Pharmacom Glossaries

In situ hybridization: Use of a DNA or RNA probe to detect the presence of the complementary DNA sequence in cloned bacterial or cultured eukaryotic cells.
In vitro: Studies performed outside a living organism such as in a laboratory.
In vivo: Studies carried out in living organisms.
Independent assortment: During meiosis each of the two copies of a gene is distributed to the germ cells independently of the distribution of other genes.
Informed consent: An individual willingly agrees to participate in an activity after first being advised of the risks and benefits.
Inherit: In genetics, to receive genetic material from parents through biological processes.
Insertion: A chromosome abnormality in which a piece of DNA is incorporated into a gene and thereby disrupts the gene's normal function.
Interference: One crossover event inhibits the chances of another crossover event. Also known as positive interference. Negative interference increases the chance of a second crossover.
Interphase: The period in the cell cycle when DNA is replicated in the nucleus; followed by mitosis.
Intron: DNA sequence that interrupts the protein-coding sequence of a gene; an intron is transcribed into RNA but is cut out of the message before it is translated into protein.
Isoenzyme: An enzyme performing the same function as another enzyme but having a different set of amino acids. The two enzymes may function at different speeds.
Return to Top

Junk DNA: Stretches of DNA that do not code for genes; most of the genome consists of so-called junk DNA which may have regulatory and other functions. Also called non-coding DNA.
Return to Top

Karyotype: A photomicrograph of an individual's chromosomes arranged in a standard format showing the number, size, and shape of each chromosome type; used in low-resolution physical mapping to correlate gross chromosomal abnormalities with the characteristics of specific diseases.
Kilobase (kb): Unit of length for DNA fragments equal to 1000 nucleotides.
Knockout: Deactivation of specific genes; used in laboratory organisms to study gene function.

Return to Top

Library: An unordered collection of clones (i.e., cloned DNA from a particular organism) whose relationship to each other can be established by physical mapping.
Linkage: The proximity of two or more markers (e.g., genes, RFLP markers) on a chromosome; the closer the markers, the lower the probability that they will be separated during DNA repair or replication processes (binary fission in prokaryotes, mitosis or meiosis in eukaryotes), and hence the greater the probability that they will be inherited together.
Linkage disequilibrium: Where alleles occur together more often than can be accounted for by chance. Indicates that the two alleles are physically close on the DNA strand.
Linkage map: A map of the relative positions of genetic loci on a chromosome, determined on the basis of how often the loci are inherited together. Distance is measured in centimorgans (cM).
Localize: Determination of the original position (locus) of a gene or other marker on a chromosome.
Locus (pl. loci): The position on a chromosome of a gene or other chromosome marker; also, the DNA at that position. The use of locus is sometimes restricted to mean expressed DNA regions.
Long-Range Restriction Mapping: Restriction enzymes are proteins that cut DNA at precise locations. Restriction maps depict the chromosomal positions of restriction-enzyme cutting sites. These are used as biochemical "signposts," or markers of specific areas along the chromosomes. The map will detail the positions where the DNA molecule is cut by particular restriction enzymes.
Return to Top

Macrorestriction map: Map depicting the order of and distance between sites at which restriction enzymes cleave chromosomes.
Mapping population: The group of related organisms used in constructing a genetic map.
Mass spectrometry: An instrument used to identify chemicals in a substance by their mass and charge.
Megabase (Mb): Unit of length for DNA fragments equal to 1 million nucleotides and roughly equal to 1 cM.
Meiosis: The process of two consecutive cell divisions in the diploid progenitors of sex cells. Meiosis results in four rather than two daughter cells, each with a haploid set of chromosomes.
Mendelian inheritance: One method in which genetic traits are passed from parents to offspring. Named for Gregor Mendel, who first studied and recognized the existence of genes and this method of inheritance.
Messenger RNA (mRNA): RNA that serves as a template for protein synthesis.
Metaphase: A stage in mitosis or meiosis during which the chromosomes are aligned along the equatorial plane of the cell.
Microarray: Sets of miniaturized chemical reaction areas that may also be used to test DNA fragments, antibodies, or proteins.
Microbial genetics: The study of genes and gene function in bacteria, archaea, and other microorganisms. Often used in research in the fields of bioremediation, alternative energy, and disease prevention.
Microinjection: A technique for introducing a solution of DNA into a cell using a fine microcapillary pipet.
Micronuclei: Chromosome fragments that are not incorporated into the nucleus at cell division.
Mitochondrial DNA: The genetic material found in mitochondria, the organelles that generate energy for the cell. Not inherited in the same fashion as nucleic DNA.
Mitosis: The process of nuclear division in cells that produces daughter cells that are genetically identical to each other and to the parent cell.
Model organisms: A laboratory animal or other organism useful for research.
Modeling: The use of statistical analysis, computer analysis, or model organisms to predict outcomes of research.
Molecular biology: The study of the structure, function, and makeup of biologically important molecules.
Molecular farming: The development of transgenic animals to produce human proteins for medical use.
Molecular genetics: The study of macromolecules important in biological inheritance.
Molecular medicine: The treatment of injury or disease at the molecular level. Examples include the use of DNA-based diagnostic tests or medicine derived from DNA sequence information.
Monogenic disorder: A disorder caused by mutation of a single gene.
Monosomy: Possessing only one copy of a particular chromosome instead of the normal two copies.
See also: cell, chromosome, gene expression, trisomy
Morbid map: A diagram showing the chromosomal location of genes associated with disease.
Multiplexing: A laboratory approach that performs multiple sets of reactions in parallel (simultaneously); greatly increasing speed and throughput.
Murine: Organism in the genus Mus. A rat or mouse.
Mutagen: An agent that causes a permanent genetic change in a cell. Does not include changes occurring during normal genetic recombination.
Mutagenicity: The capacity of a chemical or physical agent to cause permanent genetic alterations.
Mutation: Any heritable change in DNA sequence.

Return to Top

Nitrogenous base: A nitrogen-containing molecule having the chemical properties of a base. DNA contains the nitrogenous bases adenine (A), guanine (G), cytosine (C), and thymine (T).
Northern blot: A gel-based laboratory procedure that locates mRNA sequences on a gel that are complementary to a piece of DNA used as a probe.
Nuclear transfer: A laboratory procedure in which a cell's nucleus is removed and placed into an oocyte with its own nucleus removed so the genetic information from the donor nucleus controls the resulting cell. Such cells can be induced to form embryos. This process was used to create the cloned sheep "Dolly".
Nucleic acid: A large molecule composed of nucleotide subunits.
Nucleolar organizing region: A part of the chromosome containing rRNA genes.
Nucleotide: A subunit of DNA or RNA consisting of a nitrogenous base (adenine, guanine, thymine, or cytosine in DNA; adenine, guanine, uracil, or cytosine in RNA), a phosphate molecule, and a sugar molecule (deoxyribose in DNA and ribose in RNA). Thousands of nucleotides are linked to form a DNA or RNA molecule.
Nucleus: The cellular organelle in eukaryotes that contains most of the genetic material.
Return to Top

Oligogenic: A phenotypic trait produced by two or more genes working together.
Oligonucleotide: A molecule usually composed of 25 or fewer nucleotides; used as a DNA synthesis primer.
Oncogene: A gene, one or more forms of which is associated with cancer. Many oncogenes are involved, directly or indirectly, in controlling the rate of cell growth.
Open reading frame (ORF): The sequence of DNA or RNA located between the start-code sequence (initiation codon) and the stop-code sequence (termination codon).
Operon: A set of genes transcribed under the control of an operator gene.; Return to Top

P1-derived artificial chromosome (PAC): One type of vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells. Based on bacteriophage (a virus) P1 genome.
Patent: In genetics, conferring the right or title to genes, gene variations, or identifiable portions of sequenced genetic material to an individual or organization.
Pedigree: A family tree diagram that shows how a particular genetic trait or disease has been inherited.
Penetrance: The probability of a gene or genetic trait being expressed. "Complete" penetrance means the gene or genes for a trait are expressed in all the population who have the genes. "Incomplete" penetrance means the genetic trait is expressed in only part of the population. The percent penetrance also may change with the age range of the population.
Peptide: Two or more amino acids joined by a bond called a "peptide bond."
Phage: A virus for which the natural host is a bacterial cell.
Pharmacogenomics: The study of the interaction of an individual's genetic makeup and response to a drug.
Phenocopy: A trait not caused by inheritance of a gene but appears to be identical to a genetic trait.
Phenotype: The physical characteristics of an organism or the presence of a disease that may or may not be genetic.
Physical map: A map of the locations of identifiable landmarks on DNA (e.g., restriction-enzyme cutting sites, genes), regardless of inheritance. Distance is measured in base pairs. For the human genome, the lowest-resolution physical map is the banding patterns on the 24 different chromosomes; the highest-resolution map is the complete nucleotide sequence of the chromosomes.
Plasmid: Autonomously replicating extra-chromosomal circular DNA molecules, distinct from the normal bacterial genome and nonessential for cell survival under nonselective conditions. Some plasmids are capable of integrating into the host genome. A number of artificially constructed plasmids are used as cloning vectors.
Pleiotropy: One gene that causes many different physical traits such as multiple disease symptoms.
Pluripotency: The potential of a cell to develop into more than one type of mature cell, depending on environment.
Polygenic disorder: Genetic disorder resulting from the combined action of alleles of more than one gene (e.g., heart disease, diabetes, and some cancers). Although such disorders are inherited, they depend on the simultaneous presence of several alleles; thus the hereditary patterns usually are more complex than those of single-gene disorders.
Polymerase chain reaction (PCR): A method for amplifying a DNA base sequence using a heat-stable polymerase and two 20-base primers, one complementary to the (+) strand at one end of the sequence to be amplified and one complementary to the (-) strand at the other end. Because the newly synthesized DNA strands can subsequently serve as additional templates for the same primer sequences, successive rounds of primer annealing, strand elongation, and dissociation produce rapid and highly specific amplification of the desired sequence. PCR also can be used to detect the existence of the defined sequence in a DNA sample.
Polymerase, DNA or RNA: Enzyme that catalyzes the synthesis of nucleic acids on preexisting nucleic acid templates, assembling RNA from ribonucleotides or DNA from deoxyribonucleotides.
Polymorphism: Difference in DNA sequence among individuals that may underlie differences in health. Genetic variations occurring in more than 1% of a population would be considered useful polymorphisms for genetic linkage analysis.
Polypeptide: A protein or part of a protein made of a chain of amino acids joined by a peptide bond.
Population genetics: The study of variation in genes among a group of individuals.
Positional cloning: A technique used to identify genes, usually those that are associated with diseases, based on their location on a chromosome.
Premature chromosome condensation (PCC): A method of studying chromosomes in the interphase stage of the cell cycle.
Primer: Short preexisting polynucleotide chain to which new deoxyribonucleotides can be added by DNA polymerase.
Privacy: In genetics, the right of people to restrict access to their genetic information.
Probe: Single-stranded DNA or RNA molecules of specific base sequence, labeled either radioactively or immunologically, that are used to detect the complementary base sequence by hybridization.
Prokaryote: Cell or organism lacking a membrane-bound, structurally discrete nucleus and other subcellular compartments. Bacteria are examples of prokaryotes.
Promoter: A DNA site to which RNA polymerase will bind and initiate transcription.
Pronucleus: The nucleus of a sperm or egg prior to fertilization.
Protein: A large molecule composed of one or more chains of amino acids in a specific order; the order is determined by the base sequence of nucleotides in the gene that codes for the protein. Proteins are required for the structure, function, and regulation of the body's cells, tissues, and organs; and each protein has unique functions. Examples are hormones, enzymes, and antibodies.
Proteome: Proteins expressed by a cell or organ at a particular time and under specific conditions.
Proteomics: The study of the full set of proteins encoded by a genome.
Pseudogene: A sequence of DNA similar to a gene but nonfunctional; probably the remnant of a once-functional gene that accumulated mutations.
Purine: A nitrogen-containing, double-ring, basic compound that occurs in nucleic acids. The purines in DNA and RNA are adenine and guanine.
Pyrimidine: A nitrogen-containing, single-ring, basic compound that occurs in nucleic acids. The pyrimidines in DNA are cytosine and thymine; in RNA, cytosine and uracil.

Return to Top

Radiation hybrid: A hybrid cell containing small fragments of irradiated human chromosomes. Maps of irradiation sites on chromosomes for the human, rat, mouse, and other genomes provide important markers, allowing the construction of very precise STS maps indispensable to studying multifactorial diseases.
See also: sequence tagged site
Recessive gene: A gene which will be expressed only if there are 2 identical copies or, for a male, if one copy is present on the X chromosome.
Reciprocal translocation: When a pair of chromosomes exchange exactly the same length and area of DNA. Results in a shuffling of genes.
Recombinant clone: Clone containing recombinant DNA molecules.
Recombinant DNA molecules: A combination of DNA molecules of different origin that are joined using recombinant DNA technologies.
Recombinant DNA technology: Procedure used to join together DNA segments in a cell-free system (an environment outside a cell or organism). Under appropriate conditions, a recombinant DNA molecule can enter a cell and replicate there, either autonomously or after it has become integrated into a cellular chromosome.
Recombination: The process by which progeny derive a combination of genes different from that of either parent. In higher organisms, this can occur by crossing over.
Regulatory region or sequence: A DNA base sequence that controls gene expression.
Repetitive DNA: Sequences of varying lengths that occur in multiple copies in the genome; it represents much of the human genome.
Resolution: Degree of molecular detail on a physical map of DNA, ranging from low to high.
Restriction enzyme, endonuclease: A protein that recognizes specific, short nucleotide sequences and cuts DNA at those sites. Bacteria contain over 400 such enzymes that recognize and cut more than 100 different DNA sequences.
Restriction fragment length polymorphism (RFLP): Variation between individuals in DNA fragment sizes cut by specific restriction enzymes; polymorphic sequences that result in RFLPs are used as markers on both physical maps and genetic linkage maps. RFLPs usually are caused by mutation at a cutting site.
Restriction-enzyme cutting site: A specific nucleotide sequence of DNA at which a particular restriction enzyme cuts the DNA. Some sites occur frequently in DNA (e.g., every several hundred base pairs); others much less frequently (rare-cutter; e.g., every 10,000 base pairs).
Retroviral infection: The presence of retroviral vectors, such as some viruses, which use their recombinant DNA to insert their genetic material into the chromosomes of the host's cells. The virus is then propogated by the host cell.
Reverse transcriptase: An enzyme used by retroviruses to form a complementary DNA sequence (cDNA) from their RNA. The resulting DNA is then inserted into the chromosome of the host cell.
Ribose: The five-carbon sugar that serves as a component of RNA.
Ribosomal RNA (rRNA): A class of RNA found in the ribosomes of cells.
Ribosomes: Small cellular components composed of specialized ribosomal RNA and protein; site of protein synthesis.
Risk communication: In genetics, a process in which a genetic counselor or other medical professional interprets genetic test results and advises patients of the consequences for them and their offspring.
RNA (Ribonucleic acid): A chemical found in the nucleus and cytoplasm of cells; it plays an important role in protein synthesis and other chemical activities of the cell. The structure of RNA is similar to that of DNA. There are several classes of RNA molecules, including messenger RNA, transfer RNA, ribosomal RNA, and other small RNAs, each serving a different purpose.
Return to Top

Sanger sequencing: A widely used method of determining the order of bases in DNA.
Satellite: A chromosomal segment that branches off from the rest of the chromosome but is still connected by a thin filament or stalk.
Scaffold: In genomic mapping, a series of contigs that are in the right order but not necessarily connected in one continuous stretch of sequence.
Segregation: The normal biological process whereby the two pieces of a chromosome pair are separated during meiosis and randomly distributed to the germ cells.
Sequence assembly: A process whereby the order of multiple sequenced DNA fragments is determined.
Sequence tagged site (STS): Short (200 to 500 base pairs) DNA sequence that has a single occurrence in the human genome and whose location and base sequence are known. Detectable by polymerase chain reaction, STSs are useful for localizing and orienting the mapping and sequence data reported from many different laboratories and serve as landmarks on the developing physical map of the human genome. Expressed sequence tags (ESTs) are STSs derived from cDNAs.
Sequencing: Determination of the order of nucleotides (base sequences) in a DNA or RNA molecule or the order of amino acids in a protein.
Sequencing technology: The instrumentation and procedures used to determine the order of nucleotides in DNA.
Sex chromosome: The X or Y chromosome in human beings that determines the sex of an individual. Females have two X chromosomes in diploid cells; males have an X and a Y chromosome. The sex chromosomes comprise the 23rd chromosome pair in a karyotype.
Sex-linked: Traits or diseases associated with the X or Y chromosome; generally seen in males.
Shotgun method: Sequencing method that involves randomly sequenced cloned pieces of the genome, with no foreknowledge of where the piece originally came from. This can be contrasted with "directed" strategies, in which pieces of DNA from known chromosomal locations are sequenced. Because there are advantages to both strategies, researchers use both random (or shotgun) and directed strategies in combination to sequence the human genome.
Single nucleotide polymorphism (SNP): DNA sequence variations that occur when a single nucleotide (A, T, C, or G) in the genome sequence is altered.
Single-gene disorder: Hereditary disorder caused by a mutant allele of a single gene (e.g., Duchenne muscular dystrophy, retinoblastoma, sickle cell disease).
Somatic cell: Any cell in the body except gametes and their precursors.
Somatic cell gene therapy: Incorporating new genetic material into cells for therapeutic purposes. The new genetic material cannot be passed to offspring.
Somatic cell genetic mutation: A change in the genetic structure that is neither inherited nor passed to offspring. Also called acquired mutations.
Southern blotting: Transfer by absorption of DNA fragments separated in electrophoretic gels to membrane filters for detection of specific base sequences by radio-labeled complementary probes.
Spectral karyotype (SKY): A graphic of all an organism's chromosomes, each labeled with a different color. Useful for identifying chromosomal abnormalities.
Splice site: Location in the DNA sequence where RNA removes the noncoding areas to form a continuous gene transcript for translation into a protein.
Sporadic cancer: Cancer that occurs randomly and is not inherited from parents. Caused by DNA changes in one cell that grows and divides, spreading throughout the body.
Stem cell: Undifferentiated, primitive cells in the bone marrow that have the ability both to multiply and to differentiate into specific blood cells.
Structural genomics: The effort to determine the 3D structures of large numbers of proteins using both experimental techniques and computer simulation
Substitution: In genetics, a type of mutation due to replacement of one nucleotide in a DNA sequence by another nucleotide or replacement of one amino acid in a protein by another amino acid.
Suppressor gene: A gene that can suppress the action of another gene.
Syndrome: The group or recognizable pattern of symptoms or abnormalities that indicate a particular trait or disease.
Syngeneic: Genetically identical members of the same species.
Synteny: Genes occurring in the same order on chromosomes of different species.

Return to Top

Tandem repeat sequences: Multiple copies of the same base sequence on a chromosome; used as markers in physical mapping.
Targeted mutagenesis: Deliberate change in the genetic structure directed at a specific site on the chromosome. Used in research to determine the targeted region's function.
Technology transfer: The process of transferring scientific findings from research laboratories to the commercial sector.
Telomerase: The enzyme that directs the replication of telomeres.
Telomere: The end of a chromosome. This specialized structure is involved in the replication and stability of linear DNA molecules.
Teratogenic: Substances such as chemicals or radiation that cause abnormal development of a embryo.
Thymine (T): A nitrogenous base, one member of the base pair AT (adenine-thymine).
Toxicogenomics: The study of how genomes respond to environmental stressors or toxicants. Combines genome-wide mRNA expression profiling with protein expression patterns using bioinformatics to understand the role of gene-environment interactions in disease and dysfunction.
Transcription: The synthesis of an RNA copy from a sequence of DNA (a gene); the first step in gene expression.
Transcription factor: A protein that binds to regulatory regions and helps control gene expression.
Transcriptome: The full complement of activated genes, mRNAs, or transcripts in a particular tissue at a particular time
Transfection: The introduction of foreign DNA into a host cell.
Transfer RNA (tRNA): A class of RNA having structures with triplet nucleotide sequences that are complementary to the triplet nucleotide coding sequences of mRNA. The role of tRNAs in protein synthesis is to bond with amino acids and transfer them to the ribosomes, where proteins are assembled according to the genetic code carried by mRNA.
Transformation: A process by which the genetic material carried by an individual cell is altered by incorporation of exogenous DNA into its genome.
Transgenic: An experimentally produced organism in which DNA has been artificially introduced and incorporated into the organism's germ line.
Translation: The process in which the genetic code carried by mRNA directs the synthesis of proteins from amino acids.
Translocation: A mutation in which a large segment of one chromosome breaks off and attaches to another chromosome.
Transposable element: A class of DNA sequences that can move from one chromosomal site to another.
Trisomy: Possessing three copies of a particular chromosome instead of the normal two copies.

Return to Top

Uracil: A nitrogenous base normally found in RNA but not DNA; uracil is capable of forming a base pair with adenine.

Return to Top

Virus: A noncellular biological entity that can reproduce only within a host cell. Viruses consist of nucleic acid covered by protein; some animal viruses are also surrounded by membrane. Inside the infected cell, the virus uses the synthetic capability of the host to produce progeny virus.

Return to Top

Western blot: A technique used to identify and locate proteins based on their ability to bind to specific antibodies.
Wild type: The form of an organism that occurs most frequently in nature.; Return to Top

X chromosome: One of the two sex chromosomes, X and Y.
Xenograft: Tissue or organs from an individual of one species transplanted into or grafted onto an organism of another species, genus, or family. A common example is the use of pig heart valves in humans.
Return to Top

Y chromosome: One of the two sex chromosomes, X and Y.
Yeast artificial chromosome (YAC): Constructed from yeast DNA, it is a vector used to clone large DNA fragments.

Return to Top

Zinc-finger protein: A secondary feature of some proteins containing a zinc atom; a DNA-binding protein.