of energy.
adenine (A): A purine nucleobase used as one of the four standard nucleobases in both DNA and RNA molecules. Adenine forms a base pair with thymine in DNA and with uracil in RNA.
adenosine (A): One of the four standard nucleosides used in RNA molecules, consisting of an adenine base with its N₉ nitrogen bonded to the C₁ carbon of a ribose sugar. Adenine bonded to deoxyribose is known as deoxyadenosine, which is the version used in DNA.
adenosine diphosphate (ADP)
adenosine monophosphate (AMP)
adenosine triphosphate (ATP): An organic compound derived from adenine that functions as the major source of energy for chemical reactions inside living cells. It is found in all forms of life and is often referred to as the "molecular currency" of intracellular energy transfer.
A-DNA: One of three main biologically active structural conformations of the DNA double helix, along with B-DNA and Z-DNA. The A-form helix has a right-handed twist with 11 base 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 consecutive purine nucleotides (e.g. GAAGGGGA); it is also the primary conformation adopted by double-stranded RNA and RNA-DNA hybrids.^[3]
affected relative pair: Any pair of organisms which are related genetically and both affected by the same trait. For example, two cousins who both have blue eyes are an affected relative pair since they are both affected by the allele that codes for blue eyes.
alkaline lysis
allele: One of multiple alternative versions of an individual gene, each of which is a viable DNA sequence occupying a given position, or locus, on a chromosome. For example, in humans, one allele of the eye-color gene produces blue eyes and another allele of the same gene produces brown eyes.
allosome: Any chromosome that differs from an ordinary autosome in size, form, or behavior and which is responsible for determining the sex of an organism. In humans, the X chromosome and the Y chromosome are sex chromosomes.
alpha helix (α-helix): A common structural motif in the secondary structures of proteins consisting of a right-handed helix conformation resulting from hydrogen bonding between amino acid residues which are not immediately adjacent to each other.
alternative splicing: A regulated phenomenon of eukaryotic gene expression in which specific exons or parts of exons from the same primary transcript are variably included within or removed from the final, mature messenger RNA transcript. A class of post-transcriptional modification, alternative splicing allows a single gene to code for multiple protein isoforms and greatly increases the diversity of proteins that can be produced by an individual genome. See also RNA splicing.
amber: One of three stop codons used in the standard genetic code; in RNA, it is specified by the nucleotide triplet UAG. The other two stop codons are named ochre and opal.
amino acid: Any of a class of organic compounds whose basic structural formula includes a central carbon atom bonded to amine and carboxyl functional groups and to a variable side chain. Out of nearly 500 known amino acids, a set of 20 are coded for by the standard genetic code and incorporated into long polymeric chains as the building blocks of peptides and hence of polypeptides and proteins. 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.
amino terminus: See N-terminus.
aminoacyl-tRNA synthetase: Any of a set of enzymes which catalyze the transesterification reaction that results in the attachment of a specific amino acid (or a precursor) to one of its cognate transfer RNA molecules, forming an aminoacyl-tRNA. Each of the 20 different amino acids used in the genetic code is recognized and attached by its own specific synthetase enzyme, and most synthetases are cognate to several different tRNAs according to their specific anticodons.
aminoacyl-tRNA (aa-tRNA): A transfer RNA to which a cognate amino acid is chemically bonded; i.e. the product of a transesterification reaction catalyzed by an aminoacyl-tRNA synthetase. Aminoacyl-tRNAs bind to the aminoacyl site of the ribosome during translation.
amplicon: Any DNA or RNA sequence or fragment that is the source and/or product of an amplification reaction. The term is most frequently used to describe the numerous copied fragments that are the products of the polymerase chain reaction or ligase chain reaction, though it may also refer to sequences that are amplified naturally within a genome, e.g. by gene duplication.
amplification: The replication of a biomolecule, in particular the production of one or more copies of a nucleic acid sequence, known as an amplicon, either naturally (e.g. by spontaneous duplications) or artificially (e.g. by PCR), and especially implying many repeated replication events resulting in thousands, millions, or billions of copies of the target sequence, which is then said to be amplified.
anaphase: The stage of mitosis and meiosis that occurs after metaphase and before telophase, when the replicated chromosomes are segregated and each of the sister chromatids are moved to opposite sides of the cell.
anaphase lag: The failure of one or more pairs of sister chromatids or homologous chromosomes to properly migrate to opposite sides of the cell during anaphase of mitosis or meiosis due to a defective spindle apparatus. Consequently, both daughter cells are aneuploid: one is missing one or more chromosomes (creating a monosomy) while the other has one or more extra copies of the same chromosomes (creating a polysomy).
aneucentric: (of a linear chromosome or chromosome fragment) Having an abnormal number of centromeres, i.e. more than one.^[4]
aneuploidy: The condition of a cell or organism having an abnormal number of one or more particular chromosomes (but excluding abnormal numbers of complete sets of chromosomes, which instead is known as euploidy).
annealing: The hybridization of two single-stranded nucleic acid molecules containing complementary sequences, creating a double-stranded molecule with paired nucleobases. The term is used in particular to describe steps in laboratory techniques such as polymerase chain reaction, where double-stranded DNA molecules are repeatedly denatured into single strands by heating and then exposed to cooler temperatures, causing the strands to reassociate with each other or with complementary primers. The exact temperature at which annealing occurs is strongly influenced by the length and specific sequence of the individual strands.
antibody
anticodon: A series of three consecutive nucleotides within a transfer RNA which complement the three nucleotides of a codon within an mRNA transcript. During translation, each tRNA recruited to the ribosome contains a single anticodon triplet that pairs with its complementary codon from the mRNA sequence, allowing each codon to specify a particular amino acid to be added to the growing peptide chain. Anticodons containing inosine in the first position are capable of pairing with more than one codon due to a phenomenon known as wobble base pairing.
antimetabolite: Any molecule that functions as an antagonist to a metabolic process, limiting or inhibiting normal cellular metabolism; i.e. a metabolic poison.^[4]
antimitotic: Any compound that suppresses normal mitosis in a cell or population of cells.^[4]
antioncogene: A gene 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.^[5] Compare oncogene.
antiparallel: The orientation of two strands of a double-stranded nucleic acid (and more generally any pair of biopolymers) which are parallel to each other but with opposite directionality. For example, the two complementary strands of a DNA molecule run side-by-side but in opposite directions, with one strand oriented 5'-to-3' and the other 3'-to-5'.
antiporter: A transport protein which works by exchanging two different ions or small molecules across a membrane in opposite directions, either at the same time or consecutively.^[6]
antisense: See template strand.
antisense RNA (asRNA): A single-stranded non-coding RNA molecule containing an antisense sequence that is complementary to a sense strand, such as a messenger RNA, with which it readily hybridizes, thereby inhibiting the sense strand's further activity (e.g. translation into protein). Many different classes of naturally occurring RNA such as siRNA function by this principle, making them potent gene silencers in various gene regulation mechanisms. Synthetic antisense RNA has also found widespread use in gene knockdown studies, and in practical applications such as antisense therapy.
anucleate: (of a cell or organism) Lacking a nucleus, i.e. a discrete, membrane-bound organelle enclosing the cell's genomic DNA, used especially of cells which normally have a nucleus but from which the nucleus has been removed (e.g. in artificial nuclear 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. mammalian erythrocytes).
apical constriction
apoptosis: A highly regulated form of programmed cell death that occurs in multicellular organisms.
aptamer
artificial gene synthesis: A set of laboratory methods used in the de novo synthesis of a gene (or any other nucleic acid sequence) from free nucleotides, i.e. without relying on an existing template strand.
assimilatory process: Any process by which chemical compounds containing various essential elements (C, H, O, N, P, S, Se, Fe, Co, Ni, Cu, Zn, Mo, or other oligo-elements) are uptaken by microorganisms and incorporated into complex biomolecules in order to synthesize various cellular components. In contrast, a dissimilatory process uses the energy released by decomposing exogenous molecules to power the cell's metabolism and then excretes residual or toxic compounds out of the cell, instead of reusing them to build new molecules.
asynapsis: The failure of homologous chromosomes to properly pair with each other during meiosis.^[4] Contrast synapsis and desynapsis.
attached X: A single monocentric chromosome containing two or more physically attached copies of the normal X chromosome as a result of either a natural internal duplication or any of a variety of genetic 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 by meiosis and inherited by progeny. In mechanisms such as genic 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.
autolysis: The lysis or digestion of a cell by its own enzymes; or of a particular enzyme by another instance of the same enzyme.
autosome: Any chromosome that is not an allosome and hence is not involved in the determination of the sex of an organism. Unlike the sex chromosomes, the autosomes in a diploid cell exist in pairs, with the members of each pair having the same structure, morphology, and genetic loci.
autozygote: A cell or organism that is homozygous for a locus at which the two homologous alleles are identical by descent, both having been derived from a single gene in a common ancestor.^[4] Contrast allozygote.
auxesis: The growth of a multicellular organism due to an increase in the size of its cells rather than an increase in the number of cells.
axenic: Describing a cell 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.

B[edit]

B chromosome: Any supernumerary nuclear DNA molecule which is not a duplicate of nor homologous 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 are not stably inherited and thus vary widely in copy number even between closely related individuals.^[4]
back mutation: A mutation that reverses the effect of a previous mutation which had inactivated a gene, thus restoring wild-type function.^[7] See also reverse mutation.
backcrossing: The breeding of a hybrid organism with one of its parents or an individual genetically similar to one of its parents, often intentionally as a type of selective breeding, with the aim of producing offspring with a genetic identity which is closer to that of the parent. The reproductive event and the resulting progeny are both referred to as a backcross, often abbreviated in genetics shorthand with the symbol BC.
bacterial artificial chromosome (BAC)
balancer chromosome
base: An abbreviation of nitrogenous base and nucleobase.
base pair (bp): A pair of two nucleobases on complementary DNA or RNA strands which are bonded to each other by hydrogen bonds. The ability of consecutive base pairs to stack one upon another contributes to the long-chain double helix structures observed in both double-stranded DNA and double-stranded RNA molecules.
baseline: A measure of the gene expression level of a gene or genes prior to a perturbation in an experiment, as in a negative control. Baseline expression may also refer to the expected or historical measure of expression for a gene.
basic local alignment search tool (BLAST): A computer algorithm widely used in bioinformatics for aligning and comparing primary biological sequence information such as the nucleotide sequences of DNA or RNA or the amino 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 a genome 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.
B-DNA: The "standard" or classical structural conformation of the DNA double helix in vivo, thought to represent an average of the various distinct conformations assumed by very long DNA molecules under physiological conditions.^[3] The B-form double helix has a right-handed twist with a diameter of 23.7 ångströms and a pitch of 35.7 ångströms or about 10.5 base pairs per full turn, such that each nucleotide pair is rotated 36° around the helical axis with respect to its neighboring pairs. See also A-DNA and Z-DNA.
beta oxidation
bidirectional replication: A common mechanism of DNA replication in which two replication forks move in opposite directions away from the same origin; this results in a bubble-like region where the duplex molecule is locally separated into two single strands.^[4]
binary fission
binding site
bioassay
biochemical pathway
bioenergetics
biofilm: A community of symbiotic microorganisms, especially bacteria, where cells produce and embed themselves within a slimy, sticky extracellular matrix composed of various high-molecular weight biopolymers, adhering to each other and sometimes also to a substratum, which may be a biotic or abiotic surface.^[8] 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 and communicate, and subpopulations of cells may differentiate to perform specialized functions supporting the whole biofilm.^[9]
biomarker: A measurable indicator of some biological state, especially a compound or biomolecule whose presence or absence in a biological system is a reliable sign of a normal or abnormal process, condition, or disease.^[10] Direct measurements of the concentration of a particular compound or molecule in a tissue or fluid sample are often informative, but characteristic physiological, histological, or radiographic signals (e.g. a change in heart rate, or a distinct morphology under a microscope) may also serve as biomarkers. They are regularly used as predictive or diagnostic tools in clinical medicine and laboratory research.
biomolecular gradient
bivalent
blot: Any of a variety of molecular biology methods by which electrophoretically or chromatographically separated DNA, RNA, or protein samples are transferred from a support medium such as a polyacrylamide or agarose gel onto an immobilizing carrier such as a nitrocellulose or PVDF membrane. Some methods involve the transfer of molecules by capillary action (e.g. Southern and northern blotting), while others rely on the transport of charged molecules by electrophoresis (e.g. western blotting). The transferred molecules are then visualized by colorant staining, by autoradiography, or by probing for specific sequences or epitopes with hybridization probes or antibodies bound to chemiluminescent reporters.^[4]
blunt end: A term used to describe the end of a double-stranded DNA molecule where the terminal nucleobases on each strand are base-paired with each other, such that neither strand has a single-stranded "overhang" of unpaired bases, 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 when ligating multiple DNA molecules, e.g. in restriction cloning, because sticky-ended molecules will not readily anneal 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.
bromodeoxyuridine (BUDR, BrdU)

C[edit]

cadastral gene: A regulatory gene that restricts the expression of other genes to specific tissues or body parts in an organism, typically by producing gene products which variably inhibit or permit transcription of the other genes in different cell types.^[4] The term is used most commonly in plant genetics.
cadherin
callus
Calvin cycle
candidate gene: A gene whose location on a chromosome is associated with a particular phenotype (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 on a priori knowledge or speculation about their functional relevance to the trait or disease being researched.
canonical sequence: See consensus sequence.
carbohydrate
carboxyl terminus: See C-terminus.
carrier protein: A membrane protein that functions as a transporter, binding to a solute and facilitating its movement across a membrane by undergoing a series of conformational changes.^[6]
caspase
CCAAT box: A highly conserved regulatory DNA sequence located approximately 75 base pairs upstream (i.e. -75) of the site of the start of transcription for many eukaryotic genes.^[2]
cDNA: See complementary DNA.
cell
cell biology: The branch of biology that studies the structures, functions, processes, and properties of biological cells, the self-contained units of life common to all living organisms.
cell compartmentalization: The subdivision of the interior of a cell into distinct, usually membrane-bound compartments, including the nucleus and organelles (endoplasmic reticulum, mitochondria, chloroplasts, intracellular vesicles, etc.), a defining feature of the Eukarya.^[11]
cell cortex: A specialized layer of cytoplasmic proteins lining the inner face of the cell membrane in most eukaryotic cells, composed primarily of actin microfilaments and myosin motor proteins and usually 100–1000 nanometres thick, which functions as a modulator of membrane behavior and cell surface properties.
cell counting
cell culture: 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. a culture tube or Petri dish) containing a specifically formulated substrate or growth medium that supplies all of the nutrients essential for life (amino acids, carbohydrates, vitamins, minerals, etc.) plus any desirable growth factors and hormones, permits gas exchange (if necessary), and regulates the environment by maintaining consistent physico-chemical properties (e.g. pH, osmotic pressure, and temperature). Some cell types require a solid surface to which they can adhere in order to reproduce, while others can be grown freely floating in a liquid or gelatinous suspension. Most cells have a genetically determined reproduction limit, but immortalized cells will divide indefinitely if provided with optimal conditions.
cell cycle
cell division: The separation of an individual parent cell into two daughter 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 physical cleaving of the cytoplasm and plasma 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 implies reproduction via the replication 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 by mitosis and cytokinesis, while specific lineages of cells reserved for sexual reproduction can additionally divide by meiosis.^[6]
cell fusion
cell membrane: The selectively permeable membrane surrounding all prokaryotic and eukaryotic cells, defining the outermost boundary of the cell and physically separating the cytoplasm from the extracellular environment.^[12] Like all membranes, the cell membrane is a flexible, fluid, sheet-like phospholipid bilayer with membrane proteins, carbohydrates, and numerous other molecules embedded within or interacting with it from both the interior and exterior sides. Embedded molecules often have freedom 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 require active transport through special pores or channels or by endocytosis or exocytosis in order to enter or exit the cell, usually 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 the external environment, making it important in cell signaling, motility, defense, and division, among numerous other processes.
cell physiology
cell polarity
cell signaling: The diverse set of processes by which cells transmit information to and receive information from themselves, other cells, or their environment. Signal transduction occurs in all cell types, prokaryotic and eukaryotic, and is critically important to the cell's ability to navigate and survive its physical surroundings. Countless mechanisms of signaling have evolved in different organisms, and these are often categorized according to the proximity between sender and recipient (autocrine, intracrine, juxtacrine, paracrine, or endocrine).
cell surface receptor
cell wall
cell-free DNA (cfDNA): Any DNA molecule that exists outside of a cell or nucleus, freely floating in an extracellular fluid such as blood plasma.
cellular: Of, relating to, consisting of, produced by, or resembling a cell or cells.
cellular differentiation
cellular immunity
cellular noise
cellular reprogramming: The conversion of a fully differentiated cell from one tissue-specific cell type to another. This involves dedifferentiation to a pluripotent state; an example is the conversion of mouse somatic cells to an undifferentiated embryonic state, which relies on the transcription factors Oct4, Sox2, Myc, and Klf4.^[13]
cellular senescence
centimorgan (cM): A unit for measuring genetic linkage defined as the distance between chromosomal loci for which the expected average number of intervening chromosomal 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.
central dogma of molecular biology: 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 of biopolymer—DNA, RNA, and protein—can only be transferred between these three classes in certain ways, and not in others: specifically, information transfer between the nucleic 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.
centriole: A cylindrical organelle composed of microtubules, present only in certain eukaryotes. A pair of centrioles migrate to and define the two opposite poles of a dividing cell where, as part of a centrosome, they initiate the growth of the spindle apparatus.
centromere: A specialized DNA sequence within a chromosome that links a pair of sister chromatids. The primary function of the centromere is to act as the site of assembly for kinetochores, protein complexes which direct the attachment of spindle fibers to the centromere and facilitate segregation of the chromatids during mitosis or meiosis.
centromeric index: The proportion of the total length of a chromosome encompassed by its short arm, typically expressed as a percentage; e.g. a chromosome with a centromeric index of 15 is acrocentric, with a short arm comprising only 15% of its overall length.^[4]
centrosome
cfDNA: See cell-free DNA.
channel protein: A type of transmembrane protein whose shape forms an aqueous pore in a membrane, permitting the passage of specific solutes, often small ions, across the membrane in either or both directions.^[6]
Chargaff's rules: A set of axioms which state that, in the DNA of any chromosome, species, or organism, the total number of adenine (A) residues will be approximately equal to the total number of thymine (T) residues, and the number of guanine (G) residues will be equal to the number of cytosine (C) residues; accordingly, the total number of purines (A + G) will equal the total number of pyrimidines (T + C). These observations illustrate the highly specific nature of the complementary base-pairing that occurs in all duplex 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 by unrepaired mismatches, missing bases, and non-canonical bases. The presence of single-stranded DNA polymers also alters the proportions, as the sequence of an individual strand may contain any number of any of the bases.
charged tRNA: A transfer RNA to which an amino acid has been attached; i.e. an aminoacylated tRNA. Uncharged tRNAs lack amino acids.^[4]
chDNA: See chloroplast DNA.
chemiosmosis
chemokinesis: 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.
chemotaxis: 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.^[6]
chiasma: A cross-shaped junction that forms the physical point of contact between two non-sister chromatids belonging to homologous chromosomes during synapsis. As well as ensuring proper segregation of the chromosomes, these junctions are also the breakpoints at which chromosomal crossover may occur during mitosis or meiosis, which results in the reciprocal exchange of DNA between the synapsed chromatids.
chimerism: The presence of two or more populations of cells with distinct genotypes in an individual organism, known as a chimera, which has developed from the fusion of cells originating from separate zygotes; 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. by allogeneic transplantation of cells, tissues, or organs from a genetically non-identical donor); in plants, it can result from grafting or errors in cell division. It is similar to but distinct from mosaicism.
chloroplast
chloroplast DNA (cpDNA, chDNA, ctDNA): The set of DNA molecules contained within chloroplasts, a type of photosynthetic plastid organelle located within the cells of some eukaryotes such as plants and algae, representing a semi-autonomous genome separate from that within the cell's nucleus. Like other types of plastid DNA, cpDNA usually exists in the form of small circular plasmids.
chondriome: The complete set of mitochondria or of mitochondrial DNA within a cell, tissue, organism, or species.
chromatid: One copy of a newly copied chromosome, which is joined to the original chromosome by a centromere. Paired copies of the same individual chromosome are known as sister chromatids.
chromatin: A complex of DNA, RNA, and protein found in eukaryotic cells that is the primary substance comprising chromosomes. Chromatin functions as a means of packaging very long DNA molecules into highly organized and densely compacted shapes, which prevents the strands from becoming tangled, reinforces the DNA during cell division, helps to prevent DNA damage, and plays an important role in regulating gene expression and DNA replication.
chromatin immunoprecipitation (ChIP)
chromocenter: A central amorphous mass of polytene chromosomes found in the nuclei of cells of the salivary glands in Drosophila larvae and resulting from the fusion of heterochromatic regions surrounding the centromeres of the somatically paired chromosomes, with the distal euchromatic arms radiating outward.^[4]
chromomere: A region of a chromosome that has been locally compacted or coiled into chromatin, conspicuous under a microscope as a "bead", node, or dark-staining band, especially when contrasted with nearby uncompacted strings of DNA.
chromosomal crossover
chromosomal DNA: DNA contained in chromosomes, as opposed to extrachromosomal DNA. The term is generally used synonymously with genomic DNA.
chromosomal duplication: The duplication of an entire chromosome, as opposed to a segment of a chromosome or an individual gene.
chromosomal instability
chromosome: A nuclear DNA 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 the nucleus of cells and, in most eukaryotes, are composed of long strands of DNA coiled with packaging proteins which bind to and condense 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 during cell 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 during prophase due to systemic coiling and supercoiling of chromatic strands of DNA in preparation for cell division.
chromosome segregation: The process by which sister chromatids or paired homologous chromosomes separate from each other and migrate to opposite sides of the dividing cell during mitosis or meiosis.
chromosome walking: See primer walking.
cilium: A slender, thread-like, membrane-bound projection extending from the surface of a eukaryotic cell, longer than a microvillus but shorter than a flagellum. Most eukaryotic cells have at least one primary cilium serving sensory or signaling functions; some cells employ thousands of motile cilia covering their entire surface in order to achieve locomotion or to move extracellular material past the cell.
circular DNA: Any DNA molecule, single-stranded or double-stranded, which forms a continuous closed loop without ends; e.g. bacterial chromosomes, mitochondrial and plastid DNA, as well as many other varieties of extrachromosomal DNA, including plasmids and some viral DNA. Contrast linear DNA.
circulating tumor DNA (ctDNA): Any extracellular 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. Contrast trans.
cis-acting: Affecting a gene or sequence on the same nucleic acid molecule. A locus or sequence within a particular DNA molecule such as a chromosome is said to be cis-acting if it influences or acts upon other sequences located within short distances (i.e. physically nearby, usually but not necessarily downstream) 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 a homologous pair. Cis-acting factors are often involved in the regulation of gene expression by acting to inhibit or to facilitate transcription. Contrast trans-acting.
cis-dominant mutation: A mutation occurring within a cis-regulatory element (such as an operator) which alters the functioning of a nearby gene or genes on the same chromosome. Cis-dominant mutations affect the expression of genes because they occur at sites that control transcription rather than within the genes themselves.
cisgenesis
cis-regulatory element (CRE): Any sequence or region of non-coding DNA which regulates the transcription of nearby genes (e.g. a promoter, operator, silencer, or enhancer), typically by serving as a binding site for one or more transcription factors. Contrast trans-regulatory.
cisterna: Any of a class of flattened, membrane-bound vesicles or saccules of the smooth and rough endoplasmic reticulum and the Golgi 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 as phosphorylation and glycosylation, which are used as packaging signals to direct their transport to specific destinations within the cell.^[14]
cistron
citric acid cycle
classical genetics: The branch of genetics based solely on observation of the visible results of reproductive acts, as opposed to that made possible by the modern techniques and methodologies of molecular biology. Contrast molecular genetics.
cleavage
cleavage furrow
clonal selection
cloning: 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 of asexual reproduction, and cells that undergo mitosis 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, in molecular cloning, copies of DNA fragments or other molecules.
closed chromatin: See heterochromatin.
coactivator: A type of coregulator that increases the expression of one or more genes by binding to an activator.
coding strand: The strand of a double-stranded DNA molecule whose nucleotide sequence corresponds directly to that of the RNA transcript produced during transcription (except that thymine bases are substituted with uracil 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 the codons of the RNA product. Contrast template strand; see also sense.
codon: A series of three consecutive nucleotides in a coding region of a nucleic acid sequence. Each of these triplets codes for a particular amino acid or stop signal during protein synthesis. DNA and RNA molecules are each written in a language using four "letters" (four different nucleobases), but the language used to construct proteins includes 20 "letters" (20 different amino acids). Codons provide the key that allows these two languages to be translated into each other. In general, each codon corresponds to a single amino acid (or stop signal). The full set of codons is called the genetic code.
codon usage bias: The preferential use of a particular codon to code for a particular amino 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 the genetic code is degenerate, most amino acids can be specified by multiple codons. Nevertheless, certain codons tend to be overrepresented (and others underrepresented) in different species.
coenocyte: A multinucleate mass of cytoplasm bounded by a cell wall and resulting from continuous cytoplasmic growth and repeated nuclear division without cytokinesis, found in some species of algae and fungi, e.g. Vaucheria and Physarum.^[11]
coenzyme: A relatively small, independent molecule which associates with a specific enzyme and participates in the reaction that the enzyme catalyzes, often by forming a covalent bond with the substrate. Examples include biotin, NAD⁺, and coenzyme A.^[6]
coenzyme A (CoA)
cofactor: Any non-protein organic compound that is bound to an enzyme. Cofactors are required for the initiation of catalysis.
comparative genomic hybridization (CGH)
competence
complementarity: A property of nucleic acid biopolymers whereby two polymeric chains or "strands" aligned antiparallel to each other will tend to form base pairs consisting of hydrogen bonds between the individual nucleobases comprising each chain, with each type of nucleobase pairing almost exclusively with one other type of nucleobase; e.g. in double-stranded DNA molecules, A pairs only with T and C pairs only with G. Strands that are paired in such a way, and the bases themselves, are said to be complementary. The degree of complementarity between two strands strongly influences the stability of the duplex molecule; certain sequences may also be internally complementary, which can result in a single strand binding to itself. Complementarity is fundamental to the mechanisms governing DNA replication, transcription, and DNA repair.
complementary DNA (cDNA): DNA that is synthesized from a single-stranded RNA template (typically mRNA or miRNA) in a reaction catalyzed by the enzyme reverse transcriptase. cDNA is produced both naturally by retroviruses and artificially in certain laboratory techniques, particularly molecular cloning. In bioinformatics, the term may also be used to refer to the sequence of an mRNA transcript expressed as its DNA coding strand counterpart (i.e. with thymine replacing uracil).
complementation
compound X: See attached X.
conditional expression: The controlled, inducible expression of a transgene, either in vitro or in vivo.
confluency
congression: The movement of chromosomes to the spindle equator during the prometaphase and metaphase stages of mitosis.^[4]
consensus sequence: A calculated order of the most frequent residues (of either nucleotides or amino acids) found at each position in a common sequence alignment and obtained by comparing multiple closely related sequence alignments.
conservative replication: A hypothetical mode of DNA replication in which the two parental strands of the original double-stranded DNA molecule ultimately remain complemented to each other at the end of the replication process, and the two daughter strands end up forming their own separate molecule; hence one molecule is composed of both of the starting strands while the other is composed entirely of newly synthesized strands. This is in contrast to semiconservative replication, in which each molecule is a hybrid of one old and one new strand.See also dispersive replication.
conserved sequence: A nucleic acid or protein sequence that is highly similar or identical across many species or within a genome, indicating that it has remained relatively unchanged through a long period of evolutionary time.
conspecific: Belonging to the same species.
constitutive expression: 1. The continuous transcription of a gene, as opposed to facultative expression, in which a gene is only transcribed as needed. A gene that is transcribed continuously is called a constitutive gene.; 2. A gene whose expression depends only on the efficiency of its promoter in binding RNA polymerase,^[4] and not on any transcription factors or other regulatory elements which might promote or inhibit its transcription.
contact inhibition
contig: A continuous sequence of genomic DNA generated by assembling cloned fragments by means of their overlapping sequences.^[7]
cooperativity
copy DNA (cDNA): See complementary DNA.
copy error: A mutation resulting from a mistake made during DNA replication.^[4]
copy-number variation (CNV): A phenomenon in which sections of a genome are repeated and the number of repeats varies between individuals in the population, usually as a result of duplication or deletion events that affect entire genes or sections of chromosomes. Copy-number variations play an important role in generating genetic variation within a population.
coregulator: A protein that works together with one or more transcription factors to regulate gene expression.
corepressor: A type of coregulator that reduces (represses) the expression of one or more genes by binding to and activating a repressor.
cosmid
cpDNA: See chloroplast DNA.
CpG island: A region of a genome in which CpG sites occur repetitively or with high frequency.
CpG site: A sequence of DNA in which a cytosine nucleotide is immediately followed by a guanine nucleotide on the same strand in the 5'-to-3' direction; the "p" in CpG refers simply to the intervening phosphate group linking the two consecutive nucleotides.
CRISPR gene editing
crista
crossing over: See chromosomal crossover.
crosslink: An abnormal chemical bond between two or more nucleobases on opposite strands of a double-stranded DNA molecule (interstrand), or between bases on the same strand (intrastrand), specifically via the formation of covalent bonds that are stronger than the hydrogen bonds of base pairing. Crosslinks can be generated by a variety of exogenous and endogenous agents, and tend to interfere with normal cellular processes such as DNA replication and transcription. They are common targets of DNA repair pathways.
cryptic unstable transcript (CUT)
ctDNA: 1. An abbreviation of circulating tumor DNA.; 2. An abbreviation of chloroplast DNA.
C-terminus: The end of a linear chain of amino acids (i.e. a peptide) that is terminated by the free carboxyl group (–COOH) of the last amino acid to be added to the chain during translation. This amino acid is said to be C-terminal. By convention, sequences, domains, active sites, or any other structure positioned nearer to the C-terminus of the polypeptide or the folded protein it forms relative to others are described as downstream. Contrast N-terminus.
cut
C-value: The total amount of DNA contained within a haploid nucleus (e.g. a gamete) of a particular organism or species, expressed in number of base pairs or in units of mass (typically picograms); or, equivalently, one-half the amount in a diploid somatic cell. For simple diploid eukaryotes the term is often used interchangeably with genome size, but in certain cases, e.g. in hybrid polyploids descended from parents of different species, the C-value may actually represent two or more distinct genomes contained within the same nucleus. C-values apply only to genomic DNA, and notably exclude extranuclear DNA.
C-value enigma: A term used to describe a diverse variety of questions regarding the immense variation in nuclear C-value or genome 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 of genes they possess; for example, many single-celled protists have genomes containing thousands of times more DNA than the human genome. This was considered paradoxical until the discovery that eukaryotic genomes consist mostly of non-coding DNA, which lacks genes entirely. The focus of the enigma has since shifted to understanding why and how genomes came to be filled with so much non-coding DNA, and why some genomes have a higher gene content than others.
cyclic adenosine monophosphate (cAMP)
cyclosis: See cytoplasmic streaming.
cytidine (C, Cyd): One of the four standard nucleosides used in RNA molecules, consisting of a cytosine base with its N₉ nitrogen bonded to the C₁ carbon of a ribose sugar. Cytosine bonded to deoxyribose is known as deoxycytidine, which is the version used in DNA.
cytochemistry: The branch of cell biology involving the detection and identification of the various structures and components within cells by means of biochemical analysis and visualization, in particular the localization of cellular constituents by using techniques such as chemical staining and immunostaining, spectrophotometry and spectroscopy, radioautography, and electron microscopy.
cytogenetics: The branch of genetics that studies how chromosomes influence and relate to cell behavior and function, particularly during mitosis and meiosis.
cytokine
cytokinesis: The final stage of cell division in both mitosis and meiosis, usually immediately following the division of the nucleus, during which the cytoplasm of the parent cell is cleaved and divided approximately evenly between two daughter cells. In animal cells, this process occurs by the closing of a microfilament contractile ring in the equatorial region of the dividing cell. Contrast karyokinesis.
cytology: The study of the morphology, processes, and life history of living cells, particularly by means of light and electron microscopy.^[11] The term is also sometimes used as a synonym for the broader field of cell biology.
cytolysis: See lysis.
cytometer
cytomics: The interdisciplinary field that studies cell biology, cytology, and biochemistry at the level of an individual cell by making use of single-cell molecular techniques and advanced microscopy to visualize the interactions of cellular components in vivo.^[15]
cytoplasm
cytoplasmic streaming: The flow of the cytoplasm inside a cell, driven by forces exerted upon cytoplasmic fluids by the cytoskeleton. This flow functions partly to speed up the transport of molecules and organelles suspended in the cytoplasm to different parts of the cell, which would otherwise have to rely on passive diffusion for movement. It is most commonly observed in very large eukaryotic cells, for which there is a greater need for transport efficiency.
cytoplast: An enucleated 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 of nuclear transfer experiments, during which the cytoplast can sometimes remain viable in the absence of a nucleus for up to 48 hours.^[16]
cytosine (C): A pyrimidine nucleobase used as one of the four standard nucleobases in both DNA and RNA molecules. Cytosine forms a base pair with guanine.
cytosol: The soluble aqueous phase of the cytoplasm, in which small particles such as ribosomes, proteins, nucleic acids, and many other molecules are suspended or dissolved, excluding larger structures and organelles such as mitochondria, chloroplasts, lysosomes, and the endoplasmic reticulum.^[11]

D[edit]

daughter cell
de novo mutation: A spontaneous mutation in the genome of an individual organism that is new to that organism's lineage, having first appeared in a germ 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.^[4]
de novo synthesis: The assembly of a synthetic nucleic acid sequence from free nucleotides without relying on an existing template strand, i.e. de novo, by any of a variety of laboratory methods. De novo synthesis makes it theoretically possible to construct completely artificial 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-order oligonucleotide sequences such as primers.
deacetylation
decellularization
degeneracy: The redundancy of the genetic code, exhibited as the multiplicity of different codons that specify the same amino acid. For example, in the standard genetic code, the amino acid serine is specified by six unique codons (UCA, UCG, UCC, UCU, AGU, and AGC). Codon degeneracy accounts for the existence of synonymous mutations.
degranulation
deletion: A type of mutation in which one or more nucleotides are removed from a nucleic acid sequence.
demethylation
denaturation: The process by which nucleic acids or proteins lose their quaternary, tertiary, and/or secondary 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 as hydrogen 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 of double-stranded DNA molecules, for example, which breaks the hydrogen bonds between base pairs and causes the separation of the duplex molecule into two single strands, is a necessary step in DNA replication and transcription and hence is routinely performed by enzymes such as helicases. The same mechanism is also fundamental to laboratory methods such as PCR.
deoxyadenosine: One of the four standard deoxyribonucleosides used in DNA molecules, consisting of an adenine base with its N₉ nitrogen bonded to the C₁ carbon of a deoxyribose sugar. Adenine bonded to ribose forms an alternate compound known simply as adenosine, which is used in RNA.
deoxycytidine: One of the four standard deoxyribonucleosides used in DNA molecules, consisting of a cytosine base with its N₉ nitrogen bonded to the C₁ carbon of a deoxyribose sugar. Cytosine bonded to ribose forms an alternate compound known simply as cytidine, which is used in RNA.
deoxyguanosine: One of the four standard deoxyribonucleosides used in DNA molecules, consisting of a guanine base with its N₉ nitrogen bonded to the C₁ carbon of a deoxyribose sugar. Guanine bonded to ribose forms an alternate compound known simply as guanosine, which is used in RNA.
deoxyribonuclease (DNase): Any of a class of nuclease enzymes which catalyze the hydrolytic cleavage of phosphodiester bonds in DNA molecules, thereby severing strands of deoxyribonucleotides and causing the degradation of DNA polymers into smaller components. Compare ribonuclease.
deoxyribonucleic acid (DNA): A polymeric nucleic acid molecule composed of a series of deoxyribonucleotides, each of which incorporates one of four canonical nucleobases: adenine (A), guanine (G), cytosine (C), and thymine (T). DNA is most often found in double-stranded form, which consists of two complementary antiparallel nucleotide chains in which each of the nucleobases on each individual strand is paired via hydrogen bonding with one on the opposite strand; this structure commonly occurs in the shape of a double helix. DNA can also exist in single-stranded form. By storing and encoding genetic information in the sequence of its nucleotides, DNA serves as the universal molecular basis of biological inheritance and the fundamental template from which all proteins, cells, and living organisms are constructed.
deoxyribonucleotide: A nucleotide containing deoxyribose as its pentose sugar component, and the monomeric subunit of deoxyribonucleic acid (DNA) molecules. Deoxyribonucleotides canonically incorporate any of four nitrogenous bases: adenine (A), guanine (G), cytosine (C), and thymine (T). Compare ribonucleotide.
deoxyribose: A monosaccharide sugar derived from ribose by the loss of a single oxygen atom. D-deoxyribose, in its pentose ring form, is one of three primary functional groups of deoxyribonucleotides and hence of deoxyribonucleic acid (DNA) molecules.
deoxythymidine: See thymidine.
dephosphorylation
desmosome: A specialized cell junction between neighboring epithelial cells in which the cells are held together by a network of keratin filaments and structural proteins bridging the gap between the plasma membranes.^[17]
destination vector
desynapsis: The failure of homologous chromosomes that have synapsed normally during pachynema to remain paired during diplonema. Desynapsis is usually caused by the improper formation of chiasmata.^[4] Contrast asynapsis.
developmental biology
diakinesis: In meiosis, the fifth and final substage of prophase I, following diplonema and preceding metaphase I. During diakinesis, the chromosomes are further condensed, the two centrosomes reach opposite poles of the cell, and the spindle apparatus begins to extend from the poles to the equator.^[4]
dicentric: (of a linear chromosome or chromosome fragment) Having two centromeres instead of the normal one.^[2]
differentiation
dimer: A molecular aggregate consisting of two subunits. The term is often used to describe a protein complex composed of two proteins, either the same protein (a homodimer) or different proteins (a heterodimer); or to an individual protein composed of two polypeptides. Compare monomer, trimer, and tetramer.
dinucleotide: Any two nucleotides which are immediately adjacent to each other on the same strand of a nucleic acid molecule.
diploid: (of a cell or organism) Having two homologous copies of each chromosome. Contrast haploid and polyploid.
diplonema: In meiosis, the fourth of the five substages of prophase I, following pachynema and preceding diakinesis. During diplonema, the synaptonemal complex disassembles and the paired homologous chromosomes begin to separate from one another, though they remain tightly bound at the chiasmata where crossover has occurred.
direct repeat: Any two or more repetitions of a specific sequence of nucleotides occurring in the same orientation (i.e. in precisely the same order and not inverted) and on the same strand, either separated by intervening nucleotides or not. An example is the sequence TACCGnnnnnnTACCG, in which TACCG 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 a tandem repeat.
directionality: The end-to-end chemical orientation of a single linear strand or sequence of a nucleic acid polymer or a polypeptide. The nomenclature used to indicate nucleic acid directionality is based on the chemical convention of identifying individual carbon atoms in the ribose or deoxyribose sugars of nucleotides, specifically the 5' carbon and 3' carbon of the pentose 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, including DNA replication and transcription, work exclusively in the 5'-to-3' direction, because the enzymes 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. In double-stranded nucleic acids, the two paired strands must be oriented in opposite directions in order to base-pair with each other. Polypeptide directionality is similarly based on labeling the functional groups in amino acids, specifically the amino group, which forms the N-terminus, and the carboxyl group, which forms the C-terminus; amino acid sequences are assembled in the N-to-C direction during translation, and are almost always written in the same direction.
disaccharide
dispersive replication
dissimilatory process: Any exergonic process of microbial catabolism by which redox-active chemical species participate in oxidation-reduction reactions (exchange of electrons) to provide the cell with energy needed for sustaining metabolic activities. External substances are absorbed by the cell from its environment and then decomposed to release energy, with the byproducts subsequently excreted out of the cell. This is in contrast to an assimilatory process, in which the atoms of the external substances are reused in the synthesis of biomolecules or the fabrication of cellular components.
distance measure: Any quantity used to measure the dissimilarity between the gene expression levels of different genes.^[18]
DNA: See deoxyribonucleic acid.
DNA barcoding: A method of taxonomic identification in which short DNA sequences from one or more specific genes are isolated from unidentified samples and then aligned with sequences from a reference 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 widely conserved and that show greater variation between species than within species, e.g. the cytochrome c oxidase gene for eukaryotes or certain ribosomal 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 be linked to one particular species, effectively creating a unique identifier akin to a retail barcode. 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 be phylogenetically classified with confidence. The simultaneous identification of multiple different species from a mixed sample is known as metabarcoding.
DNA condensation: The process of compacting very long DNA molecules into densely packed, orderly configurations such as chromosomes, either in vivo or in vitro.
DNA fingerprinting
DNA methylation
DNA microarray: A high-throughput technology used to measure expression levels of mRNA transcripts or to detect certain changes in nucleotide sequence. It consists of an array of thousands of microscopic spots of DNA oligonucleotides, called features, each containing picomoles of a specific DNA sequence. This can be a short section of a gene or any other DNA element, and is used as a probe to hybridize a cDNA, cRNA or genomic DNA sample (called a target) under high-stringency conditions. Probe-target hybridization is usually detected and quantified by fluorescence-based detection of fluorophore-labeled targets.
DNA polymerase: Any of a class of enzymes which synthesize DNA molecules from individual deoxyribonucleotides. DNA polymerases are essential for DNA replication and usually work in pairs to create identical copies of the two strands of an original double-stranded molecule. They build long chains of DNA by adding nucleotides one at a time to the 3'-end of a DNA strand, usually relying on the template provided by the complementary strand to copy the nucleotide sequence faithfully.
DNA repair: The set of processes by which a cell identifies and corrects structural damage or mutations in the DNA molecules that encode its genome. The ability of a cell to repair its DNA is vital to the integrity of the genome and the normal functionality of the organism.
DNA replication: The process by which a DNA molecule copies itself, producing two identical copies of one original DNA molecule.
DNA sequencing: The process of determining, by any of a variety of different methods and technologies, the order of the bases in the long chain of nucleotides that constitutes a sequence of DNA.
DNA turnover: Any mechanism by which DNA sequences are exchanged non-reciprocally (e.g. via gene conversion, transposition, or unequal crossing-over) that causes continual fluctuations in the copy number of DNA motifs during an organism's lifetime. Such mechanisms are often major drivers of speciation between populations.^[16]
DNA-binding domain (DBD)
DNA-binding protein (DBP): Any polypeptide or protein containing one or more domains capable of interacting chemically with one or more parts of a DNA molecule, and consequently having a specific or general affinity for single- and/or double-stranded DNA. DNA-binding activity often depends on the presence and physical accessibility of a specific nucleobase sequence, and mostly occurs at the major groove, since it exposes more of the functional groups that 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 undergoing structural changes induced by interactions with other molecules.
DNase: See deoxyribonuclease.
domain
donor vector
dosage compensation: Any mechanism by which organisms neutralize the large difference in gene dosage caused by the presence of differing numbers of sex chromosomes in the different sexes, thereby equalizing the expression of sex-linked genes so that the members of each sex receive the same or similar amounts of the products of such genes. An example is X-inactivation in female mammals.
double helix: The shape most commonly assumed by double-stranded nucleic acid molecules, resembling a ladder that has been twisted upon its long axis, with the rungs of the ladder consisting of paired nucleobases. This secondary structure is the most energetically stable conformation of the double-stranded forms of both DNA and RNA under most naturally occurring conditions, arising as a consequence of the primary structure of the phosphodiester backbone and the stacking of the nucleotides bonded to it. In B-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 (a major groove and a minor groove) between the parallel backbones.
double-strand break (DSB): The loss of continuity of the phosphate-sugar backbone in both strands of a double-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.^[16] Contrast single-strand break.
double-stranded: Composed of two antiparallel, complementary nucleic acid molecules or strands (either DNA–DNA, RNA–RNA, or a DNA–RNA hybrid) which are held together by hydrogen bonds between the complementary nucleobases of each strand, known as base pairing. Compare single-stranded.
double-stranded DNA (dsDNA): Any DNA molecule that is composed of two antiparallel, complementary deoxyribonucleotide polymers, known as strands, which are bonded together by hydrogen bonds between the complementary nucleobases. Though it is possible for DNA to exist as a single strand, it is generally more stable and more common in double-stranded form. In most cases, the complementary base pairing causes the twin strands to coil around each other in the shape of a double helix.
double-stranded RNA (dsRNA): Any RNA molecule that is composed of two antiparallel, complementary ribonucleotide polymers, known as strands, which are bonded together by hydrogen bonds between the complementary nucleobases. Though RNA usually occurs in single-stranded form, it is also capable of forming duplexes in the same way as DNA; an example is an mRNA transcript pairing with an antisense version of the same transcript, which effectively silences the gene from which the mRNA was transcribed by preventing translation. As in dsDNA, the base pairing in dsRNA usually causes the twin strands to coil around each other in the shape of a double helix.
downregulation: Any process, natural or artificial, which decreases the level of gene expression of a certain gene. A gene which is observed to be expressed at relatively low levels (such as by detecting lower levels of its mRNA transcripts) in one sample compared to another sample is said to be downregulated. Contrast upregulation.
downstream: Towards or closer to the 3'-end of a chain of nucleotides, or to the C-terminus of a peptide chain. Contrast upstream.
dsDNA: See double-stranded DNA.
dsRNA: See double-stranded RNA.
duplex: See double-stranded.
duplication: The production of a second copy of part or all of a nucleotide sequence or amino acid sequence, either naturally or artificially, and the retention of both copies; especially when both the copy and the original sequence are retained in situ within the same molecule, often but not necessarily adjacent to each other. See also gene duplication, chromosomal duplication, and repeat.
dyad: See sister chromatids.
dysplasia: 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,^[6] an event which often precedes the development of cancer; the abnormal growth or development of a tissue or organ.

E[edit]

eat-me signal: A molecule exposed on the surface of a cell which effectively tags the cell for phagocytosis, inducing phagocytes to engulf or "eat" it. The presence of oxidized phospholipids or phosphatidylserine, or the absence of sialic acid from cell surface glycoproteins or glycolipids, are all commonly used as eat-me signals in certain cell types. See also find-me signal.
electron transport chain
electroporation: 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 achieving transformation and transfection.
elongation: The linear growth of a nucleic acid polymer by the sequential addition of individual nucleotide monomers to a nascent strand, e.g. during transcription or replication, especially when it occurs by complementary pairing with a template strand. The term is often used to describe steps in certain laboratory techniques such as the polymerase chain reaction.
embryo
emergenesis: The quality of genetic traits that results from a specific configuration of interacting genes, rather than simply their combination.
endocytosis: Any process by which a substance is actively uptaken by or brought inside of a cell, crossing the plasma membrane from an extracellular space into an intracellular space, which includes the subclasses of pinocytosis, phagocytosis, and receptor-mediated processes. All of these involve surrounding an extracellular molecule, protein, or even another cell or organism with an extension or invagination of the cell membrane, which then "buds off" or separates from the rest of the membrane on the cytoplasmic side, forming a membrane-enclosed vesicle containing the ingested materials. By this mechanism the material can cross the lipid 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 as metabolites and hormones, are transported into the cell by endocytosis. It is distinguished from alternative routes such as passing through protein channels or being chaperoned by transport proteins. The reverse process is called exocytosis.
endomembrane: Any membrane surrounding an intracellular organelle or vesicle, e.g. that of the endoplasmic reticulum, Golgi apparatus, lysosome, vacuole, nucleus (the nuclear envelope), etc.^[11]
endonuclease: Any enzyme whose activity is to cleave phosphodiester bonds within a chain of nucleotides, including those that cleave relatively nonspecifically (without regard to sequence) and those that cleave only at very specific sequences (so-called restriction endonucleases). When recognition of a specific sequence is required, endonucleases make their cuts in the middle of the sequence. Contrast exonuclease.
endoplasmic reticulum (ER)
endosome
enhancer: A region of DNA near a gene that can be bound by an activator to increase gene expression or by a repressor to decrease expression.
enhancer RNA (eRNA): A subclass of long non-coding RNAs transcribed from regions of DNA containing enhancer 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 regulation in cis or in trans.
enucleate: To artificially remove the nucleus from a cell, e.g. by micromanipulation in the laboratory or by destroying it through irradiation with ultraviolet light, rendering the cell anucleate.^[11]
envagination
enzyme: A protein which acts as a catalyst for a biological process by accelerating a specific chemical reaction, typically by binding one or more substrate molecules and decreasing the activation 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. All metabolic 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.
epigenetics
epigenome
episome: 1. Another name for a plasmid, especially one that is capable of integrating into a chromosome.; 2. In eukaryotes, any non-integrated extrachromosomal circular DNA molecule that is stably maintained and replicated in the nucleus simultaneously with the rest of the host cell. Such molecules may include viral genomes, bacterial plasmids, and aberrant chromosomal fragments.
epistasis: The collective action of multiple genes interacting during gene expression. A form of gene action, epistasis can be either additive or multiplicative in its effects on specific phenotypic traits.
epitope
ergosome: See polysome.
euchromatin: A relatively open, lightly compacted form of chromatin in which DNA is only sporadically bound in nucleosomes and thus broadly accessible to binding and manipulation by proteins and other molecules. Euchromatic regions of a genome are often enriched in genes and actively undergoing transcription, in contrast to heterochromatin, which is relatively gene-poor, nucleosome-rich, and less accessible to transcription machinery.
euploidy: The condition of a cell or organism having an abnormal number of complete sets of chromosomes, possibly excluding the sex chromosomes. Euploidy differs from aneuploidy, in which a cell or organism has an abnormal number of one or more specific individual chromosomes.
evolution: The change in the heritable characteristics of biological populations over successive generations. In the most traditional sense, it occurs by changes in the frequencies of alleles in a population's gene pool.
ex vivo: Occurring outside of a cell or organism, as with observations made or experiments performed in or on cells or tissues 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 a cell culture being grown in a laboratory). This is in contrast to in vivo observations, which are made in an entirely natural context.
excision: The enzymatic removal of a polynucleotide sequence from one or more strands of a nucleic acid, or of a polypeptide sequence from a protein, 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 most splicing and DNA repair pathways.^[4]
exocytosis: Any active transport process by which a substance is secreted from or transported out of a cell, crossing the plasma membrane from the interior of the cell into the extracellular space, especially that which occurs by the fusion of the membrane surrounding a secretory vesicle 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 the lipid 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, often metabolites or hormones 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 as endocytosis.
exome: The entire set of exons within a particular genome, including untranslated regions of mature mRNAs as well as coding regions.
exon: Any part of a gene that encodes a part of the final mature messenger RNA produced by that gene after introns have been removed by alternative splicing. The term refers to both the sequence as it exists within a DNA molecule and to the corresponding sequence in RNA transcripts.
exon skipping
exonuclease: Any enzyme whose activity is to cleave phosphodiester bonds within a chain of nucleotides, including those that cleave only upon recognition of a specific sequence (so-called restriction exonucleases). Exonucleases make their cuts at either the 3' or 5'-end of the sequence (rather than in the middle, as with endonucleases).
exosome: 1. (protein complex) An intracellular multi-protein complex which serves the function of degrading various types of RNA molecules.; 2. (vesicle) A type of membrane-bound extracellular vesicle produced in many eukaryotic cells by the inward budding of an endosome and the subsequent fusion of the endosome with the plasma 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.
exosome complex: An intracellular multi-protein complex which serves the function of degrading various types of RNA molecules.
expression vector: A type of vector, usually a plasmid or viral vector, designed specifically for the expression of a transgene insert in a target cell, rather than for some other purpose such as cloning.
extein: Any part of an amino acid sequence which is retained within a precursor polypeptide, i.e. not excised by post-translational protein splicing, and is therefore present in the mature protein, analogous to the exons of RNA transcripts. Contrast intein.
extension: See elongation.
extracellular: Outside the plasma membrane of a cell or cells; i.e. located or occurring externally to a cell. Contrast intracellular; see also intercellular.
extracellular matrix (ECM): The network of interacting macromolecules and minerals secreted by and existing outside of and between cells in multicellular structures such as tissues and biofilms, 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 them cell adhesion, motility, metabolism, division, and cell-to-cell communication. The composition and properties of the ECM vary enormously between organisms and tissue types, but generally it takes the form of a polysaccharide gel in which various fibrous proteins (especially collagen and elastin), enzymes, and glycoproteins are embedded. Cells themselves both produce the matrix components and respond constantly to local matrix composition, a source of environmental feedback which is critical for differentiation, tissue organization, and development.^[11]^[19]
extrachromosomal DNA: Any DNA that is not found in chromosomes or in the nucleus of a cell and hence is not genomic DNA. This may include the DNA contained in plasmids or organelles such as mitochondria or chloroplasts, or, in the broadest sense, DNA introduced by viral infection. Extrachromosomal DNA usually shows significant structural differences from nuclear DNA in the same organism.

F[edit]

facultative expression: The transcription of a gene only as needed, as opposed to constitutive expression, in which a gene is transcribed continuously. A gene that is transcribed as needed is called a facultative gene.
fatty acid
fermentation
filopodium
find-me signal: A molecule exposed on the surface of a cell destined for apoptosis which is used to attract phagocytes to engulf and eliminate the cell by phagocytosis. See also eat-me signal.
five-prime cap: See 5' cap.
five-prime end: See 5'-end.
five-prime untranslated region: See 5' untranslated region.
fixation: 1. (histology) The preservation of biological material by treating it with a chemical fixative that prevents or delays the natural postmortem processes of decay (e.g. autolysis and putrefaction) 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 subsequent staining 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 obtain information about molecular details that occur too rapidly or transiently to study in living samples. Common fixatives such as formaldehyde work by disabling proteolytic enzymes, coagulating and denaturing macromolecules, creating crosslinks between them, and protecting specimens from decomposition by bacteria and fungi.; 2. (population genetics) The process by which a single allele for a particular gene with multiple different alleles increases in frequency in a given population such that it becomes permanently established as the only allele at that locus within the population's gene pool.
fixative
flagellate: (of a cell) Having one or more flagella.
flagellum
fluorescence in situ hybridization (FISH)
forward genetics: An experimental approach in molecular genetics in which a researcher starts with a specific known phenotype and attempts to determine the genetic basis of that phenotype by any of a variety of laboratory techniques, commonly by inducing random mutations in the organism's genome and then screening 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 be mapped to specific genomic loci and ultimately to one or more specific candidate genes. This methodology contrasts with reverse genetics, in which a specific gene or its gene product is individually manipulated in order to identify the gene's function.
forward mutation
frameshift mutation: A type of mutation in a nucleic acid sequence caused by the insertion or deletion of a number of nucleotides 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 the reading frame of the nucleotide sequence, resulting in the sequence of codons downstream of the mutation site being completely different from the original.
freeze-drying: See lyophilization.
Functional Genomics Data (FGED) Society: 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.^[20]

G[edit]

G banding: A technique used in cytogenetics to produce a visible karyotype by staining the condensed chromosomes with Giemsa stain. The staining produces consistent and identifiable patterns of dark and light "bands" in regions of chromatin, which allows specific chromosomes to be easily distinguished.
G1
G2
gamete: A haploid cell that is the meiotic product of a progenitor germ cell and the final product of the germ line in sexually 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 single diploid zygote.
gametogenesis
GC content: See guanine-cytosine content.
gDNA: See genomic DNA.
gene: Any segment or set of segments of a nucleic acid molecule that contains the information necessary to produce a functional RNA transcript in a controlled manner. In living organisms, genes are often considered the fundamental units of heredity and are typically encoded in DNA. A particular gene can have multiple different versions, or alleles, and a single gene can result in a gene product that influences many different phenotypes.
gene dosage: The number of copies of a particular gene present in a genome. Gene dosage directly influences the amount of gene product a cell is able to express, though a variety of controls have evolved which tightly

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