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Brown TA. Genomes. 2nd edition. Oxford: Wiley-Liss; 2002.

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Genomes. 2nd edition.

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Glossary

2 μm circle

A plasmid found in the yeast Saccharomyces cerevisiae and used as the basis for a series of cloning vectors.

2-aminopurine

A base analog that can cause mutations by replacing adenine in a DNA molecule.

−25 box

A component of the bacterial promoter.

3′-OH terminus

The end of a polynucleotide that terminates with a hydroxyl group attached to the 3′-carbon of the sugar.

3′ transduction

Transfer of a segment of genomic DNA from one place to another caused by movement of a LINE element.

3′-untranslated region

The untranslated region of an mRNA downstream of the termina-tion codon.

30 nm chromatin fiber

A relatively unpacked form of chromatin consisting of a possibly helical array of nucleosomes in a fiber approximately 30 nm in diameter.

5-bromouracil

A base analog that can cause mutations by replacing thymine in a DNA molecule.

5′-P terminus

The end of a polynucleotide that terminates with a mono-, di- or triphosphate attached to the 5′-carbon of the sugar.

5′-untranslated region

The untranslated region of an mRNA upstream of the initiation codon.

(6–4) lesion

A dimer between two adjacent pyrimidine bases in a polynucleotide, formed by ultraviolet irradiation.

(6–4) photoproduct photolyase

An enzyme involved in photoreactivation repair.

α-helix

One of the commonest secondary structural conformations taken up by segments of polypeptides.

β-N-glycosidic bond

The linkage between the base and sugar of a nucleotide.

β-sheet

One of the commonest secondary structural conformations taken up by segments of polypeptides.

β-turn

A sequence of four amino acids, the second usually glycine, which causes a polypeptide to change direction.

γ-complex

A component of DNA polymerase III comprising subunit γ in association with δ, δ′, χ and ψ.

κ-homology domain

A type of RNA-binding domain.

π–π interactions

The hydrophobic interactions that occur between adjacent base pairs in a double-stranded DNA molecule.

Acceptor arm

Part of the structure of a tRNA molecule.

Acceptor site

The splice site at the 3′ end of an intron.

Acidic domain

A type of activation domain.

Acridine dye

A chemical compound that causes a frameshift mutation by intercalating between adjacent base pairs of the double helix.

Activation domain

The part of an activator that makes contact with the initiation complex.

Activator

A DNA-binding protein that stabilizes construction of the RNA polymerase II transcription initiation complex.

Acylation

The attachment of a lipid sidechain to a polypeptide.

Ada enzyme

An Escherichia coli enzyme that is involved in the direct repair of alkylation mutations.

Adaptor

A synthetic, double-stranded oligonucleotide used to attach sticky ends to a blunt-ended molecule.

Adenine

A purine base found in DNA and RNA.

Adenosine deaminase acting on RNA (ADAR)

An enzyme that edits various eukaryotic mRNAs by deaminating adenosine to inosine.

Adenylate cyclase

The enzyme that converts ATP to cyclic AMP.

A-DNA

A structural configuration of the double helix, present but not common in cellular DNA.

Affinity chromatography

A column chromatography method that makes use of a ligand that binds to the molecule being purified.

Agarose gel electrophoresis

Electrophoresis carried out in an agarose gel and used to separate DNA molecules between 100 bp and 50 kb in length.

Alkaline phosphatase

An enzyme that removes phosphate groups from the 5′ ends of DNA molecules.

Alkylating agent

A mutagen that acts by adding alkyl groups to nucleotide bases.

Allele

One of two or more alternative forms of a gene.

Allele frequency

The frequency of an allele in a population.

Allele-specific oligonucleotide (ASO) hybridization

The use of an oligonucleotide probe to determine which of two alternative nucleotide sequences is contained in a DNA molecule.

Allopolyploid

A polyploid nucleus derived from fusion between gametes from different species.

Alphoid DNA

The tandemly repeated nucleotide sequences located in the centromeric regions of human chromosomes.

Alternative splicing

The production of two or more mRNAs from a single pre-mRNA by joining together different combinations of exons.

Alu

A type of SINE found in the genomes of humans and related mammals.

Alu-PCR

A clone fingerprinting technique that uses PCR to detect the relative positions of Alu sequences in cloned DNA fragments.

Amino acid

One of the monomeric units of a protein molecule.

Amino terminus

The end of a polypeptide that has a free amino group.

Aminoacyl or A site

The site in the ribosome occupied by the aminoacyl-tRNA during translation.

Aminoacylation

Attachment of an amino acid to the acceptor arm of a tRNA.

Aminoacyl-tRNA synthetase

An enzyme that catalyzes the aminoacylation of one or more tRNAs.

Ancestral character state

A character state possessed by a remote common ancestor of a group of organisms.

Ancient DNA

DNA preserved in ancient biological material.

Annealing

Attachment of an oligonucleotide primer to a DNA or RNA template.

Anticodon

The triplet of nucleotides, at positions 34–36 in a tRNA molecule, that base-pairs with a codon in an mRNA molecule.

Anticodon arm

Part of the structure of a tRNA molecule.

Antigen

A substance that elicits an immune response.

Antitermination

A bacterial mechanism for regulating the termination of transcription.

Antiterminator protein

A protein that attaches to bacterial DNA and mediates anti-termination.

AP (apurinic/apyrimidinic) site

A position in a DNA molecule where the base component of the nucleotide is missing.

AP endonuclease

An enzyme involved in base excision repair.

Apomorphic character state

A character state that evolved in a recent ancestor of a subset of organisms in a group being studied.

Apoptosis

Programmed cell death.

Archaea

One of the two main groups of prokaryotes, mostly found in extreme environments.

Ascospore

One of the haploid products of meiosis in an ascomycete such as the yeast Saccharomyces cerevisiae.

Ascus

The structure which contains the four ascospores produced by a single meiosis in the yeast Saccharomyces cerevisiae.

Attenuation

A process used by some bacteria to regulate expression of an amino acid biosynthetic operon in accordance with the levels of the amino acid in the cell.

AU–AC intron

A type of intron found in eukaryotic nuclear genes: the first two nucleotides in the intron are 5′–AU–3′ and the last two are 5′–AC–3′.

Autonomously replicating sequence (ARS)

A DNA sequence, particularly from yeast, that confers replicative ability on a non-replicative plasmid.

Autopolyploid

A polyploid nucleus derived from fusion of two gametes from the same species, neither of which is haploid.

Autoradiography

The detection of radioactively labeled molecules by exposure of an X-ray-sensitive photographic film.

Autosome

A chromosome that is not a sex chromosome.

Auxotroph

A mutant microorganism that can grow only when supplied with a nutrient that is not needed by the wild type.

B chromosome

A chromosome possessed by some individuals in a population, but not all.

Bacteria

One of the two main groups of prokaryotes.

Bacterial artificial chromosome (BAC)

A high-capacity cloning vector based on the F plasmid of Escherichia coli.

Bacteriophage

A virus that infects a bacterium.

Bacteriophage P1 vector

A high-capacity cloning vector based on bacteriophage P1.

Barr body

The highly condensed chromatin structure taken up by an inactivated X chromosome.

Basal promoter

The position within a eukaryotic promoter where the initiation complex is assembled.

Basal promoter element

Sequence motifs that are present in many eukaryotic promoters and set the basal level of transcription initiation.

Basal rate of transcription

The number of productive initiations of transcription occurring per unit time at a particular promoter.

Base analog

A compound whose structural similarity to one of the bases in DNA enables it to act as a mutagen.

Base excision repair

A DNA repair process that involves excision and replacement of an abnormal base.

Base pair

The hydrogen-bonded structure formed by two complementary nucleotides. When abbreviated to ‘bp’, the shortest unit of length for a double-stranded DNA molecule.

Base ratio

The ratio of A to T, or G to C, in a double-stranded DNA molecule. Chargaff showed that the base ratios are always close to 1.0.

Baseless site

A position in a DNA molecule where the base component of the nucleotide is missing.

Base-pairing

The attachment of one polynucleotide to another, or one part of a polynucleotide to another part of the same polynucleotide, by base pairs.

Base-stacking

The hydrophobic interactions that occur between adjacent base pairs in a double-stranded DNA molecule.

Basic domain

A type of DNA-binding domain.

B-DNA

The commonest structural conformation of the DNA double helix in living cells.

Beads-on-a-string

An unpacked form of chromatin consisting of nucleosome beads on a string of DNA.

Bioinformatics

The use of computer methods in studies of genomes.

Biolistics

A means of introducing DNA into cells that involves bombardment with high-velocity microprojectiles coated with DNA.

Biological information

The information contained in the genome of an organism and which directs the development and maintenance of that organism.

Biotechnology

The use of living organisms, often, but not always microbes, in industrial processes.

Biotinylation

Attachment of a biotin label to a DNA or RNA molecule.

Bivalent

The structure formed when a pair of homologous chromosomes lines up during meiosis.

Blunt end

An end of a double-stranded DNA molecule where both strands terminate at the same nucleotide position with no single-stranded extension.

Bootstrap analysis

A method for inferring the degree of confidence that can be assigned to a branch point in a phylogenetic tree.

Bootstrap value

The statistical value obtained by bootstrap analysis.

Bottleneck

A temporary reduction in the size of a population.

Branch

A component of a phylogenetic tree.

Branch migration

A step in the Holliday model for homologous recombination, involving exchange of polynucleotides between a pair of recombining double-stranded DNA molecules.

Buoyant density

The density possessed by a molecule or particle when suspended in an aqueous salt or sugar solution.

C terminus

The end of a polypeptide that has a free carboxyl group.

CAAT box

A basal promoter element.

Cap

The chemical modification at the 5′ end of most eukaryotic mRNA molecules.

Cap binding complex

The complex that makes the initial attachment to the cap structure at the beginning of the scanning phase of eukaryotic translation.

CAP site

A DNA-binding site for the catabolite activator protein.

Capping

Attachment of a cap to the 5′ end of a eukaryotic mRNA.

Capsid

The protein coat that surrounds the DNA or RNA genome of a virus.

Carboxyl terminus

The end of a polypeptide that has a free carboxyl group.

CASPs (CTD-associated SR-like proteins)

Proteins thought to play regulatory roles during splicing of GU–AG introns.

Catabolite activator protein

A regulatory protein that binds to various sites in a bacterial genome and activates transcription initiation at downstream promoters.

Catabolite repression

The means by which extracellular glucose levels dictate whether genes for sugar utilization are switched on or off in bacteria.

cDNA

A double-stranded DNA copy of an mRNA molecule.

cDNA capture or cDNA selection

Repeated hybridization probing of a pool of cDNAs with the objective of obtaining a subpool enriched in certain sequences.

Cell cycle

The series of events occurring in a cell between one division and the next.

Cell cycle checkpoint

A period before entry into S or M phase of the cell cycle, a key point at which regulation is exerted.

Cell senescence

The period in a cell lineage when the cells are alive but no longer able to divide.

Cell-free protein synthesizing system

A cell extract containing all the components needed for protein synthesis and able to translate added mRNA molecules.

Cell-specific module

Sequence motifs present in the promoters of eukaryotic genes that are expressed in just one type of tissue.

Centromere

The constricted region of a chromosome that is the position at which the pair of chromatids are held together.

Chain termination method

A DNA sequencing method that involves enzymatic synthesis of polynucleotide chains that terminate at specific nucleotide positions.

Chaperonin

A multi-subunit protein that forms a structure that aids the folding of other proteins.

Character state

One of at least two alternative forms of a character used in phylogenetic analysis.

Chemical degradation sequencing

A DNA sequencing method that involves the use of chemicals that cut DNA molecules at specific nucleotide positions.

Chemical shift

The change in the rotation of a chemical nucleus, used as the basis of NMR.

Chi form

An intermediate structure seen during recombination between DNA molecules.

Chi site

A repeated nucleotide sequence in the Escherichia coli genome that is involved in the initiation of homologous recombination.

Chimera

An organism composed of two or more genetically different cell types.

Chloroplast

One of the photosynthetic organelles of a eukaryotic cell.

Chloroplast genome

The genome present in the chloroplasts of a photosynthetic eukaryotic cell.

Chromatid

The arm of a chromosome.

Chromatin

The complex of DNA and histone proteins found in chromosomes.

Chromatosome

A subcomponent of chromatin made up of a nucleosome core octamer with associated DNA and a linker histone.

Chromosome

One of the DNA–protein structures that contains part of the nuclear genome of a eukaryote. Less accurately, the DNA molecule(s) that contain(s) a prokaryotic genome.

Chromosome scaffold

A component of the nuclear matrix which changes its structure during cell division, resulting in condensation of the chromosomes into their metaphase forms.

Chromosome theory

The theory, first propounded by Sutton in 1903, that genes lie on chromosomes.

Chromosome walking

A technique that can be used to construct a clone contig by identifying overlapping fragments of cloned DNA.

Cis-displacement

Movement of a nucleosome to a new position on a DNA molecule.

Clade

A group of monophyletic organisms or DNA sequences that include all of those in the analysis that are descended from a particular common ancestor.

Cladistics

A phylogenetic approach that stresses the importance of understanding the evolutionary relevance of the characters that are studied.

Cleavage and polyadenylation specificity factor (CPSF)

A protein that plays an ancillary role during polyadenylation of eukaryotic mRNAs.

Cleavage stimulation factor (CstF)

A protein that plays an ancillary role during polyadenylation of eukaryotic mRNAs.

Clone

A group of cells that contain the same recombinant DNA molecule.

Clone contig

A collection of clones whose DNA fragments overlap.

Clone contig approach

A genome sequencing strategy in which the molecules to be sequenced are broken into manageable segments, each a few hundred kb or few Mb in length, which are sequenced individually.

Clone fingerprinting

Any one of several techniques that compare cloned DNA fragments in order to identify ones that overlap.

Clone library

A collection of clones, possibly representing an entire genome, from which individual clones of interest are obtained.

Cloning vector

A DNA molecule that is able to replicate inside a host cell and therefore can be used to clone other fragments of DNA.

Closed promoter complex

The structure formed during the initial step in assembly of the transcription initiation complex. The closed promoter complex consists of the RNA polymerase and/or accessory proteins attached to the promoter, before the DNA has been opened up by breakage of base pairs.

Cloverleaf

A two-dimensional representation of the structure of a tRNA molecule.

Coactivator

A protein that works in conjunction with an activator to stabilize construction of the RNA polymerase II transcription initiation complex.

Coding RNA

An RNA molecule that codes for a protein; an mRNA.

Codominance

The relationship between a pair of alleles which both contribute to the phenotype of a heterozygote.

Codon

A triplet of nucleotides coding for a single amino acid.

Codon–anticodon recognition

The interaction between a codon on an mRNA molecule and the corresponding anticodon on a tRNA.

Codon bias

Refers to the fact that not all codons are used equally frequently in the genes of a particular organism.

Cohesin

The protein that holds sister chromatids together during the period between genome replication and nuclear division.

Cohesive end

An end of a double-stranded DNA molecule where there is a single-stranded extension.

Co-integrate

An intermediate in the pathway resulting in replicative transposition.

Commitment complex

The initial structure formed during splicing of a GU–AG intron.

Comparative genomics

A research strategy that uses information obtained from the study of one genome to make inferences about the map positions and functions of genes in a second genome.

Competent

Refers to a culture of bacteria that have been treated, for example, by soaking in calcium chloride, so that their ability to take up DNA molecules is enhanced.

Complementary

Refers to two nucleotides or nucleotide sequences that are able to base-pair with one another.

Complementary DNA (cDNA)

A double-stranded DNA copy of an mRNA molecule.

Composite transposon

A DNA transposon comprising a pair of insertion sequences flanking a segment of DNA usually containing one or more genes.

Concatamer

A DNA molecule made up of linear genomes or other DNA units linked head to tail.

Concerted evolution

The evolutionary process that results in the members of a multigene family retaining the same or similar sequences.

Conditional-lethal mutation

A mutation that results in a cell or organism able to survive only under permissive conditions.

Conjugation

Transfer of DNA between two bacteria that come into physical contact with one another.

Conjugation mapping

A technique for mapping bacterial genes by determining the time it takes for each gene to be transferred during conjugation.

Consensus sequence

A nucleotide sequence that represents an ‘average’ of a number of related but non-identical sequences.

Conservative replication

A hypothetical mode of DNA replication in which one daughter double helix is made up of the two parental polynucleotides and the other is made up of two newly synthesized polynucleotides.

Conservative transposition

Transposition that does not result in copying of the transposable element.

Constitutive control

Control over bacterial gene expression that depends on the sequence of the promoter.

Constitutive heterochromatin

Chromatin that is permanently in a compact organization.

Constitutive mutation

A mutation that results in continuous expression of a gene or set of genes that is normally subject to regulatory control.

Context-dependent codon reassignment

Refers to the situation whereby the DNA sequence surrounding a codon changes the meaning of that codon.

Contig

A contiguous set of overlapping DNA sequences.

Contour clamped homogeneous electric fields (CHEF)

An electrophoresis method used to separate large DNA molecules.

Conventional pseudogene

A gene that has become inactive because of the accumulation of mutations.

Convergent evolution

The situation that occurs when the same character state evolves independently in two lineages.

Core enzyme

The version of Escherichia coli RNA polymerase, subunit composition α2ββ′, that carries out RNA synthesis but is unable to locate promoters efficiently.

Core octamer

The central component of a nucleosome, made up of two subunits each of histones H2A, H2B, H3 and H4, around which DNA is wound.

Core promoter

The position within a eukaryotic promoter where the initiation complex is assembled.

Co-repressor

A small molecule that must be bound to a repressor protein before the latter is able to attach to its operator site.

cos site

One of the cohesive, single-stranded extensions present at the ends of the DNA molecules of certain strains of λ phage.

Cosmid

A high-capacity cloning vector consisting of the λ cos site inserted into a plasmid.

Cotransduction

Transfer of two or more genes from one bacterium to another via a transducing phage.

Cotransformation

Uptake of two or more genes on a single DNA molecule during transformation of a bacterium.

CpG island

A GC-rich DNA region located upstream of approximately 56% of the genes in the human genome.

CREB

An important transcription factor.

Crossing-over

The exchange of DNA between chromosomes during meiosis.

Cryptic splice site

A site whose sequence resembles an authentic splice site and which might be selected instead of the authentic site during aberrant splicing.

Cryptogene

One of several genes in the trypanosome mitochondrial genome which specify abbreviated RNAs that must undergo pan-editing in order to become functional.

CTD-associated SR-like protein (CASP)

A type of protein thought to play a regulatory role during splicing of GU–AG introns.

C-terminal domain (CTD)

A component of the largest subunit of RNA polymerase II, important in activation of the polymerase.

C-value paradox

The non-equivalence between genome size and gene number that is seen when comparisons are made between some eukaryotes.

Cyanelle

A photosynthetic organelle that resembles an ingested cyanobacterium.

Cyclic AMP (cAMP)

A modified version of AMP in which an intramolecular phosphodiester bond links the 5′ and 3′ carbons.

Cyclin

A regulatory protein whose abundance varies during the cell cycle and which regulates biochemical events in a cell-cycle-specific manner.

Cyclobutyl dimer

A dimer between two adjacent pyrimidine bases in a polynucleotide, formed by ultraviolet irradiation.

Cys2His2 finger

A type of zinc-finger DNA-binding domain.

Cytochemistry

The use of compound-specific stains, combined with microscopy, to determine the biochemical content of cellular structures.

Cytosine

One of the pyrimidine bases found in DNA and RNA.

D arm

Part of the structure of a tRNA molecule.

Dark repair

A type of nucleotide excision repair process that corrects cyclobutyl dimers.

De novo methylation

Addition of methyl groups to new positions on a DNA molecule.

Deadenylation-dependent decapping

A process for degradation of eukaryotic mRNAs that is initiated by removal of the poly(A) tail.

Deaminating agent

A mutagen that acts by removing amino groups from nucleotide bases.

Degeneracy

Refers to the fact that the genetic code has more than one codon for most amino acids.

Degradosome

A multienzyme complex responsible for degradation of bacterial mRNAs.

Delayed-onset mutation

A mutation whose effect is not apparent until a relatively late stage in the life of the mutant organism.

Deletion mutation

A mutation resulting from deletion of one or more nucleotides from a DNA sequence.

Denaturation

Breakdown by chemical or physical means of the non-covalent interactions, such as hydrogen bonding, that maintain the secondary and higher levels of structure of proteins and nucleic acids.

Density gradient centrifugation

A technique in which a cell fraction is centrifuged through a dense solution, in the form of a gradient, so that individual components are separated.

Deoxyribonuclease

An enzyme that cleaves phosphodiester bonds in a DNA molecule.

Derived character state

A character state that evolved in a recent ancestor of a subset of organisms in a group being studied.

Development

A coordinated series of transient and permanent changes that occurs during the life history of a cell or organism.

Diauxie

The phenomenon whereby a bacterium, when provided with a mixture of sugars, uses up one sugar before beginning to metabolize the second sugar.

Dicer

The ribonuclease that plays a central role in RNA interference.

Dideoxynucleotide

A modified nucleotide that lacks the 3′ hydroxyl group and so terminates strand synthesis when incorporated into a polynucleotide.

Differential centrifugation

A technique that separates cell components by centrifuging an extract at different speeds.

Differential splicing

The production of two or more mRNAs from a single pre-mRNA by joining together different combinations of exons.

Differentiation

The adoption by a cell of a specialized biochemical and/or physiological role.

Dihybrid cross

A sexual cross in which the inheritance of two pairs of alleles is followed.

Dimer

A protein or other structure that comprises two subunits.

Diploid

A nucleus that has two copies of each chromosome.

Direct readout

The recognition of a DNA sequence by a binding protein that makes contacts with the outside of a double helix.

Direct repair

A DNA repair system that acts directly on a damaged nucleotide.

Direct repeat

A nucleotide sequence that is repeated twice or more frequently in a DNA molecule.

Directed evolution

A set of experimental techniques that is used to obtain novel genes with improved products.

Discontinuous gene

A gene that is split into exons and introns.

Dispersive replication

A hypothetical mode of DNA replication in which both polynucleotides of each daughter double helix are made up partly of parental DNA and partly of newly synthesized DNA.

Displacement replication

A mode of replication which involves continuous copying of one strand of the helix, the second strand being displaced and subsequently copied after synthesis of the first daughter strand has been completed.

Distance matrix

A table showing the evolutionary distances between all pairs of nucleotide sequences in a dataset.

Distance method

A rigorous mathematical approach to alignment of nucleotide sequences.

Disulfide bridge

A covalent bond linking cysteine amino acids on different polypeptides or at different positions on the same polypeptide.

D-loop

An intermediate structure formed during the Meselson–Radding model for homologous recombination. Also an intermediate formed during displacement replication.

DNA

Deoxyribonucleic acid, one of the two forms of nucleic acid in living cells; the genetic material for all cellular life forms and many viruses.

DNA adenine methylase (Dam)

An enzyme involved in methylation of Escherichia coli DNA.

DNA bending

A type of conformational change introduced into a DNA molecule by a binding protein.

DNA-binding motif

The part of a DNA-binding protein that makes contact with the double helix.

DNA-binding protein

A protein that attaches to a DNA molecule.

DNA chip

A high-density array of DNA molecules used for parallel hybridization analyses.

DNA cloning

Insertion of a fragment of DNA into a cloning vector, and subsequent propagation of the recombinant DNA molecule in a host organism.

DNA cytosine methylase (Dcm)

An enzyme involved in methylation of Escherichia coli DNA.

DNA-dependent DNA polymerase

An enzyme that makes a DNA copy of a DNA template.

DNA-dependent RNA polymerase

An enzyme that makes an RNA copy of a DNA template.

DNA glycosylase

An enzyme that cleaves the β-N-glycosidic bond between a base and the sugar component of a nucleotide as part of the base excision and mismatch repair processes. The name is a misnomer and should be DNA glycolyase, but the incorrect usage is now embedded in the literature.

DNA gyrase

A Type II topoisomerase of Escherichia coli.

DNA ligase

An enzyme that synthesizes phosphodiester bonds as part of DNA replication, repair and recombination processes.

DNA marker

A DNA sequence that exists as two or more readily distinguished versions and which can therefore be used to mark a map position on a genetic, physical or integrated genome map.

DNA methylation

Refers to the chemical modification of DNA by attachment of methyl groups.

DNA methyltransferase

An enzyme that attaches methyl groups to a DNA molecule.

DNA photolyase

A bacterial enzyme involved in photoreactivation repair.

DNA polymerase

An enzyme that synthesizes DNA.

DNA polymerase α

The enzyme that primes DNA replication in eukaryotes.

DNA polymerase δ

The main eukaryotic DNA replicating enzyme.

DNA polymerase γ

The enzyme responsible for replication of the mitochondrial genome.

DNA polymerase I

The bacterial enzyme that completes synthesis of Okazaki fragments during genome replication.

DNA polymerase II

A bacterial DNA polymerase involved in DNA repair.

DNA polymerase III

The main DNA replicating enzyme of bacteria.

DNA repair

The biochemical processes that correct mutations arising from replication errors and the effects of mutagenic agents.

DNA replication

Synthesis of a new copy of the genome.

DNase I hypersensitive site

A short region of eukaryotic DNA that is relatively easily cleaved with deoxyribonuclease I, possibly coinciding with positions where nucleosomes are absent.

DNA sequencing

The technique for determining the order of nucleotides in a DNA molecule.

DNA shuffling

A PCR-based procedure that results in directed evolution of a DNA sequence.

DNA topoisomerase

An enzyme that introduces or removes turns from the double helix by breakage and reunion of one or both polynucleotides.

DNA transposon

A transposon whose transposition mechanism does not involve an RNA intermediate.

DNA tumor virus

A virus with a DNA genome, able to cause cancer after infection of an animal cell.

Domain

A segment of a polypeptide that folds independently of other segments; also the segment of a gene coding for such a domain.

Domain duplication

Duplication of a gene segment coding for a structural domain in the protein product.

Domain shuffling

Rearrangement of segments of one or more genes, each segment coding for a structural domain in the gene product, to create a new gene.

Dominant

The allele that is expressed in a heterozygote.

Donor site

The splice site at the 5′ end of an intron.

Dot matrix

A method for aligning nucleotide sequences.

Double helix

The base-paired double-stranded structure that is the natural form of DNA in the cell.

Double heterozygote

A nucleus that is heterozygous for two genes.

Double homozygote

A nucleus that is homozygous for two genes.

Double restriction

Digestion of DNA with two restriction endonucleases at the same time.

Double-strand break repair

A DNA repair process that mends double-stranded breaks.

Double stranded

Comprising two polynucleotides attached to one another by base-pairing.

Double-stranded RNA-binding domain (dsRBD)

A common type of RNA-binding domain.

Downstream

Towards the 3′ end of a polynucleotide.

Dynamic allele-specific hybridization (DASH)

A solution hybridization technique used to type SNPs.

E site

A position within a bacterial ribosome to which a tRNA moves immediately after deacylation.

Electrophoresis

Separation of molecules on the basis of their net electrical charge.

Electrostatic interactions

Ionic bonds that form between charged chemical groups.

Elongation factor

A protein that plays an ancillary role in the elongation step of transcription or translation.

Elongator

A yeast protein, possibly with histone acetyltransferase activity, involved in the elongation phase of transcription.

Embryonic stem (ES) cell

A totipotent cell from the embryo of a mouse or other organism.

End-labeling

The attachment of a radioactive or other label to one end of a DNA or RNA molecule.

End-modification

The chemical alteration of the end of a DNA or RNA molecule.

End-modification enzyme

An enzyme used in recombinant DNA technology that alters the chemical structure at the end of a DNA molecule.

Endogenous retrovirus (ERV)

An active or inactive retroviral genome integrated into a host chromosome.

Endonuclease

An enzyme that breaks phosphodiester bonds within a nucleic acid molecule.

Endosymbiont theory

A theory that states that the mitochondria and chloroplasts of eukaryotic cells are derived from symbiotic prokaryotes.

Enhanceosome

A structure formed by DNA bending that comprises a collection of proteins involved in activation of the RNA polymerase II transcription initiation complex.

Enhancer

A regulatory sequence that increases the rate of transcription of a gene or genes located some distance away in either direction.

Episome

A plasmid that is able to integrate into the host cell’s chromosome.

Episome transfer

Transfer between cells of some or all of a bacterial chromosome by integration into a plasmid.

Ethidium bromide

A type of intercalating agent that causes mutations by inserting between adjacent base pairs in a double-stranded DNA molecule.

Ethylmethane sulfonate (EMS)

A mutagen that acts by adding alkyl groups to nucleotide bases.

Euchromatin

Regions of a eukaryotic chromosome that are relatively uncondensed, thought to contain active genes.

Eukaryote

An organism whose cells contain membrane-bound nuclei.

Excision repair

A DNA repair process that corrects various types of DNA damage by excising and resynthesizing a region of polynucleotide.

Exit site

A position within a bacterial ribosome to which a tRNA moves immediately after deacylation.

Exon

A coding region within a discontinuous gene.

Exonic splicing enhancer (ESE)

A nucleotide sequence that plays a positive regulatory role during splicing of GU–AG introns.

Exonic splicing silencer (ESS)

A nucleotide sequence that plays a negative regulatory role during splicing of GU–AG introns.

Exon–intron boundary

The nucleotide sequence at the junction between an exon and an intron.

Exon skipping

Aberrant splicing in which one or more or exons are omitted from the spliced RNA.

Exon theory of genes

An ‘introns early’ hypothesis that holds that introns were formed when the first DNA genomes were constructed.

Exon trapping

A method, based on cloning, for identifying the positions of exons in a DNA sequence.

Exonuclease

An enzyme that removes nucleotides from the ends of a nucleic acid molecule.

Exosome

A multiprotein complex involved in degradation of mRNA in eukaryotes.

Exportin

A protein involved in transport of molecules out of the nucleus.

Expressed sequence tag (EST)

A cDNA that is sequenced in order to gain rapid access to the genes in a genome.

Extein

The functional component of a discontinuous protein.

External node

The end of a branch in a phylogenetic tree, representing one of the organisms or DNA sequences being studied.

Extrachromosomal gene

A gene in a mitochondrial or chloroplast genome.

F plasmid

A fertility plasmid that directs conjugal transfer of DNA between bacteria.

Facultative heterochromatin

Chromatin that has a compact organization in some, but not all cells, thought to contain genes that are inactive in some cells or at some periods of the cell cycle.

FEN1

The ‘flap endonuclease’ involved in replication of the lagging strand in eukaryotes.

Fiber-FISH

A specialized form of FISH that enables high marker resolution.

Field inversion gel electrophoresis (FIGE)

An electrophoresis method used to separate large DNA molecules.

Fitness

The ability of an organism or allele to survive and reproduce.

Fixation

Refers to the situation that occurs when a single allele reaches a frequency of 100% in a population.

Flow cytometry

A method for the separation of chromosomes.

FLpter value

The unit used in FISH to describe the position of a hybridization signal relative to the end of the short arm of the chromosome.

Fluorescence recovery after photobleaching (FRAP)

A technique used to study the mobility of nuclear proteins.

Fluorescent in situ hybridization (FISH)

A technique for locating markers on chromosomes by observing the hybridization positions of fluorescent labels.

Flush end

An end of a double-stranded DNA molecule where both strands terminate at the same nucleotide position with no single-stranded extension.

fMet

N-formylmethionine, the modified amino acid carried by the tRNA that is used during the initiation of translation in bacteria.

Folding domain

A segment of a polypeptide that folds independently of other segments.

Folding pathway

The series of events, involving partially folded intermediates, that results in an unfolded protein attaining its correct three-dimensional structure.

Footprinting

A range of techniques used for locating bound proteins on DNA molecules.

Fosmid

A high-capacity vector carrying the F plasmid origin of replication and a λ cos site.

Fragile site

A position in a chromosome that is prone to breakage because it contains an expanded trinucleotide repeat sequence.

Frameshift mutation

A mutation resulting from insertion or deletion of a group of nucleotides that is not a multiple of three and which therefore changes the frame in which translation occurs.

Frameshifting

The movement of a ribosome from one reading frame to another at an internal position within a gene.

Functional analysis

The area of genome research devoted to identifying the functions of unknown genes.

Functional domain

A region of eukaryotic DNA around a gene or group of genes that can be delineated by treatment with deoxyribonuclease I.

Fusion protein

A protein that consists of a fusion of two polypeptides, or parts of polypeptides, normally coded by separate genes.

G1 phase

The first gap period of the cell cycle.

G2 phase

The second gap period of the cell cycle.

Gain-of-function mutation

A mutation that results in an organism acquiring a new function.

Gamete

A reproductive cell, usually haploid, that fuses with a second gamete to produce a new cell during sexual reproduction.

GAPs (GTPase activating proteins)

A set of proteins that are intermediates in the Ras signal transduction pathway.

Gap genes

Developmental genes that play a role in establishing positional information within the Drosophila embryo.

Gap period

One of two intermediate periods within the cell cycle.

GC box

A type of basal promoter element.

GC content

The percentage of nucleotides in a genome that are G or C.

Gel electrophoresis

Electrophoresis performed in a gel so that molecules of similar electrical charge can be separated on the basis of size.

Gel retardation analysis

A technique that identifies protein-binding sites on DNA molecules by virtue of the effect that a bound protein has on the mobility of the DNA fragments during gel electrophoresis.

Gel stretching

A technique for preparing restricted DNA molecules for optical mapping.

Gene

A DNA segment containing biological information and hence coding for an RNA and/or polypeptide molecule.

Gene cloning

Insertion of a fragment of DNA, containing a gene, into a cloning vector, and subsequent propagation of the recombinant DNA molecule in a host organism.

Gene conversion

A process that results in the four haploid products of meiosis displaying an unusual segregation pattern.

Gene expression

The series of events by which the biological information carried by a gene is released and made available to the cell.

Gene flow

The transfer of a gene from one organism to another.

Gene fragment

A gene relic consisting of a short isolated region from within a gene.

General recombination

Recombination between two homologous double-stranded DNA molecules.

General transcription factor (GTF)

A protein or protein complex that is a transient or permanent component of the initiation complex formed during eukaryotic transcription.

Gene substitution

The replacement of an allele that at one time was fixed in the population by a second allele, this second allele arising by mutation and increasing in frequency until itself reaching fixation.

Gene superfamily

A group of two or more evolutionarily related multigene families.

Genes-within-genes

Refers to a gene whose intron contains a second gene.

Gene therapy

A clinical procedure in which a gene or other DNA sequence is used to treat a disease.

Genetic code

The rules that determine which triplet of nucleotides codes for which amino acid during protein synthesis.

Genetic footprinting

A technique for the rapid functional analysis of many genes at once.

Genetic linkage

The physical association between two genes that are on the same chromosome.

Genetic mapping

The use of genetic techniques to construct a genome map.

Genetic marker

A gene that exists as two or more readily distinguished alleles and whose inheritance can therefore be followed during a genetic cross, enabling the map position of the gene to be determined.

Genetic profile

The banding pattern revealed after electrophoresis of the products of PCRs directed at a range of microsatellite loci.

Genetic redundancy

The situation that occurs when two genes in the same genome perform the same function.

Genetics

The branch of biology devoted to the study of genes.

Gene tree

A phylogenetic tree that shows the evolutionary relationships between a group of genes or other DNA sequences.

Genome

The entire genetic complement of a living organism.

Genome expression

The series of events by which the biological information carried by a genome is released and made available to the cell.

Genome-wide repeat

A sequence that recurs at many dispersed positions within a genome.

Genomic imprinting

Inactivation by methylation of a gene on one of a pair of homologous chromosomes.

Genotype

A description of the genetic composition of an organism.

Gigabase pair

1 000 000 kb; 1 000 000 000 bp.

Global regulation

A general down-regulation in protein synthesis that occurs in response to various signals.

Glutamine-rich domain

A type of activation domain.

Glycosylation

The attachment of sugar units to a polypeptide.

GNRPs (guanine nucleotide-releasing proteins)

A set of proteins that are intermediates in the Ras signal transduction pathway.

Green fluorescent protein

A protein that is used to label other proteins and whose gene is used as a reporter gene.

Group I intron

A type of intron found mainly in organelle genes.

Group II intron

A type of intron found in organelle genes.

Group III intron

A type of intron found in organelle genes.

GTPase activating proteins (GAPs)

A set of proteins that are intermediates in the Ras signal transduction pathway.

GU–AG intron

The commonest type of intron in eukaryotic nuclear genes. The first two nucleotides of the intron are 5′–GU–3′ and the last two are 5′–AG–3′.

Guanine

One of the purine nucleotides found in DNA and RNA.

Guanine methyltransferase

The enzyme that attaches a methyl group to the 5′ end of a eukaryotic mRNA during the capping reaction.

Guanine nucleotide releasing proteins (GNRPs)

A set of proteins that are intermediates in the Ras signal transduction pathway.

Guanylyl transferase

The enzyme that attaches a GTP to the 5′ end of a eukaryotic mRNA at the start of the capping reaction.

Guide RNA

A short RNA that specifies the positions at which one or more nucleotides are inserted into an abbreviated RNA by pan-editing.

Hammerhead

An RNA structure with ribozyme activity that is found in some viruses.

Haploid

A nucleus that has a single copy of each chromosome.

Haploinsufficiency

The situation where inactivation of a gene on one of a pair of homologous chromosomes results in a change in the phenotype of the mutant organism.

Haplotype

A collection of alleles that are usually inherited together.

Helicase

An enzyme that breaks base pairs in a double-stranded DNA molecule.

Helix–loop–helix motif

A dimerization domain commonly found in DNA-binding proteins.

Helix–turn–helix motif

A common structural motif for attachment of a protein to a DNA molecule.

Helper phage

A phage that is introduced into a host cell in conjunction with a related cloning vector, in order to provide enzymes and other proteins required for replication of the cloning vector.

Heterochromatin

Chromatin that is relatively condensed and is thought to contain DNA that is not being transcribed.

Heteroduplex

A DNA–DNA or DNA–RNA hybrid.

Heteroduplex analysis

Transcript mapping by analysis of DNARNA hybrids with a single-strand-specific nuclease such as S1.

Heterogenous nuclear RNA (hnRNA)

The nuclear RNA fraction that comprises unprocessed transcripts synthesized by RNA polymerase II.

Heteropolymer

An artificial RNA comprising a mixture of different nucleotides.

Heterozygosity

The probability that a person chosen at random from the population will be heterozygous for a particular marker.

Heterozygous

A diploid nucleus that contains two different alleles for a particular gene.

High mobility group N (HMGN) protein

A group of nuclear proteins that influence chromatin structure.

High-performance liquid chromatography (HPLC)

A column chromatography method with many applications in biochemistry.

Histone

One of the basic proteins found in nucleosomes.

Histone acetylation

Modification of chromatin structure by attachment of acetyl groups to core histones.

Histone acetyltransferase (HAT)

An enzyme that attaches acetyl groups to core histones.

Histone code

The hypothesis that the pattern of chemical modification on histone proteins influences various cellular activities.

Histone deacetylase (HDAC)

An enzyme that removes acetyl groups from core histones.

Holliday structure

An intermediate structure formed during recombination between two DNA molecules.

Holocentric chromosome

A chromosome that does not have a single centromere but instead has multiple kinetochores spread along its length.

Holoenzyme

The version of the Escherichia coli RNA polymerase, subunit composition α2ββ′σ, that is able to recognize promoter sequences.

Homeodomain

A DNA-binding motif found in many proteins involved in developmental regulation of gene expression.

Homeotic mutation

A mutation that results in the transformation of one body part into another.

Homeotic selector gene

A gene that establishes the identity of a body part such as a segment of the Drosophila embryo.

Homologous chromosomes

Two or more identical chromosomes present in a single nucleus.

Homologous genes

Genes that share a common evolutionary ancestor.

Homologous recombination

Recombination between two homologous double-stranded DNA molecules, i.e. ones which share extensive nucleotide sequence similarity.

Homology searching

A technique in which genes with sequences similar to that of an unknown gene are sought, the objective being to gain an insight into the function of the unknown gene.

Homoplasy

The situation that occurs when the same character state evolves independently in two lineages.

Homopolymer

An artificial RNA comprising just one nucleotide.

Homopolymer tailing

The attachment of a sequence of identical nucleotides (e.g. AAAAA) to the end of a nucleic acid molecule, usually referring to the synthesis of single-stranded homopolymer extensions on the ends of a double-stranded DNA molecule.

Homozygous

A diploid nucleus that contains two identical alleles for a particular gene.

Horizontal gene transfer

Transfer of a gene from one species to another.

Hormone response element

A nucleotide sequence upstream of a gene that mediates the regulatory effect of a steroid hormone.

Housekeeping protein

A protein that is continually expressed in all or at least most cells of a multicellular organism.

Hsp70 chaperone

A family of proteins that bind to hydrophobic regions in other proteins in order to aid their folding.

Human Genome Project

The publicly funded project responsible for one of the draft human genome sequences and which continues to study the functions of human genes.

Hybridization

The attachment to one another, by base-pairing, of two complementary polynucleotides.

Hybridization probing

A technique that uses a labeled nucleic acid molecule as a probe to identify complementary or homologous molecules to which it base-pairs.

Hydrogen bond

A weak electrostatic attraction between an electronegative atom such as oxygen or nitrogen and a hydrogen atom attached to a second electronegative atom.

Hydrophobic effects

Chemical interactions that result in hydrophobic groups becoming buried inside a protein.

Hypermutation

An increase in the mutation rate of a genome.

Immunocytochemistry

A technique that uses antibody probing to locate the position of a protein in a tissue.

Immunoelectron microscopy

An electron microscopy technique that uses antibody labeling to identify the positions of specific proteins on the surface of a structure such as a ribosome.

Immunoscreening

The use of an antibody probe to detect a polypeptide synthesized by a cloned gene.

Importin

A protein involved in transport of molecules into the nucleus.

In vitro mutagenesis

Techniques used to produce a specified mutation at a predetermined position in a DNA molecule.

In vitro packaging

Synthesis of infective λ phages from a preparation of λ proteins and a concatamer of λ DNA molecules.

Incomplete dominance

Refers to a pair of alleles, neither of which displays dominance, the phenotype of a heterozygote being intermediate between the phenotypes of the two homozygotes.

Indel

A position in an alignment between two DNA sequences where an insertion or deletion has occurred.

Inducer

A molecule that induces expression of a gene or operon by binding to a repressor protein and preventing the repressor from attaching to the operator.

Inferred tree

A tree obtained by phylogenetic analysis.

Informational problem

The problem tackled by the early molecular biologists concerning the nature of the genetic code.

Inhibition domain

The part of a eukaryotic repressor that makes contact with the initiation complex

Inhibitor-resistant mutant

A mutant that is able to resist the toxic effects of an antibiotic or other type of inhibitor.

Initiation codon

The codon, usually but not exclusively 5′–AUG–3′, found at the start of the coding region of a gene.

Initiation complex

The complex of proteins that initiates transcription. Also the complex that initiates translation.

Initiation factor

A protein that plays an ancillary role during initiation of translation.

Initiation of transcription

The assembly upstream of a gene of the complex of proteins that will subsequently copy the gene into RNA.

Initiation region

A region of eukaryotic chromosomal DNA within which replication initiates at positions that are not clearly defined.

Initiator (Inr) sequence

A component of the RNA polymerase II core promoter.

Initiator tRNA

The tRNA, aminoacylated with methionine in eukaryotes or N-formylmethionine in bacteria, that recognizes the initiation codon during protein synthesis.

Inosine

A modified version of adenosine, sometimes found at the wobble position of an anticodon.

Insertion mutation

A mutation that arises by insertion of one or more nucleotides into a DNA sequence.

Insertion sequence

A short transposable element found in bacteria.

Insertion vector

A λ vector constructed by deleting a segment of non-essential DNA.

Insertional editing

A less extensive form of pan-editing that occurs during processing of some viral RNAs.

Insertional inactivation

A cloning strategy whereby insertion of a new piece of DNA into a vector inactivates a gene carried by the vector.

Instability element

A sequence present in yeast mRNAs that affects degradation.

Insulator

A segment of DNA that acts as the boundary point between two functional domains.

Integrase

A Type I topoisomerase that catalyzes insertion of the λ genome into Escherichia coli DNA.

Integron

A set of genes and other DNA sequences that enable plasmids to capture genes from bacteriophages and other plasmids.

Intein

An internal segment of a polypeptide that is removed by a splicing process after translation.

Intein homing

The conversion of a gene coding for a protein that lacks an intein into one coding for an intein-plus protein, catalyzed by the spliced component of the intein.

Intercalating agent

A compound that can enter the space between adjacent base pairs of a double-stranded DNA molecule, often causing mutations.

Intergenic region

The regions of a genome that do not contain genes.

Internal node

A branch point within a phylogenetic tree, representing an organism or DNA sequence that is ancestral to those being studied.

Internal ribosome entry site (IRES)

A nucleotide sequence that enables the ribosome to assemble at an internal position in some eukaryotic mRNAs.

Interphase

The period between cell divisions.

Interphase chromosome

A chromosome, present in a cell during the period between cell divisions, which adopts a relatively uncondensed chromatin structure.

Interspersed repeat

A sequence that recurs at many dispersed positions within a genome.

Interspersed repeat element PCR (IRE-PCR)

A clone fingerprinting technique that uses PCR to detect the relative positions of genome-wide repeats in cloned DNA fragments.

Intrinsic terminator

A position in bacterial DNA where termination of transcription occurs without the involvement of Rho.

Intron

A non-coding region within a discontinuous gene.

Intron homing

The conversion of a gene lacking an intron into one that contains an intron, catalyzed by a protein coded by that intron.

Introns early

The hypothesis that introns evolved relatively early and are gradually being lost from eukaryotic genomes.

Introns late

The hypothesis that introns evolved relatively late and are gradually accumulating in eukaryotic genomes.

Inverted repeat

Two identical nucleotide sequences repeated in opposite orientations in a DNA molecule.

Iron-response element

A type of response module.

Isoaccepting tRNAs

Two or more tRNAs that are charged with the same amino acid.

Isochore

A segment of genomic DNA that has a uniform base composition which differs from that of the adjacent segments.

Isotope

One of two or more atoms that have the same atomic number but different atomic weights.

Janus kinase (JAK)

A type of kinase that plays an intermediary role in some types of signal transduction involving STATs.

Junk DNA

One interpretation of the intergenic DNA content of a genome.

Karyogram

The entire chromosome complement of a cell, with each chromosome described in terms of its appearance at metaphase.

Karyopherin

A protein involved in transport of RNA out of or into the nucleus.

Kilobase pair (kb)

1000 base pairs.

Kinetochore

The part of the centromere to which spindle microtubules attach.

Klenow polymerase

A DNA polymerase enzyme, obtained by chemical modification of Escherichia coli DNA polymerase I, used primarily in chain termination DNA sequencing.

Knockout mouse

A mouse that has been engineered so that it carries an inactivated gene.

Kornberg polymerase

The DNA polymerase I enzyme of Escherichia coli.

Kozak consensus

The nucleotide sequence surrounding the initiation codon of a eukaryotic mRNA.

Lactose operon

The cluster of three genes that code for enzymes involved in utilization of lactose by Escherichia coli.

Lactose repressor

The regulatory protein that controls transcription of the lactose operon in response to the presence or absence of lactose in the environment.

Lagging strand

The strand of the double helix which is copied in a discontinuous fashion during genome replication.

Lariat

Refers to the lariat-shaped intron RNA that results from splicing a GU–AG intron.

Lateral gene transfer

Transfer of a gene from one species to another.

Leader segment

The untranslated region of an mRNA upstream of the initiation codon.

Leading strand

The strand of the double helix which is copied in a continuous fashion during genome replication.

Leaky mutation

A mutation that results in partial loss of a characteristic.

Lethal mutation

A mutation that results in death of the cell or organism.

Leucine zipper

A dimerization domain commonly found in DNA-binding proteins.

Ligase

An enzyme that synthesizes phosphodiester bonds as part of DNA replication, repair and recombination processes.

LINE (long interspersed nuclear element)

A type of genome-wide repeat, often with transposable activity.

LINE-1

One type of human LINE.

Linkage

The physical association between two genes that are on the same chromosome.

Linkage analysis

The procedure used to assign map positions to genes by genetic crosses.

Linker DNA

The DNA that links nucleosomes: the ‘string’ in the ‘beads-on-a-string’ model for chromatin structure.

Linker histone

A histone, such as H1, that is located outside of the nucleosome core octamer.

Locus

The chromosomal location of a genetic or DNA marker.

Locus control region (LCR)

A DNA sequence that maintains a functional domain in an open active configuration.

Lod score

A statistical measure of linkage as revealed by pedigree analysis.

Long patch repair

A nucleotide excision repair process of Escherichia coli that results in excision and resynthesis of up to 2 kb of DNA.

Loss-of-function mutation

A mutation that reduces or abolishes a protein’s activity.

LTR element

A type of genome-wide repeat typified by the presence of long terminal repeats (LTRs).

Lysogenic infection cycle

The type of bacteriophage infection that involves integration of the phage genome into the host DNA molecule.

Lysozyme

A protein used to destabilize the bacterial cell wall prior to DNA purification.

Lytic infection cycle

The type of bacteriophage infection that involves lysis of the host cell immediately after the initial infection, with no integration of the phage DNA molecule into the host genome.

M phase

The stage of the cell cycle when mitosis or meiosis occurs.

Macrochromosome

One of the larger gene-deficient chromosomes seen in the nuclei of chickens and various other species.

MADS box

A DNA-binding domain found in several transcription factors involved in plant development.

Maintenance methylation

Addition of methyl groups to positions on newly synthesized DNA strands that correspond with the positions of methylation on the parent strand.

Major groove

The larger of the two grooves that spiral around the surface of the B-form of DNA.

Major histocompatibility complex (MHC)

A mammalian multigene family coding for cell surface proteins and including several multiallelic genes.

Map

A chart showing the positions of genetic and/or physical markers in a genome.

MAP kinase

A signal transduction pathway.

Mapping reagent

A collection of DNA fragments spanning a chromosome or the entire genome and used in STS mapping.

Marker

A distinctive feature on a genome map. Also a gene, carried by a cloning vector, that codes for a distinctive protein product and/or phenotype and so can be used to determine if a cell contains a copy of the cloning vector.

Mass spectrometry

An analytical technique in which ions are separated according to their charge-to-mass ratios.

Maternal-effect gene

A Drosophila gene that is expressed in the parent and whose mRNA is subsequently injected into the egg, after which it influences development of the embryo.

Mating type

The equivalent of male and female for a eukaryotic microorganism.

Mating-type switching

The ability of yeast cells to change from a to α mating type, or vice versa, by gene conversion.

Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF)

A type of mass spectrometry used in proteomics.

Matrix-associated region (MAR)

An AT-rich segment of a eukaryotic genome that acts as an attachment point to the nuclear matrix.

Maturase

A protein, coded by a gene in an intron, thought to be involved in splicing.

Maximum parsimony method

A method for construction of phylogenetic trees.

Mediator

A protein complex that forms a contact between various activators and the C-terminal domain of the largest subunit of RNA polymerase II.

Megabase pair (Mb)

1000 kb; 1  000 000 bp.

Meiosis

The series of events, involving two nuclear divisions, by which diploid nuclei are converted to haploid gametes.

Melting

Denaturation of a double-stranded DNA molecule.

Melting temperature (Tm)

The temperature at which the two strands of a double-stranded nucleic acid molecule or base-paired hybrid detach as a result of complete breakage of hydrogen bonding.

Meselson–Stahl experiment

The experiment which showed that cellular DNA replication occurs by the semiconservative process.

Messenger RNA (mRNA)

The transcript of a protein-coding gene.

Metaphase chromosome

A chromosome at the metaphase stage of cell division, when the chromatin takes on its most condensed structure and features such as the banding pattern can be visualized.

Methyl-CpG-binding protein (MeCP)

A protein that binds to methylated CpG islands and may influence acetylation of nearby histones.

MGMT (O6-methylguanine-DNA methyltransferase)

An enzyme involved in the direct repair of alkylation mutations.

Microarray

A low-density array of DNA molecules used for parallel hybridization analysis.

Microsatellite

A type of simple sequence length polymorphism comprising tandem copies of, usually, di-, tri- or tetranucleotide repeat units. Also called a simple tandem repeat (STR).

Minichromosome

One of the smaller, gene-rich chromosomes seen in the nuclei of chickens and various other species.

Minigene

The name given to the pair of exons carried by a cloning vector used in the exon-trapping procedure.

Minimal medium

A medium that provides only the minimum nutritional requirements for growth of a microorganism.

Minisatellite

A type of simple sequence length polymorphism comprising tandem copies of repeats that are a few tens of nucleotides in length. Also called a variable number of tandem repeats (VNTR).

Minor groove

The smaller of the two grooves that spiral around the surface of the B-form of DNA.

Mismatch

A position in a double-stranded DNA molecule where base-pairing does not occur because the nucleotides are not complementary; in particular, a non-base-paired position resulting from an error in replication.

Mismatch repair

A DNA repair process that corrects mismatched nucleotide pairs by replacing the incorrect nucleotide in the daughter polynucleotide.

Missense mutation

An alteration in a nucleotide sequence that converts a codon for one amino acid into a codon for a second amino acid.

Mitochondrial genome

The genome present in the mitochondria of a eukaryotic cell.

Mitochondrion

One of the energy-generating organelles of eukaryotic cells.

Mitosis

The series of events that results in nuclear division.

Model organism

An organism which is relatively easy to study and hence can be used to obtain information that is relevant to the biology of a second organism that is more difficult to study.

Modification assay

A range of techniques used for locating bound proteins on DNA molecules.

Modification interference

A technique used to identify nucleotides involved in interactions with a DNA-binding protein.

Modification protection

A technique used to identify nucleotides involved in interactions with a DNA-binding protein.

Molecular biologist

A person who studies the molecular life sciences.

Molecular chaperone

A protein that helps other proteins to fold.

Molecular clock

A device based on the inferred mutation rate that enables times to be assigned to the branch points in a gene tree.

Molecular combing

A technique for preparing restricted DNA molecules for optical mapping.

Molecular evolution

The gradual changes that occur in genomes over time as a result of the accumulation of mutations and structural rearrangements resulting from recombination and transposition.

Molecular life sciences

The area of research comprising molecular biology, biochemistry and cell biology, as well as some aspects of genetics and physiology.

Molecular phylogenetics

A set of techniques that enable the evolutionary relationships between DNA sequences to be inferred by making comparisons between those sequences.

Monohybrid cross

A sexual cross in which the inheritance of one pair of alleles is followed.

Monophyletic

Refers to two or more organisms or DNA sequences that are derived from a single ancestral organism or DNA sequence.

mRNA surveillance

A RNA degradation process in eukaryotes.

Multicopy

A gene, cloning vector or other genetic element that is present in multiple copies in a single cell.

Multicysteine zinc finger

A type of zinc-finger DNA-binding domain.

Multigene family

A group of genes, clustered or dispersed, with related nucleotide sequences.

Multiple alignment

An alignment of three or more nucleotide sequences.

Multiple alleles

The different alternative forms of a gene that has more than two alleles.

Multiple hit or multiple substitution

The situation that occurs when a single nucleotide in a DNA sequence undergoes two mutational changes, giving rise to two new alleles, both of which differ from each other and from the parent at that nucleotide position.

Multipoint cross

A genetic cross in which the inheritance of three or more markers is followed.

Multiregional evolution

A hypothesis that holds that modern humans in the Old World are descended from Homo erectus populations that left Africa over 1 million years ago.

Mutagen

A chemical or physical agent that can cause a mutation in a DNA molecule.

Mutagenesis

Treatment of a group of cells or organisms with a mutagen as a means of inducing mutations.

Mutant

A cell or organism that possesses a mutation.

Mutasome

A protein complex that is constructed during the SOS response of Escherichia coli.

Mutation

An alteration in the nucleotide sequence of a DNA molecule.

Mutation scanning

A set of techniques for detection of mutations in DNA molecules.

Mutation screening

A set of techniques for determining if a DNA molecule contains a specific mutation.

N terminus

The end of a polypeptide that has a free amino group.

Natural selection

The preservation of favorable alleles and the rejection of injurious ones.

N-degron

An N-terminal amino acid sequence that influences the degradation of a protein in which it is found.

Neighbor-joining method

A method for construction of phylogenetic trees.

Nick

A position in a double-stranded DNA molecule where one of the polynucleotides is broken as a result of the absence of a phosphodiester bond.

Nitrogenous base

One of the purines or pyrimidines that form part of the molecular structure of a nucleotide.

N-linked glycosylation

The attachment of sugar units to an asparagine in a polypeptide.

Non-coding RNA

An RNA molecule that does not code for a protein.

Non-homologous end-joining (NHEJ)

Another name for the double-strand break repair process.

Non-penetrance

The situation whereby the effect of a mutation is never observed during the lifetime of a mutant organism.

Non-polar

A hydrophobic (water-hating) chemical group.

Nonsense-mediated RNA decay (NMD)

A process for degradation of eukaryotic mRNAs that is initiated by the presence of an internal termination codon.

Nonsense mutation

An alteration in a nucleotide sequence that changes a triplet coding for an amino acid into a termination codon.

Non-synonymous mutation

A mutation that converts a codon for one amino acid into a codon for a second amino acid.

Northern blotting

The transfer of RNA from an electrophoresis gel to a membrane prior to northern hybridization.

Northern hybridization

A technique used for detection of a specific RNA molecule against a background of many other RNA molecules.

Nuclear genome

The DNA molecules present in the nucleus of a eukaryotic cell.

Nuclear magnetic resonance (NMR) spectroscopy

A technique for determining the three-dimensional structure of large molecules.

Nuclear matrix

A proteinaceous scaffold-like network that permeates the cell.

Nuclear pore complex

The complex of proteins present at a nuclear pore.

Nuclear receptor superfamily

A family of receptor proteins that bind hormones as an intermediate step in modulation of genome activity by these hormones.

Nuclease

An enzyme that degrades a nucleic acid molecule.

Nuclease protection experiment

A technique that uses nuclease digestion to determine the positions of proteins on DNA or RNA molecules.

Nucleic acid

The term first used to describe the acidic chemical compound isolated from the nuclei of eukaryotic cells. Now used specifically to describe a polymeric molecule comprising nucleotide monomers, such as DNA and RNA.

Nucleic acid hybridization

Formation of a double-stranded hybrid by base-pairing between complementary polynucleotides.

Nucleoid

The DNA-containing region of a prokaryotic cell.

Nucleolus

The region of the eukaryotic nucleus in which rRNA transcription occurs.

Nucleoside

A purine or pyrimidine base attached to a five-carbon sugar.

Nucleosome

The complex of histones and DNA that is the basic structural unit in chromatin.

Nucleosome remodeling

A change in the conformation of a nucleosome, associated with a change in access to the DNA to which the nucleosome is attached.

Nucleotide

A purine or pyrimidine base attached to a five-carbon sugar, to which a mono-, di-, or triphosphate is also attached. The monomeric unit of DNA and RNA.

Nucleotide excision repair

A repair process that corrects various types of DNA damage by excising and resynthesizing a region of a polynucleotide.

Nucleus

The membrane-bound structure of a eukaryotic cell in which the chromosomes are contained.

Octamer module

A basal promoter element.

Okazaki fragment

One of the short segments of RNA-primed DNA synthesized during replication of the lagging strand of the double helix.

Oligonucleotide

A short synthetic single-stranded DNA molecule.

Oligonucleotide-directed mutagenesis

An in vitro mutagenesis technique in which a synthetic oligonucleotide is used to introduce a predetermined nucleotide alteration into the gene to be mutated.

Oligonucleotide hybridization analysis

The use of an oligonucleotide as a hybridization probe.

O-linked glycosylation

The attachment of sugar units to a serine or threonine in a polypeptide.

Open promoter complex

A structure formed during assembly of the transcription initiation complex consisting of the RNA polymerase and/or accessory proteins attached to the promoter, after the DNA has been opened up by breakage of base pairs.

Open reading frame (ORF)

A series of codons starting with an initiation codon and ending with a termination codon. The part of a protein-coding gene that is translated into protein.

Operational taxonomic unit (OTU)

One of the organisms being compared in a phylogenetic analysis.

Operator

The nucleotide sequence to which a repressor protein binds to prevent transcription of a gene or operon.

Operon

A set of adjacent genes in a bacterial genome, transcribed from a single promoter and subject to the same regulatory regime.

Optical mapping

A technique for the direct visual examination of restricted DNA molecules.

ORF scanning

Examination of a DNA sequence for open reading frames in order to locate the genes.

Origin of replication

A site on a DNA molecule where replication initiates.

Origin recognition complex (ORC)

A set of proteins that binds to the origin recognition sequence.

Origin recognition sequence

A component of a eukaryotic origin of replication.

Orphan family

A group of homologous genes whose functions are unknown.

Orthogonal field alternation gel electrophoresis (OFAGE)

An electrophoresis system in which the field alternates between pairs of electrodes set at an angle of 45°, used to separate large DNA molecules.

Orthologous

Refers to homologous genes located in the genomes of different organisms.

Outgroup

An organism or DNA sequence that is used to root a phylogenetic tree.

Out of Africa

A hypothesis which holds that modern humans evolved in Africa, moving to the rest of the Old World between 100 000 and 50 000 years ago, displacing the descendants of Homo erectus that they encountered.

Overlapping genes

Two genes whose coding regions overlap.

P1-derived artificial chromosome (PAC)

A high-capacity vector that combines features of bacteriophage P1 vectors and bacterial artificial chromosomes.

Pair-rule genes

Developmental genes that establish the basic segmentation pattern of the Drosophila embryo.

Pan-editing

The extensive insertion of nucleotides into an abbreviated RNA, resulting in a functional molecule.

Paralogous

Refers to two or more homologous genes located in the same genome.

Paranemic

Refers to a helix whose strands can be separated without unwinding.

Parental genotype

The genotype possessed by one or both of the parents in a genetic cross.

Parsimony

An approach that decides between different phylogenetic tree topologies by identifying the one that involves the shortest evolutionary pathway.

Partial linkage

The type of linkage usually displayed by a pair of genetic and/or physical markers on the same chromosome, the markers not always being inherited together because of the possibility of recombination between them.

Partial restriction

Digestion of DNA with a restriction endonuclease under limiting conditions so that not all restriction sites are cut.

Pedigree

A chart showing the genetic relationships between the members of a human family.

Pedigree analysis

The use of pedigree charts to analyze the inheritance of a genetic or DNA marker in a human family.

P element

A DNA transposon of Drosophila.

Pentose

A sugar comprising five carbon atoms.

Peptide bond

The chemical link between adjacent amino acids in a polypeptide.

Peptide nucleic acid (PNA)

A polynucleotide analog in which the sugar–phosphate backbone is replaced by amide bonds.

Peptidyl or P site

The site in the ribosome occupied by the tRNA attached to the growing polypeptide during translation.

Peptidyl transferase

The enzyme activity that synthesizes peptide bonds during translation.

Permissive conditions

Conditions under which a conditional-lethal mutant is able to survive.

PEST sequences

Amino acid sequences that influence the degradation of proteins in which they are found.

Phage

A virus that infects a bacterium.

Phage display

A technique for identifying proteins that interact with one another.

Phage display library

A collection of clones carrying different DNA fragments, used in phage display.

Phagemid

A cloning vector comprising a mixture of plasmid and phage DNA.

Phenetics

A classificatory approach based on the numerical typing of as many characters as possible.

Phenotype

The observable characteristics displayed by a cell or organism.

Phosphodiesterase

A type of enzyme that can break phosphodiester bonds.

Phosphodiester bond

The chemical link between adjacent nucleotides in a polynucleotide.

Phosphorimaging

An electronic method for determining the positions of radioactive markers in a microarray or on a hybridization membrane.

Photobleaching

A component of the FRAP technique for studying protein mobility in the nucleus.

Photolithography

A technique that uses pulses of light to construct an oligonucleotide from light-activated nucleotide substrates.

Photolyase

An Escherichia coli enzyme involved in photoreactivation repair.

Photoproduct

A modified nucleotide resulting from treatment of DNA with ultraviolet radiation.

Photoreactivation

A DNA repair process in which cyclobutyl dimers and (6–4) photoproducts are corrected by a light-activated enzyme.

Phylogeny

A classification scheme that indicates the evolutionary relationships between organisms.

Physical mapping

The use of molecular biology techniques to construct a genome map.

Pilus

A structure involved in bringing a pair of bacteria together during conjugation; possibly the tube through which DNA is transferred.

Plaque

A zone of clearing on a lawn of bacteria caused by lysis of the cells by infecting bacteriophages.

Plasmid

A usually circular piece of DNA often found in bacteria and some other types of cell.

Plectonemic

Refers to a helix whose strands can only be separated by unwinding.

Plesiomorphic character state

A character state possessed by a remote common ancestor of a group of organisms.

Point mutation

A mutation that results from a single nucleotide change in a DNA molecule.

Polar

A hydrophilic (water-loving) chemical group.

Polyacrylamide gel electrophoresis

Electrophoresis carried out in a polyacrylamide gel and used to separate DNA molecules between 10 and 1500 bp in length.

Polyadenylate-binding protein

A protein that aids poly(A) polymerase during polyadenylation of eukaryotic mRNAs, and which plays a role in maintenance of the tail after synthesis.

Polyadenylation

The addition of a series of As to the 3′ end of a eukaryotic mRNA.

Polyadenylation editing

A form of editing that occurs with many animal mitochondrial RNAs, resulting in a termination codon being formed by adding a poly(A) tail to an mRNA that ends with the nucleotides U or UA.

Poly (A) polymerase

The enzyme that attaches a poly(A) tail to the 3′ end of a eukaryotic mRNA.

Poly (A) tail

A series of A nucleotides attached to the 3′ end of a eukaryotic mRNA.

Polymer

A compound made up of a long chain of identical or similar units.

Polymerase chain reaction (PCR)

A technique that results in exponential amplification of a selected region of a DNA molecule.

Polymorphic

Refers to a locus that is represented by a number of different alleles or haplotypes in the population as a whole.

Polynucleotide

A single-stranded DNA or RNA molecule.

Polynucleotide kinase

An enzyme that adds phosphate groups to the 5′ ends of DNA molecules.

Polypeptide

A polymer of amino acids.

Polyphyletic

A group of DNA sequences that are derived from two or more distinct ancestral sequences.

Polyprotein

A translation product consisting of a series of linked proteins which are processed by proteolytic cleavage to release the mature proteins.

Polypyrimidine tract

A pyrimidine-rich region near the 3′ end of a GU–AG intron.

Polysome

An mRNA molecule that is being translated by more than one ribosome at the same time.

Positional cloning

A procedure that uses information on the map position of a gene to obtain a clone of that gene.

Positional effect

Refers to the different levels of expression that result after insertion of a gene at different positions in a eukaryotic genome.

Post-replication complex (post-RC)

A complex of proteins, derived from a pre-RC, that forms at a eukaryotic origin of replication during the replication process and ensures that the origin is used just once per cell cycle.

POU domain

A DNA-binding motif found in a variety of proteins.

Pre-initiation complex

The structure comprising the small subunit of the ribosome, the initiator tRNA plus ancillary factors that forms the initial association with the mRNA during protein synthesis. Also the structure that forms at the core promoter of a gene transcribed by RNA polymerase II.

Pre-mRNA

The primary transcript of a protein-coding gene.

Prepriming complex

A complex of proteins formed during initiation of replication in bacteria.

Pre-replication complex (pre-RC)

A protein complex that is constructed at a eukaryotic origin of replication and enables initiation of replication to occur.

Pre-RNA

The initial product of transcription of a gene or group of genes, subsequently processed to give the mature transcript(s).

Pre-rRNA

The primary transcript of a gene or group of genes specifying rRNA molecules.

Pre-spliceosome complex

An intermediate in the splicing pathway for a GU–AG intron.

Pre-tRNA

The primary transcript of a gene or group of genes specifying tRNA molecules.

Pribnow box

A component of the bacterial promoter.

Primary structure

The sequence of amino acids in a polypeptide.

Primary transcript

The initial product of transcription of a gene or group of genes, subsequently processed to give the mature transcript(s).

Primase

The RNA polymerase enzyme that synthesizes RNA primers during bacterial DNA replication.

Primer

A short oligonucleotide that is attached to a single-stranded DNA molecule in order to provide a start point for strand synthesis.

Primosome

A protein complex involved in genome replication.

Principal component analysis

A procedure that attempts to identify patterns in a large dataset of variable character states.

Prion

An unusual infectious agent that consists purely of protein.

Processed pseudogene

A pseudogene that results from integration into the genome of a reverse-transcribed copy of an mRNA.

Processivity

Refers to the amount of DNA synthesis that is carried out by a DNA polymerase before dissociation from the template.

Programmed frameshifting

The controlled movement of a ribosome from one reading frame to another at an internal position within a gene.

Programmed mutation

The possibility that under some circumstances an organism can increase the rate at which mutations occur in a specific gene.

Prokaryote

An organism whose cells lack a distinct nucleus.

Proliferating cell nuclear antigen (PCNA)

An accessory protein involved in genome replication in eukaryotes.

Proline-rich domain

A type of activation domain.

Promiscuous DNA

DNA that has been transferred from one organelle genome to another.

Promoter

The nucleotide sequence, upstream of a gene, to which RNA polymerase binds in order to initiate transcription.

Promoter clearance

The completion of successful initiation of transcription that occurs when the RNA polymerase moves away from the promoter sequence.

Promoter escape

The stage in transcription during which the polymerase moves away from the promoter region and becomes committed to making a transcript.

Proofreading

The 3′→5′ exonuclease activity possessed by some DNA polymerases which enables the enzyme to replace a misincorporated nucleotide.

Prophage

The integrated form of the genome of a lysogenic bacteriophage.

Protease

An enzyme that degrades protein.

Proteasome

A multi-subunit protein structure that is involved in the degradation of other proteins.

Protein

The polymeric compound made of amino acid monomers.

Protein electrophoresis

Separation of proteins in an electrophoresis gel.

Protein engineering

Various techniques for making directed alterations in protein molecules, often to improve the properties of enzymes used in industrial processes.

Protein folding

The adoption of a folded structure by a polypeptide.

Protein interaction map

A map showing the interactions between all or some of the proteins in a proteome.

Protein–protein crosslinking

A technique that links together adjacent proteins in order to identify proteins that are positioned close to one another in a structure such as a ribosome.

Proteome

The collection of functioning proteins synthesized by a living cell.

Proteomics

A variety of techniques used to study proteomes.

Protogenome

An RNA genome that existed during the RNA world.

Protoplast

A cell from which the cell wall has been completely removed.

Prototroph

An organism that has no nutritional requirements beyond those of the wild type and which can grow on minimal medium.

Pseudogene

An inactivated and hence non-functional copy of a gene.

Punctuation codon

A codon that specifies either the start or the end of a gene.

Punnett square

A tabular analysis for predicting the genotypes of the progeny resulting from a genetic cross.

Purine

One of the two types of nitrogenous base found in nucleotides.

Pyrimidine

One of the two types of nitrogenous base found in nucleotides.

Pyrosequencing

A novel DNA sequencing method in which addition of a nucleotide to the end of a growing polynucleotide is detected directly by conversion of the released pyrophosphate into a flash of chemiluminescence.

Quantitative PCR

A PCR method that enables the number of DNA molecules in a sample to be estimated.

Quaternary structure

The structure resulting from the association of two or more polypeptides.

RACE (rapid amplification of cDNA ends)

A PCR-based technique for mapping the end of an RNA molecule.

Radiation hybrid

A collection of rodent cell lines that contain different fragments of a second genome, constructed by a technique involving irradiation and used as a mapping reagent, for example in studies of the human genome.

Radioactive marker

A radioactive atom incorporated into a molecule and whose radioactive emissions are subsequently used to detect and follow that molecule during a biochemical reaction.

Radiolabeling

The technique for attaching a radioactive atom to a molecule.

Random genetic drift

The process that leads to alleles gradually changing their frequency in a population.

Ras

A protein involved in signal transduction.

Reading frame

A series of triplet codons in a DNA sequence.

Readthrough mutation

A mutation that changes a termination codon into a codon specifying an amino acid, and hence results in readthrough of the termination codon.

RecA

An Escherichia coli protein involved in homologous recombination.

RecBCD enzyme

An enzyme complex involved in homologous recombination in Escherichia coli.

Recessive

The allele that is not expressed in a heterozygote.

Reciprocal strand exchange

The exchange of DNA between two double-stranded molecules, occurring as a result of recombination, such that the end of one molecule is exchanged for the end of the other molecule.

Recognition helix

An α-helix in a DNA-binding protein, one that is responsible for recognition of the target nucleotide sequence.

Recombinant

A progeny member that possesses neither of the combinations of alleles displayed by the parents.

Recombinant DNA molecule

A DNA molecule created in the test tube by ligating pieces of DNA that are not normally joined together.

Recombinant DNA technology

The techniques involved in the construction, study and use of recombinant DNA molecules.

Recombinant protein

A protein synthesized in a recombinant cell as the result of expression of a cloned gene.

Recombinase

A diverse family of enzymes that catalyze site-specific recombination events.

Recombination

A large-scale rearrangement of a DNA molecule.

Recombination frequency

The proportion of recombinant progeny arising from a genetic cross.

Recombination hotspot

A region of a chromosome where crossovers occur at a higher frequency than the average for the chromosome as a whole.

Recombination repair

A DNA repair process that mends double-stranded breaks.

Regulatory control

Control over bacterial gene expression that depends on the influence of regulatory proteins.

Regulatory mutant

A mutant that has a defect in a promoter or other regulatory sequence.

Release factor

A protein that plays an ancillary role during termination of translation.

Renaturation

The return of a denatured molecule to its natural state.

Repetitive DNA

A DNA sequence that is repeated two or more times in a DNA molecule or genome.

Repetitive DNA fingerprinting

A clone fingerprinting technique that involves determining the positions of genome-wide repeats in cloned DNA fragments.

Repetitive DNA PCR

A clone fingerprinting technique that uses PCR to detect the relative positions of genome-wide repeats in cloned DNA fragments.

Replacement vector

A λ vector designed so that insertion of new DNA is by replacement of part of the non-essential region of the λ DNA molecule.

Replica plating

A technique for transfer of colonies from one Petri dish to another, such that their relative positions on the surface of the agar medium are retained.

Replication factor C (RFC)

A multi-subunit accessory protein involved in eukaryotic genome replication.

Replication factory

A large structure attached to the nuclear matrix; the site of genome replication.

Replication fork

The region of a double-stranded DNA molecule that is being opened up to enable DNA replication to occur.

Replication licensing factors (RLFs)

A set of proteins that regulate genome replication, in particular by ensuring that only one round of genome replication occurs per cell cycle.

Replication mediator protein (RMP)

A protein responsible for detachment of single-strand binding proteins during genome replication.

Replication origin

A site on a DNA molecule where replication initiates.

Replication protein A (RPA)

The main single-strand binding protein involved in replication of eukaryotic DNA.

Replication slippage

An error in replication that leads to an increase or decrease in the number of repeat units in a tandem repeat such as a microsatellite.

Replicative form

The double-stranded form of the M13 DNA molecule found within infected Escherichia coli cells.

Replicative transposition

Transposition that results in copying of the transposable element.

Replisome

A complex of proteins involved in genome replication.

Reporter gene

A gene whose phenotype can be assayed and which can therefore be used to determine the function of a regulatory DNA sequence.

Resolution

Separation of a pair of recombining double-stranded DNA molecules.

Response module

A sequence motif found upstream of various genes that enables transcription initiation by RNA polymerase II to respond to general signals from outside of the cell.

Restriction endonuclease

An enzyme that cuts DNA molecules at a limited number of specific nucleotide sequences.

Restriction fragment length polymorphism (RFLP)

A restriction fragment whose length is variable because of the presence of a polymorphic restriction site at one or both ends.

Restriction mapping

Determination of the positions of restriction sites in a DNA molecule by analyzing the sizes of restriction fragments.

Restrictive conditions

Conditions under which a conditional-lethal mutant is unable to survive.

Retroelement

A genetic element that transposes via an RNA intermediate.

Retroposon

A retroelement that does not have LTRs.

Retrotransposition

Transposition via an RNA intermediate.

Retrotransposon

A genome-wide repeat with a sequence similar to an integrated retroviral genome and possibly with retrotransposition activity.

Retroviral-like element (RTVL)

A truncated retroviral genome integrated into a host chromosome.

Retrovirus

A virus with an RNA genome that integrates into the genome of its host cell.

Reverse transcriptase

A polymerase that synthesizes DNA on an RNA template.

Reverse transcriptase PCR (RT-PCR)

PCR in which the first step is carried out by reverse transcriptase, so RNA can be used as the starting material.

Rho

A protein involved in termination of transcription of some bacterial genes.

Rho-dependent terminator

A position in bacterial DNA where termination of transcription occurs with the involvement of Rho.

Ribbon–helix–helix motif

A type of DNA-binding domain.

Ribonuclease

An enzyme that degrades RNA.

Ribonuclease D

An enzyme involved in processing pre-tRNA in bacteria.

Ribonuclease MRP

An enzyme involved in processing eukaryotic pre-rRNA.

Ribonuclease P

An enzyme involved in processing pre-tRNA in bacteria.

Ribonucleoprotein (RNP) domain

A common type of RNA-binding domain.

Ribose

The sugar component of a ribonucleotide.

Ribosomal protein

One of the protein components of a ribosome.

Ribosomal RNA (rRNA)

The RNA molecules that are components of ribosomes.

Ribosome

One of the protein–RNA assemblies on which translation occurs.

Ribosome binding site

The nucleotide sequence that acts as the attachment site for the small subunit of the ribosome during initiation of translation in bacteria.

Ribosome recycling factor (RRF)

A protein responsible for disassembly of the ribosome at the end of protein synthesis in bacteria.

Ribozyme

An RNA molecule that has catalytic activity.

RNA

Ribonucleic acid, one of the two forms of nucleic acid in living cells; the genetic material for some viruses.

RNA-dependent DNA polymerase

An enzyme that makes a DNA copy of an RNA template; a reverse transcriptase.

RNA-dependent RNA polymerase

An enzyme that makes an RNA copy of an RNA template.

RNA editing

A process by which nucleotides not coded by a gene are introduced at specific positions in an RNA molecule after transcription.

RNA interference

An RNA degradation process in eukaryotes.

RNA polymerase

An enzyme that synthesizes RNA on a DNA or RNA template.

RNA polymerase I

The eukaryotic RNA polymerase that transcribes ribosomal RNA genes.

RNA polymerase II

The eukaryotic RNA polymerase that transcribes protein-coding and snRNA genes.

RNA polymerase III

The eukaryotic RNA polymerase that transcribes tRNA and other short genes.

RNA transcript

An RNA copy of a gene.

RNA world

The early period of evolution when all biological reactions were centered on RNA.

Rolling circle replication

A replication process that involves continual synthesis of a polynucleotide which is ‘rolled off’ of a circular template molecule.

Rooted

Refers to a phylogenetic tree that provides information on the past evolutionary events that have led to the organisms or DNA sequences being studied.

S phase

The stage of the cell cycle when DNA synthesis occurs.

S value

The unit of measurement for a sedimentation coefficient.

S1 nuclease

An enzyme that degrades single-stranded DNA or RNA molecules, including single-stranded regions in predominantly double-stranded molecules.

SAP (stress activated protein) kinase

A stress-activated signal transduction pathway.

Satellite DNA

Repetitive DNA that forms a satellite band in a density gradient.

Scaffold

A series of sequence contigs separated by sequence gaps.

Scaffold attachment region (SAR)

An AT-rich segment of a eukaryotic genome that acts as an attachment point to the nuclear matrix.

Scanning

A system used during initiation of eukaryotic translation, in which the pre-initiation complex attaches to the 5′-terminal cap structure of the mRNA and then scans along the molecule until it reaches an initiation codon.

Second messenger

An intermediate in a certain type of signal transduction pathway.

Secondary structure

The conformations, such as α-helix and β-sheet, taken up by a polypeptide.

Sedimentation analysis

The centrifugal technique used to measure the sedimentation coefficient of a molecule or structure.

Sedimentation coefficient

The value used to express the velocity at which a molecule or structure sediments when centrifuged in a dense solution.

Segment polarity genes

Developmental genes that provide greater definition to the segmentation pattern of the Drosophila embryo established by the action of the pair-rule genes.

Segregation

The separation of homologous chromosomes, or members of allele pairs, into different gametes during meiosis.

Selectable marker

A gene carried by a vector and conferring a recognizable characteristic on a cell containing the vector or a recombinant DNA molecule derived from the vector.

Selective medium

A medium that supports the growth of only those cells that carry a particular genetic marker.

Selfish DNA

DNA that appears to have no function and apparently contributes nothing to the cell in which it is found.

Semiconservative replication

The mode of DNA replication in which each daughter double helix is made up of one polynucleotide from the parent and one newly synthesized polynucleotide.

Sequenase

An enzyme used in chain termination DNA sequencing.

Sequence contig

A contiguous DNA sequence obtained as an intermediate in a genome sequencing project.

Sequence skimming

A method for rapid sequence acquisition in which a few random sequences are obtained from a cloned fragment, the rationale being that if the fragment contains any genes then there is a good chance that at least some of them will be revealed by these random sequences.

Sequence tagged site (STS)

A DNA sequence that is unique in the genome.

Serial analysis of gene expression (SAGE)

A method for studying the composition of a transcriptome.

Sex cell

A reproductive cell; a cell that divides by meiosis.

Sex chromosome

A chromosome that is involved in sex determination.

Shine–Dalgarno sequence

The ribosome binding site upstream of an Escherichia coli gene.

Short interfering RNA (siRNA)

An intermediate in the RNA interference pathway.

Short patch repair

A nucleotide excision repair process of Escherichia coli that results in excision and resynthesis of about 12 nucleotides of DNA.

Short tandem repeat (STR)

A type of simple sequence length polymorphism comprising tandem copies of, usually, di-, tri- or tetranucleotide repeat units. Also called a microsatellite.

Shotgun approach

A genome sequencing strategy in which the molecules to be sequenced are randomly broken into fragments which are then sequenced individually.

Shuttle vector

A vector that can replicate in the cells of more than one organism (e.g. in Escherichia coli and in yeast).

Signal peptide

A short sequence at the N terminus of some proteins that directs the protein across a membrane.

Signal transduction

Control of cellular activity, including genome expression, via a cell-surface receptor that responds to an external signal.

Silencer

A regulatory sequence that reduces the rate of transcription of a gene or genes located some distance away in either direction.

Silent mutation

A change in a DNA sequence that has no effect on the expression or functioning of any gene or gene product.

Similarity approach

A rigorous mathematical approach to alignment of nucleotide sequences.

Simple sequence length polymorphism (SSLP)

An array of repeat sequences that display length variations.

SINE (short interspersed nuclear element)

A type of genome-wide repeat, typified by the Alu sequences found in the human genome.

Single-copy DNA

A DNA sequence that is not repeated elsewhere in the genome.

Single nucleotide polymorphism (SNP)

A point mutation that is carried by some individuals of a population.

Single orphan

A single gene, with no homolog, whose function is unknown.

Single-strand binding protein (SSB)

One of the proteins that attach to single-stranded DNA in the region of the replication fork, preventing base pairs forming between the two parent strands before they have been copied.

Single stranded

A DNA or RNA molecule that comprises just a single polynucleotide.

Site-directed hydroxyl radical probing

A technique for locating the position of a protein in a protein–RNA complex, such as a ribosome, by making use of the ability of Fe(II) ions to generate hydroxyl radicals which cleave nearby RNA phosphodiester bonds.

Site-directed mutagenesis

Techniques used to produce a specified mutation at a predetermined position in a DNA molecule.

Site-specific recombination

Recombination between two double-stranded DNA molecules that have only short regions of nucleotide sequence similarity.

Slippage

The translocation of a ribosome along a short non-coding nucleotide sequence between the termination codon of one gene and the initiation codon of a second gene.

SMAD family

A group of proteins involved in signal transduction.

Small cytoplasmic RNA (scRNA)

A type of short eukaryotic RNA molecule with various roles in the cell.

Small nuclear ribonucleoprotein (snRNP)

Structures involved in splicing GU–AG and AU–AC introns and in other RNA processing events, comprising one or two snRNA molecules complexed with proteins.

Small nuclear RNA (snRNA)

A type of short eukaryotic RNA molecule involved in splicing GU–AG and AU–AC introns and in other RNA processing events.

Small nucleolar RNA (snoRNA)

A type of short eukaryotic RNA molecule involved in chemical modification of rRNA.

Somatic cell

A non-reproductive cell; a cell that divides by mitosis.

Sonication

A procedure that uses ultrasound to cause random breaks in DNA molecules.

SOS response

A series of biochemical changes that occur in Escherichia coli in response to damage to the genome and other stimuli.

Southern hybridization

A technique used for detection of a specific restriction fragment against a background of many other restriction fragments.

Species tree

A phylogenetic tree that shows the evolutionary relationships between a group of species.

Spliceosome

The protein–RNA complex involved in splicing GU–AG or AU–AC introns.

Splicing

The removal of introns from the primary transcript of a discontinuous gene.

Splicing pathway

The series of events that converts a discontinuous pre-mRNA into a functional mRNA.

Spontaneous mutation

A mutation that arises from an error in replication.

SR-like CTD-associated factor (SCAF)

Proteins thought to play regulatory roles during splicing of GU–AG introns.

SR protein

A protein that plays a role in splice-site selection during splicing of GU–AG introns.

STAT (signal transducer and activator of transcription)

A type of protein that responds to binding of an extracellular signaling compound to a cell surface receptor by activating a transcription factor.

Stem cell

A progenitor cell that divides continually throughout the lifetime of an organism.

Stem-loop structure

A structure made up of a base-paired stem and non-base-paired loop, which can form in a single-stranded polynucleotide that contains an inverted repeat.

Steroid hormone

A type of extracellular signaling compound.

Steroid receptor

A protein that binds a steroid hormone after the latter has entered the cell, as an intermediate step in modulation of genome activity.

Sticky end

An end of a double-stranded DNA molecule where there is a single-stranded extension.

Strong promoter

A promoter that directs a relatively large number of productive initiations per unit time.

Structural domain

A segment of a polypeptide that folds independently of other segments. Also, a loop of eukaryotic DNA, predominantly in the form of the 30 nm chromatin fiber, attached to the nuclear matrix.

STS mapping

A physical mapping procedure that locates the positions of sequence tagged sites (STSs) in a genome.

Stuffer fragment

A DNA fragment contained within a λ vector that is replaced by the DNA to be cloned.

Substitution mutation

Commonly used as a synonym for a point mutation.

Supercoiling

A conformational state in which a double helix is overwound or underwound so that superhelical coiling occurs.

Superwobble

The extreme form of wobble that occurs in vertebrate mitochondria.

Suppressor mutation

A mutation in one gene that reverses the effect of a mutation in a second gene.

Syncytium

A cell-like structure comprising a mass of cytoplasm and many nuclei.

Synonymous mutation

A mutation that changes a codon into a second codon that specifies the same amino acid.

Synteny

Refers to a pair of genomes in which at least some of the genes are located at similar map positions.

TψC arm

Part of the structure of a tRNA molecule.

T4 polynucleotide kinase

An enzyme that adds phosphate groups to the 5′ ends of DNA molecules.

TAF and initiator-dependent cofactor (TIC)

A type of protein involved in initiation of transcription by RNA polymerase II.

Tandemly repeated DNA

DNA sequence motifs that are repeated head to tail.

Tandem repeat

Direct repeats that are adjacent to each other.

TATA-binding protein (TBP)

A component of the general transcription factor TFIID, the part that recognizes the TATA box of the RNA polymerase II promoter.

TATA box

A component of the RNA polymerase II core promoter.

Tautomeric shift

The spontaneous change of a molecule from one structural isomer to another.

Tautomers

Structural isomers that are in dynamic equilibrium.

TBP-associated factor (TAF)

One of several components of the general transcription factor TFIID, playing ancillary roles in recognition of the TATA box.

TBP domain

A type of DNA-binding domain.

T-DNA

The portion of the Ti plasmid that is transferred to the plant DNA.

Telomerase

The enzyme that maintains the ends of eukaryotic chromosomes by synthesizing telomeric repeat sequences.

Telomere

The end of a eukaryotic chromosome.

Telomere binding protein (TBP)

A protein that binds to and regulates the length of a telomere.

Temperature-sensitive mutation

A type of conditional-lethal mutation, one that is expressed only above a threshold temperature.

Template

The polynucleotide that is copied during a strand synthesis reaction catalyzed by a DNA or RNA polymerase.

Template-dependent DNA polymerase

An enzyme that synthesizes DNA in accordance with the sequence of a template.

Template-dependent DNA synthesis

Synthesis of a DNA molecule on a DNA or RNA template.

Template-dependent RNA polymerase

An enzyme that synthesizes RNA in accordance with the sequence of a template.

Template-dependent RNA synthesis

Synthesis of an RNA molecule on a DNA or RNA template.

Template-independent DNA polymerase

An enzyme that synthesizes DNA without the use of a template.

Template-independent RNA polymerase

An enzyme that synthesizes RNA without the use of a template.

Template strand

The polynucleotide that acts as the template for RNA synthesis during transcription of a gene.

Terminal deoxynucleotidyl transferase

An enzyme that adds one or more nucleotides to the 3′ end of a DNA molecule.

Termination codon

One of the three codons that mark the position where translation of an mRNA should stop.

Termination factor

A protein that plays an ancillary role in termination of transcription.

Terminator sequence

One of several sequences on a bacterial genome involved in termination of genome replication.

Tertiary structure

The structure resulting from folding the secondary structural units of a polypeptide.

Test cross

A genetic cross between a double heterozygote and a double homozygote.

Thermal cycle sequencing

A DNA sequencing method that uses PCR to generate chain-terminated polynucleotides.

Thermostable

Able to withstand high temperatures.

Thymine

One of the pyrimidine bases found in DNA.

Ti plasmid

The large plasmid found in those Agrobacterium tumefaciens cells able to direct crown gall formation on certain species of plants.

Tm

Melting temperature.

Tn3-type transposon

A type of DNA transposon that does not have flanking insertion sequences.

Topology

The branching pattern of a phylogenetic tree.

Totipotent

Refers to a cell that is not committed to a single developmental pathway and can hence give rise to all types of differentiated cell.

Trailer segment

The untranslated region of an mRNA downstream of the termination codon.

Transcript

An RNA copy of a gene.

Transcription

The synthesis of an RNA copy of a gene.

Transcription bubble

The non-base-paired region of the double helix, maintained by RNA polymerase, within which transcription occurs.

Transcription-coupled repair

A nucleotide excision repair process that results in repair of the template strands of genes.

Transcription factory

A large structure attached to the nuclear matrix; the site of RNA synthesis.

Transcription initiation

The assembly, upstream of a gene, of the complex of proteins that will subsequently copy the gene into RNA.

Transcriptome

The entire mRNA content of a cell.

Transcript-specific regulation

Regulatory mechanisms that control protein synthesis by acting on a single transcript or a small group of transcripts coding for related proteins.

Trans-displacement

Transfer of a nucleosome from one DNA molecule to another.

Transduction

Transfer of bacterial genes from one cell to another by packaging in a phage particle.

Transduction mapping

The use of transduction to map the relative positions of genes in a bacterial genome.

Transfection

The introduction of purified phage DNA molecules into a bacterial cell.

Transfer-messenger RNA (tmRNA)

A bacterial RNA involved in protein degradation.

Transfer RNA (tRNA)

A small RNA molecule that acts as an adaptor during translation and is responsible for decoding the genetic code.

Transformant

A cell that has become transformed by the uptake of naked DNA.

Transformation

The acquisition by a cell of new genes by the uptake of naked DNA.

Transformation mapping

The use of transformation to map the relative positions of genes in a bacterial genome.

Transforming principle

The compound, now known to be DNA, responsible for transformation of an avirulent Streptococcus pneumoniae bacterium into a virulent form.

Transgenic mouse

A mouse that carries a cloned gene.

Transition

A point mutation that replaces a purine with another purine, or a pyrimidine with another pyrimidine.

Translation

The synthesis of a polypeptide, the amino acid sequence of which is determined by the nucleotide sequence of an mRNA in accordance with the rules of the genetic code.

Translational bypassing

A form of slippage in which a large part of an mRNA is skipped during translation, elongation of the original protein continuing after the bypassing event.

Translocation

The movement of a ribosome along an mRNA molecule during translation.

Transposable element

A genetic element that can move from one position to another in a DNA molecule.

Transposable phage

A bacteriophage that transposes as part of its infection cycle.

Transposase

An enzyme that catalyzes transposition of a transposable genetic element.

Transposition

The movement of a genetic element from one site to another in a DNA molecule.

Transposon

A genetic element that can move from one position to another in a DNA molecule.

Transposon tagging

A gene isolation technique that involves inactivation of a gene by movement of a transposon into its coding sequence, followed by the use of a transposon-specific hybridization probe to isolate a copy of the tagged gene from a clone library.

Transversion

A point mutation that involves a purine being replaced by a pyrimidine, or vice versa.

Trinucleotide repeat expansion disease

A disease that results from the expansion of an array of trinucleotide repeats in or near to a gene.

Triplet binding assay

A technique for determining the coding specificity of a triplet of nucleotides.

Triplex

A DNA structure comprising three polynucleotides.

Trisomy

The presence of three copies of a homologous chromosome in a nucleus that is otherwise diploid.

tRNA nucleotidyltransferase

The enzyme responsible for the post-transcriptional attachment of the triplet 5′–CCA–3′ to the 3′ end of a tRNA molecule.

trp RNA-binding attenuation protein (TRAP)

A protein involved in attenuation regulation of some operons in bacteria such as Bacillus subtilis.

True tree

A phylogenetic tree that depicts the actual series of evolutionary events that led to the group of organisms or DNA sequences being studied.

Truncated gene

A gene relic that lacks a segment from one end of the original, complete gene.

Tus

The protein that binds to a bacterial terminator sequence and mediates termination of genome replication.

Twintron

A composite structure made up of two or more Group II and/or Group III introns embedded in each other.

Two-dimensional gel electrophoresis

A method for separation of proteins used especially in studies of the proteome.

Type 0 cap

The basic cap structure, consisting of 7-methylguanosine attached to the 5′ end of an mRNA.

Type 1 cap

A cap structure comprising the basic 5′-terminal cap plus an additional methylation of the ribose of the second nucleotide.

Type 2 cap

A cap structure comprising the basic 5′-terminal cap plus methylation of the riboses of the second and third nucleotides.

Ubiquitin

A 76-amino-acid protein which, when attached to a second protein, acts as a tag directing that protein for degradation.

Unequal crossing-over

A recombination event that results in duplication of a segment of DNA.

Unequal sister chromatid exchange

A recombination event that results in duplication of a segment of DNA.

Unit factor

Mendel’s term for a gene.

Unrooted

Refers to a phylogenetic tree that merely illustrates relationships between the organisms or DNA sequences being studied, without providing information about the past evolutionary events that have occurred.

Upstream

Towards the 5′ end of a polynucleotide.

Upstream control element

A component of an RNA polymerase I promoter.

Upstream promoter element

Components of a eukaryotic promoter that lie upstream of the position where the initiation complex is assembled.

Uracil

One of the pyrimidine bases found in RNA.

U-RNA

A uracil-rich nuclear RNA molecule including the snRNAs and snoRNAs.

UvrABC endonuclease

A multienzyme complex involved in the short patch repair process of Escherichia coli.

V loop

Part of the structure of a tRNA molecule.

van der Waals forces

A particular type of attractive or repulsive non-covalent bond.

Variable number of tandem repeats (VNTR)

A type of simple sequence length polymorphism comprising tandem copies of repeats that are a few tens of nucleotides in length. Also called a minisatellite.

Vegetative cell

A non-reproductive cell; a cell that divides by mitosis.

Wave of advance

A hypothesis which holds that the spread of agriculture into Europe was accompanied by a large-scale movement of human populations.

Weak promoter

A promoter that directs relatively few productive initiations per unit time.

Whole-genome shotgun approach

A genome sequencing strategy which combines random shotgun sequencing with a genome map, the latter used to aid assembly of the master sequence.

Wild type

A gene, cell or organism that displays the typical phenotype and/or genotype for the species and is therefore adopted as a standard.

Winged helix–turn–helix

A type of DNA-binding domain.

Wobble hypothesis

The process by which a single tRNA can decode more than one codon.

X inactivation

Inactivation by methylation of most of the genes on one copy of the X chromosome in a female nucleus.

X-ray crystallography

A technique for determining the three-dimensional structure of a large molecule.

X-ray diffraction

The diffraction of X-rays that occurs during passage through a crystal.

X-ray diffraction pattern

The pattern obtained after diffraction of X-rays through a crystal.

Yeast artificial chromosome (YAC)

A high-capacity cloning vector constructed from the components of a yeast chromosome.

Yeast two-hybrid system

A technique for identifying proteins that interact with one other.

Z-DNA

A conformation of DNA in which the two polynucleotides are wound into a left-handed helix.

Zinc finger

A common structural motif for attachment of a protein to a DNA molecule.

Zoo blotting

A technique that attempts to determine if a DNA fragment contains a gene by hybridizing that fragment to DNA preparations from related species, on the basis that genes have similar sequences in related species and so give positive hybridization signals, whereas the regions between genes have less similar sequences and so do not hybridize.

Zygote

The cell resulting from fusion of gametes during meiosis.

Copyright © 2002, Garland Science.
Bookshelf ID: NBK21126

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