Postgrad Med J7 1997; 73: 317-318 ©) The Fellowship of Postgraduate Medicine, 1997 Glossary Postgrad Med J: first published as 10.1136/pgmj.73.859.317 on 1 May 1997. Downloaded from Common terms in molecular biology part 1 (a-f)

Janardan D Khandekar

Presently, cardiovascular surgeons cannot practise Base pair (bp) - Pairing ofA with T or C with good surgery without understanding the structure G in a double helix. Other pairs can be formed and function of the heart; similarly a modern in RNA under certain conditions. The distance physician will not be able to practise good medicine along a piece of DNA is measured in bps. without understanding the structure andffunction of genes. - Professor Paul Berg, Nobel Laureate C-value-Total amount of DNA in a haploid (paraphrased) genome. CCAAT box-Part of a conserved sequence, Molecular biology is increasingly taking centre located upstream of the starting point of the stage in all aspects of medicine, especially eukaryotic transcription site. It may be in- oncology, and may soon have therapeutic volved in binding RNA polymerase. It is only applications. Here, I present some of the one of the many protein-binding motifs in- commonly used terms in molecular biology volved in transcriptional regulation. which may be useful for oncologists in their Cap-Addition of a modified 7-methylguano- practice as well as in understanding the patho- sine nucleotide to the 5' end of the growing physiology of the diseases. The list is not all- mRNA chain. inclusive, but covers most important terms. CDC - Cell division cycle protein, involved directly in the control of the cell cycle, eg, Acute transforming retroviruses-Viruses CDC2(p34) is a kinase enzyme. that have acquired sequences from the host CdK (cyclin-dependent kinase) - Enzymes genome, giving them the property of causing with activities that are tightly regulated by tumours or transformation of cells in culture. protein phosphorylation and associated with They are also known as viral oncogenes. cyclins. Sequential activation of the cyclin/ Allele-One of several alternate forms of a CdK complexes probably governs the orderly gene occupying a locus on a chromosome. transitions of the cell cycle. Allosteric control-Ability of an interaction cDNA- Single-stranded DNA complementary at one site of a protein to influence the activity to RNA and synthesized from it by reverse http://pmj.bmj.com/ at another site. transcription, in vitro. Amplification- Induction ofadditional copies cDNA clone -Duplex DNA sequence repre- of a chromosomal sequence seen as intra- senting RNA. chromosomal or extrachromosomal DNA. cDNA libraries-A collection of clones re- Anchorage dependent-Need of normal eu- presentative of the mRNA of a given cell type karytic cells for a surface to which to attach in that is formed using reverse transcriptase.

order to grow in culture. Cell line -A cell culture composed of a single on September 23, 2021 by guest. Protected copyright. Anneal-To form hydrogen-bonded base pairs immortalised stem cell population. between complementary strands of nucleic Cellular oncogene-Altered proto-oncogene, acids. eg, by mutation, which leads it to acquire an Antiparallel-Strands of the double helix are altered cellular function that contributes to organised in opposite directions, so that the 5' carcinogenesis. end of one strand is aligned with the 3' end of CentiMorgan-Unit representing a recombi- the other strand. nation frequency of 1% or approximately 1 Antisense-This is a noncoding strand, and million base pairs in humans. serves as a template for mRNA synthesis. It is Chromosomal walking and jumping- complementary to the sense strand. Antisense Techniques of mapping segments of DNA oligonucleotides have been synthesized to (up to several hundred kb) through the block information flow at mRNA. identification of overlapping DNA fragments Apoptosis-Also known as programmed cell in a genomic DNA library. They are per- death. It is conceptualised as a preprogrammed formed to reach a particular point of Division of Medical pathway of sequential biochemical events that interest. Oncology, Evanston leads to cleavage of nuclear chromatin and Cis-acting locus -A regulatory sequence that Hospital and eventual cell death with characteristic morpho- effects activity of DNA sequences on its own Northwestern Univer- logical changes. Apoptosis is an active process molecule of DNA. sity Medical School, as compared to passive cell necrosis. - Evanston, IL 60201, Cis-configuration Two sites on the same USA molecule of DNA. JD Khandekar Bacteriophage-Bacterial viruses which have Clone - Large number of identical cells or been extensively modified for use as molecular molecules with a single ancestral cell or Accepted 24 September 1996 cloning vehicles. molecule. 318 Khandekar

Cloning vector- Plasmid or phage that is around histones (to form a nucleosome) which used as a vector for an inserted foreign gene are twisted into a 30-nm wide fibre; this fibre is

for the purpose of producing more DNA coiled into loops attached to the nuclear matrix Postgrad Med J: first published as 10.1136/pgmj.73.859.317 on 1 May 1997. Downloaded from product or characterisation of DNA. and the loops/matrix are themselves coiled into Closed reading frame- Contains termina- chromosome bands. tion codons that prevent its translation into DNA cloning-A technique involving the proteins. integration of a specific DNA sequence into a Coding sequence-That part of the genome self-replicating element (plasmid or virus) that or mRNA that is translated into protein. reproduces itself in bacteria to generate huge Codon-A triplet ofnucleotides coding for one numbers of identical copies. amino acid or termination signal. DNA library-Collection of different cDNAs Complementary bases - Bases which are or fragments of genomic DNA propagated in a hydrogen bonded specifically in a DNA duplex cloning vector (phage or plasmid) from which or in DNA/RNA heteroduplex. specific sequences can be isolated (cloned). Conditional expression - Gene expression Another term used is genomic library. that occurs only in response to certain stimuli DNA transfection- The transfer ofDNA into or specific conditions. cells in culture. Consensus sequence-An idealised nucleo- Domain-Large polypeptide chains are folded tide or amino acid sequence in which each into units and each folded unit is known as a position represents the base most often domain. Frequently used to indicate a region found when many actual sequences are of a protein that has a specific function, eg, compared. ligand-binding domain. Constitutional deletion-Deletion inherited Double minutes-Extra pairs of chromoso- in the germline from one or other parent and mal fragments visualised on metaphase present in every cell of the body (usually spreads, associated with amplification, eg, examined in lymphocytes), cf somatic. multidrug resistance, myc oncogene. Constitutive expression - A gene that is Down-regulation-Process by which a cell present and expressed at the same level for loses its sensitivity to growth factor or hormone most of the cell cycle. stimulation (often by endocytosis of growth Copy number-The number of copies of a factor receptors). gene present in genomic DNA. Downstream-Sequences proceeding further Cosmid-A lambda-derived cloning vector in the direction of expression. which can carry large fragments of DNA. Drug adducts-DNA modified by a cova- The vector contains a selectable marker, a lently bound drug or the reactive side-group of plasmid origin of replication, a polylinker, or a drug. restriction site into which DNA can be inserted. (The yeast artificial chromosome End-labelling-Addition of a radioactively system, known as the YAC system, which labelled group to one end (5' or 3') of a DNA

allows large human DNA fragments to be strand. http://pmj.bmj.com/ cloned in the yeast, is not a cosmid). Endonucleases - Enzymes which cleave CpG islands- Sequences relatively rich in the bonds within a nucleic acid chain. dinucleotide CpG; often associated with genes Enhancer element- Cis-acting sequence that and possibly involved in transcriptional regula- increases the utilisation of eukaryotic promo- tion. ters (see Cis-acting locus). Cytokines-Proteins which act as signals to Epigenetic phenomenon- Passed from a cell coordinate the cellular response. to its progeny without any alteration in the Cytoskeleton-Network of fibres in the cyto- coding sequence of DNA. on September 23, 2021 by guest. Protected copyright. plasm of the eukaryotic cells. Episome - Plasmid able to integrate into bacterial DNA. Deletion- Loss of a single base pair or a large Epitope - Antigenic determinant (there may sequence of DNA on chromosomes. be several per molecule). Denaturation- (a) of DNA; melting (separa- Euchromatin-The decondensed form of tion) of the complementary strands caused by chromatin typical of the interphase nucleus. high temperature or chemical conditions, Excision repair- System that removes a usually reversible. (b) of protein; loss of higher single-stranded DNA sequence containing order structures caused by high temperature or damaged or misplaced bases and replaces them chemical conditions, usually irreversible. in duplex with a complementary strand. Determination-A commitment to follow a Exonucleases - Enzymes which cleave nu- given developmental lineage (pathway). cleotides at the end of a polynucleotide chain, Differentiation-An increase in specialisation eg, 5' or 3' end of DNA or RNA. towards a specific function as related to Exons- Transcribed sequence not spliced out embryological development. of mature RNAs. DNAase -An enzyme that breaks bonds in the DNA. Footprinting-Technique for identifying the DNA chromatin - Structural packing ofDNA site of DNA/protein binding. double helix into nucleus. The helix is coiled