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. It is split across two articles:
This page, Glossary of cellular and molecular biology (0–L), lists terms beginning with numbers and with the letters A through L. Glossary of cellular and molecular biology (M–Z) lists terms beginning with the letters M through Z. 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.
0–9
3' untranslated region (3'-UTR) Also three-prime untranslated region, 3' non-translated region (3'-NTR), and trailer sequence.
3'-end Also three-prime end. One of two ends of a single linear strand of DNA or RNA, specifically the end at which the chain of nucleotides terminates at the third carbon atom in the furanose ring of deoxyribose or ribose (i.e. the terminus at which the 3' carbon is not attached to another nucleotide via a phosphodiester bond; in vivo, the 3' carbon is often still bonded to a hydroxyl group). By convention, sequences and structures positioned nearer to the 3'-end relative to others are referred to as downstream. Contrast 5'-end.
5' cap Also five-prime cap. A specially altered nucleotide attached to the 5'-end of some primary RNA transcripts as part of the set of post-transcriptional modifications which convert raw transcripts into mature RNA products. The precise structure of the 5' cap varies widely by organism; in eukaryotes, the most basic cap consists of a methylated guanine nucleoside bonded to the triphosphate group that terminates the 5'-end of an RNA sequence. Among other functions, capping helps to regulate the export of mature RNAs from the nucleus, prevent their degradation by exonucleases, and promote translation in the cytoplasm. Mature mRNAs can also be decapped.
5' untranslated region (5'-UTR) Also five-prime untranslated region, 5' non-translated region (5'-NTR), and leader sequence.
5-bromodeoxyuridine See bromodeoxyuridine.
5'-end Also five-prime end. One of two ends of a single linear strand of DNA or RNA, specifically the end at which the chain of nucleotides terminates at the fifth carbon atom in the furanose ring of deoxyribose or ribose (i.e. the terminus at which the 5' carbon is not attached to another nucleotide via a phosphodiester bond; in vivo, the 5' carbon is often still bonded to a phosphate group). By convention, sequences and structures positioned nearer to the 5'-end relative to others are referred to as upstream. Contrast 3'-end.
5-methyluracil See thymine.
A
acentric (of a linear chromosome or chromosome fragment) Having no centromere.
acetyl coenzyme A (acetyl-CoA) A biochemical compound consisting of a coenzyme A molecule to which an acetyl group (–COCH3) is attached via a high-energy thioester bond. Acetylation of coenzyme A occurs as part of the metabolism of proteins, carbohydrates (glycolysis), and fatty acids (beta oxidation), after which it participates as an energy carrier in several important biochemical pathways, notably the citric acid cycle, in which hydrolysis of the acetyl group releases energy which is ultimately captured in 11 ATP and one GTP.
acetylation The covalent attachment of an acetyl group (–COCH3) to a chemical compound, protein, or other biomolecule via an esterification reaction with acetic acid, either spontaneously or by enzymatic catalysis. Acetylation plays important roles in several metabolic pathways and in histone modification. Contrast deacetylation.
acetyltransferase Any of a class of transferase enzymes which catalyze the covalent bonding of an acetyl group (–COCH3) to another compound, protein, or biomolecule, a process known as acetylation.
acrocentric (of a linear chromosome or chromosome fragment) Having a centromere positioned very close to one end of the chromosome, as opposed to at the end or in the middle.
action potential The local change in voltage that occurs when the membrane potential of a specific location along the membrane of a cell rapidly depolarizes, such as when a nerve impulse is transmitted between neurons.
activation See upregulation.
activator A type of transcription factor that increases the transcription of a gene or set of genes. Most activators work by binding to a specific sequence located within or near an enhancer or promoter and facilitating the binding of RNA polymerase and other transcription machinery in the same region. See also coactivator; contrast repressor.
active site Also binding site and catalytic site. The region of an enzyme to which one or more substrate molecules bind, causing the substrate or another molecule to undergo a chemical reaction. This region usually consists of one or more amino acid residues (commonly three or four) which, when the enzyme is folded properly, are able to form temporary chemical bonds with the atoms of the substrate molecule; it may also include one or more additional residues which, by interacting with the substrate, are able to catalyze a specific reaction involving the substrate. Though the active site constitutes only a small fraction of all the residues comprising the enzyme, its specificity for particular substrates and reactions is responsible for the enzyme's biological function.
active transport Transport of a substance (such as a protein or drug) across a membrane against a concentration gradient. Unlike passive transport, active transport requires an expenditure of energy.
acylation The covalent attachment of any acyl group (e.g. acetyl or benzoyl) to a chemical compound, protein, or other biomolecule via the substitution of the acyl group for a hydrogen atom, either spontaneously or by enzymatic catalysis. Acetylation is a type of acylation.
adenine (A) A purine nucleobase used as one of the four standard nucleobases in both DNA and RNA molecules. Adenine forms a base pair with thymine in DNA and with uracil in RNA.
adenosine (A) One of the four standard nucleosides used in RNA molecules, consisting of an adenine base with its N9 nitrogen bonded to the C1 carbon of a ribose sugar. Adenine bonded to deoxyribose is known as deoxyadenosine, which is the version used in DNA.
adenosine diphosphate (ADP) A nucleoside diphosphate consisting of adenosine attached to two consecutive phosphate groups via high-energy ester bonds. ADP can be phosphorylated to produce ATP and thus is a precursor for its synthesis; it can also be dephosphorylated into AMP.
adenosine monophosphate (AMP) A nucleoside consisting of adenosine attached to a single phosphate group via a high-energy ester bond. Additional phosphate groups can be added to AMP to produce ADP and ATP; the cyclic ester of AMP serves as a second messenger in some signaling pathways.
adenosine triphosphate (ATP) A nucleoside triphosphate consisting of adenosine attached to three consecutive phosphate groups via high-energy ester bonds. The conversion of ATP into ADP or AMP via hydrolysis of these phosphates releases energy which is used to drive the majority of energy-consuming chemical reactions in all living cells, and hence ATP functions as a universal and ubiquitous energy carrier which is often referred to as the "molecular currency" of intracellular metabolism. It is continuously regenerated via phosphorylation of ADP and AMP by enzymes such as ATP synthase. Like other nucleoside triphosphates, it also serves as a precursor for nucleic acid synthesis.
adipocyte A type of mesenchymal cell found in fat tissue, containing large lipid-filled vesicles.
A-DNA One of three main biologically active structural conformations of the DNA double helix, along with B-DNA and Z-DNA. The A-form helix has a right-handed twist with 11 base pairs per full turn, only slightly more compact than B-DNA, but its bases are sharply tilted with respect to the helical axis. It is often favored in dehydrated conditions and within sequences of consecutive purine nucleotides (e.g. GAAGGGGA); it is also the primary conformation adopted by double-stranded RNA and RNA-DNA hybrids.
aerobic 1. Describing conditions in which gaseous or dissolved diatomic oxygen is present. Aerobic environments are said to be oxygenated. 2. Describing an organism, pathway, or process that requires or makes use of diatomic oxygen; e.g. aerobic respiration. Contrast anaerobic.
affected relative pair Any pair of organisms which are related genetically and both affected by the same trait. For example, two cousins who both have blue eyes are an affected relative pair since they are both affected by the allele that codes for blue eyes.
agonist Any ligand (especially a drug or hormone) that in binding to or interacting with a receptor protein causes a conformational change that converts the receptor into an active form, thereby initiating a biological response. In contrast, an inverse agonist has the opposite effect on the receptor, inactivating or disabling it, while an antagonist competes with or directly blocks the agonist, preventing it from activating the receptor.
alkaline lysis A laboratory method used in molecular biology to extract and isolate extrachromosomal DNA such as the DNA of plasmids (as opposed to genomic or chromosomal DNA) from certain cell types, commonly cultured bacterial cells.
allele One of multiple alternative versions of an individual gene, each of which is a viable DNA sequence occupying a given position, or locus, on a chromosome. For example, in humans, one allele of the eye-color gene produces blue eyes and another allele of the same gene produces brown eyes.
allosome 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.
alpha helix (α-helix) A common structural motif in the secondary structures of proteins consisting of a right-handed helix conformation resulting from hydrogen bonding between amino acid residues which are not immediately adjacent to each other.
alternative splicing Also differential splicing or simply splicing. A regulated phenomenon of eukaryotic gene expression in which specific exons or parts of exons from the same primary transcript are variably included within or removed from the final, mature messenger RNA transcript. A class of post-transcriptional modification, alternative splicing allows a single gene to code for multiple protein isoforms and greatly increases the diversity of proteins that can be produced by an individual genome. See also RNA splicing.
amber One of three stop codons used in the standard genetic code; in RNA, it is specified by the nucleotide triplet UAG. The other two stop codons are named ochre and opal.
amino acid Any of a class of organic compounds whose basic structural formula includes a central carbon atom bonded to amine and carboxyl functional groups and to a variable side chain. Out of nearly 500 known amino acids, a set of 20 are coded for by the standard genetic code and incorporated into long polymeric chains as the building blocks of peptides and hence of polypeptides and proteins. The specific sequences of amino acids in the polypeptide chains that form a protein are ultimately responsible for determining the protein's structure and function.
amino terminus See N-terminus.
aminoacyl-tRNA synthetase Also tRNA-ligase. Any of a set of enzymes which catalyze the transesterification reaction that results in the attachment of a specific amino acid (or a precursor) to one of its cognate transfer RNA molecules, forming an aminoacyl-tRNA. Each of the 20 different amino acids used in the genetic code is recognized and attached by its own specific synthetase enzyme, and most synthetases are cognate to several different tRNAs according to their specific anticodons.
aminoacyl-tRNA (aa-tRNA) Also aminoacylated tRNA and charged tRNA. A transfer RNA to which a cognate amino acid is chemically bonded; i.e. the product of a transesterification reaction catalyzed by an aminoacyl-tRNA synthetase. Aminoacyl-tRNAs bind to the aminoacyl site of the ribosome during translation.
amplicon Any DNA or RNA sequence or fragment that is the source and/or product of an amplification reaction. The term is most frequently used to describe the numerous copied fragments that are the products of the polymerase chain reaction or ligase chain reaction, though it may also refer to sequences that are amplified naturally within a genome, e.g. by gene duplication.
amplification The replication of a biomolecule, in particular the production of one or more copies of a nucleic acid sequence, known as an amplicon, either naturally (e.g. by spontaneous duplications) or artificially (e.g. by PCR), and especially implying many repeated replication events resulting in thousands, millions, or billions of copies of the target sequence, which is then said to be amplified.
anabolism Any metabolic reaction or process in which energy is expended in order to build complex substances such as macromolecules from simpler compounds, including aspects of growth and biosynthesis. Anabolic processes and pathways tend to involve reductive steps that create high-enthalpy, low-entropy compounds such as proteins and nucleic acid polymers. Contrast catabolism.
anaerobic 1. Describing conditions in which diatomic oxygen is entirely absent, as opposed to aerobic conditions. 2. Describing an organism that is able to survive and grow in the absence of diatomic oxygen, or a pathway or process characterized by the absence of diatomic oxygen; e.g. anaerobic respiration.
anaphase The stage of mitosis and meiosis that occurs after metaphase and before telophase, when the replicated chromosomes are segregated and each of the sister chromatids are moved to opposite sides of the cell.
anaphase lag The failure of one or more pairs of sister chromatids or homologous chromosomes to properly migrate to opposite sides of the cell during anaphase of mitosis or meiosis due to a defective spindle apparatus. Consequently, both daughter cells are aneuploid: one is missing one or more chromosomes (creating a monosomy) while the other has one or more extra copies of the same chromosomes (creating a polysomy).
aneucentric (of a linear chromosome or chromosome fragment) Having an abnormal number of centromeres, i.e. more than one.
aneuploidy The condition of a cell or organism having an abnormal number of one or more particular chromosomes (but excluding abnormal numbers of complete sets of chromosomes, which instead is known as euploidy).
annealing The hybridization of two single-stranded nucleic acid molecules containing complementary sequences, creating a double-stranded molecule with paired nucleobases. The term is used in particular to describe steps in laboratory techniques such as polymerase chain reaction, where double-stranded DNA molecules are repeatedly denatured into single strands by heating and then exposed to cooler temperatures, causing the strands to reassociate with each other or with complementary primers. The exact temperature at which annealing occurs is strongly influenced by the length and specific sequence of the individual strands.
antibiotic resistance gene A gene that confers resistance to one or more specific antibiotic compounds. In molecular cloning, plasmid vectors are often designed to carry antibiotic resistance genes as selectable markers alongside other genes of interest, because it permits the artificial selection of successfully transformed cell populations when the cells are cultured in the presence of the antibiotic.
antibody Any of a diverse family of glycoproteins known as immunoglobulins capable of binding specifically but reversibly via non-covalent interactions to a particular antigen or immunogen. Antibodies are generated as part of an organism's immune response to the introduction of a specific antigen into a host organism, and their binding of the antigen frequently (though not always) counteracts or inhibits any biological activity the antigen may have. Antibodies have a characteristic Y-shaped structure consisting of a heavy chain and light chain held together by disulfide bonds.
anticodon A series of three consecutive nucleotides within a transfer RNA which complement the three nucleotides of a codon within an mRNA transcript. During translation, each tRNA recruited to the ribosome contains a single anticodon triplet that pairs with its complementary codon from the mRNA sequence, allowing each codon to specify a particular amino acid to be added to the growing peptide chain. Anticodons containing inosine in the first position are capable of pairing with more than one codon due to a phenomenon known as wobble base pairing.
antigen Any exogenous agent that, upon introduction into an immunocompetent organism, stimulates a response from the organism's immune system that results in the production of one or more antibodies which can bind to it specifically; in this sense the term is synonymous with immunogen. Antigens may be pure substances, mixtures of substances, or particulate matter such as cells or cell fragments. Broader definitions may include substances that can bind to a specific antibody but are not themselves immunogenic, i.e. those which are only able to stimulate antibody production when combined with a carrier.
antimetabolite Any molecule that functions as an antagonist to a metabolic process, limiting or inhibiting normal cellular metabolism; i.e. a metabolic poison.
antimitotic Any compound that suppresses normal mitosis in a cell or population of cells.
antioncogene A gene which helps to regulate cell growth and suppress tumors when functioning correctly, such that its absence or malfunction can result in uncontrolled cell growth and possibly cancer. Compare oncogene.
antiparallel The contrasting orientations of the 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 respect to chemical numbering conventions, with one strand oriented 5'-to-3' and the other 3'-to-5'.
antiporter A transport protein which works by exchanging two different ions or small molecules across a membrane in opposite directions, either at the same time or consecutively.
antisense See template strand.
antisense RNA (asRNA) Also antisense transcript and antisense oligonucleotide (ASO). A single-stranded non-coding RNA molecule containing an antisense sequence that is complementary to a sense strand, such as a messenger RNA, with which it readily hybridizes, thereby inhibiting the sense strand's further activity (e.g. translation into protein). Many different classes of naturally occurring RNA such as siRNA function by this principle, making them potent gene silencers in various gene regulation mechanisms. Synthetic antisense RNA has also found widespread use in gene knockdown studies, and in practical applications such as antisense therapy.
anucleate Also anuclear. (of a cell or organism) Lacking a nucleus, i.e. a discrete, membrane-bound organelle enclosing the cell's genomic DNA, used especially of cells which normally have a nucleus but from which the nucleus has been removed (e.g. in artificial nuclear transfer), and also of specialized cell types that develop without nuclei despite that the cells of other tissues comprising the same organism ordinarily do have nuclei (e.g. mammalian erythrocytes).
apical constriction The process by which contraction of the apical side of a cell (and often a corresponding expansion of the opposing basal side) causes the cell to assume a wedge-shaped morphology. The process is common during early development, where it is often coordinated across many adjacent cells of an epithelial layer simultaneously in order to generate bends or folds in developing tissues.
apoptosis A highly regulated form of programmed cell death that occurs in multicellular organisms.
aptamer Any artificial DNA, RNA, or XNA oligonucleotide molecule, single-stranded or double-stranded, which functions as a ligand by binding selectively to one or more specific target molecules, usually other nucleic acids or proteins, and often a family of such molecules. The term is used in particular to describe short nucleic acid fragments which have been randomly generated and then artificially selected in vitro by procedures such as SELEX. Aptamers are useful in the laboratory as antibody mimetics, particularly in applications where conventional protein antibodies are not appropriate.
artificial gene synthesis A set of laboratory methods used in the de novo synthesis of a gene (or any other nucleic acid sequence) from free nucleotides, i.e. without relying on an existing template strand.
assimilatory process Any process by which chemical compounds containing biologically relevant elements (e.g. carbon, hydrogen, oxygen, nitrogen, phosphorus, sulfur, selenium, iron, cobalt, nickel, copper, zinc, molybdenum, etc.) 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 excretes residual or toxic compounds out of the cell, instead of reusing them to build new molecules.
aster In animal cells, a star-shaped system of non-kinetochore microtubules that radiates from a centrosome or from either of the poles of the mitotic spindle during the early stages of cell division.
asynapsis The failure of homologous chromosomes to properly pair with each other during meiosis. Contrast synapsis and desynapsis.
attached X Also compound X. A single monocentric chromosome containing two or more physically attached copies of the normal X chromosome as a result of either a natural internal duplication or any of a variety of genetic engineering methods. The resulting compound chromosome effectively carries two or more doses of all genes and sequences included on the X, yet functions in all other respects as a single chromosome, meaning that haploid 'XX' gametes (rather than the ordinary 'X' gametes) will be produced by meiosis and inherited by progeny. In mechanisms such as genic balance in which the sex of an organism is determined by the total dosage of X-linked genes, an abnormal 'XXY' zygote, fertilized by one XX gamete and one Y gamete, will develop into a female.
autolysis The lysis or digestion of a cell by its own enzymes; or of a particular enzyme by another instance of the same enzyme. See also autophagy.
autophagy Also autophagocytosis. The orderly autolytic degradation and recycling of dysfunctional or unnecessary cellular components by the cell's own enzymes as part of a carefully regulated, lysosome-dependent pathway. Autophagic programs play important roles in nutrient-deprived and senescent cells but also help maintain homeostasis in healthy cells.
autosome Any chromosome that is not an allosome and hence is not involved in the determination of the sex of an organism. Unlike the sex chromosomes, the autosomes in a diploid cell exist in pairs, with the members of each pair having the same structure, morphology, and genetic loci.
autozygote A cell or organism that is homozygous for a locus at which the two homologous alleles are identical by descent, both having been derived from a single gene in a common ancestor. Contrast allozygote.
auxesis The growth of a multicellular organism due to an increase in the size of its cells rather than an increase in the number of cells.
axenic Describing a cell culture in which only a single species, variety, or strain is present, and which is therefore entirely free of contaminating organisms including symbiotes and parasites.
B
B chromosome Any supernumerary nuclear DNA molecule which is not a duplicate of nor homologous to any of the standard complement of normal "A" chromosomes comprising a genome. Typically very small and devoid of structural genes, B chromosomes are by definition not necessary for life. Though they occur naturally in many eukaryotic species, they are not stably inherited and thus vary widely in copy number even between closely related individuals.
back mutation A mutation that reverses the effect of a previous forward mutation which had inactivated a gene, thus restoring wild-type function. See also reverse mutation.
bacterial artificial chromosome (BAC)
base An abbreviation of nitrogenous base and nucleobase.
base pair (bp) A pair of two nucleobases on complementary DNA or RNA strands which are loosely attracted to each other via hydrogen bonding, a type of non-covalent electrostatic interaction between individual atoms in the purine or pyrimidine rings of the complementing bases. This phenomenon, known as base pairing, is the mechanism underlying the hybridization that commonly occurs between nucleic acid polymers, allowing two single-stranded molecules to combine into a more energetically stable double-stranded molecule, as well as enabling certain individual strands to complement themselves. The ability of consecutive base pairs to stack one upon another contributes to the long-chain double helix structures observed in both double-stranded DNA and double-stranded RNA molecules.
baseline A measure of the gene expression level of a gene or genes prior to a perturbation in an experiment, as in a negative control. Baseline expression may also refer to the expected or historical measure of expression for a gene.
basic local alignment search tool (BLAST) A computer algorithm widely used in bioinformatics for aligning and comparing primary biological sequence information such as the nucleotide sequences of DNA or RNA or the amino acid sequences of proteins. BLAST programs enable scientists to quickly check for homology between two or more sequences by directly comparing the nucleotides or amino acids present at each position within each sequence; a common use is to search for matches between a specific query sequence and a digital sequence database such as a genome library, with the program returning a list of sequences from the database which resemble the query sequence above a specified threshold of similarity. Such comparisons can permit the identification of an organism from an unknown sample or the inference of evolutionary relationships between genes, proteins, or species.
B-DNA The "standard" or classical structural conformation of the DNA double helix in vivo, thought to represent an average of the various distinct conformations assumed by very long DNA molecules under physiological conditions. The B-form double helix has a right-handed twist with a diameter of 23.7 ångströms and a pitch of 35.7 ångströms or about 10.5 base pairs per full turn, such that each nucleotide pair is rotated 36° around the helical axis with respect to its neighboring pairs. See also A-DNA and Z-DNA.
beta bend Also β-bend, beta turn or β-turn. A short segment of a polypeptide chain in which the main direction of the chain changes, i.e. a bend or turn in an otherwise linear polymeric chain. The bend is facilitated by a span of four consecutive amino acid residues where the carboxyl group of the first residue participates in hydrogen bonding with the amino group of the fourth residue.
beta oxidation Also β-oxidation. The metabolic pathway by which fatty acid molecules are broken down into simpler molecules, generating acetyl-CoA in the process. This occurs via a series of enzyme-catalyzed reactions which oxidize the beta carbon of the fatty acid chain and ultimately convert it into a carbonyl group, which is then susceptible to nucleophilic attack by another molecule of coenzyme A, causing thiolysis of the bond between the alpha and beta carbons; this process can be repeated to sequentially digest long chains of hydrocarbons into shorter chains, generating an additional molecule of acetyl-CoA with every cycle. In prokaryotes, beta oxidation occurs in the cytosol, while in eukaryotes it primarily takes place in the inner mitochondrial membrane or in peroxisomes.
bidirectional replication A common mechanism of DNA replication in which two replication forks move in opposite directions away from the same origin; this results in a bubble-like region where the duplex molecule is locally separated into two single strands.
binary fission The separation of a single entity (e.g. a cell) into exactly two discrete entities closely resembling the original. The term refers in particular to a type of cell division used by prokaryotes such as bacteria, whereby a single parent cell divides evenly into two daughter cells which are genetically identical to each other and to the parent. Binary fission is preceded by replication of the parent cell's DNA, rapid growth of the cell wall, and various other processes which ensure even distribution of the cell's contents between the two progeny, but is generally a quicker and simpler process than the mitosis and cytokinesis that occur in eukaryotes.
binding capacity A measure of the quantity of ligand that can be chemically bound by a given amount of a particular binding agent, binding partner, or system.
binding site A region of a macromolecule such as a nucleic acid or a protein that directly participates in chemical interactions with another molecule. A wide variety of chemical interactions of varying strength and specificity can be described as "binding"; they may be long-term or transient, reversible or irreversible, and may rely upon relatively weak intermolecular forces or much stronger covalent bonds. Binding sites are defined by the spatial proximity of one or more residues having functional groups with particular chemical properties. For example, the folding of polypeptides in such a way that particular amino acids are positioned near each other in the protein's quaternary structure may confer chemical properties that permit the interaction of those residues with a particular ligand. Similarly, a specific sequence of nucleobases in a DNA molecule may function as a recognition site for a DNA-binding protein. Whether and how the binding site functions depends on the precise spatial arrangement of the interacting residues and their physical accessibility to potential binding partners; thus mutations or changes in the chemical environment such as conformational changes can dramatically alter functionality. See also active site.
bioassay Any analytical method that measures or qualifies the presence, effect, or potency of a substance within or upon a biological system, either directly or indirectly, e.g. by quantifying the concentration of a particular chemical compound within a sample obtained from living organisms, cells, or tissues, and ideally under controlled conditions that compare a sample subjected to an experimental treatment with an unmanipulated sample, so as to permit inferences about the effect of the treatment upon some measured variable.
biochemistry A subdiscipline of both biology and chemistry which studies the chemical basis of biological phenomena, focusing on understanding the chemical reactions and interactions that occur between biomolecules and give rise to the processes that define and characterize living systems. It is closely related to and largely overlaps with molecular biology.
bioenergetics The branch of biochemistry and cell biology that studies the flow of energy through living systems, in particular how organisms acquire, produce, transform, and utilize energy in order to perform biochemical work such as metabolic reactions.
biofilm A community of symbiotic microorganisms, especially bacteria, where cells produce and embed themselves within a slimy, sticky extracellular matrix composed of various high-molecular weight biopolymers, adhering to each other and sometimes also to a substratum, which may be a biotic or abiotic surface. 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.
biomarker A measurable indicator of some biological state, especially a compound or biomolecule whose presence or absence in a biological system is a reliable sign of a normal or abnormal process, condition, or disease. Things that may serve as biomarkers include direct measurements of the concentration of a particular compound or molecule in a tissue or fluid sample, or any other characteristic physiological, histological, or radiographic signal (e.g. a change in heart rate, or a distinct morphology under a microscope). They are regularly used as predictive or diagnostic tools in clinical medicine and laboratory research.
biometal Any metallic element found naturally in small but measurable amounts in biological contexts. Metal ions play important roles in many biochemical processes and some are essential for normal function in living organisms, especially iron (Fe), zinc (Zn), copper (Cu), manganese (Mn), magnesium (Mg), potassium (K), sodium (Na), and calcium (Ca).
biomolecular gradient Any difference in the concentration of biomolecules between two spaces within a biological system, whether intracellular, extracellular, across a membrane, or between different cells or different parts of a tissue or organ system. Gradients of one kind or another drive virtually all biochemical processes occurring within and between cells, as natural systems tend to move toward a thermodynamic equilibrium where concentrations are uniformly distributed in all spaces and no gradients exist. Gradients thus cause chemical reactions to occur in particular directions, which can be used by cells to accomplish essential biological functions, including metabolic energy transfer, signal transduction, and movement of ions and solutes into and out of cells and organelles. It is often necessary for cells to continuously regenerate gradients such as membrane potentials in order to permit these processes to continue.
biomolecule Also biological molecule. Any molecule or chemical compound involved in or essential to one or more biological processes within a biological system, especially large macromolecules such as proteins, nucleic acids, lipids, and carbohydrates, but also broadly inclusive of smaller molecules such as vitamins, hormones, and biometals which are consumed or produced by biochemical reactions, often as part of biochemical pathways. Most biomolecules are organic compounds; some are produced naturally within cells or tissues (endogenous compounds), while others can only be obtained from the organism's environment (exogenous compounds).
bivalent
blast cell See precursor cell.
blot Any of a variety of molecular biology methods by which electrophoretically or chromatographically separated DNA, RNA, or protein samples are transferred from a support medium such as a polyacrylamide or agarose gel onto an immobilizing carrier such as a nitrocellulose or PVDF membrane. Some methods involve the transfer of molecules by capillary action (e.g. Southern and northern blotting), while others rely on the transport of charged molecules by electrophoresis (e.g. western blotting). The transferred molecules are then visualized by colorant staining, by autoradiography, or by probing for specific sequences or epitopes with hybridization probes or antibodies conjugated to chemiluminescent reporters.
blunt end A term used to describe the end of a double-stranded DNA molecule where the terminal nucleobases on each strand are base-paired with each other, such that neither strand has a single-stranded "overhang" of unpaired bases. This is in contrast to a so-called "sticky end", where an overhang is created by one strand being one or more bases longer than the other. Blunt ends and sticky ends are relevant when ligating multiple DNA molecules, e.g. in restriction cloning, because sticky-ended molecules will not readily anneal to each other unless they have matching overhangs; blunt-ended molecules do not anneal in this way, so special procedures must be used to ensure that fragments with blunt ends are joined in the correct places.
bromodeoxyuridine (BUDR, BrdU) Also 5-bromodeoxyuridine. A synthetic nucleoside analogue with a chemical structure similar to thymidine, the only difference being the substitution of a bromine atom for the methyl group of the nucleobase.
C
cadastral gene A regulatory gene that restricts the expression of other genes to specific tissues or body parts in an organism, typically by producing gene products which variably inhibit or permit transcription of the other genes in different cell types. The term is used most commonly in plant genetics.
cadherin 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.
callus 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.
candidate gene A gene whose location on a chromosome is associated with a particular phenotype (often a disease-related phenotype), and which is therefore suspected of causing or contributing to the phenotype. Candidate genes are often selected for study based on a priori knowledge or speculation about their functional relevance to the trait or disease being researched.
canonical sequence See consensus sequence.
carbohydrate Any of a class of organic compounds having the generic chemical formula (CH2O)n, and one of several major classes of biomolecules found universally in biological systems. Carbohydrates include individual monosaccharides as well as larger polymeric oligosaccharides and polysaccharides, in which multiple monosaccharide monomers are joined by glycosidic bonds. 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- indicates a compound or process containing or involving carbohydrates, and the suffix -ose usually signifies that a compound is a carbohydrate or a derivative.
carboxyl terminus See C-terminus.
carrier protein 1. A membrane protein that functions as a transporter, binding to a solute and facilitating its movement across the membrane by undergoing a series of conformational changes. 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. 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. For example, in many blotting techniques, albumin is intentionally allowed to bind non-specifically to the