Gene regulation, genomics and biotechnology definitions

Control of gene expression

Gene expression

The process by which the information in a gene is used to produce a functional product, usually a polypeptide.

Transcription factor

A protein that binds to a specific base sequence in DNA, usually in or near a promoter region, and so increases or decreases the rate of transcription of that gene.

Promoter

A region of DNA at the start of a gene to which RNA polymerase and transcription factors bind.

Inducible enzyme

An enzyme synthesised only when its substrate is present, because the substrate or a derivative of it inactivates the repressor of its gene, as allolactose does for β-galactosidase.

Repressible enzyme

An enzyme synthesised continuously until the product of its pathway accumulates and activates a repressor, switching transcription of its gene off.

Oestrogen response element

A specific base sequence near a target gene to which an oestrogen-receptor complex binds, increasing the rate of transcription.

Steroid hormone

A lipid-soluble hormone that crosses the cell-surface membrane by simple diffusion and acts on an intracellular receptor.

Epigenetics

Heritable changes in gene expression caused by chemical modifications to DNA and to the histones associated with it, without any change to the base sequence.

Epigenome

The full set of chemical marks on a cell's DNA and histones at a given time.

Histone acetylation

The addition of acetyl groups to histone tails, which reduces their positive charge, loosens the chromatin and increases transcription.

DNA methylation

The addition of methyl groups to cytosine bases; heavy methylation of a promoter reduces or prevents transcription of that gene.

siRNA

Small interfering RNA: short double-stranded RNA fragments, one strand of which guides a protein complex to a complementary mRNA so that the mRNA is broken down and cannot be translated.

RNA interference

The inhibition of gene expression by small RNA molecules binding to complementary mRNA.

Mutation, gene expression and cancer

Chromosome mutation

A change in the structure of a chromosome, or in the number of chromosomes, that can affect many genes at once.

Translocation (chromosome)

A chromosome mutation in which a section of one chromosome breaks off and joins a non-homologous chromosome.

Balanced translocation carrier

A person with a reciprocal translocation who has lost and gained no genes, is usually healthy, but can produce unbalanced gametes.

Mutation

A change in the base sequence of DNA. Whether the protein changes depends on which base changes and where in the transcript it lies.

Silent mutation

A base substitution that produces a triplet coding for the same amino acid, so the primary structure of the polypeptide is unchanged.

Frame shift

The displacement of the reading frame caused by insertion or deletion of a number of bases that is not a multiple of three.

Control sequence

A region of DNA that is not translated but determines whether, when and how strongly a gene is transcribed.

CFTR protein

A chloride ion channel in the cell-surface membrane of epithelial cells; when it is faulty, too little chloride and water are secreted and mucus becomes thick and sticky.

Proto-oncogene

A normal gene whose product stimulates cell division in response to a growth signal.

Oncogene

A mutated or over-expressed proto-oncogene whose product stimulates division continuously.

Tumour suppressor gene

A gene whose product slows the cell cycle or triggers apoptosis; loss of both alleles removes that control.

Metastasis

The spread of cells from a malignant tumour through the blood or lymph to form secondary tumours.

Recombinant DNA technology

Reverse transcriptase

An enzyme, obtained from retroviruses, which catalyses the synthesis of DNA from an RNA template.

Complementary DNA (cDNA)

DNA made from an mRNA template by reverse transcriptase, and therefore containing no introns.

Recombinant DNA

DNA made by joining together sequences from two different organisms.

Transgenic organism

An organism containing DNA transferred into it from another species.

Restriction enzyme

A restriction endonuclease: an enzyme that cuts DNA at one specific base sequence, its recognition sequence, often leaving sticky ends.

Sticky end

A short single-stranded overhang left on a DNA fragment by an offset cut, which pairs with any complementary overhang.

DNA ligase

An enzyme that joins DNA fragments by catalysing the formation of phosphodiester bonds between their sugar-phosphate backbones.

Viral vector

A virus with its replication and disease-causing genes removed and a chosen gene inserted, used to carry that gene into host cells.

Gene gun

A device that fires microscopic gold or tungsten particles coated with DNA into cells, used chiefly to transform plant tissue.

Polymerase chain reaction (PCR)

A method of copying a chosen length of DNA many millions of times in vitro, by repeated cycles of denaturation at 95 °C, primer annealing at about 55 to 60 °C and extension by Taq polymerase at 72 °C.

Primer

A short single strand of DNA complementary to a sequence at one end of the target region. It gives DNA polymerase a starting point and defines the stretch that PCR copies.

Gel electrophoresis

A technique that separates DNA fragments by length. The negatively charged fragments move through a gel towards the positive electrode, and shorter fragments travel further in a given time.

Knockout mouse

A mouse in which both alleles of a chosen gene have been deliberately inactivated, so that the gene's function can be inferred from what changes.

Animal model

An animal with a condition that resembles a human disease, used to study the disease and test treatments.

High-oleic soya

Soya genetically modified so that the enzyme converting oleic acid to linoleic acid is silenced, giving an oil with more monounsaturated fat that resists oxidation.

DNA ladder

A mixture of DNA fragments of known lengths, run in one lane of a gel so that the lengths of fragments in the other lanes can be read against it.

Loading dye

A dense, coloured solution mixed with DNA samples so that they sink into the wells of a gel and their progress during the run can be seen.

Genome analysis, genetic screening and gene therapy

DNA probe

A short single-stranded length of DNA, labelled radioactively or fluorescently, with a base sequence complementary to a target sequence.

Hybridisation

The binding of a probe to a complementary single-stranded target sequence by hydrogen bonds between complementary bases.

DNA microarray

A plate carrying many different DNA probes at known positions, allowing thousands of sequences to be tested for at once.

Personalised medicine

Choosing which drug to give a patient, and at what dose, using their genotype or the genotype of their tumour, rather than treating everyone with the same diagnosis alike; also called stratified medicine.

Pharmacogenomics

The study of how a person's genotype affects the way they respond to a drug, including how quickly they break it down.

Companion diagnostic

A test carried out to decide whether a particular drug should be given to a particular patient, such as testing a tumour for HER2 before prescribing trastuzumab.

Industrial biotechnology and fermentation

Biotechnology

The use of living organisms, usually microorganisms, or of their components such as enzymes, in industrial processes that make useful products.

Fermentation (industrial)

The large-scale culture of microorganisms in a fermenter to make a product. The industrial word covers aerobic processes as well as the anaerobic pathway the respiration unit gave the same name.

Single-cell protein

Protein-rich food produced from cultured microorganisms, eaten by humans or fed to livestock.

Mycoprotein

Single-cell protein made from the hyphae of the fungus Fusarium venenatum, grown in continuous culture and textured to resemble meat.

Fermenter

A vessel in which microorganisms are cultured at large scale under controlled conditions of temperature, pH, oxygen and nutrient supply.

Aseptic conditions

Conditions from which unwanted microorganisms are excluded, achieved in a fermenter by steam-sterilising the vessel and medium and filtering the incoming air.

Broth

A liquid culture medium, used to grow large numbers of microorganisms and to follow their growth over time.

Selective medium

A culture medium containing a substance, or lacking a nutrient, so that only certain kinds of microorganism can grow on it.

Colony

A visible mass of microorganisms on a solid medium, all descended from a single cell or a small clump of cells.

Total count

A count of all the cells in a sample, living and dead, as made with a haemocytometer.

Viable count

A count of the living cells in a sample, as made by dilution plating, where each living cell grows into one colony.

Serial dilution

A series of dilutions in which each step dilutes the previous one by the same factor, usually tenfold.

Turbidity

The cloudiness of a suspension, measured as absorbance in a colorimeter, which rises as a culture grows.

Exponential growth rate constant

The number of generations per unit time in the log phase: k = (log₁₀ N − log₁₀ N₀) ÷ 0.301t, where N₀ grows to N in time t.

Mean generation time

The time a population takes to double during the log phase, equal to 1 ÷ k.

Inoculum

The small measured volume of culture added to a sterile medium to start a new culture.

Streak plate

An agar plate on which a culture has been spread in a series of areas, each with fewer cells than the last, so that single colonies grow in the final areas.

Pure culture

A culture containing only one species, grown from a single isolated colony.

Zone of inhibition

The clear area round a disc on a lawn of bacteria, where a substance diffusing from the disc has stopped the bacteria growing.

Bacterial lawn

An even layer of bacteria grown over the whole surface of an agar plate from a spread liquid culture.

Pharming, recombinant medicines and synthetic biology

Recombinant medicine

A protein drug produced by cells carrying an introduced copy of the human gene, rather than extracted from blood or tissue.

Factor VIII

The clotting protein deficient in haemophilia A, produced recombinantly in mammalian cell culture since the 1990s.

Adenosine deaminase

The enzyme missing in ADA-deficient severe combined immunodeficiency, supplied to patients as a recombinant protein.

Pharming

The use of genetically modified organisms, including plants and animals, to produce pharmaceutical substances; in livestock, classically in milk.

Mammary-specific promoter

The promoter of a milk protein gene, placed in front of an introduced gene so that the gene is transcribed only in mammary gland cells during lactation.

Plant-made pharmaceutical

A medicine, usually a protein, produced by genetically modified plants or plant cells carrying the gene for it.

Transient expression

Production of a protein from a gene delivered into cells for a few days without being inserted into their chromosomes.

Synthetic biology

The design and construction of new biological parts, devices and pathways, and the redesign of existing organisms, treating DNA as a specifiable engineering material.

Standard part

A DNA sequence with a defined function, catalogued and designed to be assembled with any other standard part.