Adenine symbol A or Ado; adenine riboside; 9-β-D-ribofuranosyladenine; a ribonucleoside found widely distributed in cells of every type as the free nucleoside and in combination with nucleic acids and various nucleoside coenzymes. A potent regulator of physiological transmission in both central and peripheral nervous system. Base-Pair symbol bp; any of the possible pairings between two bases in opposing strands of double-stranded DNA or RNA molecules. Adenine (A) forms a base pair with Thymine (T) in DNA or Uracil (U) in RNA and Guanine (G) with Cytosine (C); hence the number of adenine residues equals the number of thymine (and/or Uracil) residues while the number of Guanine residues equals that of the Cytosine residues. Cancer any malignant neoplasm. Cancers are usually divided into carcinomas, derived from epithelial cells and sarcomas, derived from connective tissues. Some 300 genes are known to be involved in carcinogenesis. Cell The basic structural unit of all living organisms; it typically comprises of small, usually microscopic, discrete mass of organelle-containing cytoplasm, bounded externally by a membrane. In plants, the cell usually includes cell-walls. Each cell is capable of interacting with other cells and performing all the fundamental functions of life. Central Dogma a fundamental principle of molecular biology; first articulated by British molecular biologist Francis Crick in 1958. The central dogma states that once ‘information has passed into protein, it cannot get out again. In more detail, the transfer of information from nucleic acid to nucleic acid or from nucleic acid to protein may be possible, but transfer from protein to protein or from protein to nucleic acid is impossible. Information means there is precise determination of sequence of amino acids or of base-pairs.’ The dogma has been taken to relate primarily to the following transfer of information that can occur in all cells: DNA to RNA to Protein. Chemotaxis a movement of motile cell or organism in response to a specific chemical concentration gradient. Movement can be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis). Chitosan the cationic polymeric carbohydrate obtained by the deacetylation of chitin. Chromosome a structure composed of very long molecule of DNA and associated with proteins that carries hereditary information. Chromosomes are especially evident in plant or animal cells, undergoing mitosis or meiosis, where each chromosome becomes condensed into a compact, readily visible thread. In non-dividing cells, chromosomes typically assume a more dispersed form called ‘chromatin’. Coenzyme any of the various non-protein organic cofactors that are required in addition to an enzyme and a substrate for an enzymatic reaction to proceed. Cytoplasm all the protoplasm of a living cell excluding the nucleus and the plasma membrane but including the other intracellular organelles and structures. Cytosine symbol C or Cyt; 4-amino-2-hydroxypyrimidine; 4-amino-2(1H)-pyrimidinone; a pyrimidine derivative that is one of the five main bases found in nucleic acids. It occurs widely in cytidine derivatives. Dicer a multidomain endonuclease of ribonuclease III-type that is involved in generation of small interfering RNAs (siRNAs) and other forms of microRNA (miRNA) species.. It is important for normal development in C. elegans. The human and Drosophila enzymes are homologous and contain a DEXH-box-ATP dependent RNA helicase domain. In animals, Dicer and its cofactors are absent in differentiated cells. DNA abbr and common name for deoxyribonucleate or deoxyribonucleic acid; one of the two main types of nucleic acid, consisting of a long, un-branched macromolecule formed from one or more commonly, two strands of linked deoxyribonucleotides, the 3’-phosphate group of each constituent deoxyribonucleotide being joined in 3’,5’-phosphodiester linkage to 5’-hydroxyl group of the deoxyribose moiety of the next one. DNA Double Helix or Watson-Crick model of DNA the main features of this model are that DNA consists of two anti-parallel helical polynucleotide chains coiled around the same axis to form a double helix. Deoxyribose-phosphate backbones are on the outer side of the helix and purine and pyrimidine bases lie approximately at right angles to the central axis on the inside of the helix. The diameter of the helix is 2 nm and there is a residue on each chain every 0.34 nm. The angle between each residue on the same chain is 360, so that the structure repeats after every 10 residues (3.4 nm) on each chain. The two chains are held together by hydrogen bonds between pairs of bases, each member of the pair belonging to a different polynucleotide chain. Drosha a nuclear RNase III rhat is specific for dsRNA. It contains a dsRBM (a dsRNA-binding motif) and 2 RNase III domains and processes pri-miRNA to a pre-miRNA. It interacts with Pasha in the nuclear microprocessor complex. Drug any naturally occurring or synthetic substance, other than a nutrient that, when administered or applied to any organism, affects the structure or functioning of the organism; in particular, any such substance used in diagnosis, prevention or treatment of disease. Enzymes any naturally occurring or synthetic macromolecular substance composed of protein, that catalyses, more or less specifically, one or more biochemical reactions at relatively low temperatures. Eukaryotes any organism whose cells contain a eukaryon (a type of nucleus bounded by a nuclear membrane and containing true chromosomes) and undergo meiosis. Evolution a process of cumulative change occurring in the form and mode of existence of a population of organism in the course of successive generations related by descent. Expression Vector any vector designed to enable the expression of a cloned gene. Functional Genomics the systematic analysis of genes, their coded proteins and the relationships between gene activity and cell function at the level of whole genomes. Gene in classical genetics, a statistical entity that correlates with a particular phenotypic characteristic; the functional unit of heredity. Before their biochemical nature was understood, genes were defined in terms of units of mutation and/or recombination. Discovery of the role of DNA in genetic processes, followed by elaboration of the central dogma of protein synthesis, led to enunciation of the ‘one gene – one protein hypothesis. In current molecular genetics, the concept of gene requires modification in a number of ways – such as association with promoters, concept of polyproteins and alternative splicing. Gene Amplification the selective, repeated replication of a certain gene or genes without a proportional increase in other genes in the genome. Gene Expression the process by which the information carried by a gene or genes becomes manifest as the phenotype. It involves transcription of the gene into complementary RNA sequences and for the structural genes , subsequent translation of mRNA into polypeptide chains and their assembly into the ultimate protein products. Gene expression is tightly regulated by promoters, enhancers and transcriptional factors. Gene Therapy the treatment of disease by incorporating into a person’s genome DNA that encodes a specific therapeutic protein or that corrects deficiency of a normal protein due to gene mutation. Genome the whole of the genetic information of an organism. It is contained as DNA in eukaryotes and prokaryotes, and as either DNA or RNA in viruses. A given organism has only one genome regardless of whether the organism is haploid, diploid or polyploidy. The term was originally used to denote one haploid set of chromosomes in eukaryotic organism. Genomics the systematic sequencing and characterization of complete genomes. Guanine symbol: G or Gua; 2-amino-6-hydroxypurine; 2-amino-1,7-dihydro-6H-purin-6-one; a purine that is one of the five main bases found in nucleic acids and a component of a number of phosphorylated guanosine derivatives whole metabolic or regulatory functions are important. Hairpin any part of linear molecular structure in which two adjacent segments of the molecule are folded back one on the other and held in that conformation by secondary molecular forces such as hydrogen bonds or van der Waals interactions. Hairpin DNA contains inverted repeats; when denatured it renatures extremely rapidly by intrachain base-pairing between complementary sequences of the inverted repeat. Similar structures occur in RNA molecules. High-Throughput describing a process that is scaled up, usually via increased levels of automation using robots. High-throughput screening refers to the rapid in vitro screening of large number of compound libraries using robotic screening assays. High-throughput sequencing involves the application of rapid sequencing technology at the scale of whole genomes. Inflammation the immediate defensive reaction of vertebrate tissue to infection or to injury by chemical or physical agents. The part affected is characterized by pain, heat, redness, swelling and loss-of-function; there is local vasodilation, extravasation of plasma into the intercellular spaces, and accumulation of white blood cells and other macrophages in the injured part. Plasma enzyme systems are important sources of inflammatory mediators; which include complement, blood coagulation, fibrinolytic and kinin system etc. Inhibitor any substance that inhibits an enzyme reaction. Innate Immunity an immune response in both – vertebrates and invertebrates to a pathogen that involves the pre-existing defences of the body – the innate immune system – such as barriers formed by skin and mucosa, antimicrobial molecules and phagocytes. Such a response is not specific for the pathogen. The agents are either small proteins or peptides, many of which have been detected in insects, which lack the immune system of higher animals. For example, cecropin, attracin, defensins etc. Integrins any member of the large family of transmembrane proteins that act as receptors for cell-adhesion molecules. Integrins are heterodimeric molecules in which the α and β subunits are non-covalently bonded. Ligation joining together with a bond to co-ordinate functions. Metazoan any animal of sub-kingdom Metazoa; consisting of multicellular animals whose cells are organized into tissues and their activites co-ordinated by nervous system. It includes all organisms except Protozoa and Parazoa. miRNA abbr. for microRNA; other name; tiny RNA; any of various RNA species that are 21-25 nt long and may be single or double-stranded. They have been found in animals, including Drosophila and C. elegans and in plants. The term encompasses small interfering RNAs and small temporal RNAs as well as miRNA proper. They exhibit diverse developmental and tissue-specific expression profiles amd are involved in a wide-range of gene regulatory processes. mRNA abbr. for messenger RNA; a class of naturally occurring RNA molecules that carry the information embodied in the genes of DNA Nanotechnology the creation and control of objects in nanometre scales. In nanotechnology, a particle is defined as a small object that behaves as a whole unit in terms of its transport and properties. Ultrafine particles, or nanoparticles are sized between 100 to 1 nanometres. |
Nitrogen bases or Nitrogenous bases derivatives of two parent compounds – purines (Adenine and Guanine) and pyrimidines (Cytosine, Thymine and Uracil). They are non-polar and planar. The nitrogen bases form hydrogen bonds between the anti-parallel strands of DNA to form rungs of the twisted ladder aka the double-helix of DNA or of a coenzyme moiety. Adenine forms bonds with Guanine and Cytosine bonds with Thymine (in case of DNA) or Uracil (in case of RNA). Nuclear Pore any opening in the nuclear envelope of a eukaryotic cell, where the inner and the outer nuclear membranes are joined. The nuclear pores are the central feature of a complex in higher eukaryotes and are estimated to contain about 100 different polypeptides. The complex constitutes a diffusion channel about 9 nm in diameter through which proteins enter the nucleus and ribonucleoproteins leave. Entry of larger proteins is controlled by their containing one or more clusters of basic amino acids which comprise the nuclear localization sequence (NLS). This involves binding to the nuclear envelope, followed by energy-dependent transit through the pores.Nucleic Acids abbr. NA; any single- or double-stranded polynucleotide of molar mass in the range 20KDa to 40kDa or more. Nucleic acids are either deoxyribonucleic acids (DNA) or ribonucleic acids (RNA). The phosphoric residues linking any constituent mononucleotide residue to the next bears one free hydroxyl group, which is weakly acidic. They are universal components of living matter and are concerned with the storage, transmission and transfer of genetic information. Nucleosides any glycosylamine that is a component of a nucleic acid and that consists of a nitrogenous base linked either to β-D-ribofuranose (forming a ribonucleoside in RNA) or 2-deoxy-β-D-ribofuranose (forming a deoxyribonucleoside in DNA). The base is either a purine (linked at N-9) or a pyrimidine (linked at N-1). Nucleotides any compound that consists of a nucleoside esterified with [ortho]phosphate at either 3’- or at 5’-hydroxyl group of its glycose moiety. Nucleotides are the constitutional units into which nucleic acids are broken down by partial hydrolysis and from which they are considered to be build up. Nucleus the most conspicuous organelle of a eukaryotic cell; it contains the chromosomes and with exceptions of mitochondria and chloroplast, is an sole site of DNA replication and RNA synthesis in the cell. Usually a spheroidal body, it is separated from the cytoplasm by the nuclear envelope. piRNA abbr. PIWI-interacting RNA; largest class of small non-coding RNA molecules that is expressed in animal cells. piRNA form RNA-protein complexes through interactions with piwi proteins. These complexes have been linked to both epigenetic and post-transcriptional gene silencing of retrotransposons and other genetic elements in germ line cells; particularly those in spermatogenesis. They lack sequence conservation and are more complex in nature as compared to other small RNAs. Plasmid strictly any extra-chromosomal genetic element; however mitochondrial and chloroplast DNA are commonly excluded, hence the term plasmid refers to any extra-chromosomal covalently continuous double-stranded DNA molecule that occurs in bacteria and rarely in other microorganisms. Natural plasmids vary from <5kb to over 100kb in size. Plasmid genes may include drug resistance genes for catabolic enzymes, genes for antibiotic synthesis and genes for toxin production. Plasmids are popular choice for cloning vectors, and are greatly influenced by the origin of replication sequence and the copy number. Polymerase a general name for any transferase enzyme that catalyzes the formation of biological polymers; especially of polynucleotides. Polymerase Chain Reaction abbr. PCR; a method whereby a specific sequence of nucleotides within a double-stranded DNA in amplified. The sequence is identified by the use of short synthetic oligonucleotide primers that are complementary to the two terminal regions of the DNA sequence to be amplified; these oligonucleotides are extended by the thermostable Taq DNA polymerase on the DNA template. The effect is that the new chains span the region delimited by the two chosen termini. There are three phases in a single cycle of PCR reaction: the nascent chains are heat denatured at 940C; the temperature is then decreased to allow annealing of the primers to the template strands; and then the temperature is increased to 72oC for extension. The theoretical yield of amplified product is 2n where n is the number of cycles. The method was first described by Kary B. Mullis in 1984. Post-Transcriptional Modification abbr. PTM; any enzyme catalysed change to a protein made after it is synthesized by the translation of messenger RNA. For example, glycosylation, prenylation, phosphorylation etc. Promoter symbol P; a DNA sequence located at 5’ to a gene that indicates the site of for initiation of transcription. It may influence the amount of mRNA produced and the tissue specificity of expression. In prokaryotes, consensus sequences centred at -10 and -35 nucleotides (The Pribnow box) upstream from the transcriptional promoters are recognized by RNA polymerase. Eukaryotic promoters have sequence element that are recognized by general transcription factors such as TFIIA, TFIIB, TFIIC, TFIID (i.e. TATA-binding protein) etc. Protein any large group of organic compounds found as major macromolecular constituents of living organisms. All enzymes are proteins. A protein is a linear polymer of amino acids linked by peptide bonds in a specific sequence. The amino acid residues may be subsequently modified so that the chains may contain a much wider variety of residues, amounting to nearly 200. The modifications may involve the covalent attachment of various groups, such as carbohydrates and phosphate; these are simple proteins. Other substances loosely associated with polypeptide chains, such as heme or lipid, giving rise to conjugated proteins. Four hierarchies have been defined for polypeptide chains, termed primary structure, secondary structure, tertiary structure and quaternary structure. Reporter Gene a gene used to disclose the function of potential regulatory sequences. These sequences are placed in plasmids, upstream of the reporter gene. The chimeric plasmids are introduced into cells and the expression of the reporter gene is measured as an index of the function of the regulatory sequences under the conditions being investigated. Retrovirus or ribodeoxyvirus or RNA-DNA virus any virus belonging to the family Retroviridae. This comprises of single-stranded RNA animal viruses whose genome is diploid, consisting of two copies of the RNA, which is transcribed by the virion-associated enzyme reverse-transcriptase into DNA. This double-stranded DNA or provirus can then integrate into the host genome and be passes from parent cell to progeny cell as a component of the host genome. Recombinant DNA Technology an area of biotechnology concerned with manipulation of recombinant DNA. It has several important applications including DNA sequencing, synthesis of recombinant protein, production of DNA probes etc. Reverse Genetics another name for positional cloning; a term coined to describe the study of the biological consequences to an organism of artificial alteration of its DNA. The changes may be either gross (e.g. deletion, insertion or transposition of segments of DNA effected by recombinant DNA technology) or limited to specific loci (e.g. base substitution through site-directed mutagenesis). RNA abbr. and common name for ribonucleate or ribonucleic acid; one of the two main types of nucleic acids, consisting of long, un-branched macromolecule formed from ribonucleotides, the 3’-phosphate group of each constituent ribonucleotide being joined in 3’-5’-phosphodiester linkage to 5’-hydroxyl group on each ribose moiety of the next one. The presence of a free 2’-hydroxyl group on each ribose moiety renders these phosphodiester bonds susceptible to hydrolytic attack by alkali, in contrast to those of DNA. The RNA chain has polarity, with one 5’ end and one 3’ end. Two purines (Adenine and Guanine) and two pyrimidines (Cytosine and Uracil) are the major bases usually present. RNA is fundamental to protein biosynthesis in all living cells. There are several types of RNA involved in a wide range of functions viz., mRNA, rRNA, tRNA, snoRNA, hnRNA, mtRNA, siRNA, miRNA, nRNA etc. RISC abbr. for RNA-induced silencing complex; s ribonucleoprotein complex that targets its perfectly (or partially) complementary mRNA for either cleavage or translational repression. Short interfering RISCs (siRISCs) are programmed by siRNA and microRISCs are programmed by miRNAs. Both siRISCs and miRISCs are of two types – cleaving and non-cleaving. It is likely that its specificity is determined by one of the argonaute proteins. RNAi abbr. for RNA Interference a general mechanism for silencing transcript of an active gene in many organisms. The interference is initiated by siRNA as a part of an RNA-induced silencing complex – RISC – that is specific for the nucleotide sequence of the target transcript. There is no evidence that this type of silencing occurs in normally growing animals, but it has been demonstrated in C. elegans and is used by plants to combat virus infections. Sequencing the act, or the process of determining sequence of proteins or nucleic acids. siRNA abbr. for small interfering RNA; a form of microRNA that associated with RNA helicase and RNase molecules to form a complex called RISC. The siRNA unwinds and directs precise, sequence-specific degradation of mRNA. siRNAs are 21-23 bp long generated by Dicer from a dsRNA precursor and are highly specific for the nucleotide sequence of their target mRNA. They require Argonaute to function. Thymine or Thymidine symbol dT or dThd; thymine 2’-deoxyriboside; 1-(2—deoxy-β-D-ribofuranosyl)-5-methyluracill a deoxyribonucleotide very widely distributed almost entirely as phosphoric esters in deoxyribonucleotides and DNA. Because thymine is absent from ribonucleates, the incorporation of radioisotope-labelled thymidine into cells is the basis of procedure for measuring the rates of DNA synthesis and cell growth. Transcription the synthesis of RNA on a template of DNA. In transcription of dsDNA, RNA is formed on a template comprising of only one strand, the transcribed strand. This is called the anti-sense strand since the other strand is termed sense strand. Transcription is a multistep process. Transfection originally the process of infection of competent bacterial cells by free bacteriophage or plasmid nucleic acid that result in the subsequent production of normal bacteriophage or plasmids in the infected bacterial cell. It has to come to mean the process of bringing about genetic alteration of any cell or organism using recombinant DNA technology. Translation the process by which a particular sequence of bases in messenger RNA (mRNA) determines the sequence of amino acids in a polypeptide chain during protein and peptide biosynthesis. One or more specific base triplets or codons code for each of the 20 amino acids. Each codon of the mRNA molecule is recognized by the corresponding anti-codon on the transfer RNAs (tRNAs) to which amino acids are attached. The tRNA binds on the site on the large subunit of ribosome, which is associated to the smaller subunit of ribosome to which each mRNA is bound. The first codon (the initiation codon) of each mRNA is AUG, which codes for fomylmethionine (in prokaryotes and mitochondria) or methionine (in eukaryotes). Completion of translation is signalled by termination codons. Tumour a mass of proliferating cells lacking, to varying degrees, normal growth control. Tumours maybe benign i.e. growing slowly or malignant i.e. growing aggressively, invading the neighbouring tissues, and spreading to distant parts of the body by releasing cells into the bloodstream or lymph. These cells then form secondary tumours. Uracil symbol U or Ura; a 2,4-dioxopyrimidine; 2-4-pyrimidinediol; a pyrimidine base occurring in RNA but not in DNA. Vector an organism or DNA from a different species used as a vehicle to transfer foreign genetic material into another cell. The four major vectors are plasmids, viruses, cosmids and artificial chromosomes. A vector contains an origin of replication sequence, a multiple cloning site with sites for restriction enzymes and a selectable marker. The purpose of a vector which transfers genetic information to another cell is typically to isolate, multiply or express the insert in the target cells. Insertion of vector into the target cell brings about transformation for bacterial cells or transfection for eukaryotic cells, and insertion of a viral vector is called a transduction process. Courtesy 'Oxford Dictionary of Biochemistry and Molecular Biology, Second Edition (2006), Oxford University Press'. © 2012, Saie Mogre. All Rights Reserved. |
