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.
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 to
Glossary of genetics and evolutionary biology, which contains many overlapping and related terms; other related glossaries include
Glossary of virology and
Glossary of chemistry.
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.
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
methylatedguaninenucleoside 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.
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.
Any of a class of
transferaseenzymes which catalyze the covalent bonding of an
acetyl group (–COCH 3) to another compound, protein, or biomolecule, a process known as
acetylation.
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.
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.
One of three main biologically active
structural conformations of the
DNAdouble 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]
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.
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.
Also sex chromosome, heterochromosome, or idiochromosome.
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.
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.
Any of a class of organic compounds whose basic structural formula includes a central carbon atom bonded to
amine and
carboxylfunctional 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.
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.
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.
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).
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.
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.
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'.
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]
Also antisense transcript and antisense oligonucleotide (ASO).
A
single-strandednon-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.
(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).
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
excretesresidual or toxic compounds out of the cell, instead of reusing them to build new molecules.
A single
monocentricchromosome 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.
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.
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.
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.
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.
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.
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.
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.
The "standard" or classical
structural conformation of the
DNAdouble helixin 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.
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]
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.
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.
A
regulatorygene 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.
Any of a class of
transmembrane proteins which are dependent on calcium ions (Ca2+) and whose extracellular
domains function as mediators of cell–cell adhesion at
adherens junctions in eukaryotic tissues.
An unorganized mass of
parenchymal cells that forms naturally at the site of wounds in plant tissues, and which is commonly artificially induced to form in plant
tissue culture as a means of initiating
somatic embryogenesis.[11]
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.
Any of a class of organic compounds having the generic chemical formula (CH 2O) n, and one of several major classes of
biomolecules found universally in biological systems. Carbohydrates include individual
monosaccharides as well as the larger
polymers they form (
oligosaccharides,
polysaccharides, etc.) when multiple monosaccharide units are joined by
glycosidic bonds.[11] Abundant and ubiquitous, these compounds are involved in numerous essential biochemical processes and
pathways; they are widely used as an energy source for cellular
metabolism, as a form of energy storage, as
signaling molecules, and as
biomarkers to
label or modify the activity of other molecules. Carbohydrates are often colloquially described as "sugars"; the prefix glyco- is used to indicate a compound or process containing or related to carbohydrates, and the suffix -ose usually signifies that a compound is a carbohydrate or a derivative.
2. A protein to which a specific
ligand or
hapten has been conjugated and which thereby carries an
antigen capable of eliciting an
antibody response.[12]
3. A protein which is included in an
assay at high concentrations in order to prevent non-specific interactions of the assay's reagents with vessel surfaces, sample components, or other reagents.[12] For example, in many
blotting techniques,
albumin is intentionally allowed to bind non-specifically to the blotted membrane prior to
fluorescent labelling, so as to "block" potential off-target binding of the
fluorophore 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 DNA
vector with an annotated sequence and precisely positioned
regulatory elements, into which one or more
fragments can be readily
inserted or recombined by various
genetic engineering methods. Recombinant
plasmid vectors containing reliable
promoters,
origins of replication, and antibiotic resistance genes are commonly manufactured and sold as cassettes to allow scientists to easily replace one
gene of interest with another by swapping it into and out of an active "slot" or locus within the plasmid. See also multiple cloning site.
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.
A specialized layer of
cytoplasmic proteins lining the inner face of the
cell membrane in most eukaryotic cells, composed primarily of
actinmicrofilaments and
myosinmotor 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 of
cells within a biological sample or
culture by any of a variety of methods. Counting cells is an important aspect of
cytometry used widely in research and clinical medicine. It is generally achieved by using a manual or digital
cytometer to count the number of cells present in small fractions of a sample, and then extrapolating to estimate the number present in the entire sample. The resulting quantification is typically expressed as a 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. 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.
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]
The merging or coalescence of two or more cells into a single cell, as occurs in the fusion of
gametes to form a
zygote. Generally this occurs by the destabilization of each cell's
plasma membrane and the formation of
cytoplasmic bridges between them which then expand until the two cytoplasms are completely mixed; intercellular structures or
organelles such as
nuclei may or may not fuse as well. Cells can also be artificially induced to fuse with each other by treating them with a fusogen such as
polyethylene glycol or by passing an electric current through them.[11]
Also plasma membrane, cytoplasmic membrane, and plasmalemma.
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.[13] 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.
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).
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.
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.
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.
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]
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]
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
complementarybase-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
unrepairedmismatches, 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.
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.[6]
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.
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.
A type of small, lens-shaped
plastidorganelle found in the cells of green algae and plants which contains light-sensitive
photosynthetic pigments and in which the series of biochemical reactions that comprise
photosynthesis takes place. Like
mitochondria, chloroplasts are bound by a double membrane, contain their own
internal circular DNA molecules from which they direct transcription of a unique set of genes, and replicate independently of the nuclear genome.[11][12]
The set of
DNA molecules contained within
chloroplasts, a type of photosynthetic
plastidorganelle 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.
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.
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.
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]
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.
A
nuclearDNA 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.
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.
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.
Any of a class of flattened, membrane-bound
vesicles or
saccules of the
smooth and
roughendoplasmic 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.[15]
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.
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.
Also sense strand, positive (+) sense strand, and nontemplate 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.
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.
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.
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]
A property of
nucleic acidbiopolymers 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-strandedDNA 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.
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).
In
cell culture, a measure of the proportion of the surface area of a
culture vessel that is covered by adherent cells, commonly expressed as a percentage. A culture in which the entire surface is completely covered by a continuous
monolayer, 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. Different cell lines exhibit differences in growth rate or
gene expression depending on the degree of confluence. Because of
contact inhibition, most show a significant reduction in the rate of
cell division as they approach complete confluence, though some
immortalized cells may continue to divide, expanding vertically rather than horizontally by stacking themselves on top of the
parent cells, until all available nutrients are depleted.[11][12]
conformation
The three-dimensional spatial configuration of the atoms comprising a molecule or
macromolecular structure.[11] The conformation of a
protein is the physical shape into which its
polypeptide chains arrange themselves during
protein folding, which is not necessarily rigid and may
change with the protein's particular chemical environment.
A change in the spatial
conformation 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 the
tertiary structures of proteins can affect whether or how strongly they bind
ligands or
substrates; 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.[12]
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.
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.
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.
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.
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.
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.
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.
The total amount of
DNA contained within a
haploidnucleus (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
diploidsomatic 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.
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.
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.
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.
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.[16]
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.
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.[17]
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]
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.
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.
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.
A
polymericnucleic acid molecule composed of a series of covalently linked
deoxyribonucleotides, each of which incorporates one of four
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 assumes the shape of a
double helix. DNA can also exist in
single-stranded form. By storing and encoding genetic information in the
sequence 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.
A
monosaccharidepentose sugar derived from
ribose 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 of
deoxyribonucleotides and hence of
deoxyribonucleic acid (DNA) molecules.
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. by
mass spectroscopy or
chromatography), or of
labelling it by attaching a detectable chemical moiety (e.g. a fluorescent tag) to make it easier to identify and track in vivo. Molecules modified in this way are described as derivatives of their naturally occurring counterparts and are said to have been derivatized.[12]
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.[12]
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]
A molecular
dimer consisting of exactly two covalently linked
nucleotides; or any two nucleotides which are immediately adjacent to each other on the same
strand of a longer
nucleic acid polymer.
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.
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
polymerases 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 comprising
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 by convention are written in the same direction.
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]
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.
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
DNAoligonucleotides, 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.
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.
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.
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.
A protein
domain containing at least one structural motif capable of recognizing and interacting with the
nucleotides of a
double-stranded or
single-strandedDNA molecule. DNA-binding domains may bind to specific sequences or have a non-specific affinity for DNA. They are the primary functional components of
DNA-binding proteins, including many
transcription factors and regulatory proteins.
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 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 undergoing
conformational changes induced by interactions with other molecules.
A discrete, usually continuous region of a
protein, or the corresponding
amino acid sequence of a
polypeptide, which serves a particular function or is defined by particular physico-chemical properties (e.g.
hydrophobic, polar, non-polar,
globular, etc.),[12] and especially one which assumes a unique, recognizable spatial
conformation as part of the protein's
tertiary structure and which contributes to or defines its biological activity. Large proteins are generally composed of several domains linked together by short, intervening polypeptide sequences.[6] 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 of
nucleic acid sequences and
chromosomes.[17]
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.
The shape most commonly assumed by
double-strandednucleic acid molecules, resembling a ladder that has been twisted upon its long axis, with the rungs of the ladder consisting of
pairednucleobases. 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.
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.[17] Contrast single-strand break.
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.
The abnormal growth or development of a
tissue 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,[6] an event which often precedes the development of
cancer.
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.
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.
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.
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]
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.
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.
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.
The specific site or region within an
antigenicmacromolecule such as a
protein or
carbohydrate which is recognized by
B or
T cells of the immune system, against which a specific
antibody is produced, and with which the antibody's
paratope specifically interacts or binds. In proteins, epitopes are typically
motifs of 4–5 amino acid residues, sequential or discontiguous, which by virtue of the distinct spatial
conformation they adopt upon
protein folding are able to uniquely interact with a particular paratope. In this sense they may be considered
binding 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 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.
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.
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.
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]
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.
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.
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.
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]
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.
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.
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.
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.
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.
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.
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]
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.
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
diploidzygote.
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.
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
regulategene expression. Changes in gene dosage caused by mutations include
copy-number variations.
The set of processes by which the information encoded in a
gene is used in the synthesis of a
gene product, such as a protein or
non-coding RNA, or otherwise made available to influence one or more
phenotypes. Canonically, the first step is
transcription, which produces a
messenger RNA molecule complementary to the
DNA molecule in which the gene is encoded; for protein-coding genes, the second step is
translation, in which the messenger RNA is read by the
ribosome to produce 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.
The union, either by natural mutation or by
recombinant laboratory techniques, of two or more previously independent genes that code for different gene products such that they become subject to control by the same
regulatory systems. The resulting hybrid sequence is known as a
fusion gene.[4]
Any of a variety of methods used to precisely identify the
location of a particular
gene within a DNA molecule (such as a chromosome) and/or the physical or
linkage distances between it and other genes.
gene of interest (GOI)
A
gene being studied in a scientific experiment, especially one that is the focus of a
genetic engineering technique such as
cloning.
Any of the biochemical material resulting from the
expression of a
gene, most commonly interpreted as the functional
mRNA transcript produced by
transcription of the gene or the fully constructed
protein produced by
translation of the transcript, though
non-coding RNA molecules such as
transfer 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 or
expression of specific
gene products, such as
RNA or
proteins. 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 drives
cellular differentiation and
morphogenesis in the
embryo, enabling the creation of a diverse array of cell types from the same
genome.
Any mechanism of
gene regulation which drastically reduces or completely prevents the
expression of a particular gene. Gene silencing may occur naturally during either
transcription or
translation. Laboratory techniques often exploit natural silencing mechanisms to achieve
gene knockdown.
The insertion of a functional or
wild-type gene or part of a gene into an organism (especially a patient) with the intention of correcting a
genetic defect, either by direct substitution of the defective gene or by supplementation with a second, functional version.[17]
1. In any given organism, a single
reproductive 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 particular
lineage 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 given
common ancestor by virtue of the same number of reproductive events having occurred between them and the ancestor.[17]
Any illness, disease, or other health problem directly caused by one or more abnormalities in an organism's
genome which are
congenital (present at birth) and not acquired later in life. Causes may include a
mutation to one or more
genes, or a
chromosomal abnormality such as an
aneuploidy of a particular chromosome. The mutation responsible
may occur spontaneously during embryonic development or may be
inherited from one or both parents, in which case the genetic disorder is also classified as a
hereditary 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 simply
increase the risk of developing it.
A measure of the genetic divergence between species, populations within a species, or individuals, used especially in
phylogenetics to express either the time elapsed since the existence of a
common ancestor or the degree of differentiation in the
DNA sequences comprising the
genomes of each population or individual.
Also genetic modification or genetic manipulation.
The direct, deliberate manipulation of an organism's genetic material using any of a variety of biotechnology methods, including the insertion or
removal of
genes, the transfer of genes within and between species, the
mutation of existing sequences, and the construction of novel sequences using
artificial 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 and
expression of individual genes, to produce hormones, vaccines, and other drugs, and to create
genetically modified organisms for use in research and agriculture.
A specific, easily identifiable, and usually highly
polymorphicgene or other
DNAsequence with a known location on a
chromosome that can be used to identify the individual or species possessing it.
The redundant encoding of two or more distinct
gene 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 any
loss of function and obviate any
gain of function.
A
graph that represents the regulatory complexity of
gene expression. The vertices (nodes) are represented by various regulatory elements and
gene products while the edges (links) are represented by their interactions. These network structures also represent functional relationships by approximating the rate at which genes are
transcribed.
A broad class of various procedures used to identify features of an individual's particular chromosomes, genes, or proteins in order to determine parentage or
ancestry, diagnose vulnerabilities to heritable diseases, or detect
mutant alleles associated with increased risks of developing
genetic disorders. Genetic testing is widely used in human medicine, agriculture, and biological research.
Any organism whose genetic material has been altered using
genetic engineering techniques, particularly in a way that does not occur naturally by mating or by natural
genetic recombination.
The entire complement of genetic material contained within the
chromosomes of an organism,
organelle, or
virus. The term is also used to refer to the collective set of genetic
loci shared by every member of a population or species, regardless of the different
alleles that may be present at these loci in different individuals.
The total amount of
DNA contained within one copy of a
genome, typically measured by
mass (in picograms or
daltons) or by the total number of
base pairs (in
kilobases or
megabases). For
diploid organisms, genome size is often used interchangeably with
C-value.
An
epigenetic phenomenon that causes
genes to be
expressed in a manner dependent upon the particular parent from which the gene was inherited. It occurs when epigenetic marks such as
DNA or
histone methylation are established or "imprinted" in the
germ cells of a parent organism and subsequently maintained through cell divisions in the
somatic 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.
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, or
point mutations), which may or may not result in a permanent
mutation. Though all
mutagens are genotoxic, not all genotoxic compounds are mutagenic.
The process of determining differences in the
genotype of an individual by examining the
DNA sequences in the individual's
genome using
bioassays and comparing them to another individual's sequences or a reference sequence.
Any
cell that gives rise to the
gametes of a
sexually 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 from
somatic cells, which are entirely separate from the
germ 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 from
somatic cells, which cannot pass on their genetic material except to their own immediate
mitotic daughter cells. Cells of the germ line are called
germ cells.
2. The
lineage of germ cells, spanning many generations, that contains the genetic material which has been passed on to an individual from its ancestors.
The chain of
metabolic reactions that results in the generation of
glucose from some non-carbohydrate carbon substrates, including the
glucogenic amino acids. It is one of two primary
pathways used by most animals to maintain blood sugar levels (the other being
glycogenolysis), especially during periods of fasting, starvation, and intense exercise.
The
metabolic pathway in which
carbohydrate sugars such as
glucose 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 of
pyruvate, with the free energy liberated in this process simultaneously being used to form high-energy bonds in two molecules of reduced
nicotinamide adenine dinucleotide (NADH) and two molecules of
adenosine triphosphate (ATP). In
aerobic conditions pyruvate and NADH are further oxidized in the
mitochondria; in
anaerobic conditions NADH itself subsequently reduces pyruvate to
lactate.
A
protein with one or more
carbohydrate molecules, typically short
oligosaccharide chains, covalently attached to one or more of its amino acid side chains.[6] Proteins which are exposed on the outer surface of the
plasma membrane or are secreted into the extracellular space are commonly
glycosylated in this way.
Any chemical compound in which a
carbohydrate molecule is covalently bonded to another molecule containing a
hydroxyl group (including other carbohydrates) via one or more C–Oglycosidic bonds. When both molecules are carbohydrates, the glycoside is a
disaccharide or
polysaccharide.[11]
The proportion of
nitrogenous bases in a
nucleic acid that are either
guanine (G) or
cytosine (C), typically expressed as a percentage. DNA and RNA molecules with higher GC-content are generally more
thermostable than those with lower GC-content due to molecular interactions that occur during base stacking.[23]
In a
diploid organism, having just one
allele at a given
genetic locus (where there would ordinarily be two). Hemizygosity may be observed when only one copy of a
chromosome is present in a normally diploid cell or organism, or when a segment of a chromosome containing one copy of an allele is
deleted, or when a gene is located on a
sex chromosome in the
heterogametic sex (in which the sex chromosomes do not exist in matching pairs); for example, in human males with normal chromosomes, almost all
X-linked genes are said to be hemizygous because there is only one
X chromosome and few of the same genes exist on the
Y chromosome.
The storage, transfer, and expression of molecular information in biological organisms,[17] as manifested by the passing on of
phenotypic traits from parents to their
offspring, either through
sexual or
asexual reproduction. Offspring cells or organisms are said to inherit the genetic information of their parents.
The
expression of a foreign
gene or any other foreign DNA sequence within a host organism which does not naturally contain the same gene. Insertion of foreign
transgenes into heterologous hosts using
recombinantvectors is a common biotechnology method for studying gene structure and function.
In a
diploid organism, having two different
alleles at a given
genetic locus. In genetics shorthand, heterozygous
genotypes are represented by a pair of non-matching letters or symbols, often an uppercase letter (indicating a
dominant allele) and a lowercase letter (indicating a
recessive allele), such as "Aa" or "Bb". Contrast homozygous.
The study or analysis of the microscopic anatomy of biological
tissues or of
cells 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 include
cytology.
The complex of eight
histone proteins around which double-stranded DNA wraps within a
nucleosome. The canonical histone octamer consists of two each of histones
H2A,
H2B,
H3, and
H4, which pair with each other symmetrically to form a ball-shaped cluster around which DNA winds through interactions with the histones' surface
domains, though
variant histones may replace their analogues in certain contexts.
(of a linear
chromosome or chromosome fragment) Having no single
centromere but rather multiple
kinetochore assembly sites dispersed along the entire length of the chromosome. During cell division, the
chromatids of holocentric chromosomes move apart in parallel and do not form the classical V-shaped structures typical of
monocentric chromosomes.
Any of a class of DNA
sequences approximately 180 base pairs in length occurring near the
3'‐end of certain eukaryotic genes and encoding a
60-amino acid domain which is capable of
binding to DNA or RNA via a characteristic helix-turn-helix motif in proteins containing it. Homeobox-containing genes are translated into homeodomain-containing proteins, which commonly
regulate transcription or translation by binding to other genes or messenger RNAs containing specific
homeobox responsive elements. The products of many homeotic genes, exemplified by the
Hox genes, are of critical importance in developmental pathways.[4]
homeobox responsive element (HRE)
Also homeodomain responsive element.
Any DNA or RNA
sequence that is specifically
recognized and bound by the
homeodomain of a homeodomain-containing protein.
A set of two matching
chromosomes, one maternal and one paternal, which pair up with each other inside the nucleus during
meiosis. They have the same
genes at the same
loci, but may have different
alleles.
In a
diploid organism, having two identical
alleles at a given
genetic locus. In genetics shorthand, homozygous
genotypes are represented by a pair of matching letters or symbols, such as "AA" or "aa". Contrast heterozygous.
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.
Any
constitutive gene that is
transcribed at a relatively constant level across many or all known conditions and cell types. The
products 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 highly
conservedhomeobox-containing
genes which are essential for the proper organization of the
body plan in developing animal embryos, ensuring that the correct structures are formed in the correct places. Hox genes are usually arranged on a chromosome in
tandem arrays and are
expressed 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.[4]
A collaborative international scientific research project with the goal of
sequencing all of the
chromosomal DNA and identifying and
mapping all of the
genes within human cells, and ultimately of assembling a complete
reference 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 a
mosaic of sequences obtained by sampling DNA from thousands of individuals across the world and does not represent any one individual.
The
offspring that results from combining the qualities of two organisms of different
genera,
species,
breeds, or varieties through
sexual reproduction. Hybrids may occur naturally or artificially, as during
selective 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 in
speciation.
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 a
complementaryhybridization probe.
Soluble in or having an affinity for water or other
polar compounds; describing a polar molecule, or a moiety or functional group within a molecule, which participates in intermolecular interactions such as
hydrogen bonding with other polar molecules and therefore readily dissolves in polar solvents such as water or
aqueous solutions.[6] Unlike
hydrophobic compounds, hydrophilic compounds can form energetically favorable contacts with the aqueous phase of biological fluids and so can often be suspended directly in the
cytosol or exposed to extracellular spaces.[12] Together, the contrasting properties of hydrophilicity and hydrophobicity play major roles in determining the structural
conformations and functions of most
biomolecules.
Having a low
solubility in or affinity for water or other
polar solvents; describing a
non-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, instead
clustering 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 from
aqueous 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 spatial
conformations assumed by
macromolecules such as
proteins and
lipids, the binding of
ligands and
substrates to proteins, and the structure and properties of lipid
membranes.[11][6] Contrast hydrophilic.
A mutant
allele 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.[4]
A naturally occurring non-canonical
purinenucleobase that is used in some
RNA molecules and pairs with standard nucleobases in a phenomenon known as
wobble base pairing. Its
nucleoside form is known as
inosine, which is the reason it is commonly abbreviated with the letter I in sequence reads.
A diagrammatic or schematic
karyotype of the entire set of
chromosomes within a cell or genome, in which annotated illustrations depict each chromosome in its most idealized form (e.g. with straight lines and obvious
centromeres) 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.
(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 or
in an artificial environment.
(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 to
inside a living organism or
in 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. Contrast ex vivo and in vitro.
1. (of a gene or sequence) Read or transcribed in the same
reading frame as another gene or sequence; not requiring a shift in reading frame to be intelligible or to result in a functional
peptide.
Any nucleotide sequence that is
inserted naturally or artificially into another sequence. The term is used in particular to refer to the part of a
transposable element that codes for those proteins directly involved in the transposition process, e.g. the
transposase enzyme. The coding region in a transposable insertion sequence is usually flanked by short
inverted 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 the
insertion 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 a
gene product or biochemical pathway, or they may be
neutral, leading to no substantive changes at all. Many
genetic engineering techniques rely on the insertion of exogenous genetic material into host cells in order to study gene function and expression.[4]
Any of a class of
integral membrane proteins which span the entirety of the
cell membrane, extending from the interior or
cytosolic side of the membrane to the exterior or
extracellular side. Transmembrane proteins typically have hydrophilic
domains exposed to each side as well as one or more hydrophobic domains crossing the nonpolar space inside the
lipid bilayer, by which they are further classified as single-pass or multipass membrane proteins. As such many transmembrane proteins function as
gated channels or
transporters to permit or prohibit the movement of specific molecules or ions across the membrane, often undergoing conformational changes in the process, or as
receptors in
cell signaling pathways. Contrast integral monotopic protein.
A
mobile genetic element consisting of a
gene cassette containing the gene for a
site-specific recombinase,
integrase-specific recognition sites, and a
promoter that governs the expression of one or more genes conferring adaptive traits on the host cell. Integrons usually exist in the form of circular
episomal DNA fragments, through which they facilitate the rapid adaptation of bacteria by enabling
horizontal gene transfer of antibiotic resistance genes between different bacterial species.[4]
The insertion, naturally or artificially, of chemical compounds between the planar
bases of a
DNA molecule, which generally disrupts the
hydrogen bonding necessary for
base pairing.
The abbreviated pause in activities related to cell division that occurs during
meiosis in some species, between the first and second meiotic divisions (i.e. meiosis I and meiosis II). No
DNA replication occurs during interkinesis, unlike during the normal
interphase that precedes meiosis I and
mitosis.[4]
A sequence present in some
messenger RNAs that permits recognition by the
ribosome and thus the initiation of
translation even in the absence of a
5' cap, which in eukaryotes is otherwise required for assembly of the initiation complex. IRES elements are often located in the
5' untranslated region, but may also be found in other positions.
The infolding of a
membrane toward the interior of a cell or organelle, or of a sheet of cells toward the interior of a developing
embryo,
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-bound
vesicle within the cell, as in
endocytosis.[11]
A
nucleotide sequence followed
downstream on the same
strand by its own
reverse 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 a
palindromic sequence. Inverted repeats are
self-complementary by definition, a property which involves them in many biological functions and dysfunctions. Contrast direct repeat.
Any chemical compound or macromolecule that facilitates the movement of
ions across biological membranes, or more specifically, any chemical species that reversibly binds electrically charged atoms or molecules. Many ionophores are lipid-soluble
proteins that catalyze the transport of monovalent and divalent cations across the hydrophobic
lipid bilayers surrounding cells and vesicles.[11]
A large region of
genomic DNA with a relatively homogeneous composition of
base pairs, distinguished from other regions by the proportion of pairs that are G-C or A-T. The genomes of most plants and vertebrates are composed of different classes of GC-rich and AT-rich isochores.[4]
A type of
abnormalchromosome in which the arms of the chromosome are mirror images of each other. Isochromosome formation is equivalent to simultaneous
duplication and
deletion events such that two copies of either the
long arm or the
short arm comprise the resulting chromosome.
Any of a class of
enzymes which catalyze the conversion of a molecule from one
isomer 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 more
genes that are equivalent and redundant in the sense that, despite coding for distinct
gene products, they each result in the same
phenotype when set within the same
genetic background. If several isomeric genes are present in a single
genotype they may be either cumulative or non-cumulative in their contributions to the phenotype.[17]
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 the
genome in which it is located. The term was once more broadly used to refer to all
non-coding DNA, though much of this was later discovered to have a function; in modern usage it typically refers to broken or vestigial sequences and
selfish genetic elements, including
introns,
pseudogenes,
intergenic DNA, and fragments of
transposons and
retroviruses, 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 by
natural selection.
junk RNA
Any RNA-encoded sequence, especially a
transcript, 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 remaining
untranslated, many
non-coding RNAs still serve important functions, whereas junk RNAs are truly useless: often they are the product of accidental transcription of a
junk DNA sequence, or they may result from
post-transcriptional processing of
primary transcripts, as with
spliced-outintrons. Junk RNA is usually quickly degraded by
ribonucleases and other cytoplasmic enzymes.
A
karyotype which depicts the entire set of
chromosomes in a cell or organism by using photomicrographs of the actual chromosomes as they appear in vivo (usually during
metaphase, in their most condensed forms), as opposed to the idealized illustrations of chromosomes used in
idiograms. 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 the
nucleus of a dying cell, during which the
nuclear envelope is destroyed and the contents of the nucleus, including
chromatin, are dispersed throughout the
cytoplasm and degraded by enzymes. Karyorrhexis is usually preceded by
pyknosis and may occur as a result of
apoptosis,
cellular senescence, or
necrosis.
The number and appearance of
chromosomes within the
nucleus of a eukaryotic cell, especially as depicted in an organized
karyogram or
idiogram (in pairs and arranged by size and by position of the
centromere). 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.
Any of a class of
enzymes which catalyze the transfer of
phosphate groups from high-energy, phosphate-donating molecules such as
ATP to one or more specific
substrates, a process known as
phosphorylation. The opposite process, known as
dephosphorylation, is catalyzed by
phosphatase enzymes.
Any 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 is often defined as any non-specific, non-directional response, in contrast to
taxis and
tropism.
In
cytogenetics, an enlarged, heavily staining
chromomere that can be used as a visual marker, allowing specific chromosomes to be easily identified in the nucleus.[4]
A
genetic engineering technique by which the normal rate of
expression of one or more of an organism's
genes is reduced, either through direct modification of a DNA sequence or through treatment with a
reagent such as a short DNA or RNA
oligonucleotide with a sequence
complementary to either an
mRNA transcript or a gene.
A
genetic engineering technique in which an organism is modified to carry
genes that have been made inoperative ("knocked out"), such that their
expression is disrupted at some point in the pathway that produces their
gene products and the organism is deprived of their normal effects. Contrast knockin.
The chemical attachment of a highly selective substance, known as a label, tag, or probe, to a particular cell, protein, amino acid, or other molecule of interest, either naturally or artificially, in vivo or in vitro. Natural labelling is a primary mechanism by which biomolecules specifically identify and interact with other biomolecules; important examples include
methylation,
acetylation, and
ubiquitination. Labelling is also a common laboratory technique, where the label is typically a reactive derivative of a naturally fluorescent 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 easily detected, identified, quantified, or isolated for further study.
In
DNA replication, the nascent
strand for which
DNA polymerase's direction of synthesis is away from the
replication fork, which necessitates a complex and discontinuous process in contrast to the streamlined, continuous synthesis of the other nascent strand, known as the
leading strand, which occurs simultaneously. Because DNA polymerase works only in the
5' to
3' 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 a
primase enzyme synthesizes short
RNAprimers complementary to the template DNA, and DNA polymerase then extends the primed segments into short chains of nucleotides known as
Okazaki fragments. The RNA primers are then removed and replaced with DNA, and the Okazaki fragments are joined by
DNA ligase.
In
DNA replication, the nascent
strand for which both the direction of synthesis by
DNA polymerase and the direction of overall chain elongation are toward the
replication fork; i.e. both occur in the
5' to
3' direction, resulting in a single, continuous elongation process with few or no interruptions. By contrast, the other nascent strand, known as the
lagging strand, is assembled in a discontinuous process involving the ligation of short
DNA fragments synthesized in the opposite direction, away from the replication fork.[4]
left splicing junction
Also donor splicing junction or donor splicing site.
In
meiosis, the first of five substages of
prophase I, following
interphase and preceding
zygonema. During leptonema, the replicated chromosomes condense from diffuse
chromatin into long, thin strands that are much more visible within the
nucleus.
A common structural
motif in
DNA-bindingtranscription factors and some other types of proteins, approximately 35 amino acids in length, characterized chiefly by the recurrence of the amino acid
leucine every seven residues. When modeled in an idealized
alpha-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, facilitating
dimerization and the formation of a complex resembling a zipper.[12]
In biochemistry, any molecule that binds to or interacts with a
specific site on a
protein or other
biomolecule, usually reversibly via intermolecular forces;[6] 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 many
biochemical pathways; for example, protein–ligand binding may result in the protein undergoing a
conformational change which alters its function or affinity for other molecules.
A class of enzymes which catalyze the joining of large molecules such as
nucleic acids by forming one or more chemical bonds between them, typically C–C, C–O, C–S, or C–N bonds via
condensation reactions. An example is
DNA ligase, which catalyzes the formation of
phosphodiester bonds between adjacent
nucleotides on one or both strands of a DNA molecule, a reaction known as
ligation.
The tendency of DNA sequences which are physically near to each other on the same chromosome to be
inherited together during
meiosis. Because the physical distance between them is relatively small, the chance that any two nearby parts of a DNA sequence (often
loci or
genetic markers) will be separated on to different
chromatids during
chromosomal crossover is statistically very low; such loci are then said to be more linked than loci that are farther apart. Loci that exist on entirely different chromosomes are said to be perfectly unlinked. The standard unit for measuring genetic linkage is the
centimorgan (cM).
1. A short, synthetic DNA duplex containing the
recognition sequence for a particular
restriction enzyme.[4] In
molecular cloning, linkers are often deliberately included in
recombinant molecules in order to make them easily modifiable by permitting cleavage and
insertion of foreign sequences at precise locations. A segment of an engineered
plasmid containing many such restriction sites is sometimes called a
polylinker.
The number of times that the two strands of a circular
double-helicalDNA molecule cross each other, equivalent to the
twisting number (which measures the torsion of the double helix) plus the
writhing 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 as topological isomers.[4]
Any of a heterogeneous class of organic compounds, including
glycerides (fats),
waxes,
sterols, and some vitamins, united only by their
amphipathic or
hydrophobic nature and consequently their very low solubility in water.[12] Some lipids such as
phospholipids tend to form lamellar structures or
micelles in aqueous environments, where they serve as the primary constituents of biological
membranes. Others such as
fatty acids can be
metabolized for energy, have important functions in energy storage, or serve as
signaling 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 amphipathic
lipid molecules packed together in two back-to-back sheets or layers, with their
hydrophobicfatty acid "tails" directed inward and their
hydrophilic "heads" exposed on the outer surface. This is the basic structural motif for all biological
membranes, including the
plasma membrane surrounding all cells as well as the membranes surrounding
organelles and
vesicles. Though bilayers are sometimes colloquially described as phospholipid bilayers,
phospholipids are just one of several classes of
membrane lipids which form bilayers; most membranes are actually a
fluid, heterogeneous mixture of phospholipids,
glycolipids, and
cholesterols, interspersed and studded with various other molecules such as
integral proteins.[12]
In condensed
chromosomes where the positioning of the
centromere creates two segments or "arms" of unequal length, the longer of the two arms of a
chromatid. Contrast short arm.
Any of a large family of non-
LTRretrotransposons which together comprises one of the most widespread
mobile genetic elements in eukaryotic genomes. Each LINE
insertion is on average about 7,000 base pairs in length.
The disruption and decomposition of the
plasma membrane surrounding a cell, or more generally of any membrane-bound
organelle or
vesicle, especially by
osmotic,
enzymatic, or other chemical or mechanical processes which compromise the membrane's integrity and thereby cause the unobstructed interchange of the contents of
intracellular and
extracellular 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 the
cytosol, and therefore the death of the cell. Such a cell is said to be lysed, and a fluid containing the contents of lysed cells (usually including
nucleic acids,
proteins, and many other organic molecules) is called a lysate. Lysis may occur both naturally and artificially, and is a normal part of the cellular life cycle.
^
abcdefghijklmnAlberts, Bruce; Johnson, Alexander; Lewis, Julian; Raff, Martin; Roberts, Keith; Walter, Peter (2002). "Glossary".
Molecular Biology of the Cell(Available from the National Center for Biotechnology Information) (4th ed.). New York: Garland Science.
^
abLewin, Benjamin (2003). Genes VIII. Upper Saddle River, NJ: Pearson Prentice Hall.
ISBN0-13-143981-2.
^
abcdefghijklmLackie, J. M. (2013). The Dictionary of Cell and Molecular Biology (5th ed.). Amsterdam: Academic Press/Elsevier.
ISBN978-0-12-384931-1.
^SwissBioPics.
"Animal cell". www.swissbiopics.org. Swiss Institute of Bioinformatics (SIB).
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.
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 to
Glossary of genetics and evolutionary biology, which contains many overlapping and related terms; other related glossaries include
Glossary of virology and
Glossary of chemistry.
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.
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
methylatedguaninenucleoside 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.
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.
Any of a class of
transferaseenzymes which catalyze the covalent bonding of an
acetyl group (–COCH 3) to another compound, protein, or biomolecule, a process known as
acetylation.
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.
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.
One of three main biologically active
structural conformations of the
DNAdouble 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]
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.
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.
Also sex chromosome, heterochromosome, or idiochromosome.
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.
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.
Any of a class of organic compounds whose basic structural formula includes a central carbon atom bonded to
amine and
carboxylfunctional 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.
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.
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.
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).
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.
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.
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'.
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]
Also antisense transcript and antisense oligonucleotide (ASO).
A
single-strandednon-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.
(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).
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
excretesresidual or toxic compounds out of the cell, instead of reusing them to build new molecules.
A single
monocentricchromosome 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.
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.
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.
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.
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.
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.
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.
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.
The "standard" or classical
structural conformation of the
DNAdouble helixin 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.
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]
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.
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.
A
regulatorygene 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.
Any of a class of
transmembrane proteins which are dependent on calcium ions (Ca2+) and whose extracellular
domains function as mediators of cell–cell adhesion at
adherens junctions in eukaryotic tissues.
An unorganized mass of
parenchymal cells that forms naturally at the site of wounds in plant tissues, and which is commonly artificially induced to form in plant
tissue culture as a means of initiating
somatic embryogenesis.[11]
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.
Any of a class of organic compounds having the generic chemical formula (CH 2O) n, and one of several major classes of
biomolecules found universally in biological systems. Carbohydrates include individual
monosaccharides as well as the larger
polymers they form (
oligosaccharides,
polysaccharides, etc.) when multiple monosaccharide units are joined by
glycosidic bonds.[11] Abundant and ubiquitous, these compounds are involved in numerous essential biochemical processes and
pathways; they are widely used as an energy source for cellular
metabolism, as a form of energy storage, as
signaling molecules, and as
biomarkers to
label or modify the activity of other molecules. Carbohydrates are often colloquially described as "sugars"; the prefix glyco- is used to indicate a compound or process containing or related to carbohydrates, and the suffix -ose usually signifies that a compound is a carbohydrate or a derivative.
2. A protein to which a specific
ligand or
hapten has been conjugated and which thereby carries an
antigen capable of eliciting an
antibody response.[12]
3. A protein which is included in an
assay at high concentrations in order to prevent non-specific interactions of the assay's reagents with vessel surfaces, sample components, or other reagents.[12] For example, in many
blotting techniques,
albumin is intentionally allowed to bind non-specifically to the blotted membrane prior to
fluorescent labelling, so as to "block" potential off-target binding of the
fluorophore 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 DNA
vector with an annotated sequence and precisely positioned
regulatory elements, into which one or more
fragments can be readily
inserted or recombined by various
genetic engineering methods. Recombinant
plasmid vectors containing reliable
promoters,
origins of replication, and antibiotic resistance genes are commonly manufactured and sold as cassettes to allow scientists to easily replace one
gene of interest with another by swapping it into and out of an active "slot" or locus within the plasmid. See also multiple cloning site.
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.
A specialized layer of
cytoplasmic proteins lining the inner face of the
cell membrane in most eukaryotic cells, composed primarily of
actinmicrofilaments and
myosinmotor 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 of
cells within a biological sample or
culture by any of a variety of methods. Counting cells is an important aspect of
cytometry used widely in research and clinical medicine. It is generally achieved by using a manual or digital
cytometer to count the number of cells present in small fractions of a sample, and then extrapolating to estimate the number present in the entire sample. The resulting quantification is typically expressed as a 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. 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.
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]
The merging or coalescence of two or more cells into a single cell, as occurs in the fusion of
gametes to form a
zygote. Generally this occurs by the destabilization of each cell's
plasma membrane and the formation of
cytoplasmic bridges between them which then expand until the two cytoplasms are completely mixed; intercellular structures or
organelles such as
nuclei may or may not fuse as well. Cells can also be artificially induced to fuse with each other by treating them with a fusogen such as
polyethylene glycol or by passing an electric current through them.[11]
Also plasma membrane, cytoplasmic membrane, and plasmalemma.
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.[13] 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.
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).
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.
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.
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.
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]
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]
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
complementarybase-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
unrepairedmismatches, 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.
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.[6]
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.
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.
A type of small, lens-shaped
plastidorganelle found in the cells of green algae and plants which contains light-sensitive
photosynthetic pigments and in which the series of biochemical reactions that comprise
photosynthesis takes place. Like
mitochondria, chloroplasts are bound by a double membrane, contain their own
internal circular DNA molecules from which they direct transcription of a unique set of genes, and replicate independently of the nuclear genome.[11][12]
The set of
DNA molecules contained within
chloroplasts, a type of photosynthetic
plastidorganelle 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.
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.
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.
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]
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.
A
nuclearDNA 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.
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.
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.
Any of a class of flattened, membrane-bound
vesicles or
saccules of the
smooth and
roughendoplasmic 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.[15]
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.
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.
Also sense strand, positive (+) sense strand, and nontemplate 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.
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.
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.
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]
A property of
nucleic acidbiopolymers 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-strandedDNA 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.
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).
In
cell culture, a measure of the proportion of the surface area of a
culture vessel that is covered by adherent cells, commonly expressed as a percentage. A culture in which the entire surface is completely covered by a continuous
monolayer, 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. Different cell lines exhibit differences in growth rate or
gene expression depending on the degree of confluence. Because of
contact inhibition, most show a significant reduction in the rate of
cell division as they approach complete confluence, though some
immortalized cells may continue to divide, expanding vertically rather than horizontally by stacking themselves on top of the
parent cells, until all available nutrients are depleted.[11][12]
conformation
The three-dimensional spatial configuration of the atoms comprising a molecule or
macromolecular structure.[11] The conformation of a
protein is the physical shape into which its
polypeptide chains arrange themselves during
protein folding, which is not necessarily rigid and may
change with the protein's particular chemical environment.
A change in the spatial
conformation 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 the
tertiary structures of proteins can affect whether or how strongly they bind
ligands or
substrates; 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.[12]
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.
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.
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.
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.
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.
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.
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.
The total amount of
DNA contained within a
haploidnucleus (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
diploidsomatic 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.
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.
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.
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.
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.[16]
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.
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.[17]
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]
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.
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.
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.
A
polymericnucleic acid molecule composed of a series of covalently linked
deoxyribonucleotides, each of which incorporates one of four
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 assumes the shape of a
double helix. DNA can also exist in
single-stranded form. By storing and encoding genetic information in the
sequence 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.
A
monosaccharidepentose sugar derived from
ribose 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 of
deoxyribonucleotides and hence of
deoxyribonucleic acid (DNA) molecules.
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. by
mass spectroscopy or
chromatography), or of
labelling it by attaching a detectable chemical moiety (e.g. a fluorescent tag) to make it easier to identify and track in vivo. Molecules modified in this way are described as derivatives of their naturally occurring counterparts and are said to have been derivatized.[12]
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.[12]
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]
A molecular
dimer consisting of exactly two covalently linked
nucleotides; or any two nucleotides which are immediately adjacent to each other on the same
strand of a longer
nucleic acid polymer.
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.
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
polymerases 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 comprising
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 by convention are written in the same direction.
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]
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.
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
DNAoligonucleotides, 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.
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.
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.
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.
A protein
domain containing at least one structural motif capable of recognizing and interacting with the
nucleotides of a
double-stranded or
single-strandedDNA molecule. DNA-binding domains may bind to specific sequences or have a non-specific affinity for DNA. They are the primary functional components of
DNA-binding proteins, including many
transcription factors and regulatory proteins.
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 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 undergoing
conformational changes induced by interactions with other molecules.
A discrete, usually continuous region of a
protein, or the corresponding
amino acid sequence of a
polypeptide, which serves a particular function or is defined by particular physico-chemical properties (e.g.
hydrophobic, polar, non-polar,
globular, etc.),[12] and especially one which assumes a unique, recognizable spatial
conformation as part of the protein's
tertiary structure and which contributes to or defines its biological activity. Large proteins are generally composed of several domains linked together by short, intervening polypeptide sequences.[6] 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 of
nucleic acid sequences and
chromosomes.[17]
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.
The shape most commonly assumed by
double-strandednucleic acid molecules, resembling a ladder that has been twisted upon its long axis, with the rungs of the ladder consisting of
pairednucleobases. 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.
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.[17] Contrast single-strand break.
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.
The abnormal growth or development of a
tissue 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,[6] an event which often precedes the development of
cancer.
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.
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.
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.
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]
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.
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.
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.
The specific site or region within an
antigenicmacromolecule such as a
protein or
carbohydrate which is recognized by
B or
T cells of the immune system, against which a specific
antibody is produced, and with which the antibody's
paratope specifically interacts or binds. In proteins, epitopes are typically
motifs of 4–5 amino acid residues, sequential or discontiguous, which by virtue of the distinct spatial
conformation they adopt upon
protein folding are able to uniquely interact with a particular paratope. In this sense they may be considered
binding 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 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.
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.
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.
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]
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.
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.
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.
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]
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.
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.
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.
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.
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.
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.
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]
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.
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
diploidzygote.
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.
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
regulategene expression. Changes in gene dosage caused by mutations include
copy-number variations.
The set of processes by which the information encoded in a
gene is used in the synthesis of a
gene product, such as a protein or
non-coding RNA, or otherwise made available to influence one or more
phenotypes. Canonically, the first step is
transcription, which produces a
messenger RNA molecule complementary to the
DNA molecule in which the gene is encoded; for protein-coding genes, the second step is
translation, in which the messenger RNA is read by the
ribosome to produce 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.
The union, either by natural mutation or by
recombinant laboratory techniques, of two or more previously independent genes that code for different gene products such that they become subject to control by the same
regulatory systems. The resulting hybrid sequence is known as a
fusion gene.[4]
Any of a variety of methods used to precisely identify the
location of a particular
gene within a DNA molecule (such as a chromosome) and/or the physical or
linkage distances between it and other genes.
gene of interest (GOI)
A
gene being studied in a scientific experiment, especially one that is the focus of a
genetic engineering technique such as
cloning.
Any of the biochemical material resulting from the
expression of a
gene, most commonly interpreted as the functional
mRNA transcript produced by
transcription of the gene or the fully constructed
protein produced by
translation of the transcript, though
non-coding RNA molecules such as
transfer 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 or
expression of specific
gene products, such as
RNA or
proteins. 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 drives
cellular differentiation and
morphogenesis in the
embryo, enabling the creation of a diverse array of cell types from the same
genome.
Any mechanism of
gene regulation which drastically reduces or completely prevents the
expression of a particular gene. Gene silencing may occur naturally during either
transcription or
translation. Laboratory techniques often exploit natural silencing mechanisms to achieve
gene knockdown.
The insertion of a functional or
wild-type gene or part of a gene into an organism (especially a patient) with the intention of correcting a
genetic defect, either by direct substitution of the defective gene or by supplementation with a second, functional version.[17]
1. In any given organism, a single
reproductive 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 particular
lineage 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 given
common ancestor by virtue of the same number of reproductive events having occurred between them and the ancestor.[17]
Any illness, disease, or other health problem directly caused by one or more abnormalities in an organism's
genome which are
congenital (present at birth) and not acquired later in life. Causes may include a
mutation to one or more
genes, or a
chromosomal abnormality such as an
aneuploidy of a particular chromosome. The mutation responsible
may occur spontaneously during embryonic development or may be
inherited from one or both parents, in which case the genetic disorder is also classified as a
hereditary 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 simply
increase the risk of developing it.
A measure of the genetic divergence between species, populations within a species, or individuals, used especially in
phylogenetics to express either the time elapsed since the existence of a
common ancestor or the degree of differentiation in the
DNA sequences comprising the
genomes of each population or individual.
Also genetic modification or genetic manipulation.
The direct, deliberate manipulation of an organism's genetic material using any of a variety of biotechnology methods, including the insertion or
removal of
genes, the transfer of genes within and between species, the
mutation of existing sequences, and the construction of novel sequences using
artificial 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 and
expression of individual genes, to produce hormones, vaccines, and other drugs, and to create
genetically modified organisms for use in research and agriculture.
A specific, easily identifiable, and usually highly
polymorphicgene or other
DNAsequence with a known location on a
chromosome that can be used to identify the individual or species possessing it.
The redundant encoding of two or more distinct
gene 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 any
loss of function and obviate any
gain of function.
A
graph that represents the regulatory complexity of
gene expression. The vertices (nodes) are represented by various regulatory elements and
gene products while the edges (links) are represented by their interactions. These network structures also represent functional relationships by approximating the rate at which genes are
transcribed.
A broad class of various procedures used to identify features of an individual's particular chromosomes, genes, or proteins in order to determine parentage or
ancestry, diagnose vulnerabilities to heritable diseases, or detect
mutant alleles associated with increased risks of developing
genetic disorders. Genetic testing is widely used in human medicine, agriculture, and biological research.
Any organism whose genetic material has been altered using
genetic engineering techniques, particularly in a way that does not occur naturally by mating or by natural
genetic recombination.
The entire complement of genetic material contained within the
chromosomes of an organism,
organelle, or
virus. The term is also used to refer to the collective set of genetic
loci shared by every member of a population or species, regardless of the different
alleles that may be present at these loci in different individuals.
The total amount of
DNA contained within one copy of a
genome, typically measured by
mass (in picograms or
daltons) or by the total number of
base pairs (in
kilobases or
megabases). For
diploid organisms, genome size is often used interchangeably with
C-value.
An
epigenetic phenomenon that causes
genes to be
expressed in a manner dependent upon the particular parent from which the gene was inherited. It occurs when epigenetic marks such as
DNA or
histone methylation are established or "imprinted" in the
germ cells of a parent organism and subsequently maintained through cell divisions in the
somatic 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.
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, or
point mutations), which may or may not result in a permanent
mutation. Though all
mutagens are genotoxic, not all genotoxic compounds are mutagenic.
The process of determining differences in the
genotype of an individual by examining the
DNA sequences in the individual's
genome using
bioassays and comparing them to another individual's sequences or a reference sequence.
Any
cell that gives rise to the
gametes of a
sexually 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 from
somatic cells, which are entirely separate from the
germ 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 from
somatic cells, which cannot pass on their genetic material except to their own immediate
mitotic daughter cells. Cells of the germ line are called
germ cells.
2. The
lineage of germ cells, spanning many generations, that contains the genetic material which has been passed on to an individual from its ancestors.
The chain of
metabolic reactions that results in the generation of
glucose from some non-carbohydrate carbon substrates, including the
glucogenic amino acids. It is one of two primary
pathways used by most animals to maintain blood sugar levels (the other being
glycogenolysis), especially during periods of fasting, starvation, and intense exercise.
The
metabolic pathway in which
carbohydrate sugars such as
glucose 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 of
pyruvate, with the free energy liberated in this process simultaneously being used to form high-energy bonds in two molecules of reduced
nicotinamide adenine dinucleotide (NADH) and two molecules of
adenosine triphosphate (ATP). In
aerobic conditions pyruvate and NADH are further oxidized in the
mitochondria; in
anaerobic conditions NADH itself subsequently reduces pyruvate to
lactate.
A
protein with one or more
carbohydrate molecules, typically short
oligosaccharide chains, covalently attached to one or more of its amino acid side chains.[6] Proteins which are exposed on the outer surface of the
plasma membrane or are secreted into the extracellular space are commonly
glycosylated in this way.
Any chemical compound in which a
carbohydrate molecule is covalently bonded to another molecule containing a
hydroxyl group (including other carbohydrates) via one or more C–Oglycosidic bonds. When both molecules are carbohydrates, the glycoside is a
disaccharide or
polysaccharide.[11]
The proportion of
nitrogenous bases in a
nucleic acid that are either
guanine (G) or
cytosine (C), typically expressed as a percentage. DNA and RNA molecules with higher GC-content are generally more
thermostable than those with lower GC-content due to molecular interactions that occur during base stacking.[23]
In a
diploid organism, having just one
allele at a given
genetic locus (where there would ordinarily be two). Hemizygosity may be observed when only one copy of a
chromosome is present in a normally diploid cell or organism, or when a segment of a chromosome containing one copy of an allele is
deleted, or when a gene is located on a
sex chromosome in the
heterogametic sex (in which the sex chromosomes do not exist in matching pairs); for example, in human males with normal chromosomes, almost all
X-linked genes are said to be hemizygous because there is only one
X chromosome and few of the same genes exist on the
Y chromosome.
The storage, transfer, and expression of molecular information in biological organisms,[17] as manifested by the passing on of
phenotypic traits from parents to their
offspring, either through
sexual or
asexual reproduction. Offspring cells or organisms are said to inherit the genetic information of their parents.
The
expression of a foreign
gene or any other foreign DNA sequence within a host organism which does not naturally contain the same gene. Insertion of foreign
transgenes into heterologous hosts using
recombinantvectors is a common biotechnology method for studying gene structure and function.
In a
diploid organism, having two different
alleles at a given
genetic locus. In genetics shorthand, heterozygous
genotypes are represented by a pair of non-matching letters or symbols, often an uppercase letter (indicating a
dominant allele) and a lowercase letter (indicating a
recessive allele), such as "Aa" or "Bb". Contrast homozygous.
The study or analysis of the microscopic anatomy of biological
tissues or of
cells 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 include
cytology.
The complex of eight
histone proteins around which double-stranded DNA wraps within a
nucleosome. The canonical histone octamer consists of two each of histones
H2A,
H2B,
H3, and
H4, which pair with each other symmetrically to form a ball-shaped cluster around which DNA winds through interactions with the histones' surface
domains, though
variant histones may replace their analogues in certain contexts.
(of a linear
chromosome or chromosome fragment) Having no single
centromere but rather multiple
kinetochore assembly sites dispersed along the entire length of the chromosome. During cell division, the
chromatids of holocentric chromosomes move apart in parallel and do not form the classical V-shaped structures typical of
monocentric chromosomes.
Any of a class of DNA
sequences approximately 180 base pairs in length occurring near the
3'‐end of certain eukaryotic genes and encoding a
60-amino acid domain which is capable of
binding to DNA or RNA via a characteristic helix-turn-helix motif in proteins containing it. Homeobox-containing genes are translated into homeodomain-containing proteins, which commonly
regulate transcription or translation by binding to other genes or messenger RNAs containing specific
homeobox responsive elements. The products of many homeotic genes, exemplified by the
Hox genes, are of critical importance in developmental pathways.[4]
homeobox responsive element (HRE)
Also homeodomain responsive element.
Any DNA or RNA
sequence that is specifically
recognized and bound by the
homeodomain of a homeodomain-containing protein.
A set of two matching
chromosomes, one maternal and one paternal, which pair up with each other inside the nucleus during
meiosis. They have the same
genes at the same
loci, but may have different
alleles.
In a
diploid organism, having two identical
alleles at a given
genetic locus. In genetics shorthand, homozygous
genotypes are represented by a pair of matching letters or symbols, such as "AA" or "aa". Contrast heterozygous.
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.
Any
constitutive gene that is
transcribed at a relatively constant level across many or all known conditions and cell types. The
products 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 highly
conservedhomeobox-containing
genes which are essential for the proper organization of the
body plan in developing animal embryos, ensuring that the correct structures are formed in the correct places. Hox genes are usually arranged on a chromosome in
tandem arrays and are
expressed 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.[4]
A collaborative international scientific research project with the goal of
sequencing all of the
chromosomal DNA and identifying and
mapping all of the
genes within human cells, and ultimately of assembling a complete
reference 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 a
mosaic of sequences obtained by sampling DNA from thousands of individuals across the world and does not represent any one individual.
The
offspring that results from combining the qualities of two organisms of different
genera,
species,
breeds, or varieties through
sexual reproduction. Hybrids may occur naturally or artificially, as during
selective 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 in
speciation.
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 a
complementaryhybridization probe.
Soluble in or having an affinity for water or other
polar compounds; describing a polar molecule, or a moiety or functional group within a molecule, which participates in intermolecular interactions such as
hydrogen bonding with other polar molecules and therefore readily dissolves in polar solvents such as water or
aqueous solutions.[6] Unlike
hydrophobic compounds, hydrophilic compounds can form energetically favorable contacts with the aqueous phase of biological fluids and so can often be suspended directly in the
cytosol or exposed to extracellular spaces.[12] Together, the contrasting properties of hydrophilicity and hydrophobicity play major roles in determining the structural
conformations and functions of most
biomolecules.
Having a low
solubility in or affinity for water or other
polar solvents; describing a
non-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, instead
clustering 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 from
aqueous 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 spatial
conformations assumed by
macromolecules such as
proteins and
lipids, the binding of
ligands and
substrates to proteins, and the structure and properties of lipid
membranes.[11][6] Contrast hydrophilic.
A mutant
allele 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.[4]
A naturally occurring non-canonical
purinenucleobase that is used in some
RNA molecules and pairs with standard nucleobases in a phenomenon known as
wobble base pairing. Its
nucleoside form is known as
inosine, which is the reason it is commonly abbreviated with the letter I in sequence reads.
A diagrammatic or schematic
karyotype of the entire set of
chromosomes within a cell or genome, in which annotated illustrations depict each chromosome in its most idealized form (e.g. with straight lines and obvious
centromeres) 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.
(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 or
in an artificial environment.
(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 to
inside a living organism or
in 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. Contrast ex vivo and in vitro.
1. (of a gene or sequence) Read or transcribed in the same
reading frame as another gene or sequence; not requiring a shift in reading frame to be intelligible or to result in a functional
peptide.
Any nucleotide sequence that is
inserted naturally or artificially into another sequence. The term is used in particular to refer to the part of a
transposable element that codes for those proteins directly involved in the transposition process, e.g. the
transposase enzyme. The coding region in a transposable insertion sequence is usually flanked by short
inverted 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 the
insertion 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 a
gene product or biochemical pathway, or they may be
neutral, leading to no substantive changes at all. Many
genetic engineering techniques rely on the insertion of exogenous genetic material into host cells in order to study gene function and expression.[4]
Any of a class of
integral membrane proteins which span the entirety of the
cell membrane, extending from the interior or
cytosolic side of the membrane to the exterior or
extracellular side. Transmembrane proteins typically have hydrophilic
domains exposed to each side as well as one or more hydrophobic domains crossing the nonpolar space inside the
lipid bilayer, by which they are further classified as single-pass or multipass membrane proteins. As such many transmembrane proteins function as
gated channels or
transporters to permit or prohibit the movement of specific molecules or ions across the membrane, often undergoing conformational changes in the process, or as
receptors in
cell signaling pathways. Contrast integral monotopic protein.
A
mobile genetic element consisting of a
gene cassette containing the gene for a
site-specific recombinase,
integrase-specific recognition sites, and a
promoter that governs the expression of one or more genes conferring adaptive traits on the host cell. Integrons usually exist in the form of circular
episomal DNA fragments, through which they facilitate the rapid adaptation of bacteria by enabling
horizontal gene transfer of antibiotic resistance genes between different bacterial species.[4]
The insertion, naturally or artificially, of chemical compounds between the planar
bases of a
DNA molecule, which generally disrupts the
hydrogen bonding necessary for
base pairing.
The abbreviated pause in activities related to cell division that occurs during
meiosis in some species, between the first and second meiotic divisions (i.e. meiosis I and meiosis II). No
DNA replication occurs during interkinesis, unlike during the normal
interphase that precedes meiosis I and
mitosis.[4]
A sequence present in some
messenger RNAs that permits recognition by the
ribosome and thus the initiation of
translation even in the absence of a
5' cap, which in eukaryotes is otherwise required for assembly of the initiation complex. IRES elements are often located in the
5' untranslated region, but may also be found in other positions.
The infolding of a
membrane toward the interior of a cell or organelle, or of a sheet of cells toward the interior of a developing
embryo,
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-bound
vesicle within the cell, as in
endocytosis.[11]
A
nucleotide sequence followed
downstream on the same
strand by its own
reverse 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 a
palindromic sequence. Inverted repeats are
self-complementary by definition, a property which involves them in many biological functions and dysfunctions. Contrast direct repeat.
Any chemical compound or macromolecule that facilitates the movement of
ions across biological membranes, or more specifically, any chemical species that reversibly binds electrically charged atoms or molecules. Many ionophores are lipid-soluble
proteins that catalyze the transport of monovalent and divalent cations across the hydrophobic
lipid bilayers surrounding cells and vesicles.[11]
A large region of
genomic DNA with a relatively homogeneous composition of
base pairs, distinguished from other regions by the proportion of pairs that are G-C or A-T. The genomes of most plants and vertebrates are composed of different classes of GC-rich and AT-rich isochores.[4]
A type of
abnormalchromosome in which the arms of the chromosome are mirror images of each other. Isochromosome formation is equivalent to simultaneous
duplication and
deletion events such that two copies of either the
long arm or the
short arm comprise the resulting chromosome.
Any of a class of
enzymes which catalyze the conversion of a molecule from one
isomer 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 more
genes that are equivalent and redundant in the sense that, despite coding for distinct
gene products, they each result in the same
phenotype when set within the same
genetic background. If several isomeric genes are present in a single
genotype they may be either cumulative or non-cumulative in their contributions to the phenotype.[17]
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 the
genome in which it is located. The term was once more broadly used to refer to all
non-coding DNA, though much of this was later discovered to have a function; in modern usage it typically refers to broken or vestigial sequences and
selfish genetic elements, including
introns,
pseudogenes,
intergenic DNA, and fragments of
transposons and
retroviruses, 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 by
natural selection.
junk RNA
Any RNA-encoded sequence, especially a
transcript, 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 remaining
untranslated, many
non-coding RNAs still serve important functions, whereas junk RNAs are truly useless: often they are the product of accidental transcription of a
junk DNA sequence, or they may result from
post-transcriptional processing of
primary transcripts, as with
spliced-outintrons. Junk RNA is usually quickly degraded by
ribonucleases and other cytoplasmic enzymes.
A
karyotype which depicts the entire set of
chromosomes in a cell or organism by using photomicrographs of the actual chromosomes as they appear in vivo (usually during
metaphase, in their most condensed forms), as opposed to the idealized illustrations of chromosomes used in
idiograms. 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 the
nucleus of a dying cell, during which the
nuclear envelope is destroyed and the contents of the nucleus, including
chromatin, are dispersed throughout the
cytoplasm and degraded by enzymes. Karyorrhexis is usually preceded by
pyknosis and may occur as a result of
apoptosis,
cellular senescence, or
necrosis.
The number and appearance of
chromosomes within the
nucleus of a eukaryotic cell, especially as depicted in an organized
karyogram or
idiogram (in pairs and arranged by size and by position of the
centromere). 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.
Any of a class of
enzymes which catalyze the transfer of
phosphate groups from high-energy, phosphate-donating molecules such as
ATP to one or more specific
substrates, a process known as
phosphorylation. The opposite process, known as
dephosphorylation, is catalyzed by
phosphatase enzymes.
Any 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 is often defined as any non-specific, non-directional response, in contrast to
taxis and
tropism.
In
cytogenetics, an enlarged, heavily staining
chromomere that can be used as a visual marker, allowing specific chromosomes to be easily identified in the nucleus.[4]
A
genetic engineering technique by which the normal rate of
expression of one or more of an organism's
genes is reduced, either through direct modification of a DNA sequence or through treatment with a
reagent such as a short DNA or RNA
oligonucleotide with a sequence
complementary to either an
mRNA transcript or a gene.
A
genetic engineering technique in which an organism is modified to carry
genes that have been made inoperative ("knocked out"), such that their
expression is disrupted at some point in the pathway that produces their
gene products and the organism is deprived of their normal effects. Contrast knockin.
The chemical attachment of a highly selective substance, known as a label, tag, or probe, to a particular cell, protein, amino acid, or other molecule of interest, either naturally or artificially, in vivo or in vitro. Natural labelling is a primary mechanism by which biomolecules specifically identify and interact with other biomolecules; important examples include
methylation,
acetylation, and
ubiquitination. Labelling is also a common laboratory technique, where the label is typically a reactive derivative of a naturally fluorescent 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 easily detected, identified, quantified, or isolated for further study.
In
DNA replication, the nascent
strand for which
DNA polymerase's direction of synthesis is away from the
replication fork, which necessitates a complex and discontinuous process in contrast to the streamlined, continuous synthesis of the other nascent strand, known as the
leading strand, which occurs simultaneously. Because DNA polymerase works only in the
5' to
3' 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 a
primase enzyme synthesizes short
RNAprimers complementary to the template DNA, and DNA polymerase then extends the primed segments into short chains of nucleotides known as
Okazaki fragments. The RNA primers are then removed and replaced with DNA, and the Okazaki fragments are joined by
DNA ligase.
In
DNA replication, the nascent
strand for which both the direction of synthesis by
DNA polymerase and the direction of overall chain elongation are toward the
replication fork; i.e. both occur in the
5' to
3' direction, resulting in a single, continuous elongation process with few or no interruptions. By contrast, the other nascent strand, known as the
lagging strand, is assembled in a discontinuous process involving the ligation of short
DNA fragments synthesized in the opposite direction, away from the replication fork.[4]
left splicing junction
Also donor splicing junction or donor splicing site.
In
meiosis, the first of five substages of
prophase I, following
interphase and preceding
zygonema. During leptonema, the replicated chromosomes condense from diffuse
chromatin into long, thin strands that are much more visible within the
nucleus.
A common structural
motif in
DNA-bindingtranscription factors and some other types of proteins, approximately 35 amino acids in length, characterized chiefly by the recurrence of the amino acid
leucine every seven residues. When modeled in an idealized
alpha-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, facilitating
dimerization and the formation of a complex resembling a zipper.[12]
In biochemistry, any molecule that binds to or interacts with a
specific site on a
protein or other
biomolecule, usually reversibly via intermolecular forces;[6] 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 many
biochemical pathways; for example, protein–ligand binding may result in the protein undergoing a
conformational change which alters its function or affinity for other molecules.
A class of enzymes which catalyze the joining of large molecules such as
nucleic acids by forming one or more chemical bonds between them, typically C–C, C–O, C–S, or C–N bonds via
condensation reactions. An example is
DNA ligase, which catalyzes the formation of
phosphodiester bonds between adjacent
nucleotides on one or both strands of a DNA molecule, a reaction known as
ligation.
The tendency of DNA sequences which are physically near to each other on the same chromosome to be
inherited together during
meiosis. Because the physical distance between them is relatively small, the chance that any two nearby parts of a DNA sequence (often
loci or
genetic markers) will be separated on to different
chromatids during
chromosomal crossover is statistically very low; such loci are then said to be more linked than loci that are farther apart. Loci that exist on entirely different chromosomes are said to be perfectly unlinked. The standard unit for measuring genetic linkage is the
centimorgan (cM).
1. A short, synthetic DNA duplex containing the
recognition sequence for a particular
restriction enzyme.[4] In
molecular cloning, linkers are often deliberately included in
recombinant molecules in order to make them easily modifiable by permitting cleavage and
insertion of foreign sequences at precise locations. A segment of an engineered
plasmid containing many such restriction sites is sometimes called a
polylinker.
The number of times that the two strands of a circular
double-helicalDNA molecule cross each other, equivalent to the
twisting number (which measures the torsion of the double helix) plus the
writhing 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 as topological isomers.[4]
Any of a heterogeneous class of organic compounds, including
glycerides (fats),
waxes,
sterols, and some vitamins, united only by their
amphipathic or
hydrophobic nature and consequently their very low solubility in water.[12] Some lipids such as
phospholipids tend to form lamellar structures or
micelles in aqueous environments, where they serve as the primary constituents of biological
membranes. Others such as
fatty acids can be
metabolized for energy, have important functions in energy storage, or serve as
signaling 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 amphipathic
lipid molecules packed together in two back-to-back sheets or layers, with their
hydrophobicfatty acid "tails" directed inward and their
hydrophilic "heads" exposed on the outer surface. This is the basic structural motif for all biological
membranes, including the
plasma membrane surrounding all cells as well as the membranes surrounding
organelles and
vesicles. Though bilayers are sometimes colloquially described as phospholipid bilayers,
phospholipids are just one of several classes of
membrane lipids which form bilayers; most membranes are actually a
fluid, heterogeneous mixture of phospholipids,
glycolipids, and
cholesterols, interspersed and studded with various other molecules such as
integral proteins.[12]
In condensed
chromosomes where the positioning of the
centromere creates two segments or "arms" of unequal length, the longer of the two arms of a
chromatid. Contrast short arm.
Any of a large family of non-
LTRretrotransposons which together comprises one of the most widespread
mobile genetic elements in eukaryotic genomes. Each LINE
insertion is on average about 7,000 base pairs in length.
The disruption and decomposition of the
plasma membrane surrounding a cell, or more generally of any membrane-bound
organelle or
vesicle, especially by
osmotic,
enzymatic, or other chemical or mechanical processes which compromise the membrane's integrity and thereby cause the unobstructed interchange of the contents of
intracellular and
extracellular 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 the
cytosol, and therefore the death of the cell. Such a cell is said to be lysed, and a fluid containing the contents of lysed cells (usually including
nucleic acids,
proteins, and many other organic molecules) is called a lysate. Lysis may occur both naturally and artificially, and is a normal part of the cellular life cycle.
^
abcdefghijklmnAlberts, Bruce; Johnson, Alexander; Lewis, Julian; Raff, Martin; Roberts, Keith; Walter, Peter (2002). "Glossary".
Molecular Biology of the Cell(Available from the National Center for Biotechnology Information) (4th ed.). New York: Garland Science.
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abLewin, Benjamin (2003). Genes VIII. Upper Saddle River, NJ: Pearson Prentice Hall.
ISBN0-13-143981-2.
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abcdefghijklmLackie, J. M. (2013). The Dictionary of Cell and Molecular Biology (5th ed.). Amsterdam: Academic Press/Elsevier.
ISBN978-0-12-384931-1.
^SwissBioPics.
"Animal cell". www.swissbiopics.org. Swiss Institute of Bioinformatics (SIB).