B

Base Pair

The chemical structure that forms the units of DNA and RNA and that encode genetic information. The bases that make up the base pairs are adenine (A), guanine (G), thymine (T), cytosine (C), and uracil (U) (see DNA). Binding Site

Regions on macromolecules which are sequence and structure specific and complementary that enable any two or more macromolecules to mechanically bind and interact. Bioinformatics

The collection, organization, and analysis of large amounts of biological data, using networks of computers and databases. Historically, bioinformatics concerned itself with the analysis of the sequences of genes and their products (proteins), but the field has since expanded to the management, processing, analysis, and visualization of large quantities of data from genomics, proteomics, drug screening, and medicinal chemistry. Bioinformatics also includes the integration and "mining" (detailed searching) of the ever-expanding databases of information from these disciplines.

Chromosome

One of the physically separate segments that together forms the genome, or total genetic material, of a cell. Chromosomes are long strands of genetic material, or DNA, that have been packaged and compressed by wrapping around proteins. The number and size of chromosomes varies from species to species. In humans, there are 23 pairs of chromosomes (a pair has one chromosome from each parent). One pair are called the sex chromosomes because they contain genes that determine sex. The chromosome carrying the male determining genes is designated Y and the corresponding female one is the X chromosome. The remaining pairs are called autosomes. Chromosome 1 is the largest and chromosome 22 the smallest. Each chromosome has two "arms" designated p and q.

Complementary DNA (cDNA)

DNA that is synthesized from a messenger RNA template; the single-stranded form is often used as a probe in physical mapping or for detecting RNA. Since cDNA is constructed from messenger RNA (after introns have been spliced out), it does not contain introns.

Cosmid

Artificially constructed cloning vector containing the cos gene of lambda phage (a virus). Cosmids can be packaged in lambda phage particles for infection into E. coli; this permits cloning of larger DNA fragments (up to 45 kb) than can be introduced into bacterial hosts in plasmid vectors.

Deoxyribonucleic Acid (DNA)

The chemical that forms the basis of the genetic material in virtually all living organisms. Structurally, DNA is composed of two strands that intertwine to form a springlike structure called the double helix. Attached to each backbone are chemical structures called bases (or nucleotides), which protrude away from the backbone toward the center of the helix, and which come in four types—adenine, cytosine, guanine, and thymine (designated A, C, G, and T). In DNA, cytosine only forms optimal hydrogen bonding with guanine, and adenine only with thymine. These interactions across the many nucleotides in each strand hold the two strands together.

Electrophoresis

The use of electrical fields to separate charged biomolecules such as DNA, RNA, and proteins. DNA and RNA carry a net negative charge because of the numerous phosphate groups in their structure. In the process of gel electrophoresis, these biomolecules are put into wells of a solid matrix typically made of an inert substance such as agarose. When this gel is placed into a bath and an electrical charge applied across the gel, the biomolecules migrate and separate according to size in proportion to the amount of charge they carry. The biomolecules can be stained for viewing and isolated and purified from the gels for further analysis. Electrophoresis can be used to isolate pure biomolecules from a mixture or to analyze biomolecules (such as for DNA sequencing). Enzyme

A protein that catalyzes chemical reactions in a living cell. Enzymes are protein molecules whose function it is to speed the making and breaking of chemical bonds required for essential physiochemical reactions.

Exon

The protein-coding DNA sequences of a gene (see Intron). Expressed Sequence Tags (EST)

A set of single-pass sequenced cDNAs from an mRNA population derived from a specified cell population (e.g., a tumor or a particular muscle type). ESTs provide one estimate of which DNA sequences are actually transcribed and therefore potentially functional as genes.

Functional genomics

The use of genetic technology to determine the function of newly discovered genes by determining their role in one or more model organisms. Functional genomics uses as its starting point the isolated gene whose function is to be determined, and then selects a model organism in which a homolog of that gene exists. This model organism can be as simple as a yeast cell or as complex as a nematode worm, fruit fly, or even a mouse.

Gene

The basic unit of heredity; the sequence of DNA that encodes all the information to make a protein. A gene may be "activated" or "switched on" to make protein—this activation is referred to as gene expression—by these proteins which control when, where, and how much protein is expressed from the gene. In the human genome, there are an estimated 30,000 genes (although recent studies suggest a larger number). Gene product

The biochemical material, either RNA or protein, resulting from expression of a gene. The amount of gene product is used to measure how active a gene is; abnormal amounts can be correlated with disease-causing alleles. As gene products include all the alternative splicing products, there are estimated to be at least 100,000 distinct such products. Gene therapy

The technology that uses genetic material for therapeutic purposes. This genetic material can be in the form of a gene, representative of a gene or cDNA, RNA, or even a small fragment of a gene. The introduced genetic material can be therapeutic in several ways: It can make a protein that is defective or missing in the patient's cells (as would be the case in a genetic disorder), or that will correct or modify a particular cellular function, or that elicits an immune response.

High-throughput screening

The use of miniaturized, robotics-based technology to screen large compound libraries against an isolated target protein, cell, or tissue in order to identify binders that may be potential new drugs. In conjunction with genomics and combinatorial chemistry (the production of large numbers of medicinally relevant compounds), high-throughput screening has revolutionized the capacity of pharmaceutical and biotechnology companies to identify potential new drugs. Typically, high-throughput screening has relied on 96-well plates as the standard, although higher-density formats (384, 1536) are possible. Recently, advances in miniaturization and micro fluidics have allowed screening of up to 100,000 compounds against a target on a single chip daily.

Hybridization

The interaction of complementary nucleic acid strands. Since DNA is a double-stranded structure held together by complementary interactions (in which C always binds to G, and A to T), complementary strands favorably reanneal or "hybridize" to each other when separated.

Intron

Noncoding portion of the gene that is spliced out from the nascent RNA transcript in the process of making an mRNA transcript. Frequently includes regulator elements (i.e., binding sites) in addition to those of the promoter.

Microfluidics

Microfluidics is the miniaturization of fluid-based biochemistry to very small volumes such that a large series of chemical reactions can be performed in parallel in a microarray format. The essential issue with developing microfluidics based devices is the ability to maintain adequate access to the solutions needed in each element of the array. Several companies have manufactured "labs-on-a-chip" that allow the high-throughput chemistries needed in screening, synthesis, and probing of biological molecules. Mutation

Any alteration to DNA that can potentially result in a change in the function of one or more genes. Mutations can be a change in a single base of DNA (point mutation) or a loss of base pairs (deletion) affecting a single gene, or a movement of chromosomal regions (translocation) affecting many genes. Some changes in DNA occur naturally and lead to no harmful effects; these changes in a population are called polymorphisms.

Northern Blot

RNA from a sample is spatially separated and distributed by mass on a gel. Radioactively labelled DNA or RNA strands with sequence complementary to the RNA segments from the sample are used to locate the position of those RNA segments.

Oligonucleotide

A short molecule consisting of several linked nucleotides (typically between 10 and 60) chained together and attached by covalent bonds. Open Reading Frame

Regions in a nucleotide sequence that are bounded by start and stop codons and are therefore possible gene coding regions.

Pharmacogenomics

Pharmacogenomics is the study of the pharmacological response to a drug by a population based on the genetic variation of that population. It has long been known that different individuals in a population respond to the same drug differently, and that these variations are due to variations in the molecular receptors being affected by the drug, or to differences in metabolic enzymes that clear the drug. Pharmacogenomics is the science of studying these variations at the molecular level. Applications of pharmacogenomics include reducing side effects, customizing drugs, improvement of clinical trials, and the rescue of some drugs that have been banned due to severe side effects in a small percentage of the eligible population. Polymorphism

Difference in nucleotide sequence among individuals. Single nucleotide polymorphisms (SNP) are thought to be the principal component of inherited genetic variation. There is approximately one SNP every 300 to 1000 nucleotide of the human genome.

Probe

Any biochemical agent that is labeled or tagged in some way so that it can be used to identify or isolate a gene, RNA, or protein. Typically refers to the immobilized specified nucleic acid in a detection system [8]. Promoter

Regions of DNA typically upstream or before a gene which contain transcription factor binding sites (see Transcription Factor), but also include elements for specific initiation of transcription. That is, there are stretches of DNA to which transcription factors may bind and thereby modulate transcription but which are not promoters, because they do not include the elements of transcriptional initiation. Protein family

A set of proteins that share a common evolutionary origin reflected by their relatedness in function, which is usually reflected by similarities in sequence, or in primary, secondary, or tertiary structure. A set of proteins with related structure and function. Proteomics

The study of the entire protein complement or "protein universe" of the cell. Mirroring genomics, proteomics aims to determine the entire suite of expressed proteins in a cell. This includes determining the number, level, and turnover of all expressed proteins, their sequence and any post-translational modifications to the sequence, and protein-protein and protein-other molecule interactions within the cell, across the cell membrane, and among (secreted) proteins. Polymerase chain reaction (PCR)

A technique used to amplify or generate large amounts of replica DNA or a segment of any DNA whose "flanking" sequences are known. Oligonucleotide primers that bind these flanking sequences are used by an enzyme to copy the sequence in between the primers. Cycles of heat to break apart the DNA strands, cooling to allow the primers to bind, and heating again to allow the enzyme to copy the intervening sequence lead to doubling of the DNA present at each cycle.

Serial Analysis of Gene Expression (SAGE)

The use of short 10-14 bp sequence tags linked together to identify sequences in a sample. The count of the instances of each sequence in a specific sample is a number that bears (in theory) a direct relationship to the number of transcripts of a particular genes (see section 7.1.4).

Single nucleotide polymorphism (SNP)

Variations in single base pairs scattered throughout the human genome that serve as measures of genetic diversity in humans. About 1 million SNPs are estimated to be present in the human genome, and SNPs are useful markers for gene mapping and disease studies. Southern Blot

DNA from a sample is cut with restriction enzymes and the position of the fragments (e.g. on a gel) is determined by the fragment's molecular weight. Complementary strands of radioactively labelled DNA are used to identify the position of the DNA fragments on the gel.

Transcription Factor

A molecute, typically a protein, which binds to promoter (see Promoter) or other DNA binding sites with some regulatory role in transcription. The binding (or unbinding) of a transcription factor from a promoter eventually leads to a change of transcription activity in the gene controlled by that promoter.

Target

The free nucleic acid that is being interrogated [8].

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