Some of the definitions in this glossary have been modified or taken directly from the glossaries of the following books:

Wolpert L, Beddington R, Jessell T, Lawrence P, Meyerowitz E, Smith J. 2002. Principles of Development, 2nd ed. Oxford University Press, New York.

Alberts B, Bray D, Lewis J, Raff M, Roberts K, Watson JD. 1994. Molecular Biology of the Cell, 3rd ed. Garland Publishing Inc., New York.

32P: A radioactive isotope of phosphorus. Term used sloppily in molecular biology to indicate any chemical compound containing 32P made for the purposes of labelling biological molecules such as DNA and RNA. For some reason, normally referred to as “P32.”

Adenovirus: A medium-sized virus with a linear double-stranded DNA genome. Causes a wide range of human illnesses such as respiratory infections and conjunctivitis.

Allele: One of a set of alternative forms of a gene. In most cells, each gene will have two alleles, each occupying the same position (locus) on homologous (paired) chromosomes.

Amino acid: Organic molecule containing both an amino group and a carboxyl group. The building blocks of proteins.

Amino terminus: The front end of a polypeptide chain or protein.

Anterior: In developmental biology, the head end of an embryo. The antero–posterior axis defines which is the head end and which is the tail end of an animal or structure (in the limb, the thumb is anterior, the little finger is posterior).

Antibody: Protein produced by the body in response to a foreign molecule or organism. In the laboratory, is used to detect and bind tightly to its antigen.

Antigen: Molecule that provokes an immune response, including the production of antibodies.

Antiserum: Blood serum containing a mixture of antibodies.

Apoptosis: Programmed cell death.

ATP: Adenosine 5′ triphosphate, used by many enzymes as an energy source.

ATPase: An enzyme that catalyses the conversion of ATP into adenosine diphosphate, in the process generating energy. ATPases tend to be the power sources driving molecular machinery such as the complexes that replicate DNA.

Autocrine: A form of signalling in which a cell secretes a molecule such as a growth factor that then binds and signals back into the same cell. Tumours use autocrine signalling to force their own growth.

Autosome: Any chromosome except the X or Y sex chromosomes.

Bacteriophage: Tiny virus able to infect bacteria. The foundation upon which molecular biology was built.

Base (A, C, G, T): Used in this book to refer to the purines (A, adenine; G, guanine) and pyrimidines (C, cytosine; T, thymidine; and U, uracil) in DNA and RNA.

Biochemistry: The chemistry of living things.

Blotting: The process by which, subsequent to gel electrophoresis, whole gels can be transferred to membranes. The membranes can be probed with labelled DNA or RNA or antibodies, to visualise specific bands. Southern blotting: The original gel was loaded with DNA. Northern blotting: The gel was loaded with RNA. Western blotting: The gel was loaded with protein.

Branch migration: The process in which a crossover point between two DNA double helices slides along the helices.

Buffer: Generic name for the solutions, containing various mixes of chemicals, in which experiments are performed. Called buffers because they contain chemicals that hold the pH of the solution steady.

Carboxyl terminus: The back end of a polypeptide chain or protein.

Cell cycle: The period between the formation of a cell by division of its mother cell and the time when the cell itself divides to form two daughters.

Checkpoint: Point in the cell cycle where progress can be halted until conditions are suitable for the cell to proceed to the next stage. Thus, checkpoint control: the mechanism by which the cell detects damage or unfavourable events and halts the cycle.

Cloning: Exact duplication of a molecule or organism. Also used as a verb: “to clone a gene,” meaning to produce many copies of a gene by repeated cycles of replication.

Cloning vector: A genetic element, usually a plasmid, bacteriophage, or virus, that is used to carry a fragment of DNA into a recipient cell for the purpose of gene cloning.

Codon: Sequence of three nucleotides in a DNA or messenger RNA molecule that represents the instruction for incorporation of a specific amino acid into a growing polypeptide chain.

Complementary strand: Two strands of DNA are said to be complementary if they can form a perfect base-paired double helix with one another.

Complementation: In genetics, complementation is used to test whether two mutant strains that produce the same phenotype (e.g., a change in wing structure in flies), carry dud copies of the same or different genes. The test only works if the mutation is homozygous recessive; that is, if it only shows up when both copies of the gene are mutated. If, when the strains are crossed with each other, some offspring look normal, then the two mutations must be in different genes; the mutant copy of each gene is being rescued (“complemented”) by the normal copy from the other parent.

Conditional mutant: A mutant that only kicks in under certain physiological conditions such as increased temperature.

Cyclins: Proteins that periodically rise and fall in concentration in step with the eukaryotic cell cycle. Cyclins activate crucial protein kinases (called cyclin-dependent protein kinases, or CDKs) and thereby help control progression from one stage of the cell cycle to the next.

Cyclin-dependent protein kinase (CDK): A protein kinase that has to be complexed with a cyclin protein in order to act; different Cdk–cyclin complexes control progression of many of the cellular reactions involved in the regulation and execution of the cell cycle.

Cytoplasm: Contents of a cell that are contained within its outer plasma membrane, but, in the case of eukaryotic cells, outside the nucleus.

Dephosphorylation: The process of stripping phosphate groups off proteins or other biological molecules. Catalysed by enzymes called phosphatases.

Diploid: Containing two sets of homologous chromosomes and hence two copies of each gene.

DNA: Deoxyribonucleic acid. The carrier of genetic information.

DNA sequence: The order of nucleotides in a DNA molecule. Thus, DNA sequencing, the process of determining the order of nucleotides in a DNA molecule.

DNA tumour virus: Double-stranded DNA eukaryotic-specific virus able to cause cancer.

Dorsal: The upper surface, or back, of an embryo. As opposed to the ventral, or under surface. The dorso–ventral axis defines the relation of the back to the under surface of an organism or structure.

Enzyme: Protein that catalyses (accelerates, but is not changed by) a specific chemical reaction.

Eukaryote: Living organism composed of one or more cells with a distinct nucleus and cytoplasm. Includes all forms of life except viruses, bacteria, and archaea.

Excision repair: Process by which DNA is repaired by cutting out the damaged section and filling it in again using the opposite strand of DNA as a template.

Extract (protein, cell-free): What you get if you pop cells open. Depending on the method of preparation, extracts can be full of proteins, DNA, and/or RNA, just the contents of the nucleus, just the contents of the cytoplasm, and so on.

Fibroblast: Common cell type found in connective tissue. Migrates and proliferates readily in wounded tissue and in tissue culture.

Floor plate: Part of the developing neural tube (which goes on to become the spinal cord). Composed of nonneural cells and vitally important for patterning of the ventral part of the neural tube.

G1 phase: Gap 1 phase of the eukaryotic cell cycle, between the end of cell division and the start of DNA synthesis.

G2 phase: Gap 2 phase of the eukaryotic cell cycle, between the end of DNA synthesis and the beginning of mitosis.

Gap genes: Zygotic genes (i.e., those present in the fertilised egg, not coming from the mother) coding for transcription factors expressed in early Drosophila development that subdivide the embryo into regions along the antero–posterior (i.e., head to tail) axis.

Gel electrophoresis: A method for separation and analysis of DNA, RNA, and proteins, and their fragments, based on their size and charge. Molecules are separated by applying an electric field to move the negatively charged molecules through a gel matrix. Smaller molecules move faster and therefore migrate farther than larger ones.

Gene: Region of DNA that controls a single hereditary characteristic.

Genome: Total genetic information carried by a cell or an organism.

Genotype: Genetic makeup of a cell or an organism.

Germline: The lineage of germ cells, that is, those cells that contribute to the formation of a new generation of organisms; distinct from somatic cells, which form the body and leave no descendants in the next generation.

Gradient (e.g., sucrose, lactose): Running molecules down a gradient is a method of separating DNA, RNA, or proteins by centrifugation, based on their buoyant density. Gradients are made using buffers containing varying amounts of viscous molecules such as sucrose or lactose. The sample is loaded on top of the gradient in a test tube, and the tube is spun at high g force over set periods of time. Different-sized molecules migrate down the gradient until they reach the point at which the density of the gradient is the same as their own.

Growth factor: Extracellular polypeptide signalling molecule that stimulates a cell to grow or proliferate. Most growth factors have other actions beside the induction of cell growth or proliferation, depending on the circumstances in which they find themselves.

Holliday junction: A mobile junction between four strands of DNA. The structure is named after Robin Holliday, who proposed it in 1964 to account for a particular type of exchange of genetic information that he observed in yeast known as homologous recombination. Holliday junctions are highly conserved structures, from prokaryotes to mammals.

Homeobox: Region of DNA in homeotic genes that encodes a DNA-binding domain called the homeodomain. Genes containing this motif are called homeobox genes. The homeodomain is present in a large number of transcription factors that are important in development.

Homeotic mutation: A mutation that gives rise to a homeotic transformation—the transformation of one structure into another.

Homologous chromosome: One of two copies of a particular chromosome in a diploid cell, each copy being derived from a different parent.

Homologous genes: Genes sharing significant similarity in their nucleotide sequences indicating that they are derived from a common ancestor.

Homologous recombination: The recombination of two DNA molecules at a specific site of sequence similarity.

Homologues: Genes from different species that share a common ancestry or have a common function.

Homology: Morphological or structural similarity due to common ancestry.

Immortalise: To generate a cell line capable of an unlimited number of cell divisions.

Immunoglobulin: An antibody molecule.

Immunoprecipitation: The method by which a specific protein can be fished out of a general mix, using as bait an antibody directed against it.

In vitro: Term used by biochemists to describe a process taking place in an isolated cell-free extract. Also used to describe cells growing in culture as opposed to in an organism.

In vivo: In an intact cell or organism.

Insert (n): A fragment of DNA carried in a cloning vector.

Journal hierarchy: Publishing in certain journals carries a great deal of prestige with it. Nature and Science are the generalist journals that sit at the top of the heap, with Cell not far behind. Proceedings of the National Academy of Science USA (PNAS) used to be a way of getting interesting data out fast, because Academy members could submit a few papers a year without review. The preeminence of certain journals, and therefore their editors, is a matter of enduring irritation to many scientists, who nevertheless collaborate with a system they dislike in the interests of career advancement.

Junction resolution: Process by which a Holliday junction is cut and resolved into two separate double helices.

Kinase: An enzyme catalysing the addition of a phosphate group to a protein or other molecule. Kinases and phosphatases are the regulatory kings of the cell because phosphorylation can rapidly and dramatically alter the properties of a molecule.

Library: In this book, used to describe a set of fragments of DNA, cloned into an appropriate vector, which together encompass all or a large part of the genes present in a given organism.

Licensing Factor: The name given to the protein factor that determines when cells started replicating their DNA. Biochemically, it is the highly regulated replication complex that binds to origins and initiates replication.

Ligase: An enzyme that joins together two molecules in an energy-dependent process. DNA ligase links two DNA molecules together through a phosphodiester bond. Used in the last step of repair reactions and also as a vital component of DNA cloning, where it is used to glue fragments together.

Linkage: Coinheritance of two genetic loci that lie near each other on the same chromosome; the greater the linkage, the lower the frequency of recombination between the two loci, and the nearer they must be.

Locus: In genetics, the position of a gene on a chromosome. Different alleles of the same gene all occupy the same locus.

Lysis: Rupture of a cell's plasma membrane, leading to the release of cytoplasm and the death of the cell. Many viruses lyse cells as part of their life cycle, and it is also used in the laboratory to get at the cell's contents for a lysate, or extract.

Mass spectrometer: An instrument that can measure the masses and relative concentrations of atoms and molecules. It makes use of the basic magnetic force on a moving charged particle. It can be used as a way of identifying proteins, which all have unique signatures.

Media: Generic name for the solutions needed for growing cells.

Mercaptoethanol: A somewhat toxic chemical smelling strongly of rotten eggs. Beloved of biochemists because it helps stabilise proteins taken out of their natural milieu.

Messenger RNA (mRNA): RNA molecule that specifies the amino acid sequence of a protein. Produced by RNA splicing (in eukaryotes) from a larger RNA molecule made by RNA polymerase as a complementary copy of DNA. It is translated into protein in a process catalysed by ribosomes.

Mitosis: Division of the nucleus of a eukaryotic cell, involving condensation of the DNA into visible chromosomes.

Molecular biology: The branch of biology that deals with the molecular basis of biological activity.

Monoclonal antibody: Antibody secreted by a hybridoma clone. Because each such clone is derived from a single B cell, all of the antibody molecules it makes are identical.

Morphogen: Any substance active in pattern formation whose spatial concentration varies and to which cells respond differently at different threshold concentrations.

Neurulation: The process in vertebrates in which the ectoderm of the future brain and spinal cord—the neural plate—develops folds (neural folds) and forms the neural tube.

Neuron: A nerve cell. The electrically excitable cells of the nervous system that convey information in the form of electrical signals.

Notochord: In vertebrate embryos, a rod-like cellular structure that runs from head to tail and lies centrally beneath the future central nervous system.

Nuclease: An enzyme able to cut nucleic acids, either RNA, in which case they are called RNases, or DNA, in which case they are DNases.

Nucleoprotein: Any protein that is structurally associated with DNA or RNA.

Nucleosome: Structural, beadlike unit of a eukaryotic chromosome composed of a short length of DNA wrapped around a core of histone proteins; the fundamental subunit of chromatin.

Nucleoside: Compound composed of a purine or pyrimidine base linked to either a ribose or a deoxyribose sugar (in DNA, the sugar is a deoxyribose, and in RNA, it is a ribose).

Nucleotide: Nucleoside with one or more phosphate groups joined to its sugar moiety. DNA and RNA are polymers of nucleotides.

Nucleus: The central compartment of a eukaryotic cell, containing DNA organised into chromosomes.

O levels: Between 1950 and 1988, the exams taken by 15–16 year olds in Britain. Typically sat in eight to 12 subjects. Followed by a smaller number of A levels, taken at 17–18 years of age, and necessary for university entrance.

Oligonucleotide: Polymerised nucleotides. Generally used to describe short pieces of DNA.

Oncogene: Gene capable of causing cancer. Typically, a mutant form of a normal gene (proto-oncogene) involved in the control of cell growth or division.

Oncoprotein: Protein product of an oncogene.

Organiser: In developmental biology, a signalling centre that directs the development of a whole embryo or of part of the embryo, such as a limb.

Origin of replication: Specific region in a DNA molecule from which replication starts. In bacteria, there is just one origin of replication. In mammals, there are tens of thousands.

Pair-rule gene: Drosophila gene involved in specifying the boundaries of parasegments. They are expressed in transverse stripes in the blastoderm, each pair-rule gene being expressed in alternate parasegments.

Parasegments: In the developing Drosophila embryo, parasegments are independent developmental units that give rise to the segments of the larva and adult.

Peptide: Very short linear polymer of amino acids.

Phage: See bacteriophage.

Phenotype: The observable or measurable characters and features of a cell or organism.

Phosphorylation: Process of adding phosphate groups onto another molecule. Accomplished by kinases.

Plasmid: A small circular DNA molecule that replicates independently of the bacterial genome. Used by molecular biologists for cloning genes.

Platelet: Cell fragment, lacking a nucleus, that breaks off from a megakaryocyte in the bone marrow and is found in large numbers in the bloodstream. It helps initiate blood clotting when blood vessels are injured.

Polymerase: Enzyme capable of synthesising polymers of nucleic acids.

Polyoma: Small, double-stranded DNA tumour virus.

Polypeptide: Linear polymer composed of multiple amino acids. Proteins are large polypeptides, and the two terms can be used interchangeably.

Positional cloning: The cloning or identification of a gene for a particular disease based on its location in the genome.

Positional information: Can take the form of, for example, a gradient of an extracellular signalling molecule such as Sonic hedgehog, which tells the cells where they are in a developing structure and instructs them to develop into the right cell type for their location.

Posttranslational modifications: Modifications made to proteins after they've been made; includes actions such as phosphorylation and ubiquitination.

Postdoc: Someone at the post-PhD (i.e., postdoctoral) stage of their scientific career. Also used as a job definition and a verb. Postdocs are on short-term contracts, typically for 2 or 3 years; postdoc contracts are renewable but never permanent.

Posterior: In developmental biology, the tail end of an embryo. The antero–posterior axis defines which is the head end and which is the tail end of an animal or structure (in the limb, the thumb is anterior, the little finger is posterior).

Primary cells: Cells taken straight out of an organism into tissue culture. Will grow in tissue culture for only a few generations, or not at all, if you're unlucky.

Prokaryote: Organism made of simple cells that lack a well-defined membrane-enclosed nucleus; bacteria or archaea.

Protease: An enzyme that can digest proteins.

Protein: The major macromolecule constituent of cells. A linear polymer of amino acids linked together by peptide bonds in a specific sequence.

Proto-oncogene: Normal gene, usually concerned with control of cell proliferation, which when mutated into an oncogene can cause cancer.

Pseudo-autosomal: The regions on the X and Y sex chromosomes that are similar enough to be able to pair with each other.

Ras: One of a large family of GTP-binding proteins that help relay signals from the cell-surface receptors into the nucleus. First identified in several mutant forms as the oncogene of several different rat sarcoma viruses.

Reading frame: The phase in which nucleotides are read in sets of three to encode a protein; an mRNA molecule can be read in any one of three reading frames.

Receptor: Molecule able to recognise and bind to a specific extracellular signalling molecule (ligand) to initiate a response in the cell. Cell-surface receptors, rather like Winnie the Pooh after too much honey, are stuck in the plasma membrane with their ligand-binding domains exposed to the outside of the cell and their signalling domains hanging in the cytoplasm. Intracellular receptors also exist, which bind the ligand once it has diffused through the plasma membrane into the cell.

Recombinant DNA: Any DNA molecule formed by joining DNA segments from different sources. Recombinant DNAs are widely used in the cloning of genes, in the genetic modification of organisms, and in molecular biology in general.

Recombination: Process by which chromosomes or DNA molecules are broken and the fragments rejoined in new combinations. Can occur in the living cell or in the test tube using purified DNA and enzymes that break and religate DNA strands.

Replication: Process by which a cell makes a new copy of its genome, before cell division.

Resolvase: The enzyme that cuts Holliday junctions, resolving the four-way structure into two separate double helices.

Restriction enzyme: One of a large number of nucleases that can cleave a DNA molecule at any site where a specific short sequence of nucleotides occurs. The workhorse enzymes of molecular cloning and analysis of DNA.

Restriction map: Diagrammatic representation of a DNA molecule, indicating the sites where various restriction enzymes can cleave.

Restriction site: Each restriction enzyme has a specific sequence it likes to cut, known as its restriction site.

Retrovirus: RNA-containing virus that replicates in a cell by first making a double-stranded DNA intermediate.

Reverse genetics: In reverse genetics, the functional study of a gene starts with the gene sequence rather than a mutant phenotype. Using various techniques, a gene's function is altered, and the effect on the development or behaviour of the organism is then analysed.

Reverse transcriptase: Enzyme, present in retroviruses, that makes a double-stranded DNA copy from a single-stranded RNA template. The only transgressor of Crick's Central Dogma that DNA makes RNA makes protein.

RNA: Ribonucleic acid. Polymer formed from ribonucleotide monomers.

RNA splicing: Process in which intron sequences are excised from RNA molecules in the nucleus during formation of messenger RNA.

RNA tumour viruses: A subset of viruses of the retrovirus family, able to cause tumours in the animals they infect. Source of retroviral oncogenes.

S phase: Period of the eukaryotic cell cycle during which DNA is replicated.

Segment polarity gene: In Drosophila, involved in patterning the parasegments and segments.

Segmentation: The division of the body of an organism into a series of morphologically similar units or segments.

Sequencing: Process of determining the linear sequence of DNA, RNA, or protein.

Serum: What is left from blood after all of the blood cells and clotting factors are removed. Serum includes all proteins not used in blood clotting and all the electrolytes, antibodies, antigens, hormones, and growth factors. It is a rich source of nutrition for tissue culture cells.

Signal transduction: The process by which a cell converts an extracellular signal into a series of intracellular responses, often leading to changes in gene expression.

Sister-chromatid cohesion: A chromatid is one copy of a replicated chromosome that is still joined at the centromere to the other copy, its sister chromatid. Cohesion refers to the process by which they are joined. Sister chromatids are separated at mitosis, when they are allotted to the new daughter cells.

Somatic cell: Any cell other than a germ cell. In most animals, the somatic cells are diploid.

Somatic mutation: Genetic alteration acquired by a cell that can be passed to the progeny of the mutated cell in the course of cell division. Working out how to engineer somatic mutations was the breakthrough that started the human genetics revolution, amongst other things.

Southern blotting: Technique in which DNA fragments, separated by electrophoresis, are immobilised on a membrane. Specific molecules are then detected with a labelled nucleic acid probe. Named after its inventor, Ed Southern.

Strand exchange: Process by which homologous recombination is initiated by RecA in bacteria and Rad51 in eukaryotes. A single invading DNA strand extends its partial pairing with its complementary strand and displaces the resident strand from a DNA double helix.

Substrate: The molecule on which an enzyme acts.

Supernatant: The liquid lying above a solid pellet following centrifugation.

SV40: Small double-stranded DNA tumour virus.

Sympathetic ganglia: A ganglion is a biological tissue mass, most commonly a mass of nerve cell bodies. Sympathetic ganglia are therefore ganglia of the sympathetic nervous system. They deliver information to the body about stress and impending danger and are responsible for the fight-or-flight response. They contain approximately 20,000–30,000 nerve cell bodies and are located close to and on either side of the spinal cord in long chains.

Syncytiotrophoblast: The epithelial covering of the embryonic placental villi, which invades the wall of the uterus to establish nutrient circulation between the embryo and the mother.

TDF (testis determining factor): The gene responsible for maleness. Shown by Peter Goodfellow and Robin Lovell-Badge's laboratories to be SRY.

Temperature-sensitive (ts) mutant: Organism or cell carrying a genetically altered protein or RNA molecule that performs normally at one temperature but is abnormal at another (usually higher) temperature.

Tissue culture: The process of growing cells or tissues outside the body. Generally refers to animal cells.

Transcription: Copying of one strand of DNA into a complementary RNA sequence by the enzyme RNA polymerase.

Transcription factor: Loose term applied to any protein required to initiate or regulate transcription. Includes both regulatory proteins as well as proteins involved in the actual transcription machinery. In terms of the regulatory proteins, transcriptional activators switch on transcription, and transcriptional repressors inhibit it.

Transfection: Technique for introducing foreign DNA into mammalian and other animal cells. The introduced DNA is sometimes incorporated permanently into the host cell's DNA.

Transfer RNA (tRNA): Set of small RNA molecules used in protein synthesis as adaptors between mRNA and amino acids. Each type of tRNA molecule is responsible for bringing one particular amino acid to be incorporated into a growing peptide chain.

Transformation: Heritable alteration in the properties of a eukaryotic cell, usually referring to the acquisition of cancer-like properties following treatment with a virus or carcinogen, or expression of oncogenes. The next step beyond immortalisation. Transformed cell lines are used to study cancer in vitro.

Transformation (yeast): Introduction of a foreign DNA molecule into a yeast cell; usually followed by expression of one or more genes from the newly introduced DNA.

Transgenic: An animal (or plant) that has stably incorporated DNA from another organism and can pass it on to successive generations. The DNA may encode a gene, engineered to be expressed in the transgenic animal and therefore called a transgene.

Translation: Process by which the sequence of nucleotides in a messenger RNA molecule directs the incorporation of amino acids into protein; occurs on a ribosome.

Tritium: A radioactive isotope of hydrogen. Also written as 3H, but always called tritium.

Tumour-suppressor genes: Genes whose function is to protect the cell from cancer. If both copies of such genes are inactivated, the cell is at far greater risk of becoming cancerous. Also known as anti-oncogenes. p53, RB, BRCA1, and BRCA2 belong to this class of gene.

Tyrosine kinase: Enzyme that specifically phosphorylates the amino acid tyrosine in proteins. Extremely important for regulation of a multitude of cellular processes, including signal transduction.

Ubiquitin: A small protein that is attached to other proteins as a post-translational modification. Ubiquitination is a sort of address label for proteins. Depending on how many ubiquitin molecules are bound, and where, ubiquitinated proteins are sorted into different pathways, which can move them into, out of, or around the cell, or send them to be scrapped.

Vector: In molecular biology, an agent (virus or plasmid) used to transmi genetic material into a cell or organism. Used to clone DNA fragments.

Ventral: In developmental biology, the underside of an embryo or animal. The dorso–ventral axis defines the relation of the back to the front of an organism or structure.

Zone of polarising activity: The polarising region at the posterior margin of the limb bud. Responsible for producing the signals that specify positional information for the antero–posterior (thumb to little finger) axis of the limb.