Glossary

10-nm fiber

A linear array of nucleosomes generated by unfolding from the natural condition of chromatin.

–10 element

The consensus sequence centered about 10 bp before the start point of a bacterial gene. It is involved in melting DNA during the initiation reaction.

14-3-3 adaptors

A family of seven evolutionarily conserved and highly homologous adaptors that form homo- or heterodimers and/or tetramers and that bind a multitude of protein and DNA ligands through either the amphipathic groove or the outer surface. They regulate diverse cell homeostasis events, such as signal transduction, survival, cell cycle progression, and DNA replication, as well as cell differentiation processes, such as class switch recombination (CSR).

2R hypothesis

The hypothesis that the early vertebrate genome underwent two rounds of duplication.

3′ untranslated region (UTR)

The region in an mRNA between the termination codon and the end of the message.

30-nm fiber

A coil of nucleosomes. It is the basic level of organization of nucleosomes in chromatin.

–35 element

The consensus sequence centered about 35 bp before the start point of a bacterial gene. It is involved in initial recognition by RNA polymerase.

5′-AGCT-3′

Repeats that recur at a high frequency in Ig switch regions, but not in the genome at large. They are specifically bound by 14-3-3 adaptors and other class switch recombination (CSR) elements. They are important for CSR targeting.

5′-end resection

The generation of 3′ overhanging single-stranded regions that occurs via exonucleolytic digestion of the 5′ ends at a double-strand break.

5′ untranslated region (UTR)

The region in an mRNA between the start of the message and the first codon.

A complex

The second splicing complex; it is formed by the binding of U2 snRNP to the E complex.

A domain

The conserved 11-bp sequence of A-T base pairs in the yeast ARS element that comprises the replication origin.

A site

The site of the ribosome that an aminoacyl-tRNA enters to base pair with the codon.

Abortive initiation

Describes a process in which RNA polymerase starts transcription but terminates before it has left the promoter. It then reinitiates. Several cycles may occur before the elongation stage begins.

Abundance

The average number of mRNA molecules per cell.

Abundant mRNA

Consists of a small number of individual molecular species, each present in a large number of copies per cell.

Ac (Activator) element

An autonomous transposable element in maize.

Acentric fragment

A fragment of a chromosome (generated by breakage) that lacks a centromere and is lost at cell division.

Acridines

Mutagens that act on DNA to cause the insertion or deletion of a single base pair. They were useful in defining the triplet nature of the genetic code.

Activation-induced (cytidine) deaminase (AID)

An enzyme that removes the amino group from the cytidine base in DNA; mediates DNA damage that leads to the initiation of immunoglobulin (Ig) diversification.

Activator

A protein that stimulates the expression of a gene, typically by interacting with a promoter to stimulate RNA polymerase. In eukaryotes, the sequence to which it binds in the promoter is called an enhancer.

Activator (Ac) element

An autonomous transposable element in maize.

Adaptive (acquired) immunity

The response mediated by lymphocytes that are activated by their specific interaction with antigen. The response develops over several days as lymphocytes with antigen-specific receptors are stimulated to proliferate and become effector cells. It is responsible for immunological memory.

Addiction system

A survival mechanism used by plasmids. The mechanism kills the bacterium upon loss of the plasmid.

Agropine plasmids

Plasmids that carry genes coding for the synthesis of opines of the agropine type. The tumors usually die early.

AID

See activation-induced (cytidine) deaminase (AID).

Allele

One of several alternative forms of a gene occupying a given locus on a chromosome.

Allelic exclusion

The expression in any particular lymphocyte of only one allele coding for the expressed immunoglobulin heavy or light chain. This is caused by feedback from the first immunoglobulin allele to be expressed that prevents activation of the allele on the other chromosome.

Allolactose

A by-product of β-galactosidase (encoded by LacZ), the true inducer of the lac operon.

Allopolyploidy

Polyploidization resulting from hybridization between two different but reproductively compatible species.

Allosteric control

The ability of a protein to change its conformation (and therefore activity) at one site as the result of binding a small molecule to a second site located elsewhere on the protein.

Alternative splicing

The production of different RNA products from a single product by changes in the usage of splicing junctions.

Alu element

One of a set of dispersed, related sequences, each approximately 300 bp long, in the human genome (members of the SINE family). The individual members have Alu cleavage sites at each end.

Amber codon

The triplet UAG, one of the three termination codons that end polypeptide translation.

Amplicon

The precise, primer-to-primer, double-stranded nucleic acid product of a PCR or RT-PCR reaction.

Amyloid fibers

Insoluble fibrous protein polymers with a cross β-sheet structure generated by prions or other dysfunctional protein aggregations (such as in Alzheimer’s disease).

Annealing

The renaturation of a duplex structure from single strands that were obtained by denaturing duplex DNA.

Anti-Sm

An autoimmune antiserum that defines the Sm domain that is common to a group of proteins found in snRNPs that are involved in RNA splicing.

Antibody

A protein that is produced by B lymphocytes and that binds a particular antigen. Consists of two identical light chains disulfide bond–linked to two identical heavy chains. They are synthesized in membrane-bound and secreted forms. Those produced during an immune response recruit effector functions to help neutralize and eliminate the pathogen.

Antigen

A molecule that can bind specifically to an antigen receptor, such as a B cell receptor or an antibody, and can induce a specific immune response.

Antigen-presenting cells (APCs)

Cells of the immune system that are very efficient at internalizing antigen either by phagocytosis or by receptor-mediated endocytosis, and then displaying a fragment of the antigen, bound to a class II MHC molecule, on their membrane. Examples include dendritic cells, macrophages, and B cells.

Antigenic determinant

The site or region on the surface of a macromolecular antigen that induces an antibody response.

Antiparallel

Strands of the double helix are organized in opposite orientation so that the 5′ end of one strand is aligned with the 3′ end of the other strand.

Antirepressor

A positive regulator that functions in opening chromatin.

Antisense RNA

RNA that has a complementary sequence to an RNA that is its target.

Antisense strand

See template strand.

Antitermination

A mechanism of transcriptional control in which termination is prevented at a specific terminator site, allowing RNA polymerase to read into the genes beyond it.

Antitermination complex

Proteins that allow RNA polymerase to transcribe through certain terminator sites.

Anucleate cell

Bacteria that lack a nucleoid but are of similar shape to wild-type bacteria.

Apoptosis

Programmed cell death triggered by a cellular stimulus through a signal transduction pathway.

Aptamer

An RNA domain that binds a small molecule; this can result in a conformation change in the RNA.

Apurinic/apyrimidinic endonuclease (APE)

A DNA base excision repair (BER) pathway enzyme that nicks the phosphodiester backbone of an abasic site generated by DNA glycosylase. Nicks generated in proximity on opposite DNA strands are critical for the generation of double-strand breaks in switch regions of the immunoglobulin locus.

Architectural protein

A protein that, when bound to DNA, can alter the structure of the DNA (e.g., introduce a bend). These proteins appear to have no other function.

ARE

See AU-rich element (ARE).

ARS

An origin for replication in yeast. The common feature among different examples of these sequences is a conserved 11-bp sequence called the A domain.

Assembly factors

Proteins that are required for formation of a macromolecular structure but are not themselves part of that structure.

ATP-dependent chromatin remodeling complex

A complex of one or more proteins associated with an ATPase of the SWI2/SNF2 superfamily that uses the energy of ATP hydrolysis to alter or displace nucleosomes.

attachment (att) sites

The loci on a lambda phage and the bacterial chromosome at which recombination integrates the phage into, or excises it from, the bacterial chromosome.

Attenuation

The regulation of bacterial operons by controlling termination of transcription at a site located before the first structural gene.

Attenuator

A terminator sequence at which attenuation occurs.

AU-rich element (ARE)

A eukaryotic mRNA cis sequence consisting largely of A and U ribonucleotides that acts as a destabilizing element.

Autonomous transposons

An active transposon with the ability to transpose (i.e., encode a functional transposase).

Autonomously replicating sequence

A DNA sequence element that contains an origin of replication.

Autopolyploidy

Polyploidization resulting from mitotic or meiotic errors within a species.

Autoradiography

A method of capturing an image of radioactive materials on film.

Autoregulation

A site or mutation that affects only the properties of its own molecule of DNA, often indicating that a site does not code for a diffusible product.

Autosplicing (self-splicing)

The ability of an intron to excise itself from an RNA by a catalytic action that depends only on the sequence of RNA in the intron.

Axial element

A proteinaceous structure around which the chromosomes condense at the start of synapsis.

B cell

A lymphocyte that produces antibodies. Developed primarily in the bone marrow. Those lymphocytes emerging from the marrow undergo further differentiation in the bloodstream and peripheral lymphoid organs.

B cell receptor (BCR)

Receptor composed of the antigen-binding membrane immunoglobulin and the Igα and Igβ signaling coreceptors. It has the same structure and specificity of the antibody that will be produced by the same B cell after its activation by antigen.

Back mutation

A mutation that reverses the effect of a mutation that had inactivated a gene; thus, it restores the original sequence or function of the gene product.

Bacteriophage

A bacterial virus.

Balbiani rings

Exceptionally large puffs on polytene chromosomes that are the sites of RNA transcription. They are useful in studying the structure of active genes and synthesis and transport of RNA molecules.

Bam islands

A series of short, repeated sequences found in the nontranscribed spacer of Xenopus rDNA genes.

Bands

Portions of polytene chromosomes visible as dense regions that contain the majority of DNA; they include active genes.

Basal apparatus

The complex of transcription factors that assembles at the promoter before RNA polymerase is bound.

Basal transcription factors

Transcription factors required by RNA polymerase II to form the initiation complex at all RNA polymerase II promoters. Factors are identified as TFIIX, where X is a letter.

Base excision repair (BER)

DNA repair systems that directly remove the damaged base and replace it with the correct base within the DNA.

Base pairing

Binding of nucleotide bases such that each base pair consists of a purine and pyrimidine held together by one or more hydrogen bonds. In DNA, the purine adenine (A) binds to the pyrimidine thymine (T) and the purine guanine (G) binds to the pyrimidine cytosine (C). In RNA, the pyrimidine uracil (U) is substituted for thymine.

Bent DNA

Curves in DNA often associated with poly(A) stretches on the same side of the double helix that are thought to assist with both activation and repression of transcription.

Bidirectional replication

A system in which an origin generates two replication forks that proceed away from the origin in opposite directions.

Bivalent

The structure containing all four chromatids (two representing each homologue) at the start of meiosis.

Blocked reading frame

See closed (blocked) reading frame.

Blotting

Technique used to transfer proteins, DNA, or RNA onto a carrier such as nitrocellulose or nylon. Following the blotting, the molecules can be visualized through a number of different techniques (e.g., staining).

Boundary (insulator) element

A DNA sequence element bound by proteins that prevents the spread of open or closed chromatin.

Branch migration

The ability of a DNA strand partially paired with its complement in a duplex to extend its pairing by displacing the resident strand with which it is homologous.

Branch site

A short sequence just before the end of an intron at which the lariat intermediate is formed in splicing by joining the 5′ nucleotide of the intron to the 2′ position of an adenosine.

Breakage and reunion

The mode of genetic recombination in which two DNA duplex molecules are broken at corresponding points and then rejoined crosswise (involving formation of a length of heteroduplex DNA around the site of joining).

Bromodomain

A domain of 110 amino acids that binds to acetylated lysines (often in histones).

Brownian ratchet

Stochastic fluctuations that can be locked into a productive structure.

bZIP (basic zipper)

A protein with a basic DNA-binding region adjacent to a leucine zipper dimerization motif.

C-value

The total amount of DNA in the genome (per haploid set of chromosomes).

C-value paradox

The lack of relationship between the DNA content of an organism and its coding potential.

cAMP

See cyclic AMP (cAMP).

Cap

The structure at the 5′ end of eukaryotic mRNA; it is introduced after transcription by linking the terminal phosphate of 5′ guanosine triphosphate (GTP) to the terminal base of the mRNA.

Capsid

The external protein coat of a virus particle.

Carboxy-terminal domain (CTD)

The domain of eukaryotic RNA polymerase II that is phosphorylated at initiation and is involved in coordinating several activities with transcription.

Cascade

A sequence of events, each of which is stimulated by the previous one. In transcriptional regulation, as seen in sporulation and phage lytic development, it means that regulation is divided into stages and that at each stage one of the genes that is expressed codes for a regulator needed to express the genes of the next stage.

Catabolite regulation

The ability of glucose to prevent the expression of a number of genes. In bacteria this is a positive control system; in eukaryotes, it is completely different.

Catabolite repression

A mechanism that enables bacteria to utilize a preferred carbon source first even in the presence of high levels of a non-preferred carbon source; for example, the presence of glucose results in repression of the lac operon even in the presence of lactose.

Catabolite repressor protein (CRP)

A positive regulator protein activated by cyclic AMP. It is needed for RNA polymerase to initiate transcription of many operons of Escherichia coli.

Catenate

To link together two circular molecules, as in a chain.

CCCTC-binding factor (CTCF)

A transcription factor involved in regulation of chromatin architecture, V(D)J recombination, insulator activity, and transcription regulation. It binds together DNA strands, thus forming chromatin loops, and anchors DNA to cellular structures such as the nuclear lamina. It also defines the boundaries between active and heterochromatic DNA.

cDNA

A single-stranded DNA complementary to an RNA, synthesized from it by reverse transcription in vitro.

Central dogma

Information cannot be transferred from protein to protein or protein to nucleic acid but can be transferred between nucleic acids and from nucleic acid to protein.

Central element

A structure that lies in the middle of the synaptonemal complex, along which the lateral elements of homologous chromosomes align; it is formed from Zip proteins.

Centromere

A constricted region of a chromosome that includes the site of attachment (the kinetochore) to the mitotic or meiotic spindle. It consists of unique DNA sequences and proteins not found anywhere else in the chromosome.

Checkpoint

A biochemical control mechanism that prevents the cell from progressing from one stage to the next unless specific goals and requirements have been met.

Chemical proofreading

A proofreading mechanism in which the correction event occurs after the addition of an incorrect subunit to a polymeric chain by means of reversing the addition reaction.

Chiasma (pl. chiasmata)

A site at which two homologous chromosomes synapse during meiosis.

Chromatid

Either of the two threadlike strands formed when a chromosome duplicates during the early stages of cell division. The two strands are held together at the centromere and separate into daughter chromosomes during anaphase.

Chromatin

The combination of DNA and proteins that make up the contents of the nucleus of a cell. Its primary functions are to package DNA into a smaller volume to fit in the cell, to strengthen the DNA to allow mitosis and meiosis and prevent DNA damage, and to control gene expression and DNA replication and repair. The primary protein components are histones that compact the DNA.

Chromatin remodeling

The energy-dependent displacement or reorganization of nucleosomes that occurs in conjunction with activation of genes for transcription.

Chromatosomes

Nucleosomes that contain linker histones.

Chromocenter

An aggregate in the nucleus of heterochromatin from different chromosomes.

Chromodomain

Domains of approximately 60 amino acids that recognize various methylated states of lysines in histones and other proteins; some have other functions, such as RNA binding.

Chromomeres

Densely staining granules visible in chromosomes under certain conditions, especially early in meiosis, when a chromosome may appear to consist of a series of such granules.

Chromosomal domain

A region of altered chromosome structure that includes at least one active transcription unit.

Chromosome

A discrete unit of the genome carrying many genes. Each consists of a very long molecule of duplex DNA and an approximately equal mass of proteins (in eukaryotes). It is visible as a morphological entity only during cell division.

Chromosome pairing

The coupling of the homologous chromosomes at the start of meiosis.

Chromosome scaffold

A proteinaceous structure in the shape of a sister chromatid pair, generated when chromosomes are depleted of histones.

Chromosome territories

The discrete three-dimensional spaces occupied by individual chromosomes in the interphase nucleus.

Chroperon

Multigene complex in eukaryotes that brings together various genes from distant loci into close proximity.

cis-acting

A site that affects the activity only of sequences on its own molecule of DNA (or RNA); this property usually implies that the site does not code for protein.

cis-dominant

A site or mutation that affects the properties only of its own molecule of DNA, often indicating that a site does not code for a diffusible product.

Cistron

The genetic unit defined by the complementation test; it is equivalent to a gene.

Clamp

A protein complex that forms a circle around the DNA. By connecting to DNA polymerase, it ensures that the enzyme action is processive.

Clamp loader

A five-subunit protein complex that is responsible for loading the β clamp onto DNA at the replication fork.

class switch recombination (CSR)

A somatic change in the Ig gene locus organization in which the constant region of the heavy chain is changed but the variable region (and therefore antigen specificity) remains the same. This allows different progeny B cells from the same activated B cell to produce antibodies of different classes or isotypes. Naïve mature B cells express IgM and IgD. After activation by antigen, they undergo class switching to IgG, IgA, or IgE. Class switching is effected by DNA recombination between the switch regions lying upstream of different C heavy chain gene clusters.

Class switching

See class switch recombination.

Clonal selection

The process by which only lymphocyte(s) that bind a given antigen through their surface B cell receptor are stimulated to proliferate and differentiate to produce antibodies that specifically bind the same antigen. Requires that each lymphocyte expresses on its surface B cell receptors of a single, typically unique specificity. Thus, the antigen “selects” the lymphocytes to be activated. Originally a theory, but now an established principle in immunology.

Clone

An exact replica or copy, whether it is Dolly the sheep or a fragment of DNA.

Cloning

Propagation of a DNA sequence by incorporating it into a hybrid construct that can be replicated in a host cell.

Cloning vector

DNA (often derived from a plasmid or a bacteriophage genome) that can be used to propagate an incorporated DNA sequence in a host cell; vectors contain selectable markers and replication origins to allow identification and maintenance of the vector in the host.

Closed (blocked) reading frame

A reading frame that cannot be translated into protein because of the occurrence of termination codons.

Closed complex

The stage of initiation of transcription before RNA polymerase causes the two strands of DNA to separate to form the “transcription bubble.” The DNA is double stranded.

Cluster rule

Rule discovered by Erwin Chargaff that purines tend to cluster on one DNA strand and pyrimidines tend to cluster on the other. As applied to exons, the purines, A and G, tend to be clustered in one DNA strand of the DNA duplex (usually the nontemplate strand) and these are complemented by clusters of the pyrimindines, T and C, in the template strand.

Coactivator

Factors required for transcription that do not bind DNA but are required for (DNA-binding) activators to interact with the basal transcription factors.

Coding end

Constitutes an intermediate during recombination of immunoglobulin and T cell receptor V(D)J gene segments. It identifies with the termini of the cleaved V, D, and J DNA regions. The subsequent joining yields coding joint(s).

Coding region

A part of a gene that codes for a polypeptide sequence.

Coding strand

The DNA strand that has the same sequence as the mRNA and is related by the genetic code to the protein sequence that it represents.

Codon

(1) A triplet of nucleotides that codes for an amino acid. (2) A termination signal.

Codon bias

A higher usage of one codon in genes to encode amino acids for which there are several synonymous codons.

Codon usage

A description of the relative abundance of tRNAs for each codon.

Cognate tRNAs

tRNAs recognized by a particular aminoacyl-tRNA synthetase. All are charged with the same amino acid.

Cohesins

Proteins that regulate the separation of sister chromatids during cell division. They hold the sister chromatids together after DNA replication until anaphase, at which point their removal leads to the separation of the sister chromatids.

Coincidental evolution

See concerted (coincidental) evolution.

Cointegrate

A structure that is produced by fusion of two replicons, one originally possessing a transposon and the other lacking it; the product has copies of the transposon present at both junctions of the replicons, oriented as direct repeats.

Colinear

The relationship that describes the 1:1 correspondence of a sequence of triplet nucleotides to a sequence of amino acids.

Comparative genomics

Field of study that examines similarities and differences among DNA sequences, genes, gene order, regulatory sequences, and other genomic landmarks to determine how organisms are related to each other.

Compatibility group

A group of plasmids that contains members unable to coexist in the same bacterial cell.

Complement

A set of approximately 20 proteins that function through a cascade of proteolytic actions that lead to generation of intermediates (membrane attack complex) that lyse target cells and/or chemotactic fragments that attract macrophages, neutrophils, or lymphocytes.

Complementary

Base pairs that match up in the pairing reactions in double helical nucleic acids (A with T in DNA or with U in RNA, and C with G).

Complementary DNA (cDNA)

The double-stranded DNA that is synthesized from a single-stranded RNA template through a reaction catalyzed by reverse transcriptase.

Complementation group

Mutant genes that do not complement each other, thus indicating that the mutations occur on the same gene. Complementation tests are used to determine whether two mutations are in the same or different genes.

Complementation test

A test that determines whether two mutations are alleles of the same gene. It is accomplished by crossing two different recessive mutations that have the same phenotype and determining whether the wild-type phenotype can be produced. If so, the mutations are said to complement each other and are probably not mutations in the same gene.

Complex mRNA

mRNA that consists of a large number of individual mRNA species, each present in very few copies per cell. This accounts for most of the sequence complexity in RNA.

Composite transposons (Tn)

Segments of DNA that have similar function as simple transposons and IS elements in that they have protein-coding DNA segments flanked by inverted, repeated sequences that can be recognized by transposase enzymes.

Concerted (coincidental) evolution

The ability of two or more related genes to evolve together as though constituting a single locus.

Condensins

Class of ATPases that are involved in the control of the condensation of genetic material into compact chromosomes at mitosis. They form complexes that have a core of the heterodimer SMC2–SMC4 associated with other (non-SMC) proteins.

Conditional lethal

A mutation that is lethal under one set of conditions but not lethal under a second set of conditions, such as temperature.

Conjugation

A process in which two cells come in contact and transfer genetic material. In bacteria, DNA is transferred from a donor to a recipient cell. In protozoa, DNA passes from each cell to the other.

Consensus sequence

An idealized sequence in which each position represents the base most often found when many actual sequences are compared.

Conserved sequence

Sequences in which many examples of a particular nucleic acid or protein are compared and the same individual bases or amino acids are always found at particular locations.

Constant (C) genes

Genes that encode the constant regions of immunoglobulin heavy or light chain.

Constant (C) region

The part of an immunoglobulin or T cell receptor that varies least in amino acid sequence between different molecules. C regions are encoded by C gene segments. In antibodies, the heavy chain regions identify the class or subclass of immunoglobulin and mediate effector functions. Humans have five Ig classes, or isotypes: IgM, IgD, IgG (IgG1, IgG2, IgG3, and IgG4), IgA, and IgE.

Constitutive expression

Describes a state in which a gene is expressed continuously.

Constitutive gene

A gene that is (theoretically) expressed in all cells because it provides basic functions needed for sustenance of all cell types.

Constitutive heterochromatin

The inert state of particular (often repetitive) DNA sequences, such as satellite DNA.

Context

The fact that neighboring sequences may change the efficiency with which a codon is recognized by its aminoacyl-tRNA or is used to terminate polypeptide translation.

Controlling elements

Transposable units in maize originally identified solely by their genetic properties. They may be autonomous (able to transpose independently) or nonautonomous (able to transpose only in the presence of an autonomous element).

Conventional phenotype

The effect of a single gene on the organism carrying it, usually as a result of the polypeptide it encodes.

Copy number

The number of copies of a plasmid that is maintained in a bacterium (relative to the number of copies of the origin of the bacterial chromosome).

Core DNA

Region of nucleosomal DNA that has an invariant length of 146 bp, the minimum length of DNA needed to form a stable monomeric nucleosome, and is relatively resistant to digestion by nucleases.

Core enzyme

The complex of RNA polymerase subunits needed for elongation. It does not include additional subunits or factors that may be needed for initiation or termination.

Core histone

One of the four types of histone (H2A, H2B, H3, and H4 and their variants) found in the core particle derived from the nucleosome. (This excludes linker histones.)

Core promoter

The shortest sequence at which an RNA polymerase can initiate transcription (typically at a much lower level than that displayed by a promoter containing additional elements). For RNA polymerase II, it is the minimal sequence at which the basal transcription apparatus can assemble, and it includes three sequence elements: the Inr, the TATA box, and the downstream promoter element (DPE). It is typically approximately 40 bp long.

Core sequence

The segment of DNA that is common to the attachment sites on both the phage lambda and bacterial genomes. It is the location of the recombination event that allows phage lambda to integrate.

Corepressor

A molecule that triggers repression of transcription by binding to a regulator protein.

Cosmid

Cloning vector derived from a bacterial plasmid by incorporating the cos sites of phage lambda, which make the plasmid DNA a substrate for the lambda packaging system.

Countertranscript

An RNA molecule that prevents an RNA primer from initiating transcription by base pairing with the primer.

Coupled transcription/translation

The process in bacteria where a message is simultaneously being translated while it is still being transcribed.

cpDNA

The DNA found in the chloroplast.

CpG islands

Stretches of 1 to 2 kb in mammalian genomes that are enriched in CpG dinucleotides; frequently found in promoter regions of genes.

CRISPRs

Clusters of regularly interspersed short palindromic repeats in prokaryotes that are transcribed and processed into short RNAs that function in RNA interference.

Crossover fixation

A possible consequence of unequal crossing over that allows a mutation in one member of a tandem cluster to spread through the whole cluster (or to be eliminated).

Crown gall disease

A tumor that can be induced in many plants by infection with the bacterium Agrobacterium tumefaciens.

CRP

See catabolite repressor protein (CRP).

Cryptic satellite

A satellite DNA sequence not identified as such by a separate peak on a density gradient; that is, it remains present in main band DNA.

Cryptic unstable transcripts (CUTs)

Non-protein-coding RNAs transcribed by RNA Pol II, frequently generated from the 3′ ends of genes (resulting in antisense transcripts) and rapidly degraded after synthesis.

C-terminal domain (CTD)

The domain of RNA polymerase that is involved in stimulating transcription by contact with regulatory proteins.

ctDNA

The DNA found in the chloroplast.

CUTs

See cryptic unstable transcripts (CUTs).

Cyclic AMP (cAMP)

The coregulator of catabolite repressor protein (CRP); it has an internal 3′–5′ phosphodiester bond. Its concentration is inverse to the concentration of glucose.

Cyclin-dependent kinases

Serine-threonine protein kinases that are synthesized in an inactive form and activated by binding a cyclin protein subunit.

Cyclins

Cell cycle–dependent proteins that have no intrinsic enzymatic activity but when bound to an inactive cyclin-dependent kinase can activate it.

Cytological map

A schematic representation of chromosomes that indicates the arrangement of individual genes. Created by analyzing the banding patterns of chromosomes that have undergone changes such as deletions and mutations.

Cytoplasmic domain

The part of a transmembrane protein that is exposed to the cytosol.

Cytotoxic T cell (CTL)

A T lymphocyte, usually CD8+, that can kill target cells expressing specifically recognized antigens, such as virus-encoded glycoproteins expressed on the surface of virus-infected cells.

Cytotype

A cytoplasmic condition that affects P element activity; it results from the presence or absence of a repressor of transposition, which is provided by the mother to the egg.

D-loop

(1) A region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region. (2) The displacement of a region of one strand of duplex DNA by a complementary single-stranded invader.

D segments

Coding sequences in the Ig heavy chain and TCRβ and TCRδ loci. They lie in cluster between the variable (V) and joining (J) gene segment clusters. Not present in Iδ, Igλ, and TCRα and TCRγ loci.

de novo methyltransferase

An enzyme that adds a methyl group to an unmethylated target sequence on DNA.

Deacylated tRNA

tRNA that has no amino acid or polypeptide chain attached because it has completed its role in protein synthesis and is ready to be released from the ribosome.

Deadenylase (or poly[A] nuclease)

An exoribonuclease that is specific for digesting poly(A) tails.

Decapping enzyme

An enzyme that catalyzes the removal of the 7-methyl guanosine cap at the 5′ end of eukaryotic mRNAs.

Degradosome

A complex of bacterial enzymes, including RNAase and helicase activities, that is involved in degrading mRNA.

Delayed early genes

Genes in phage lambda that are equivalent to the middle genes of other phages. They cannot be transcribed until regulator protein(s) coded by the immediate early genes have been synthesized.

Demethylase

A casual name for an enzyme that removes a methyl group, typically from DNA, RNA, or protein.

Denaturation

A molecule’s conversion from the physiological conformation to some other (inactive) conformation. In DNA, this involves the separation of the two strands due to breaking of hydrogen bonds between bases.

Dendritic cell (DC)

The most powerful antigen-presenting cell. Its main function is to process antigen material and present it to T cells to initiate an immune response. They account for less than 1% of blood mononuclear cells and are present in small quantities in tissues that are in contact with the external environment. In the skin, they are called Langerhans cells.

Destabilizing element (DE)

Any one of many different cis sequences, present in some mRNAs, that stimulates rapid decay of that mRNA.

Dicer

An endonuclease that processes double-stranded precursor RNA to 21- to 23-nucleotide RNAi molecules.

Dideoxy sequencing

A popular DNA sequencing method that relies on synthetic primers. It is also called the Sanger technique. DNA polymerases are used to copy a single-stranded DNA template by adding nucleotides to the growing chain. The chain elongates at the 3′ end of a primer, which is an oligonucleotide that anneals to the template. The deoxynucleotides added to the extension are determined by base-pair matching to the template.

Dideoxynucleotide (dNTP)

A chain-terminating nucleotide that lacks a 3′–OH group and therefore is not a substrate for DNA polymerization. Used in DNA sequencing and as an antiviral drug.

Direct repeats

Identical (or closely related) sequences present in two or more copies in the same orientation in the same molecule of DNA.

Directional cloning

Method of directing the orientation of inserts into vectors by digesting a DNA insert or vector molecule with two restriction endonuclease enzymes to create either blunt or noncomplementary sticky ends at both ends of each restriction fragment. The insert can then be ligated to the vector (plasmid or bacteriophage) in a specific, fixed orientation.

Displacement loop

A region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region. The same term is also used to describe the displacement of a region of one strand of duplex DNA by a complementary single-stranded invader.

Dissociator (Ds) element

A nonautonomous transposable element in maize, related to the autonomous Activator (Ac) element.

Distributive (nuclease)

An enzyme that catalyzes the removal of only one or a few nucleotides before dissociating from the substrate.

Divergence

The corrected percent difference in nucleotide sequence between two related DNA sequences or in amino acid sequences between two proteins.

DNA forensics

Technique used to identify individuals by characteristics of their DNA for the purposes of paternity testing or criminal investigations. Although approximately 99.9% of human DNA sequences are the same in every person, there are enough differences in a person’s DNA that it is possible to distinguish one individual from another (unless they are monozygotic twins). Identification is based on the small set of DNA variations that is likely to differ between unrelated individuals.

DNA ligase

The enzyme that makes a bond between an adjacent 3′–OH and 5′–phosphate end where there is a nick in one strand of duplex DNA.

DNA methyltransferase

An enzyme that adds a methyl group to a DNA substrate.

DNA mutants

Temperature-sensitive replication mutants in Escherichia coli that identify a set of loci called the dna genes.

DNA polymerase

An enzyme that synthesizes a daughter strand(s) of DNA (under direction from a DNA template). Any particular enzyme may be involved in repair or replication (or both).

DNA profiling

Technique used to identify individuals by characteristics of their DNA for the purposes of paternity testing or criminal investigations. Although approximately 99.9% of human DNA sequences are the same in every person, there are enough differences in a person’s DNA that it is possible to distinguish one individual from another (unless they are monozygotic twins). Identification is based on the small set of DNA variations that is likely to differ between unrelated individuals.

DNA repair

The removal and replacement of damaged DNA by the correct sequence.

DNA replicase

See DNA polymerase.

DNase

An enzyme that degrades DNA.

Domain

In reference to a chromosome, it may refer either to a discrete structural entity defined as a region within which supercoiling is independent of other regions or to an extensive region including an expressed gene that has heightened sensitivity to degradation by the enzyme DNase I. In a protein, it is a discrete continuous part of the amino acid sequence that can be equated with a particular function.

Dominant gain of function mutation

A type of mutation in which the altered product possesses a new molecular function or pattern of gene expression.

Dominant negative

A mutation that results in a mutant gene product that prevents the function of the wild-type gene product, causing loss or reduction of gene activity in cells containing both the mutant and wild-type alleles. The most common cause is that the gene codes for a homomultimeric protein whose function is lost if only one of the subunits is a mutant.

Dosage compensation

Mechanisms employed to compensate for the discrepancy between the presence of two X chromosomes in one sex but only one X chromosome in the other sex.

Double-strand breaks (DSBs)

Breaks that occur when both strands of a DNA duplex are cleaved at the same site. Genetic recombination is initiated by such breaks. The cell also has repair systems that act on breaks that are created at other times.

Doubling time

The period (usually measured in minutes) that it takes for a bacterial cell to reproduce.

Down mutation

A mutation in a promoter that decreases the rate of transcription.

Downstream

Sequences proceeding farther in the direction of expression within the transcription unit.

Downstream promoter element (DPE)

A common component of RNA polymerase II promoters that do not contain a TATA box.

Drosha

An endonuclease that processes double-stranded primary RNAs into short (approximately 70-bp) precursors for Dicer processing.

Ds (Dissociator) element

A nonautonomous transposable element in maize, related to the autonomous Activator (Ac) element.

E complex

The first complex to form at a splice site, consisting of U1 snRNP bound at the splice site together with factor ASF/SF2, U2AF bound at the branch site, and the bridging protein SF1/BBP.

E site

The site of the ribosome that briefly holds deacylated tRNAs before their release.

Early genes

Genes that are transcribed before the replication of phage DNA. They code for regulators and other proteins needed for later stages of infection.

Early infection

The part of the phage lytic cycle between entry and replication of the phage DNA. During this time, the phage synthesizes the enzymes needed to replicate its DNA.

EF-Tu

The elongation factor that binds aminoacyl-tRNA and places it into the A site of a bacterial ribosome.

EGFR

A member of the erbB family of receptors that binds Epidermal Growth Factor (EGF).

EJC

See exon junction complex (EJC).

Electroporation

Technique whereby an electric pulse is applied to a cell to create temporary pores in the cell membrane, increasing the membrane’s permeability to chemicals, drugs, or DNA. Can be used to transform bacteria and yeast or to introduce new DNA into tissue cultures, especially of mammalian cells.

Elongation

The stage in a macromolecular synthesis reaction (replication, transcription, or translation) when the nucleotide or polypeptide chain is extended by the addition of individual subunits.

Elongation factors

Proteins that associate with ribosomes cyclically during the addition of each amino acid to the polypeptide chain.

Endonuclease

An enzyme that cleaves bonds within a nucleic acid chain; it may be specific for RNA or for single- or double-stranded DNA.

Endoreduplication

Successive replications of a synapsed diploid pair of chromosomes that do not separate, thus remaining attached in their extended state. Results in production of giant chromosomes.

Endoribonuclease

A ribonuclease that cleaves an RNA at internal site(s).

Enhancer

A cis-acting sequence that increases the utilization of (most) eukaryotic promoters and can function in either orientation and in any location (upstream or downstream) relative to the promoter.

Epidermal growth factor (EGF)

Peptide hormone that binds to EGFR in a lock-and-key type mechanism.

Epigenetic

Changes that influence the phenotype without altering the genotype. They consist of changes in the properties of a cell that are inherited but that do not represent a change in genetic information.

Episome

A plasmid able to integrate into bacterial DNA.

Epitope

The site or region on the surface of a macromolecular antigen that induces an antibody response.

Epitope tag

A polypeptide that has been added to a protein that allows its identification by an antibody.

eRNAs

Relatively short noncoding RNA molecules transcribed from the DNA sequence of enhancer regions. Evidence suggests that they play a role in regulation of transcription.

Error-prone polymerase

A DNA polymerase that incorporates noncomplementary bases into the daughter strand.

Error-prone synthesis

A repair process in which noncomplementary bases are incorporated into the daughter strand.

Euchromatin

Regions that comprise most of the genome in the interphase nucleus, are less tightly coiled than heterochromatin, and contain most of the active or potentially active single-copy genes.

Excision

Release of phage or episome or other sequence from the host chromosome as an autonomous DNA molecule.

Excision repair

A type of repair system in which one strand of DNA is directly excised and then replaced by resynthesis using the complementary strand as a template.

Exon

Any segment of an interrupted gene that is represented in the mature RNA product.

Exon definition

The process in which a pair of splicing sites are recognized by interactions involving the 5′ site of the intron and also the 5′ site of the next intron downstream.

Exon junction complex (EJC)

A protein complex that assembles at exon–exon junctions during splicing and assists in RNA transport, localization, and degradation.

Exon shuffling

The hypothesis that genes have evolved by the recombination of various exons coding for functional protein domains.

Exon trapping

Inserting a genomic fragment into a vector whose function depends on the provision of splicing junctions by the fragment.

Exonuclease

An enzyme that cleaves nucleotides one at a time from the end of a polynucleotide chain; it may be specific for either the 5′ or 3′ end of DNA or RNA.

Exoribonuclease

A ribonuclease that removes terminal ribonucleotides from RNA.

Exosome

An exonuclease complex involved in nuclear processing and nuclear/cytoplasmic RNA degradation.

Expressed sequence tag (EST)

A short-sequenced fragment of a cDNA sequence that can be used to identify an actively expressed gene.

Expression vector

A cloning vehicle containing a promoter that can drive expression of an attached gene.

Extein

A sequence that remains in the mature protein that is produced by processing a precursor via protein splicing.

Extranuclear genes

Genes that reside outside the nucleus in organelles such as mitochondria and chloroplasts.

F plasmid

An episome that can be free or integrated in Escherichia coli, and that can sponsor conjugation in either form.

Facultative heterochromatin

The inert state of sequences that also exist in active copies (e.g., one mammalian X chromosome in females).

First parity rule

Rule discovered by Erwin Chargaff that applies to most regions of DNA whereby base A in one strand of the duplex is matched by a complementary base (T) in the other strand, and base G in one strand of the duplex is matched by a complementary base (C) in the other strand. Rule applies to single bases as well as to dinucleotides, trinucleotides, and oligonucleotides.

Fixation

The process by which a new allele replaces the allele that was previously predominant in a population.

Fluorescence resonant energy transfer (FRET)

A process whereby the emission from an excited fluorophore is captured and reemitted at a longer wavelength by a nearby second fluorophore whose excitation spectrum matches the emission frequency of the first fluorophore.

Fold pressure

The genome-wide pressure for single-stranded nucleic acid, whether in free form or extruded from duplex forms, to adopt secondary and higher order stem-loop structures.

Footprinting

A technique for identifying the site on DNA bound by some protein by virtue of the protection of bonds in this region against attack by nucleases.

Forward mutation

A mutation that inactivates a functional gene.

Forward strand

The strand of DNA that is synthesized continuously in the 5′ to 3′ direction.

Frameshift mutation

A genetic mutation formed through the addition or deletion of nucleotide bases such that the reading frame is thrown off. The resulting polypeptide formed is usually abnormally short or abnormally long and most likely nonfunctional.

Fully methylated

A site that is a palindromic sequence that is methylated on both strands of DNA.

Fusion proteins

Chimeric proteins that are produced due to the joining of two or more genes that originally coded for separate proteins.

γ-H2AX

Denotes the form of the histone variant H2AX when it is phosphorylated on a SQEL/Y motif at the site of a double-strand break.

G-bands

Bands generated on eukaryotic chromosomes by staining techniques that appear as a series of lateral striations. They are used for karyotyping (i.e., identifying chromosomes and chromosomal regions by the banding pattern).

G quadruplex

Nucleic acids that are rich in guanine and can fold into a four-strand structure stabilized by hydrogen bonds that can be stacked.

Gain-of-function mutation

A mutation that causes an increase in the normal gene activity. It sometimes represents acquisition of certain abnormal properties. It is often, but not always, dominant.

Gap repair

A type of DNA repair in which one DNA duplex may act as a donor of genetic information that directly replaces the corresponding sequences in the recipient duplex by a process of gap generation, strand exchange, and gap filling.

GC pressure

The tendency of a species’ genome to conform to its optimal GC content.

GC rule

Rule discovered by Erwin Chargaff that the overall proportion of guanine (G) and cytosine (C) in a genome tends to be a species-specific character and that the GC content tends to be greater in exons than in introns.

Gene cluster

A group of adjacent genes that are identical or related.

Gene conversion

The alteration of one strand of a heteroduplex DNA to make it complementary with the other strand at any position(s) where there were mispaired bases or the complete replacement of genetic material at one locus by a homologous sequence.

Gene conversion bias

Process whereby the guanine (G) and cytosine (C) content of DNA increases due to gene conversion during recombination.

Gene expression

The process by which the information in a sequence of DNA in a gene is used to produce an RNA or polypeptide, involving transcription and (for polypeptides) translation.

Gene family

A set of genes within a genome that code for related or identical proteins or RNAs. The members were derived by duplication of an ancestral gene followed by accumulation of changes in sequence between the copies. Most often the members are related but not identical.

Genetic code

The correspondence between triplets in DNA (or RNA) and amino acids in polypeptide.

Genetic drift

The chance fluctuation (without selective pressure) of the frequencies of alleles in a population.

Genetic engineering

Direct manipulation of an organism’s genome through the use of biotechnology to insert or delete genes. Often involves production and use of recombinant DNA to transfer genes between organisms.

Genetic hitchhiking

The change in frequency of a genetic variant due to its linkage to a selected variant at another locus.

Genetic map

See linkage map.

Genetic recombination

A process by which separate DNA molecules are joined into a single molecule due to such processes as crossing over or transposition.

Genome

The complete set of sequences in the genetic material of an organism. It includes the sequence of each chromosome plus any DNA in organelles.

Genome phenotype

The structure of the genome as influenced by factors other than the effects of products of its genes.

Genome-wide association study (GWAS)

Examination of a genome-wide set of genetic variants in different individuals to determine whether a particular variant is associated with a trait.

Glycosylase

A repair enzyme that removes damaged bases by cleaving the bond between the base and the sugar.

GMP-PCP

An analog of guanosine triphosphate (GTP) that cannot be hydrolyzed. It is used to test which stage in a reaction requires hydrolysis of GTP.

Gratuitous inducer

Inducers that resemble authentic inducers of transcription but that are not substrates for the induced enzymes.

Growing point

See replication fork.

Growth factor receptor

Recruits the exchange factor SOS to the cell membrane to activate the RAS protein as part of the signal transduction pathway that ultimately cases the cell to begin replication and growth.

GU-AG rule

The rule that describes the presence of these constant dinucleotides at the first two and last two positions of introns of nuclear genes.

Guide RNA

A small RNA whose sequence is complementary to the sequence of an RNA that has been edited. It is used as a template for changing the sequence of the pre-edited RNA by inserting or deleting nucleotides.

Gyrase

An enzyme that changes the number of times the two strands in a closed DNA molecule cross each other. It does this by cutting the DNA, passing DNA through the break, and then resealing the DNA.

Hairpin

An RNA sequence that can fold back on itself, forming double-stranded RNA.

Half-life (RNA)

The time taken for the concentration of a given population of RNA molecules to decrease by half, in the absence of new synthesis.

Haplotype

The particular combination of alleles in a defined region of some chromosome—in effect, the genotype in miniature. Originally used to describe combinations of major histocompatibility complex (MHC) alleles, it now may be used to describe particular combinations of restriction fragment length polymorphisms (RFLPs), single nucleotide polymorphisms (SNPs), or other markers.

Hapten

A small molecule that can elicit an immune response only when conjugated with a carrier, such as a large protein or a microbe-associated molecular pattern (MAMP).

HAT

Histone acetylase transferase, an enzyme that adds an acetate group to histone proteins.

Hb anti-Lepore

A fusion gene produced by unequal crossing over that has the N-terminal part of β globin and the C-terminal part of δ globin.

Hb Kenya

A fusion gene produced by unequal crossing over between the γ and β globin genes.

Hb Lepore

An unusual globin protein that results from unequal crossing over between the β and δ genes. The genes become fused together to produce a single β-like chain that consists of the N-terminal sequence of δ joined to the C-terminal sequence of β.

HbH disease

A condition in which there is a disproportionate amount of the abnormal tetramer β4 relative to the amount of normal hemoglobin (α2β2).

HDAC

Histone deacetylase, an enzyme that removes acetate groups from acetylated lysine amino acids in histone proteins.

Heat-shock genes

A set of loci activated in response to an increase in temperature (and other stresses to the cell). All organisms have them. Their products usually include chaperones that act on denatured proteins.

Heat-shock response

See heat-shock genes.

Helicase

An enzyme that uses energy provided by ATP hydrolysis to separate the strands of a nucleic acid duplex.

Helix-loop-helix (HLH)

The motif that is responsible for dimerization of a class of transcription factors called HLH proteins. A bHLH protein has a basic DNA-binding sequence close to the dimerization motif.

Helix-turn-helix

The motif that describes an arrangement of two α-helices that form a site that binds to DNA, one fitting into the major groove of DNA and the other lying across it.

Helper virus

A virus that provides functions absent from a defective virus, enabling the latter to complete the infective cycle during a mixed infection with the helper virus.

Hemimethylated DNA

DNA that is methylated on one strand of a target sequence that has a cytosine on each strand.

Heterochromatin

Regions of the genome that are highly condensed, are not transcribed, and are late replicating. It is divided into two types: constitutive and facultative.

Heteroduplex DNA

DNA that is generated by base pairing between complementary single strands derived from the different parental duplex molecules; it occurs during genetic recombination.

Heterogeneous nuclear RNA (hnRNA)

RNA that comprises nuclear transcripts made primarily by RNA polymerase II; it has a wide size distribution and variable stability.

Heteromultimer

A protein composed of two or more different polypeptide chains.

Heteroplasmy

Having more than one mitochondrial allelic variant in a cell.

HflA protein

An Esherichia coli gene that controls the stability of the bacteriophage CII protein during an infection which determines whether the phage will enter the lytic or lysogenic cycle.

Hfr

A bacterium that has an integrated F plasmid within its chromosome. Hfr stands for high frequency recombination, referring to the fact that chromosomal genes are transferred from an Hfr cell to an F cell much more frequently than from an F+ cell.

Highly repetitive DNA

Very short DNA sequences (typically < 100 bp) that are present many thousands of times in the genome, often organized as long regions of tandem repeats.

Histone acetyltransferase (HAT)

An enzyme that modifies histones by addition of acetyl groups; some transcriptional coactivators have this activity. Also known as lysine acetyltransferase (KAT).

Histone code

The hypothesis that combinations of specific modifications on specific histone residues act cooperatively to define chromatin function.

Histone deacetylase (HDAC)

Enzyme that removes acetyl groups from histones; may be associated with repressors of transcription.

Histone fold

A motif found in all four core histones in which three α-helices are connected by two loops.

Histone octamer

The complex of two copies each of the four different core histones (H2A, H2B, H3, and H4); DNA wraps around this complex to form the nucleosome.

Histone tails

Flexible amino- or carboxy-terminal regions of the core histones that extend beyond the surface of the nucleosome; they are sites of extensive posttranslational modification.

Histone variant

Any of a number of histones closely related to one of the core histones (H2A, H2B, H3, or H4) that can assemble into a nucleosome in the place of the related core histone; many have specialized functions or localization. There are also numerous linker variants.

Histones

Conserved DNA-binding proteins that form the basic subunit of chromatin in eukaryotes. H2A, H2B, H3, and H4 form an octameric core around which DNA coils to form a nucleosome. Linker histones are external to the nucleosome.

hnRNP

The ribonucleoprotein form of hnRNA (heterogeneous nuclear RNA) in which the hnRNA is complexed with proteins. Pre-mRNAs are not exported until processing is complete; thus, they are found only in the nucleus.

Holliday junction

An intermediate structure in homologous recombination in which the two duplexes of DNA are connected by the genetic material exchanged between two of the four strands, one from each duplex. A joint molecule is said to be resolved when nicks in the structure restore two separate DNA duplexes.

Holocentric

Type of chromosome in some species whereby the centromeres are diffuse and spread out along the entire length of the chromosome. Species with these chromosomes still make spindle fiber attachments for mitotic chromosome separation, but do not require one and only one regional or point centromere per chromosome.

Holoenzyme

(1) The DNA polymerase complex that is competent to initiate replication. (2) The RNA polymerase form that is competent to initiate transcription. It consists of the five subunits of the core enzyme (α2ββ′ω) and sigma factor.

Homeodomain

A DNA-binding motif that typifies a class of transcription factors.

Homolog

See homologous genes (homologs).

Homologous genes (homologs)

Related genes in the same species, such as alleles on homologous chromosomes or multiple genes in the same genome sharing common ancestry.

Homologous recombination

Recombination involving a reciprocal exchange of sequences of DNA, for example, between two chromosomes that carry the same genetic loci.

Homomultimer

A molecular complex (such as a protein) in which the subunits are identical.

Horizontal transfer

The transfer of DNA from one cell to another by a process other than cell division, such as bacterial conjugation.

Hotspots

A site in the genome at which the frequency of mutation (or recombination) is very much increased, usually by at least an order of magnitude relative to neighboring sites.

Housekeeping gene

A gene that is (theoretically) expressed in all cells because it provides basic functions needed for sustenance of all cell types.

Human artificial chromosome (HAC)

An engineered mini-chromosome that can act as a new chromosome in a human cell. The new chromosome has the potential to act as a gene delivery vector in humans.

Human leukocyte antigen (HLA)

Gene complex that encodes the major histocompatibility complex (MHC) proteins in humans.

Hybrid dysgenesis

The inability of certain strains of Drosophila melanogaster to interbreed, because the hybrids are sterile (although otherwise they may be phenotypically normal).

Hybridization

The pairing of complementary RNA and DNA strands to give an RNA–DNA hybrid.

Hydrops fetalis

A fatal disease resulting from the absence of the hemoglobin α gene.

Hypersensitive site

A short region of chromatin detected by its extreme sensitivity to cleavage by DNase I and other nucleases; it comprises an area from which nucleosomes are excluded.

IF-1

A bacterial initiation factor that stabilizes the initiation complex for polypeptide translation.

IF-2

A bacterial initiation factor that binds the initiator tRNA to the initiation complex for polypeptide translation.

IF-3

A bacterial initiation factor required for 30S ribosomal subunits to bind to initiation sites in mRNA. It also prevents 30S subunits from binding to 50S ribosomal subunits.

IgA

One of the five classes of immunoglobulin that are defined by the type of CH region. These immunoglobulins are abundant on mucosal surfaces and on secretions in the respiratory tract and the intestine.

IgE

One of the five classes of immunoglobulin that are defined by the type of CH region. These immunoglobulins are associated with the allergic response and with defense against parasites.

IgG

One of the five classes of immunoglobulin that are defined by the type of CH region. These immunoglobulins are the most abundant immunoglobulins in circulation and are able to pass into extravascular spaces.

Immediate early genes

Genes in phage lambda that are equivalent to the early class of other phages. They are transcribed immediately upon infection by the host RNA polymerase.

Immunity

In phages, the ability of a prophage to prevent another phage of the same type from infecting a cell. In plasmids, the ability of a plasmid to prevent another of the same type from becoming established in a cell. It can also refer to the ability of certain transposons to prevent others of the same type from transposing to the same DNA molecule.

Immunity region

A segment of the phage genome that enables a prophage to inhibit additional phage of the same type from infecting the bacterium. This region has a gene that encodes for the repressor, as well as the sites to which the repressor binds.

Immunoglobulin (Ig)

A protein (antibody) that is produced by B cells and in large amounts by plasma cells and that binds to a particular antigen.

Immunoglobulin heavy (H) chain

One of two types of identical subunits in an antibody tetramer. Each antibody contains two of them. The –NH2 end forms part of the antigen recognition site, whereas the –COOH end determines the class or isotype.

Immunoglobulin light (L) chain

One of two types of identical subunits in an antibody tetramer. Each antibody contains two of them. The –H2 end forms part of the antigen recognition site, whereas the –COOH end determines the class, κ or λ.

Imprecise excision

Occurs when the transposon removes itself from the original insertion site but leaves behind some of its sequence.

Imprinting

A change in a gene that occurs during passage through the sperm or egg with the result that the paternal and maternal alleles have different properties in the very early embryo. This is caused by methylation of DNA.

In situ hybridization

Hybridization performed by denaturing the DNA of cells squashed on a microscope slide so that reaction is possible with an added single-stranded RNA or DNA; the added preparation is radioactively labeled and its hybridization is followed by autoradiography.

In vitro complementation

A functional assay used to identify components of a process. The reaction is reconstructed using extracts from a mutant cell. Fractions from wild-type cells are then tested for restoration of activity.

Indirect end labeling

A technique for examining the organization of DNA by making a cut at a specific site and identifying all fragments containing the sequence adjacent to one side of the cut; it reveals the distance from the cut to the next break(s) in DNA.

Induced mutations

Mutations that result from the action of a mutagen. The mutagen may act directly on the bases in DNA or it may act indirectly to trigger a pathway that leads to a change in DNA sequence.

Inducer

A molecule that triggers gene transcription by binding to a regulator protein.

Inducible gene

A gene that is turned on by the presence of its substrate.

Induction

The ability to synthesize certain enzymes only when their substrates are present; applied to gene expression, it refers to switching on transcription as a result of interaction of the inducer with the regulator protein.

Induction of phage

A phage’s entry into the lytic (infective) cycle as a result of destruction of the lysogenic repressor, which leads to excision of free phage DNA from the bacterial chromosome.

Initiation

The stages of transcription up to synthesis of the first bond in RNA. This includes binding of RNA polymerase to the promoter and melting a short region of DNA into single strands.

Initiation codon

A special codon (usually AUG) used to start synthesis of a polypeptide.

Initiation factors (IFs)

Proteins that associate with the small subunit of the ribosome specifically at the stage of initiation of polypeptide translation.

Initiator (Inr)

The sequence at the start point of transcription of a pol II promoter between −3 and +5 that has the general sequence Py2CAPy5.

Innate immunity

A response triggered by receptors whose specificity is predefined for certain common motifs found in bacteria and other infectious agents. The receptor that triggers the response is typically a member of the Toll-like receptor (TLR) family, and the pathway resembles the signaling pathway triggered by the Toll receptor of Drosophila. The pathway culminates in activation of transcription factors that induce the expression of genes, whose products inactivate the infective agent, typically by permeabilizing its membrane.

Insert

A piece of DNA inserted into a larger DNA vector, such as a plasmid, through recombinant DNA techniques.

Insertion sequence (IS)

A small bacterial transposon that carries only the genes needed for its own transposition.

Insulator

A sequence that prevents an activating or inactivating effect from passing from one side to the other.

Integrase

An enzyme that is responsible for a site-specific recombination that inserts one molecule of DNA into another.

Integration

Insertion of a viral or another DNA sequence into a host genome as a region covalently linked on either side to the host sequences.

Intein

The part that is removed from a protein that is processed by protein splicing.

Interactome

The complete set of protein complexes/protein–protein interactions present in a cell, tissue, or organism.

Interallelic complementation

The change in the properties of a heteromultimeric protein brought about by the interaction of subunits coded by two different mutant alleles; the mixed protein may be more or less active than the protein consisting of subunits of only one or the other type.

Interbands

The relatively dispersed regions of polytene chromosomes that lie between the bands.

Intercistronic region

The distance between the termination codon of one gene and the initiation codon of the next gene.

Intergenic control region 1 (IGCR1)

An insulator element characterized by two CTCF binding sites that is located between the VH and DHJH regions. Helps to equalize antibody repertoires by suppressing transcription of proximal VH regions and their recombination with DH elements that have not yet joined with JH regions.

Internal ribosome entry site (IRES)

A eukaryotic messenger RNA sequence that allows a ribosome to initiate polypeptide translation without migrating from the 5′ end.

Interrupted gene

A gene in which the coding sequence is not continuous due to the presence of introns.

Intrinsic terminator

Terminators that are able to terminate transcription by bacterial RNA polymerase in the absence of any additional factors.

Intron

A segment of DNA that is transcribed but later removed from within the transcript by splicing together the sequences (exons) on either side of it.

Intron definition

The process in which a pair of splicing sites are recognized by interactions involving only the 5′ site and the branchpoint/3′ site.

Intron homing

The ability of certain introns to insert themselves into a target DNA. The reaction is specific for a single target sequence.

Introns early hypothesis

The hypothesis that the earliest genes contained introns and some genes subsequently lost them.

Introns late hypothesis

The hypothesis that the earliest genes did not contain introns, and that introns were subsequently added to some genes.

Inversely palindromic

Two different segments of the double helix that read the same but in opposite directions; that is, a sequence of nucleotides is followed downstream by its reverse complement.

Inverted terminal repeats

The short, related or identical sequences present in reverse orientation at the ends of some transposons.

IRES

See internal ribosome entry site (IRES).

Iron-response element (IRE)

A cis sequence found in certain mRNAs whose stability or translation is regulated by cellular iron concentration.

Isoaccepting tRNAs

See cognate tRNAs.

Isoelectric focusing

Technique that separates molecules based on their isoelectric point, which is the pH at which a protein has no net charge. Often performed on proteins in gels.

Isopycnic banding

The formation of one or more bands of molecules of the same density during isopycnic centrifugation.

Isoschizomers

Different restriction enzymes that share the same recognition sequence.

J (joining) segment

Gene segments that code sequences in the immunoglobulin and T cell receptor loci. They lie as the only element or in clusters between the variable (V) and constant (C) gene segment clusters.

Joint molecule

A pair of DNA duplexes that are connected together through a reciprocal exchange of genetic material.

Junk DNA

Term used to describe the excess of DNA in some genomes that lack any apparent function.

KAT

Lysine acetyltransferase; an enzyme that transfers an acetate group to a lysine amino acid.

Kinetic proofreading

A proofreading mechanism that depends on incorrect events proceeding more slowly than correct events, so that incorrect events are reversed before a subunit is added to a polymeric chain.

Kinetochore

A small organelle associated with the surface of the centromere that attaches a chromosome to the microtubules of the mitotic spindle. Each mitotic chromosome contains two “sisters” that are positioned on opposite sides of its centromere and face in opposite directions.

Kirromycin

An antibiotic that inhibits protein synthesis by acting on EF-Tu.

Klenow fragment

A large protein fragment (68 kD) produced when DNA polymerase I is cleaved by a protease. It is used in synthetic reactions in vitro. It retains polymerase and proofreading 3′–5′ exonuclease activities.

Knockdown

A process by which a gene is downregulated by introducing a silencing vector or molecule to reduce the expression (usually translation) of the target gene.

Knock-in

A process similar to a knockout, in which new genes or genes containing more subtle mutations are inserted into the genome.

Knockout

A process in which a functional gene is eliminated, usually by replacing most of the coding sequence with a selectable marker in vitro and transferring the altered gene to the genome by homologous recombination.

Kuru

A human neurological disease caused by prions. It may be caused by eating infected brains.

lac repressor

A negative gene regulator encoded by the lacI gene that turns off the lac operon.

Lagging strand

The strand of DNA that must grow overall in the 3′ to 5′ direction and that is synthesized discontinuously in the form of short fragments (5′–3′) that are later connected covalently.

Lampbrush chromosomes

The extremely extended meiotic bivalents of certain amphibian oocytes.

Lariat

An intermediate in RNA splicing in which a circular structure with a tail is created by a 5′ to 2′ bond.

Late genes

Genes transcribed when phage DNA is being replicated. They encode components of the phage particle.

Late infection

The part of the phage lytic cycle from DNA replication to lysis of the cell. During this time, the DNA is replicated and structural components of the phage particle are synthesized.

Lateral element

A structure in the synaptonemal complex that forms when a pair of sister chromatids condenses on to an axial element.

LCR

See locus control region (LCR).

Leader (5′ UTR)

The untranslated sequence at the 5′ end of mRNA that precedes the initiation codon.

Leader peptide

The product that would result from translation of a short coding sequence used to regulate transcription of an operon by controlling ribosome movement.

Leading strand

The strand of DNA that is synthesized continuously in the 5′ to 3′ direction.

Leaky mutations

A less severe type of mutation where the amino acid substitution does not completely deactivate a certain function of the protein, but rather decreases its function or makes it less effective.

Leghemoglobin

A hemoprotein that acts as an oxygen carrier in the nitrogen-fixing root nodules of leguminous plants. Facilitates the diffusion of oxygen in order to promote nitrogen fixation.

Lesion bypass

Replication by an error-prone DNA polymerase on a template that contains a damaged base. The polymerase can incorporate a noncomplementary base into the daughter strand.

Leucine-rich region

A motif found in the extracellular domains of some surface receptors in animal and plant cells that consists of repeating stretches of 20 to 30 amino acids that are unusually rich in the hydrophobic amino acid leucine. These repeats are frequently involved in the formation of protein–protein interactions.

Leucine zipper

A dimerization motif that is found in a class of transcription factors.

Licensing factor

A factor located in the nucleus and necessary for replication; it is inactivated or destroyed after one round of replication. New factors must be provided for further rounds of replication to occur.

lincRNA

A type of hnRNA; long intergenic noncoding RNA.

LINEs

See long-interspersed nuclear elements (LINEs).

Linkage

The tendency of genes to be inherited together as a result of their location on the same chromosome; measured by percent recombination between loci.

Linkage disequilibrium

A nonrandom association between alleles at two different loci, often as a result of linkage.

Linkage map

A map of the positions of loci or other genetic markers on a chromosome obtained by measuring recombination frequencies between markers.

Linker DNA

Nonnucleosomal DNA present between nucleosomes.

Linker histones

A family of histones (such as histone H1) that are not components of the nucleosome core; linker histones bind nucleosomes and/or linker DNA and promote 30-nm fiber formation.

Linking number (L)

In a closed molecule of DNA, the number of times one strand crosses over another in space.

Linking number paradox

The discrepancy between the existence of –1.67 supercoils in the path of DNA on the nucleosome compared with the measurement of –1 supercoil released when the restraining protein is removed.

Lipopolysaccharide (LPS)

Large molecules consisting of a lipid and a polysaccharide joined by a covalent bond; they are found in the outer membrane of Gram-negative bacteria, act as endotoxins, and elicit strong immune responses in animals. Also known as lipoglycans.

Liposome

A spherical vesicle with at least one lipid bilayer that can be used to introduce nucleic acids into targeted cells.

Locus

The position on a chromosome at which the gene for a particular trait resides; it may be occupied by any one of the alleles for the gene.

Locus control region (LCR)

The region that is required for the expression of several genes in a domain.

Long-interspersed nuclear elements (LINEs)

A major class of retrotransposons that occupy approximately 21% of the human genome (see also retrotransposon).

Long noncoding RNA (lncRNA)

Evolutionarily conserved noncoding RNA molecules that are longer than 200 nucleotides and are located within the intergenic loci or regions overlapping antisense transcripts of protein coding genes. They are involved in numerous cellular functions, including transcriptional regulation, RNA processing, RNA modification, and epigenetic silencing. They have recently been shown to play an important role in the targeting of the class switch recombination machinery.

Long terminal repeat (LTR)

The sequence that is repeated at each end of the provirus (integrated retroviral sequence).

Loss-of-function mutation

A mutation that eliminates or reduces the activity of a gene. It is often, but not always, recessive.

LTR

See long terminal repeat (LTR).

Luxury gene

A gene encoding a specialized function, synthesized (usually) in large amounts in particular cell types.

Lyase

A repair enzyme (usually also a glycosylase) that opens the sugar ring at the site of a damaged base.

Lysine (K) acetyltransferase (KAT)

An enzyme (typically present in large complexes) that acetylates lysine residues in histones (or other proteins). Previously known as histone acetyltransferase (HAT).

Lysis

The death of bacteria at the end of a phage infective cycle when they burst open to release the progeny of an infecting phage (because phage enzymes disrupt the bacterium’s cytoplasmic membrane or cell wall). The same term also applies to eukaryotic cells (e.g., when infected cells are attacked by the immune system).

Lysogeny

The ability of a phage to survive in a bacterium as a stable prophage component of the bacterial genome.

Lytic infection

Infection of a bacterium by a phage that ends in the destruction of the bacterium with release of progeny phage.

Maintenance methyltransferase

An enzyme that adds a methyl group to a target site that is already hemimethylated.

Macrodomains

Large contiguous regions on chromosomes that appear to act as independent units. Four such regions have been identified in Escherichia coli.

Major groove

A fissure running the length of the DNA double helix that is 22 Å across.

Major histocompatibility complex (MHC)

A chromosomal region containing genes that are involved in the immune response. The genes encode proteins for antigen presentation, cytokines, and complement, as well as other functions. It is highly polymorphic. Its genes and proteins are divided into three classes.

Male-specific region

Region on the Y chromosome that does not undergo crossing over with the X chromosome. Contains three types of sequences: X-transposed sequences, X-degenerate segments, and ampliconic segments.

Maternal inheritance

The preferential survival in the progeny of genetic markers provided by one parent.

Maternal mRNA granules

Oocyte particles containing translationally repressed mRNAs awaiting activation later in development.

Mating-type cassette

Yeast mating type is determined by a single active locus (the active cassette) and two inactive copies of the locus (the silent cassettes). Mating type is changed when an active cassette of one type is replaced by a silent cassette of the other type.

Matrix attachment region (MAR)

A region of DNA that attaches to the nuclear matrix. It is also known as a scaffold attachment site (SAR).

Maturase

A protein encoded by a group I or group II intron that is needed to assist the RNA to form the active conformation that is required for self-splicing.

Mature transcript

A modified RNA transcript. Modification may include the removal of intron sequences and alterations to the 5′ and 3′ ends.

MCS

See multiple cloning site (MCS).

Mediator

A large protein complex associated with yeast RNA polymerase II. It contains factors that are necessary for transcription from many or most promoters.

Melting temperature

The midpoint of the temperature range over which the strands of DNA separate.

Messenger RNA (mRNA)

The intermediate that represents one strand of a gene coding for polypeptide. Its coding region is related to the polypeptide sequence by the triplet genetic code.

MHC

See major histocompatibility complex (MHC).

Microarray

An arrayed series of thousands of tiny DNA oligonucleotide samples imprinted on a small chip. mRNAs can be hybridized to microarrays to assess the amount and level of gene expression.

Microbe-associated molecular patterns (MAMPs)

Broadly conserved microbial components, including bacterial flagellin and lipopolysaccharides, that are recognized by pattern-recognition receptors, which critically initiate innate immune responses.

Micrococcal nuclease (MNase)

An endonuclease that cleaves DNA; in chromatin, DNA is cleaved preferentially between nucleosomes.

Microinjection

Technique that uses a small glass micropipette to insert genetic material, proteins, or macromolecules directly into cell cytoplasm, an embryo, or a nucleus.

microRNA (miRNA)

Small (21 to 23 nucleotides), evolutionarily conserved noncoding RNAs that function in RNA silencing and posttranscriptional regulation of gene expression. Bind to complementary sequences within the 3′ untranslated region (UTR) of their target mRNAs and negatively regulate protein expression by accelerating mRNA degradation and inhibiting mRNA translation.

Microsatellite

DNAs consisting of tandem repetitions of very short (typically less than 10 bp) units repeated a small number of times.

Microtubule organizing center (MTOC)

The structure in eukaryotic cells from which the microtubules emerge. It organizes flagella/cilia and the mitotic and meiotic spindle apparatus.

Middle genes

Phage genes that are regulated by the proteins encoded by early genes. Some proteins coded by them catalyze replication of the phage DNA; others regulate the expression of a later set of genes.

Minicell

An anucleate bacterial (Escherichia coli) cell produced by a division that generates a cytoplasm without a nucleus.

Minisatellite

DNAs consisting of tandemly repeated copies of a short, repeating sequence, with more repeat copies than a microsatellite but fewer than a satellite. The length of the repeating unit is measured in tens of base pairs. The number of repeats varies between individual genomes.

Minor groove

A fissure running the length of the DNA double helix that is 12 Å across.

Minus-strand DNA

The single-stranded DNA sequence that is complementary to the viral RNA genome of a plus-strand virus.

Mismatch repair (MMR)

Repair that corrects recently inserted bases that do not pair properly. The process preferentially corrects the sequence of the daughter strand by distinguishing the daughter strand and parental strand, sometimes on the basis of their states of methylation.

Missense suppressor

A suppressor that codes for a tRNA that has been mutated to recognize a different codon. By inserting a different amino acid at a mutant codon, the tRNA suppresses the effect of the original mutation.

Moderately repetitive DNA

Sequences of DNA that are repeated 10 to 1,000 times throughout the genome and interspersed with other sequences.

Molecular clock

An approximately constant rate of evolution that occurs in DNA sequences, such as by the genetic drift of neutral mutations.

Monocistronic mRNA

mRNA that codes for one polypeptide.

mRNA decay

mRNA degradation, assuming that the degradation process is stochastic.

mtDNA

Mitochondrial DNA.

Multicopy replication control

Occurs when the control system allows the plasmid to exist in more than one copy per individual bacterial cell.

Multiforked chromosome

A bacterial chromosome that has more than one set of replication forks, because a second initiation has occurred before the first cycle of replication has been completed.

Multiple alleles

A non-Mendelian pattern of inheritance where more than two alleles code for a trait. In most cases, the result is that more than two phenotypes are possible based on the dominance pattern of the individual alleles.

Multiple cloning site (MCS)

A sequence of DNA containing a series of tandem restriction endonuclease sites that can be used in cloning vectors for creating recombinant molecules.

Mutagens

Substances that increase the rate of mutation by inducing changes in DNA sequence, directly or indirectly.

Mutation hotspot

A site in the genome at which the frequency of mutation (or recombination) is very much increased, usually by at least an order of magnitude relative to neighboring sites.

Mutator

A mutation or a mutated gene that increases the basal level of mutation. Such genes often code for proteins that are involved in repairing damaged DNA.

Myoglobin

A small hemoprotein found in muscle cells that binds to oxygen. Highly conserved protein, containing 153 amino acids and the iron cofactor heme.

N nucleotide

A short, nontemplated sequence that is added randomly by the enzyme TdT at coding joints during rearrangement of immunoglobulin and T cell receptor genes. They increase the degree of diversity of the antigen receptors’ V(D)J sequences.

n – 1 rule

The rule that states that only one X chromosome is active in female mammalian cells; any others are inactivated.

N-formyl-methionyl-tRNA

The aminoacyl-tRNA that initiates bacterial polypeptide translation. The amino group of the methionine is formylated.

Nascent RNA

A ribonucleotide chain that is still being synthesized so that its 3′ end is paired with DNA where RNA polymerase is elongating.

ncRNAs

See noncoding RNAs (ncRNAs).

Negative complementation

Occurs when interallelic complementation allows a mutant subunit to suppress the activity of a wild-type subunit in a multimeric protein.

Negative control

A mechanism of gene regulation in which a regulator is required to turn the gene off.

Negative inducible

A control circuit in which an active repressor is inactivated by the substrate of the operon.

Negative repressible

A control circuit in which an inactive repressor is activated by the product of the operon.

Negative (purifying) selection

Type of selection whereby an individual with a disadvantageous mutation is less able to survive and produce fertile progeny relative to those without the mutation. Results in selective removal of rare, deleterious alleles from the population.

Negative supercoiling

The left-handed, double-helical form of DNA. Creates tension in the DNA that is relieved by the unwinding of the double helix. The result is the generation of a region in which the two strands of DNA have separated.

Nested gene

A gene located within an intron of another gene.

Neuronal granules

Particles containing translationally repressed mRNAs in transit to final cell destinations.

Neutral mutation

A mutation that has no significant effect on evolutionary fitness and usually has no effect on the phenotype.

Neutral substitutions

Substitutions in a protein that cause changes in amino acids that do not affect activity.

NF-κB

A protein complex that functions as a transcription factor. Is found in most cells and mediates signaling in response to a variety of immunological, inflammatory, and microbial stimuli or viral antigens. Dysregulation of its expression has been associated with cancer, inflammatory and autoimmune diseases, and abnormal immune system development.

Nick translation

The ability of Escherichia coli DNA polymerase I to use a nick as a starting point from which one strand of a duplex DNA can be degraded and replaced by resynthesis of new material; it is used to introduce radioactively labeled nucleotides into DNA in vitro.

No-go decay (NGD)

A pathway that rapidly degrades an mRNA with ribosomes stalled in its coding region.

Non-Mendelian inheritance

A pattern of inheritance that does not follow that expected by Mendelian principles (each parent contributing a single allele to offspring). This pattern of inheritance is exhibited by extranuclear genes.

Nonallelic genes

Two (or more) copies of the same gene that are present at different locations in the genome (contrasted with alleles, which are copies of the same gene derived from different parents and present at the same location on the homologous chromosomes).

Nonautonomous transposons

A transposon that encodes a nonfunctional transposase; it can transpose only in the presence of a trans-acting autonomous member of the same family.

Noncoding RNAs (ncRNAs)

RNA that does not contain an open reading frame.

Nonhistone

Any structural protein found in a chromosome except one of the histones.

Nonhomologous end joining (NHEJ)

The process that ligates blunt ends. It is common to many repair pathways and to certain recombination pathways (such as immunoglobulin recombination).

Nonprocessed pseudogene

An inactive gene copy that arises by incomplete gene duplication or duplication followed by inactivating mutations.

Nonproductive rearrangement

Occurs as a result of the recombination of V(D)J gene segments if the rearranged gene segments are not in the correct reading frame. It occurs when nucleotide addition or subtraction disrupts the reading frame or when a functional protein is not produced.

Nonrepetitive DNA

DNA that is unique (present only once) in a genome.

Nonreplicative transposition

The movement of a transposon that leaves a donor site (usually generating a double-strand break) and moves to a new site.

Nonsense-mediated decay (NMD)

A pathway that degrades an mRNA that has a nonsense mutation prior to the last exon.

Nonsense suppressor

A gene coding for a mutant tRNA that is able to respond to one or more of the termination codons and insert an amino acid at that site.

Nonstop decay (NSD)

A pathway that rapidly degrades an mRNA that lacks an in-frame termination codon.

Nonsynonymous mutation

Mutations have altered the amino acid that is encoded.

Nontemplate strand

See coding strand.

Nontranscribed spacer

The region between transcription units in a tandem gene cluster.

Nopaline plasmids

Ti plasmids of Agrobacterium tumefaciens that carry genes for the synthesis of the opine nopaline. They retain the ability to differentiate into early embryonic structures.

Northern blotting

Technique used to detect the presence of particular mRNA in a sample. RNA are separated by size and detected on a membrane using a hybridization probe with a base sequence complementary to the sequence of the target mRNA.

Nuclease

An enzyme that can break a phosphodiester bond.

Nucleation center

A duplex hairpin in TMV (tobacco mosaic virus) in which assembly of coat protein with RNA is initiated.

Nucleoid

The structure in a prokaryotic cell that contains the genome. The DNA is bound to proteins and is not enclosed by a membrane.

Nucleolar organizer

The region of a chromosome carrying genes coding for rRNA.

Nucleolus

A discrete region of the nucleus where ribosomes are produced.

Nucleoside

A molecule consisting of a purine or pyrimidine base linked to the 1′ carbon of a pentose sugar.

Nucleosome

The basic structural subunit of chromatin, consisting of approximately 200 bp of DNA and an octamer of histone proteins.

Nucleosome positioning

The placement of nucleosomes at defined sequences of DNA instead of at random locations with regard to sequence.

Nucleotide

A molecule consisting of a purine or pyrimidine base linked to the 1′ carbon of a pentose sugar and a phosphate group linked to either the 5′ or 3′ (or, rarely, 2′) carbon of the sugar.

Nucleotide excision repair (NER)

A repair pathway that entails excision of a large region of DNA containing a site of (typically helix-distorting) damage such as ultraviolet-induced photoproducts. In humans, defects in XP genes involved in this repair process result in the disease xeroderma pigmentosum.

Null mutation

A mutation that completely eliminates the function of a gene.

Nut (N utilization) site

The sequence of DNA that is recognized by the N antitermination actor.

Ochre codon

The triplet UAA, one of the three termination codons that end polypeptide translation.

Octopine plasmids

Plasmids of Agrobacterium tumefaciens that carry genes coding the synthesis of opines of the octopine type. The tumors are undifferentiated.

Okazaki fragment

Short stretches of 1,000 to 2,000 bases produced during discontinuous replication; they are later joined into a covalently intact strand.

Oligo(A) tail

A short poly(A) tail, generally referring to a stretch of less than 15 adenylates.

Oncogenes

A gene that when mutated may cause cancer. The mutation is a dominant gain of function mutation.

One gene–one enzyme hypothesis

Beadle and Tatum’s hypothesis that a gene is responsible for the production of a single enzyme.

One gene–one polypeptide hypothesis

A modified version of the not generally correct one gene–one enzyme hypothesis; the hypothesis that a gene is responsible for the production of a single polypeptide.

Opal codon

The triplet UGA, one of the three termination codons that end polypeptide translation. It has evolved to code for an amino acid in a small number of organisms or organelles.

Open complex

The stage of initiation of transcription when RNA polymerase causes the two strands of DNA to separate to form the “transcription bubble.”

Open reading frame (ORF)

A sequence of DNA consisting of triplets that can be translated into amino acids starting with an initiation codon and ending with a termination codon.

Operator

The site on DNA at which a repressor protein binds to prevent transcription from initiating at the adjacent promoter.

Operon

A unit of bacterial gene expression and regulation, including structural genes and control elements in DNA recognized by regulator gene product(s).

Opine

A derivative of arginine that is synthesized by plant cells infected with crown gall disease.

ori

A sequence of DNA at which replication is initiated.

Origin

A sequence of DNA at which replication is initiated.

Origin recognition complex (ORC)

Found in eukaryotes, a multiprotein complex that binds to the replication origin, the autonomously replicating sequence (ARS), and remains associated with it throughout the cell cycle.

Orthologous genes (orthologs)

Related genes in different species.

Outgroup

In comparative genomics, a species that is less closely related to the species being investigated, but close enough to show substantial similarity.

Overlapping gene

A gene in which part of the sequence is found within part of the sequence of another gene.

Overwound

B-form DNA that has more than 10.5 base pairs per turn of the helix.

P element

A type of transposon in Drosophila melanogaster.

P nucleotide

A short palindromic (inverted repeat) sequence that is generated during rearrangement of immunoglobulin and T cell receptor V(D)J gene segments. They are produced at coding joints when RAG proteins cleave the hairpin ends generated during V(D)J rearrangement.

P site

The site in the ribosome that is occupied by peptidyl-tRNA, the tRNA carrying the nascent polypeptide chain, still paired with the codon to which it is bound in the A site.

Packing ratio

The ratio of the length of DNA to the unit length of the fiber containing it.

Palindrome

A symmetrical sequence that reads the same forward and backward.

Paralogous genes

Genes that share a common ancestry due to gene duplication.

Paralogs

Genes that share a common ancestry due to gene duplication.

Partition complex

The complex of ParB (and IHF in some cases) with parS in some plasmids, such as P1. Its formation enables further molecules of ParB to bind cooperatively, resulting in the formation of a very large protein–DNA complex.

Patch recombinant

DNA that results from a Holliday junction being resolved by cutting the exchanged strands. The duplex is largely unchanged, except for a DNA sequence on one strand that came from the homologous chromosome.

Pathogenicity islands

DNA segments that are present in pathogenic bacterial genomes but absent in their nonpathogenic relatives.

Pattern recognition receptors (PRRs)

Receptors that recognize highly conserved microbe-associated molecular patterns (MAMPs) found in bacteria, viruses, and other infectious agents. They are found on innate immune cells such as neutrophils, macrophages, and dendritic cells (DCs) and cause the pathogen to be phagocytosed and killed. Some are also expressed in cells important for adaptive immune responses, such as all B lymphocytes and some T lymphocyte subsets.

Peptidyl transferase

The activity of the large ribosomal subunit that synthesizes a peptide bond when an amino acid is added to a growing polypeptide chain. The actual catalytic activity is a property of the rRNA.

Peptidyl-tRNA

The tRNA to which the nascent polypeptide chain has been transferred following peptide bond synthesis during polypeptide translation.

Phage

An abbreviation of bacteriophage or bacterial virus.

Phosphatase

An enzyme that can break a phosphomonoester bond, cleaving a terminal phosphate.

Phosphorelay

A pathway in which a phosphate group is passed along a series of proteins.

Photoreactivation

A repair mechanism that uses a white light–dependent enzyme to split cyclobutane pyrimidine dimers formed by ultraviolet light.

Pili

A surface appendage on a bacterium that allows the bacterium to attach to other bacterial cells. It appears as a short, thin, flexible rod. During conjugation, it is used to transfer DNA from one bacterium to another.

Pilin

The subunit that is polymerized into the pilus in bacteria.

Pioneer round of translation

The first translation event for a newly synthesized and exported mRNA.

piRNA

Piwi RNA, a special form of miRNA found in germ cells.

Plant homeodomain (PHD)

Domain of approximately 50 to 80 amino acids. Many of these domains bind various methylation states of lysines in histones. Also called the PHD finger.

Plasmid

Circular, extrachromosomal DNA. It is autonomous and can replicate itself.

Plus-strand DNA

The strand of the duplex sequence representing a retrovirus that has the same sequence as that of the RNA.

Plus-strand virus

A virus with a single-stranded nucleic acid genome whose sequence directly codes for the protein products.

Point mutation

A mutation within a gene in which only one nucleotide base is altered through substitution, insertion, or deletion.

Polarity

The effect of a mutation in one gene in influencing the expression (at transcription or translation) of subsequent genes in the same transcription unit.

Poly(A) tail

A stretch of adenylic acid that is added to the 3′ end of mRNA following its synthesis.

Poly(A)-binding protein (PABP)

The protein that binds to the 3′ stretch of poly(A) on a eukaryotic mRNA.

Poly(A) nuclease (or deadenylase)

An exoribonuclease that is specific for digesting poly(A) tails.

Poly(A) polymerase (PAP)

The enzyme that adds the stretch of polyadenylic acid to the 3′ end of eukaryotic mRNA. It does not use a template.

Polycistronic mRNA

mRNA that includes coding regions representing more than one gene.

Polymerase chain reaction (PCR)

A process for the amplification of a defined nucleic acid section through repeated thermal cycles of denaturation, annealing, and polymerase extension.

Polymerase switch

The transition from initiation to elongation of DNA replication by substitution of an enzyme that will extend the chain. On the leading strand, this is DNA polymerase ε; on the lagging strand this is DNA polymerase δ.

Polymorphism

The simultaneous occurrence in the population of alleles showing variations at a given position.

Polynucleotide

A chain of nucleotides, such as DNA or RNA.

Polyploidization

An event that results in an increase in the number of haploid chromosome sets in the cell, typically from diploid to tetraploid, and usually as a result of fertilization of unreduced gametes.

Polyribosome (or polysome)

An mRNA that is simultaneously being translated by multiple ribosomes.

Polysome

See polyribosome.

Polytene chromosomes

Chromosomes that are generated by successive replications of a chromosome set without separation of the replicas.

Position-effect variegation (PEV)

Silencing of gene expression that occurs as the result of proximity to heterochromatin.

Positional information

The localization of certain cell structures in specific places.

Positive control

This describes a system in which a gene is not expressed unless some action turns it on.

Positive inducible

A control circuit in which an inactive positive regulator is converted into an active regulator by the substrate of the operon.

Positive repressible

A control circuit in which an active positive regulator is inactivated by the product of the operon.

Positive selection

Type of selection whereby an individual with an advantageous mutation survives (i.e., is able to produce more fertile progeny) relative to those without the mutation.

Positive supercoiling

The right-handed, double-helical form of DNA. Both strands of the double helix coil together in the same direction as the coiling of the strands.

Postreplication complex

A protein–DNA complex in Saccharomyces cerevisiae that consists of the ORC complex bound to the origin.

Posttranscriptional modification

All changes made to the nucleotides of RNA after their initial incorporation into the polynucleotide chain.

ppGpp

Guanosine tetraphosphate, a signaling molecule in bacteria to reduce transcription of rRNA (and some other) genes when the amount of acylated tRNA is reduced.

Pre-mRNA

The nuclear transcript that is processed by modification and splicing to give an mRNA.

Precise excision

The removal of a transposon plus one of the duplicated target sequences from the chromosome. Such an event can restore function at the site where the transposon inserted.

Preinitiation complex

In eurkaryotic transcription, the assembly of transcription factors at the promoter before binding of RNA polymerase.

Premature termination

The termination of protein or of RNA synthesis before the chain has been completed. In translation it can be caused by mutations that create stop codons within the coding region. In RNA synthesis it is caused by various events that act on RNA polymerase.

Prereplication complex

A protein–DNA complex at the origin in Saccharomyces cerevisiae that is required for DNA replication. The complex contains the ORC complex, Cdc6, and the MCM proteins.

Presynaptic filaments

Single-stranded DNA bound in a helical nucleoprotein filament with a strand transfer protein such as Rad51 or RecA.

Primary RNA transcript

The initial product of transcription that consists of an RNA extending from the promoter to the terminator and possesses the original 3′ and 5′ ends.

Primase

A type of RNA polymerase that synthesizes short segments of RNA that will be used as primers for DNA replication.

Primer

A short sequence (often of RNA) that is paired with one strand of DNA and that provides a free 3′–OH end at which a DNA polymerase starts synthesis of a deoxyribonucleotide chain.

Primosome

A protein complex required to synthesize an RNA primer during replication.

Prion

A proteinaceous infectious agent that behaves as an inheritable trait, although it contains no nucleic acid. Examples are PrPSc, the agent of scrapie in sheep and bovine spongiform encephalopathy, and Psi, which confers an inherited state in yeast.

pRNA

Promoter upstream transcripts, short RNAs produced from both strands of DNA from active promoters.

Probe

A radioactive nucleic acid, DNA or RNA, used to identify a complementary fragment.

Processed pseudogene

An inactive gene copy that lacks introns, contrasted with the interrupted structure of the active gene. Such genes originate by reverse transcription of mRNA and insertion of a duplex copy into the genome.

Processing body (PB)

A particle containing multiple mRNAs and proteins involved in mRNA degradation and translational repression, occurring in many copies in the cytoplasm of eukaryotes.

Processive (nuclease)

An enzyme that remains associated with the substrate while catalyzing the sequential removal of nucleotides.

Processivity

The ability of an enzyme to perform multiple catalytic cycles with a single template instead of dissociating after each cycle.

Productive rearrangement

Occurs as a result of the recombination of V(D)J gene segments if all the rearranged gene segments are in the correct reading frame.

Programmed cell death (PCD)

Apoptosis triggered by a cellular stimulus through a signal transduction pathway.

Programmed frameshifting

Frameshifting that is required for expression of the polypeptide sequences encoded beyond a specific site at which a +1 or −1 frameshift occurs at some typical frequency.

Promoter

A region of DNA where RNA polymerase binds to initiate transcription.

PROMPTs

Promoter upstream transcripts, short RNAs produced from both strands of DNA from active promoters.

Proofreading

A mechanism for correcting errors in DNA synthesis that involves scrutiny of individual units after they have been added to the chain.

Prophage

A phage genome covalently integrated as a linear part of the bacterial chromosome.

Protein splicing

The autocatalytic process by which an intein is removed from a protein and the exteins on either side become connected by a standard peptide bond.

Proteome

The complete set of proteins that is expressed by the entire genome. Sometimes the term is used to describe the complement of proteins expressed by a cell at any one time.

Proto-oncogenes

Genes that code for elements of the signal transduction pathway that when altered may cause cancer.

Provirus

A duplex sequence of DNA integrated into a eukaryotic genome that represents the sequence of the RNA genome of a retrovirus.

Pseudoautosomal regions

Regions on the Y chromosome that frequently exchange with the X chromosome during male meiosis.

Pseudogenes

Inactive but stable components of the genome derived by mutation of an ancestral active gene. Usually they are inactive because of mutations that block transcription or translation or both.

Puff

An expansion of a band of a polytene chromosome associated with the synthesis of RNA at some locus in the band.

Purine

A double-ringed nitrogenous base, such as adenine or guanine.

Purine-loading (AG) pressure

The tendency of a species’ AG (purine) content at the first, second, and third positions of the codons of its genes to conform to an optimal value.

Puromycin

An antibiotic that terminates protein synthesis by mimicking a tRNA and becoming linked to the nascent protein chain.

Pyrimidine

A single-ringed nitrogenous base, such as cytosine, thymine, or uracil.

Pyrimidine dimer

A dimer that forms when ultraviolet irradiation generates a covalent link directly between two adjacent pyrimidine bases in DNA. It blocks DNA replication and transcription.

Pyrosequencing

DNA sequencing technique based on the detection of the release of pyrophosophate when nucleotides are incorporated into a single-stranded DNA. A chemoluminescent enzyme is used to detect the activity of DNA polymerase. The method allows for the sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting the base added at each step. Solutions of A, C, G, and T nucleotides are sequentially added and removed from the reaction. Light is produced only when the nucleotide solution complements the first unpaired base of the template. The sequence of solutions that produce chemiluminescent signals allows the determination of the sequence of the template.

Quantitative PCR (qPCR)

See real-time PCR (rt-PCR).

Quick-stop mutant

Temperature-sensitive replication mutants that are defective in replication elongation during synthesis of DNA.

R segments

The sequences that are repeated at the ends of a retroviral RNA. They are called R-U5 and U3-R.

RAG1

Protein required for DNA cleavage in V(D)J recombination. It recognizes the nonamer consensus sequences for recombination. It works together with RAG2 to undertake the catalytic reactions of cleaving and rejoining DNA, and also provides a structural framework within which the whole recombination reaction occurs.

RAG2

Protein required for DNA cleavage in V(D)J recombination. It is recruited by RAG1 and cleaves DNA at the heptamer. It works together with RAG1 to undertake the catalytic reactions of cleaving and rejoining DNA, and also provides a structural framework within which the whole recombination reaction occurs.

Random priming

Use of a random hexamer to prepare labeled DNA probes from templates for hybridization and to prime mRNAs with or without poly(A) for first strand cDNA synthesis.

rasiRNA

A germline subset of miRNA transcribed from transposable elements and other repeated elements that is used to silence them.

rDNA

Genes encoding ribosomal RNA (rRNA).

Reading frame

One of three possible ways of reading a nucleotide sequence. Each divides the sequence into a series of successive triplets.

Readthrough

Occurs at transcription or translation when RNA polymerase or the ribosome, respectively, ignores a termination signal because of a mutation of the template or the behavior of an accessory factor.

Real-time PCR (rt-PCR)

Technique with continuous monitoring of product formation as the process proceeds, usually through fluorometric methods. Also known as quantitative PCR (qPCR). Not to be confused with reverse transcription PCR (RT-PCR), which is a method that allows detection of RNAs by PCR.

Recoding

Events that occur when the meaning of a codon or series of codons is changed from that predicted by the genetic code. It may involve altered interactions between aminoacyl-tRNA and mRNA that are influenced by the ribosome.

Recognition helix

One of the two helices of the helix-turn-helix motif that makes contacts with DNA that are specific for particular bases. This determines the specificity of the DNA sequence that is bound.

Recombinant DNA

A DNA molecule composed of sequences from two different sources.

Recombinant joint

The point at which two recombining molecules of duplex DNA are connected (the edge of the heteroduplex region).

Recombinase

Enzyme that catalyzes site-specific recombination.

Recombination activating genes (RAG1, RAG2)

Genes that encode enzymes that play an important role in the rearrangement and recombination of the genes of immunoglobulin and T cell receptor molecules during the process of V(D)J recombination. The cellular expression of two recombination activating gene products, RAG1 and RAG2, is restricted to developing lymphocytes.

Recombination nodules (nodes)

Dense objects present on the synaptonemal complex; they may represent protein complexes involved in crossing over.

Recombination-repair

A mode of filling a gap in one strand of duplex DNA by retrieving a homologous single strand from another duplex.

Recombination signal sequences (RSSs)

Consist of conserved nonamers:12 or 23 spacer:heptamer sequences flanking one end of the coding sequence of Ig and TCR V(D)J genes.

Redundancy

The concept that two or more genes may fulfill the same function, so that no single one of them is essential.

Regulator gene

A gene that codes for a product (typically protein) that controls the expression of other genes (usually at the level of transcription).

Relaxase

An enzyme that cuts one strand of DNA and binds to the free 5′ end.

Relaxed mutants

In Escherichia coli, these do not display the stringent response to starvation for amino acids (or other nutritional deprivation).

Relaxosome

A bacterial complex assembled for the purpose of conjugation, transferring genetic material between bacteria.

Release factor (RF)

A protein required to terminate polypeptide translation to cause release of the completed polypeptide chain and the ribosome from mRNA.

Renaturation

The reassociation of denatured complementary single strands of a DNA double helix.

Repetitive DNA

DNA that is present in many (related or identical) copies in a genome.

Replication bubble

A region in which DNA has been replicated within a longer, unreplicated region.

Replication-coupled pathway

The pathway for assembling chromatin from an equal mix of old and new histones during the S phase of the cell cycle.

Replication defective

A virus that cannot sustain the infective cycle by itself but that is perpetuated in the company of a helper virus that provides the missing viral functions.

Replication-defective virus

A virus that cannot perpetuate an infective cycle because some of the necessary genes are absent (replaced by host DNA in a transducing virus) or mutated.

Replication fork

The point at which strands of parental duplex DNA are separated so that replication can proceed. A complex of proteins including DNA polymerase is found there.

Replication-independent pathway

Pathway for assembling nucleosomes during phases of the cell cycle that do not involve DNA synthesis; may be necessary due to damage to the DNA or because of displacement of the nucleosome during transcription.

Replicative transposition

The movement of a transposon by a mechanism in which first it is replicated, and then one copy is transferred to a new site.

Replicon

A unit of the genome in which DNA is replicated. Each contains an origin for initiation of replication.

Replisome

The multiprotein structure that assembles at the bacterial replication fork to undertake synthesis of DNA. It contains DNA polymerase and other enzymes.

Reporter gene

A gene attached to another promoter and/or gene that encodes a product that is easily identified or measured.

Repressible gene

A gene that is turned off by its product.

Repression

The ability to prevent synthesis of certain enzymes when their products are present; more generally, it refers to inhibition of transcription (or translation) by binding of repressor protein to a specific site on DNA (or mRNA).

Repressor

A protein that inhibits expression of a gene. It may act to prevent transcription by binding to an enhancer or silencer.

Resolution

Process that occurs by a homologous recombination reaction between the two copies of the transposon in a cointegrate. The reaction generates the donor and target replicons, each with a copy of the transposon.

Resolvase

The enzyme activity involved in site-specific recombination between two copies of a transposon that has been duplicated.

Restriction endonuclease

An enzyme that recognizes specific short sequences of DNA and cleaves the duplex (sometimes at the target site, sometimes elsewhere, depending on type).

Restriction enzymes

Enzymes that cut the DNA molecule at a particular location. The enzyme locates a particular sequence (usually four to six nucleotides) on the DNA strand and then stops and cuts at or near the recognition nucleotide sequence. In bacteria, these enzymes provide a defense against invading viruses. They are also used as a tool in genetic engineering to extract genes from organisms that can then be inserted into other organisms.

Restriction map

Determination of a linear array of sites on DNA cleaved by various restriction endonucleases.

Restriction point

The point in G1 of the cell cycle when the cell becomes committed to S phase.

Retrotransposon (retroposon)

A transposon that mobilizes via an RNA form; the DNA element is transcribed into RNA, and then reverse-transcribed into DNA, which is inserted at a new site in the genome. It does not have an infective (viral) form.

Retrovirus

An RNA virus with the ability to convert its sequence into DNA by reverse transcription.

Reverse transcriptase

An enzyme that uses single-stranded RNA as a template to synthesize a complementary DNA strand.

Reverse transcription

Synthesis of DNA on a template of RNA. It is accomplished by the enzyme reverse transcriptase.

Reverse transcription polymerase chain reaction (RT-PCR)

A technique for the detection and quantification of expression of a gene by reverse transcription and amplification of RNAs from a cell sample.

Revertants

Reversions of a mutant cell or organism to the wild-type phenotype.

RF1

The bacterial release factor that recognizes UAA and UAG as signals to terminate polypeptide translation.

RF2

The bacterial release factor that recognizes UAA and UGA as signals to terminate polypeptide translation.

RF3

A polypeptide translation termination factor related to the elongation factor EF-G. It functions to release the factors RF1 or RF2 from the ribosome when they act to terminate polypeptide translation.

Rho-dependent termination

Transcriptional termination by bacterial RNA polymerase in the presence of the rho factor.

Rho factor

A protein involved in assisting Escherichia coli RNA polymerase to terminate transcription at certain terminators (called rho-dependent terminators).

Ri plasmid

Plasmids found in Agrobacterium tumefaciens. Like Ti plasmids, they carry genes that cause disease in infected plants. The disease may take the form of either hairy root disease or crown gall disease.

Ribonuclease

An enzyme that cleaves phosphodiester linkages between RNA ribonucleotides.

Ribonucleoprotein (RNP)

A complex of RNA and proteins. Larger complexes are sometimes called ribonucleoprotein particles.

Ribosomal RNAs (rRNAs)

A major component of the ribosome.

Ribosome

A large assembly of RNA and proteins that synthesizes proteins under direction from an mRNA template.

Ribosome-binding site

A sequence on bacterial mRNA that includes an initiation codon that is bound by a 30S subunit in the initiation phase of polypeptide translation.

Ribosome stalling

The inhibition of movement that occurs when a ribosome reaches a codon for which there is no corresponding charged aminoacyl-tRNA.

Riboswitch

A catalytic RNA whose activity responds to a small ligand.

Ribozyme

An RNA that has catalytic activity.

RISC

RNA-induced silencing complex, a ribonucleoprotein particle composed of a short, single-stranded siRNA and a nuclease that cleaves mRNAs complementary to the siRNA. It receives siRNA from Dicer and delivers it to the mRNA.

RITS

RNA-induced transcriptional silencing. Small RNAs that can downregulate transcription of specific genes at the level of chromatin modification.

RNA-binding protein (RBP)

A protein containing one or more domains that confer an affinity for RNA, usually in an RNA sequence- or structure-specific manner.

RNA-dependent RNA polymerase (RDRP)

An RNA polymerase that uses RNA as the template to synthesize a new strand.

RNA editing

A change of sequence at the level of RNA following transcription.

RNA-induced transcriptional silencing (RITS)

A mechanism of gene expression silencing carried out by microRNAs.

RNA interference (RNAi)

A process by which short 21- to 23-nucleotide antisense RNAs, derived from longer double-stranded RNAs, can modulate expression of mRNA by translation inhibition or degradation.

RNA ligase

An enzyme that functions in tRNA splicing to make a phosphodiester bond between the two exon sequences that are generated by cleavage of the intron.

RNA polymerase

An enzyme that synthesizes RNA using a DNA template.

RNA processing

Modifications to RNA transcripts of genes. This may include alterations to the 3′ and 5′ ends and the removal of introns.

RNA regulon

A set of RNAs that are coregulated by the same set of RNA-binding proteins that control their splicing, stability, localization, etc.

RNA silencing

The ability of an RNA, especially ncRNA, to alter chromatin structure in order to prevent gene transcription.

RNA splicing

The process of excising introns from RNA and connecting the exons into a continuous mRNA.

RNA surveillance systems

Systems that check RNAs (or RNPs) for errors. The system recognizes an invalid sequence or structure and triggers a response.

RNase

An enzyme that degrades RNA.

Rolling circle

A mode of replication in which a replication fork proceeds around a circular template for an indefinite number of revolutions; the DNA strand newly synthesized in each revolution displaces the strand synthesized in the previous revolution, giving a tail containing a linear series of sequences complementary to the circular template strand.

Rotational positioning

The location of the histone octamer relative to turns of the double helix that determines which face of DNA is exposed on the nucleosome surface.

RSSs

See recombination signal sequences (RSSs).

rut

The sequence of RNA that is recognized by the rho termination factor.

S phase

The restricted part of the eukaryotic cell cycle during which synthesis of DNA occurs.

S region

See switch (S) region.

Satellite DNA

DNA that consists of many tandem repeats (identical or related) of a short, basic repeating unit. See also virusoid.

Scaffold attachment regions (SARs)

DNA sites attached to proteinaceous structures in both metaphase and interphase nuclei. Chromatin appears to be attached to an underlying structure in vivo; evidence suggests that this attachment is necessary for transcription or replication

Scarce mRNA

mRNA that consists of a large number of individual mRNA species, each present in very few copies per cell. This accounts for most of the sequence complexity in RNA.

Scrapie

A disease caused by an infective agent made of protein (a prion).

ScRNA

Highly abundant cytoplasmic RNAs of approximately 300 nucleotides.

Scyrps (small cytoplasmic RNAs; scRNAs)

Complexes of small cytoplasmic RNAs and proteins that make up the spliceosome.

Second parity rule

Rule discovered by Edwin Chargaff that, to a close approximation, there are equal amounts of adenine (A) and thymine (T) and equal amounts of cytosine (C) and guanine (G) in each single strand of the DNA duplex.

Second-site reversion

A second mutation suppressing the effect of a first mutation.

Selfish DNA

DNA sequences that do not contribute to the phenotype of the organism but that have self-perpetuation within the genome as their sole function.

Self-splicing

See autosplicing.

Semiconservative replication

DNA replication accomplished by separation of the strands of a parental duplex, each strand then acting as a template for synthesis of a complementary strand.

Semidiscontinuous replication

The mode of replication in which one new strand is synthesized continuously while the other is synthesized discontinuously.

Septal ring

A complex of several proteins coded by fts genes of Escherichia coli that forms at the midpoint of the cell. It gives rise to the septum at cell division. The first of the proteins to be incorporated is FtsZ, which gave rise to the original name of the Z-ring.

Septum

The structure that forms in the center of a dividing bacterium, providing the site at which the daughter bacteria will separate. The same term is used to describe the cell wall that forms between plant cells at the end of mitosis.

Sequence context

The sequence surrounding a consensus sequence. It may modulate the activity of the consensus sequence.

Severe combined immunodeficiency (SCID)

Syndrome that stems from mutations in different genes that result in B and/or T cell deficiency.

Shelterin

A complex of six telomeric proteins in mammals that function to protect telomeres from DNA damage repair pathways and to regulate telomere length control by telomerase.

Shine–Dalgarno sequence

The polypurine sequence AGGAGG centered about 10 bp before the AUG initiation codon on bacterial mRNA. It is complementary to the sequence at the 3′ end of 16S rRNA.

Short-interspersed nuclear elements (SINEs)

A major class of short (less than 500 bp) nonautonomous retrotransposons that occupy approximately 13% of the human genome (see also retrotransposon).

SHM

See somatic hypermutation (SHM).

Shuttle vectors

A cloning vector that can be used in more than one species of host cell.

Sigma factor

The subunit of bacterial RNA polymerase needed for initiation; it is the major influence on selection of promoters.

Signal end

End produced at the termini of the cleaved fragment containing the recombination signal sequences during recombination of immunoglobulin and T cell receptor genes. Their subsequent joining yields a signal joint.

Signal transduction pathway

The process by which a stimulus or cellular state is sensed by and transmitted to pathways within the cell.

Silencer

A short sequence of DNA that can inactivate expression of a gene in its vicinity.

Silent mutation

A mutation that does not change the sequence of a polypeptide because it produces synonymous codons.

Simple sequence DNA

Short, repeating units of DNA sequence.

single copy

A type of replication control in bacteria resulting from the fact that a genome in a bacterial cell has a single replication origin and thus constitutes a single replicon. Because units of replication and segregation coincide, initiation at a single origin sponsors replication of the entire genome, once for every cell division.

Single-copy replication control

A control system in which there is only one copy of a replicon per unit bacterium. The bacterial chromosome and some plasmids have this type of regulation.

Single nucleotide polymorphism (SNP)

A polymorphism (variation in sequence between individuals) caused by a change in a single nucleotide. This is responsible for most of the genetic variation between individuals.

Single-strand binding protein (SSB)

The protein that attaches to single-stranded DNA, thereby preventing the DNA from forming a duplex.

Single-strand exchange

A reaction in which one of the strands of a duplex of DNA leaves its former partner and instead pairs with the complementary strand in another molecule, displacing its homologue in the second duplex.

Single-strand invasion (or single-strand assimilation)

The process in which a single strand of DNA displaces its homologous strand in a duplex.

Single X hypothesis

The theory that describes the inactivation of one X chromosome in female mammals.

siRNA

Short interfering RNA, an miRNA that prevents gene expression.

Sister chromatid

Each of two identical copies of a replicated chromosome; this term is used as long as the two copies remain linked at the centromere. They separate during anaphase in mitosis or anaphase II in meiosis.

Site-directed mutagenesis

Method used to create targeted changes in the DNA sequence of a gene or a gene product. Basic technique relies on the introduction of a synthetic primer that contains the mutation and that is complementary to the template DNA around the mutation site.

Site-specific recombination

Recombination that occurs between two specific sequences, as in phage integration/excision or resolution of cointegrate structures during transposition.

SKI proteins

A set of protein factors that target nonstop decay (NSD) substrates for degradation.

Slow-stop mutant

Temperature-sensitive replication mutants that are defective in initiation of replication.

SL RNA

See spliced leader RNA (SL RNA).

Small cytoplasmic RNAs (scRNA; scyrps)

RNAs that are present in the cytoplasm (and sometimes also in the nucleus).

Small nuclear RNA (snRNA)

One of many small RNA species confined to the nucleus; several of them are involved in splicing or other RNA-processing reactions.

Small nucleolar RNA (snoRNA)

A small nuclear RNA that is localized in the nucleolus.

Snurps (small nuclear ribonucleoproteins; snRNPs)

Complexes of snRNAs and proteins that make up the spliceosome.

Somatic DNA recombination

The process of joining V(D)J gene segments in a B or T lymphocyte to generate a B or T cell receptor. Also underlies Ig class switching.

Somatic hypermutation (SHM)

An active process of mutation in B cells but not T cells. It introduces mutations in rearranged immunoglobulin V(D)J genes at a rate that is at least 106 higher than that of spontaneous mutations in the genome at large. These mutations can change the sequence of the antibody, especially in its antigen-binding site.

Somatic mutation

A mutation occurring in a somatic cell, therefore affecting only its daughter cells; it is not inherited by descendants of the organism.

Somatic recombination

Recombination that occurs in nongerm cells (i.e., it does not occur during meiosis). Most commonly used to refer to recombination in the immune system, in which case it refers to the process of joining V(D)J gene segments in a B or T lymphocyte to generate a B or T cell receptor; in this case it is also called V(D)J recombination. Process also underlies Ig class switching.

Southern blotting

A process for the transfer of DNA bands separated by gel electrophoresis from the gel matrix to a solid support matrix such as a nylon membrane for subsequent probing and detection.

Spindle

A structure made up of microtubules that guides the movements of the chromosomes during mitosis.

Splice recombinant

DNA that results from a Holliday junction being resolved by cutting the nonexchanged strands. Both strands of DNA before the exchange point come from one chromosome; the DNA after the exchange point come from the homologous chromosome.

Spliced leader RNA (SL RNA)

A small RNA that donates an exon in the trans-splicing reaction of trypanosomes and nematodes.

Spliceosome

A complex that is required for RNA splicing, formed by snRNPs and additional protein factors.

Splicing

The process of excising introns from RNA and connecting the exons into a continuous mRNA.

Splicing factor

A protein component of the spliceosome that is not part of one of the snRNPs.

Spontaneous mutations

Mutations occurring in the absence of any added reagent to increase the mutation rate, as the result of errors in replication (or other events involved in the reproduction of DNA) or by random changes to the chemical structure of bases.

Sporulation

The generation of a spore by a bacterium (by morphological conversion) or by a yeast (as the product of meiosis).

SR protein

A protein that has a variable length of a Ser-Arg–rich region and is involved in splicing.

sRNA

A small bacterial RNA that functions as a regulator of gene expression.

Stabilizing element (SE)

One of a variety of cis sequences present in some mRNAs that confers a long half-life on that mRNA.

Start point

The position on DNA corresponding to the first base incorporated into RNA.

Steady state (molecular concentration)

The concentration of population of molecules when the rates of synthesis and degradation are constant.

Stem-loop

A secondary structure that appears in RNAs consisting of a base-paired region (stem) and a terminal loop of single-stranded RNA. Both are variable in size.

Steroid receptor

Transcription factors that are activated by binding of a steroid ligand.

Stop codon

One of three triplets (UAG, UAA, or UGA) that cause polypeptide translation to terminate. They are also known historically as nonsense codons. The UAA codon is called ochre and the UAG codon is called amber, after the names of the nonsense mutations by which they were originally identified.

Strand displacement

A mode of replication of some viruses in which a new DNA strand grows by displacing the previous (homologous) strand of the duplex.

Stress granules

Cytoplasmic particles containing translationally inactive mRNAs that form in response to a general inhibition of translation initiation.

Stringency

A measure of the exactness of complementarity required between two DNA strands to allow them to hybridize. It is related to buffer ionic strength and reaction temperature above or below TM, with lower ionic strengths and higher temperatures having higher values (i.e., greater exactness required).

Stringent factor

The protein RelA, which is associated with ribosomes; synthesizes ppGpp and pppGpp when an uncharged tRNA enters the ribosome.

Stringent response

The ability of a bacterium to shut down synthesis of ribosomes and tRNA in a poor growth medium.

stRNA

Short temporal RNA, a form of miRNA in eukaryotes that modulates mRNA expression during development.

Structural gene

A gene that codes for any RNA or polypeptide product other than a regulator.

Subclone

The process of breaking a cloned fragment into smaller fragments for further cloning.

Supercoiling

The coiling of a closed duplex DNA in space so that it crosses over its own axis.

Superfamily

A set of genes all related by presumed descent from a common ancestor but now showing considerable variation.

Suppression mutation

A second event eliminates the effects of a mutation without reversing the original change in DNA.

Switch (S) region

A sequence involved in immunoglobulin class switch DNA recombination. Consists of repetitive 3- to 5-kb sequences upstream of the each cluster of gene segments encoding the heavy chain constant regions.

Synapsis

The association of the two pairs of sister chromatids (representing homologous chromosomes) that occurs at the start of meiosis; the resulting structure is called a bivalent.

Synaptonemal complex

The morphological structure of synapsed chromosomes.

Synonymous codons

Codons that have the same meaning (specifying the same amino acid, or specifying termination of translation) in the genetic code.

Synonymous mutation

A mutation in a coding region that does not alter the amino acid sequence of the polypeptide product.

Synteny

A relationship between chromosomal regions of different species where homologous genes occur in the same order.

Synthetic genetic array analysis (SGA)

An automated technique in budding yeast whereby a mutant is crossed to an array of approximately 5,000 deletion mutants to determine whether the mutations interact to cause a synthetic lethal phenotype.

Synthetic lethal

Two mutations that are viable by themselves but lethal when combined.

T cell receptor (TCR)

The antigen receptor on T lymphocytes; it is clonally expressed and binds to a complex of MHC class I or class II protein and antigen-derived peptide.

T cells

Lymphocytes of the T (thymic) lineage. They differentiate in the thymus from stem cells of bone marrow origin. They are grouped into several functional types (subsets) according to their phenotype, mainly expression of surface CD4, CD8, or CD25. Different subsets are involved in different cell-mediated immune responses.

T-DNA

The part of the Ti plasmid that is transferred from Agrobacterium into a plant cell. It is required for infection.

t-loop

Structure characterized by a series of TTAGGG repeats that are displaced to form a single-stranded region, and the tail of the telomere is paired with the homologous strand.

TAFs

The subunits of TFIID that assist TBP in binding to DNA. They also provide points of contact for other components of the transcription apparatus.

Tandem duplication

Generation of a chromosome segment that is identical to the segment immediately adjacent to it.

TATA-binding protein (TBP)

The subunit of transcription factor TFIID that binds to the TATA box in the promoter and is positioned at the promoters that do not contain a TATA box by other factors.

TATA box

A conserved AT-rich octamer found about 25 bp before the start point of each eukaryotic RNA polymerase II transcription unit; it is involved in positioning the enzyme for correct initiation.

TATA-less promoter

A gene promoter that does not have a TATA box in the sequence upstream of its start point.

TCR

See T cell receptor (TCR).

TdT

See terminal deoxynucleotidyl transferase (TdT).

Telomerase

The ribonucleoprotein enzyme that creates repeating units of one strand at the telomere by adding individual bases to the DNA 3′ end, as directed by an RNA sequence in the RNA component of the enzyme.

Telomere

The natural end of a chromosome; the DNA sequence consists of a simple repeating unit with a protruding single-stranded end.

Telomeric silencing

The repression of gene activity that occurs in the vicinity of a telomere.

Temperate phage

A bacteriophage that can follow the lytic or lysogenic pathway.

Template strand

The DNA strand that is copied by the polymerase.

ter

The DNA sequence that signals for the termination of replication.

Teratoma

A growth in which many differentiated cell types—including skin, teeth, bone, and others—grow in a disorganized manner after an early embryo is transplanted into one of the tissues of an adult animal.

Terminal deoxynucleotidyl transferase (TdT)

An enzyme that catalyzes the insertion of unencoded (N) nucleotides into V-D-J coding sequences during V(D)J recombination.

Terminal protein

A protein that allows replication of a linear phage genome to start at the very end. It attaches to the 5′ end of the genome through a covalent bond, is associated with a DNA polymerase, and contains a cytosine residue that serves as a primer.

Terminase

An enzyme that cleaves multimers of a viral genome and then uses hydrolysis of ATP to provide the energy to translocate the DNA into an empty viral capsid starting with the cleaved end.

Termination

A separate reaction that ends a macromolecular synthesis reaction (replication, transcription, or translation) by stopping the addition of subunits and (typically) causing disassembly of the synthetic apparatus.

Termination codon

One of the three codons (UAA, UAG, UGA) that signal the termination of translation of a polypeptide.

Terminator

A sequence of DNA that causes RNA polymerase to terminate transcription.

Terminus

A segment of DNA at which replication ends.

Ternary complex

The complex in initiation of transcription that consists of RNA polymerase and DNA as well as a dinucleotide that represents the first two bases in the RNA product.

Tetrad

A four-part structure that forms during the prophase of meiosis. Consists of two homologous chromosomes, each composed of two sister chromatids.

TFIID

The transcription factor that binds to the TATA sequence upstream of the start point of promoters for RNA polymerase II. It consists of TBP (TATA-binding protein) and the TAF subunits that bind to TBP.

Thalassemia

A disease of red blood cells resulting from lack of either α or β globin.

Third-base degeneracy

The lesser effect on codon meaning of the nucleotide present in the third (3′) codon position.

Threshold cycle (CT)

The thermocycle number in a real-time PCR or RT-PCR reaction at which the product signal rises above a specified cutoff value to indicate that amplicon production is occurring.

Ti plasmid

An episome of the bacterium Agrobacterium tumefaciens that carries the genes responsible for the induction of crown gall disease in infected plants.

Tiling array

An array of immobilized nucleic acid sequences that together represent the entire genome of an organism. The shorter each array spot is, the larger the total number of spots required, but the greater the genetic resolution of the array.

TLR

See Toll-like receptors (TLRs).

TLS DNA polymerase

Enzyme that plays a role in a DNA damage tolerance process that enables replication past lesions such as thymine dimers or areas of stalled DNA replication.

TM

The theoretical melting temperature of a duplex nucleic acid segment into separate strands. It is dependent on parameters such as sequence composition, duplex length, and buffer ionic strength.

tmRNA

A tRNA–mRNA hybrid that allows recycling of stalled ribosomes.

Toll/interleukin-1/resistance (TIR)

A key signaling domain that is unique to the Toll-like receptor (TLR) system. Located in the cytosolic face of each TLR, and also in the TLR signaling adaptors. Similar to the TLRs, the adaptors are conserved across many species. The five known adaptors are MyD88, MyD88-adaptor-like (MAL, also known as TIRAP), TIR-domain-containing adaptor protein inducing IFN-β (TRIF; also known as TICAM1), TRIF-related adaptor molecule (TRAM; also known as TICAM2), and sterile armadillo-motif-containing protein (SARM).

Toll-like receptors (TLRs)

A family of proteins that play a fundamental role in recognition of microbes and activation of innate immunity. These transmembrane proteins are expressed on the cell surface and the endocytic compartment and recognize microbe-associated molecular patterns (MAMPs) on microorganisms.

Topoisomerase

An enzyme that changes the number of times the two strands in a closed DNA molecule cross each other. It does this by cutting the DNA, passing DNA through the break, and resealing the DNA.

Topological isomers

Molecules with the same chemical formula but different bond connectivities, thus resulting in different topologic structures. Examples include DNA, which can have different numbers of supercoils.

Trailer (3′ UTR)

An untranslated sequence at the 3′ end of an mRNA following the termination codon.

TRAMP

A protein complex that identifies and polyadenylates aberrant nuclear RNAs in yeast, recruiting the nuclear exosome for degradation.

trans-acting

A product that can function on any copy of its target DNA. This implies that it is a diffusible protein or RNA.

Transcription

Synthesis of RNA from a DNA template.

Transcription unit

The sequence between sites of initiation and termination by RNA polymerase; it may include more than one gene.

Transcriptional interference (TI)

The phenomenon in which transcription from one promoter interferes directly with transcription from a second, linked promoter.

Transcriptome

The complete set of RNAs present in a cell, tissue, or organism. Its complexity is due mostly to mRNAs, but it also includes noncoding RNAs.

Transducing virus

A virus that carries part of the host genome in place of part of its own sequence. The best known examples are retroviruses in eukaryotes and DNA phages in Escherichia coli.

Transfection

In eukaryotic cells, it is the acquisition of new genetic markers by incorporation of added DNA.

Transfer region

A large (approximately 33 kb) region of an F plasmid that is required for bacterial conjugation. It contains genes that are required for the transmission of DNA.

Transfer RNA (tRNA)

The intermediate in protein synthesis that interprets the genetic code. Each molecule can be linked to an amino acid. It has an anticodon sequence that is complementary to a triplet codon representing the amino acid.

Transformation

In bacteria, it is the acquisition of new genetic material by incorporation of added DNA.

Transforming principle

DNA that is taken up by a bacterium and whose expression then changes the properties of the recipient cell.

Transgenerational epigenetics

Transmission of nongenetic information (epigenetic states) from an organism to its offspring.

Transgenic

Organism created by introducing DNA prepared in test tubes into the germline. The DNA may be inserted into the genome or exist in an extrachromosomal structure.

Transition

A mutation in which one pyrimidine is replaced by the other, or in which one purine is replaced by the other.

Translation

Synthesis of protein on an mRNA template.

Translational positioning

The location of a histone octamer at successive turns of the double helix that determines which sequences are located in linker regions.

Translesion DNA synthesis (TLS) polymerase

Involved in bypass of base damage in DNA. In general, displays low fidelity and low processivity and is error prone when copying undamaged DNA templates.

Translesion synthesis

A DNA damage tolerance process that can bypass replication blocks caused by damaged DNA by switching out regular DNA polymerases for specialized translesion polymerases that are able to replicate DNA over the damaged area.

Translocation

(1) The movement of the ribosome one codon along mRNA after the addition of each amino acid to the polypeptide chain. (2) The reciprocal or nonreciprocal exchange of chromosomal material between nonhomologous chromosomes.

Transmembrane region (domain)

The part of a protein that spans the membrane bilayer. It is hydrophobic and in many cases contains approximately 20 amino acids that form an α-helix.

Transposase

The enzyme activity involved in insertion of transposon at a new site.

Transposition

The movement of a transposon to a new site in the genome.

Transposon

A DNA sequence able to insert itself (or a copy of itself) at a new location in the genome without having any sequence relationship with the target locus.

Transversion

A mutation in which a purine is replaced by a pyrimidine or vice versa.

tRNAfMet

The special RNA used to initiate polypeptide translation in bacteria. It mostly uses AUG but can also respond to GUG and CUG.

tRNAmMet

The bacterial tRNA that inserts methionine at internal AUG codons.

True activator

A positive transcription faction that functions by making contact, direct or indirect, with the basal apparatus to activate transcription.

True reversion

A mutation that restores the original sequence of the DNA.

Tudor domain

A type of methyl-lysine binding domain characterized by a specific sequence of approximately 60 amino acids.

Tumor suppressor

A class of proteins that guard the cell cycle, ensuring that the cell size and absence of DNA damage criteria are met. These proteins act as brakes on the cell cycle, preventing the cell from progressing from G1 to S.

Twisting number (T)

In the DNA double helix, the rotation of one strand about the other.

U3

The repeated sequence at the 3′ end of a retroviral RNA.

U5

The repeated sequence at the 5′ end of a retroviral RNA.

UAS

See upstream activating sequence (UAS).

Underwound

B-form DNA that has fewer than 10.5 base pairs per turn of the helix.

Unequal crossing over (nonreciprocal recombination)

The result of an error in pairing and crossing over in which nonequivalent sites are involved in a recombination event. It produces one recombinant with a deletion of material and one with a duplication.

Ung

Enzyme required for both class switch recombination (CSR) and somatic hypermutation (SHM). It deglycosylates the deoxyuridines generated by the deamination of deoxycytidines to give rise to abasic sites. B cells that are deficient in this enzyme have a 10-fold reduction in CSR, suggesting that the enzyme is critical for the generation of double-strand breaks (DSBs). Different events follow in the CSR and SHM processes.

Unidentified reading frame (URF)

An open reading frame with an as yet undetermined function.

Unidirectional replication

The movement of a single replication fork from a given origin.

Uninducible

A mutant in which the affected gene(s) cannot be expressed.

Unit evolutionary period (UEP)

The time in millions of years that it takes for 1% divergence in evolutionary divergent sequences.

UP element

A sequence in bacteria adjacent to the promoter, upstream of the −35 element, that enhances transcription.

UPF proteins

A set of protein factors that target nonsense-mediated decay (NMD) substrates for degradation.

Upstream

Sequences in the opposite direction from expression.

Upstream activating sequence (UAS)

The equivalent in yeast of the enhancer in higher eukaryotes that is bound by transcriptional activator proteins; a UAS cannot function downstream of the promoter.

Up mutation

A mutation in a promoter that increases the rate of transcription.

Uracil-DNA glycosylase (Ung)

A member of a highly conserved and specific class of DNA repair enzymes. Biological function is the specific removal of the normal RNA base uracil from DNA. It eliminates uracil from DNA molecules and generates abasic sites, thereby initiating the base excision repair (BER) pathway. This enzyme has been identified in a variety of prokaryotic and eukaryotic organisms and in different families of viruses. In class switch recombination and somatic hypermutation, it deglycosylates deoxyuridines emerging from AID-mediated deamination of deoxycytosines.

Variable number tandem repeat (VNTR)

Very short repeated sequences, including microsatellites and mini-satellites.

Variable (V) region

An antigen-binding site of an immunoglobulin or T cell receptor molecule. They are composed of the variable domains of the component chains. They are coded by V gene segments and vary extensively among antigen receptors as the result of multiple, different genomic copies and of changes introduced during synthesis.

Vector

An engineered DNA molecule used to transfer and propagate various insert DNAs.

Vegetative phase

The period of normal growth and division of a bacterium. For a bacterium that can sporulate, this contrasts with the sporulation phase, when spores are being formed.

Viroid

A small infectious nucleic acid that does not have a protein coat.

Virulent mutations (λvir)

Phage mutants that are unable to establish lysogeny.

Virulent phage

A bacteriophage that can only follow the lytic cycle.

Virusoid (satellite RNA)

A small infectious nucleic acid that is encapsidated by a plant virus together with its own genome.

Western blotting

Analytical technique used to detect specific proteins in a sample of tissue homogenate or extract. Artificial antibodies are introduced to the sample that will react with a specific target protein. The sample is then placed on a membrane. If a stained band appears after gel electrophoresis is performed on the sample, then the specific protein is present in the sample.

Wobble hypothesis

The ability of a tRNA to recognize more than one codon by unusual (non–G-C, non–A-T) pairing with the third base of a codon.

Writhing number (W)

In DNA, the turning of the axis of the duplex in space.

Xeroderma pigmentosum (XP)

A disease caused by mutation in one of the XP genes, which results in hypersensitivity to sunlight (particularly ultraviolet light), skin disorders, and cancer predisposition.

Yeast artificial chromosome (YAC)

A cloning vector used in yeast that can hold up to 3,000 kb of DNA and that contains a centromere, telomeres, and origin of replication.

Z-ring

See septal ring.

Zinc finger

A DNA-binding motif that typifies a class of transcription factor.

Zipcode (or localization signal)

Any of the number of mRNA cis elements involved in directing cellular localization.