Glossary 1.13 2004/09/10 11:21:37 GMT-5 2007/10/09 06:21:42.329 GMT-5 Lukasz Marek Wita lwita@tlen.pl Ewa Alina Paszek epaszek@liv.ac.uk Ewa Alina Paszek epaszek@liv.ac.uk glossary This course is a short series of lectures on Statistical Bioinformatics. Topics covered are listed in the Table of Contents. The notes were prepared by Ewa Paszek, Lukasz Wita and Marek Kimmel. The development of this course has been supported by NSF 0203396 grant.

Alphabet A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

ADENINE One of the four bases in DNA that make up the letters ATGC, adenine is the "A". The others are guanine, cytosine, and thymine. Adenine always pairs with thymine. (from National Human Genome Research Institute) ALA (ALANINE)(A) One of the twenty naturally occurring amino acids. (from BioTech Dictionary) AMINO ACIDS A group of 20 different kinds of small molecules that link together in long chains to form proteins. Often referred to as the "building blocks" of proteins. (from National Human Genome Research Institute) ANAPHASE the stage of meiosis or mitosis when chromosomes move toward opposite ends of the nuclear spindle. (from WordNet) ARG (ARGININE)(R) One of the twenty naturally occurring amino acids. (from BioTech Dictionary) ASN (ASPARAGINE)(N) One of the twenty naturally occurring amino acids. (from BioTech Dictionary) ASP (ASPARTIC ACID)(D) One of the twenty naturally occurring amino acids. (from BioTech Dictionary) ASX (ASPARAGINE OR ASPARTIC ACID)(B) One of the twenty naturally occurring amino acids. (from BioTech Dictionary) BASE PAIR Two bases which form a "rung of the DNA ladder." A DNA nucleotide is made of a molecule of sugar, a molecule of phosphoric acid, and a molecule called a base. The bases are the "letters" that spell out the genetic code. In DNA, the code letters are A, T, G, and C, which stand for the chemicals adenine, thymine, guanine, and cytosine, respectively. In base pairing, adenine always pairs with thymine, and guanine always pairs with cytosine. (from National Human Genome Research Institute) CENTROMERE The constricted region near the center of a human chromosome. This is the region of the chromosome where the two sister chromatids are joined to one another. (from National Human Genome Research Institute) CODON Three bases in a DNA or RNA sequence which specify a single amino acid. (from National Human Genome Research Institute) COMPLEMENTARY DNA (CDNA) a single-stranded DNA synthesized from a mature mRNA template. cDNA is often used to clone eukaryotic genes in prokaryotes. (from Wikipedia) CHROMATID one of two identical strands into which a chromosome splits during mitosis. (from WordNet) CHROMATIN (CHROMATIN GRANULE) the readily stainable substance of a cell nucleus consisting of DNA and RNA and various proteins; during mitotic division the chromatin condenses into chromosomes(from WordNet) CHROMOSOME One of the threadlike "packages" of genes and other DNA in the nucleus of a cell. Different kinds of organisms have different numbers of chromosomes. Humans have 23 pairs of chromosomes, 46 in all: 44 autosomes and two sex chromosomes. Each parent contributes one chromosome to each pair, so children get half of their chromosomes from their mothers and half from their fathers. (from National Human Genome Research Institute) CLUSTER (GENE CLUSTER) A set of closely related genes that code for the same or similar proteins and which are usually grouped together on the same chromosome. (from BioTech Dictionary) COVALENT BOND A bond between two or more atoms that is provided by electrons that travel between the atoms' nuclei, holding them together but keeping them a stable distance apart. (from BioTech Dictionary) CROSSING OVER The breaking during meiosis of one maternal and one paternal chromosome, the exchange of corresponding sections of DNA, and the rejoining of the chromosomes. This process can result in an exchange of alleles between chromosomes. (from Human Genome Project Information) CROSSLINKING The linking of two strands of DNA by covalent bonds (as opposed to the normal hydrogen bonds between base pairs ), which can occur by exposure to X-rays. (from BioTech Dictionary) CYS (CYSTEINE)(C) One of the twenty naturally occurring amino acids. (from BioTech Dictionary) CYTOPLASM All the contents of a cell, including the plasma membrane, but not including the nucleus. (from UCMP Glossary) CYTOSINE One of the four bases in DNA that make up the letters ATGC, cytosine is the "C". The others are adenine, guanine, and thymine. Cytosine always pairs with guanine. (from National Human Genome Research Institute) DNA The chemical inside the nucleus of a cell that carries the genetic instructions for making living organisms. (from National Human Genome Research Institute) DNA MICROARRAY (DNA CHIP) a piece of glass or plastic on which single-stranded pieces of DNA have been affixed in a microscopic array. (from Wikipedia) ENHANCER a short region of DNA which can be bound with proteins (namely, the trans-acting factors, much like a set of transcription factors) to enhance transcription levels of nearby genes (hence the name) in a gene-cluster. (from Wikipedia) EXON The region of a gene that contains the code for producing the gene's protein. Each exon codes for a specific portion of the complete protein. In some species (including humans), a gene's exons are separated by long regions of DNA (called introns or sometimes "junk DNA") that have no apparent function. (from National Human Genome Research Institute) EXPRESSION (GENE EXPRESSION) The process by which a gene's coded information is converted into the structures present and operating in the cell. Expressed genes include those that are transcribed into mRNA and then translated into protein and those that are transcribed into RNA but not translated into protein. (from BioTech Dictionary) GAMETE Mature male or female reproductive cell (sperm or ovum) with a haploid set of chromosomes (23 for humans). (from Human Genome Project Information) GENE The functional and physical unit of heredity passed from parent to offspring. Genes are pieces of DNA, and most genes contain the information for making a specific protein. (from National Human Genome Research Institute) GENOME All the DNA contained in an organism or a cell, which includes both the chromosomes within the nucleus and the DNA in mitochondria. (from National Human Genome Research Institute) GENETIC MAP (LINKAGE MAP) a chromosome map of a species that shows the position of its known genes and/or markers relative to each other, rather than as specific physical points on each chromosome. (from National Human Genome Research Institute) GLN (GLUTAMINE)(Q) One of the twenty naturally occurring amino acids. (from BioTech Dictionary) GLU (GLUTAMIC ACID)(E) One of the twenty naturally occurring amino acids. (from BioTech Dictionary) GLX (GLUTAMINE OR GLUTAMIC ACID)(Z) One of the twenty naturally occurring amino acids. (from BioTech Dictionary). GLY (GLYCINE)(G) One of the twenty naturally occurring amino acids. (from BioTech Dictionary) GUANINE One of the four bases in DNA that make up the letters ATGC, guanine is the "G". The others are adenine, cytosine, and thymine. Guanine always pairs with cytosine. (from National Human Genome Research Institute) HIS (HISTIDINE)(H) One of the twenty naturally occurring amino acids. (from BioTech Dictionary) HYBRIDIZATION A genetics lab technique used to identify which colonies of bacteria on a plate contain a particular sequence of DNA or a particular gene. The technique involves pressing a nylon or nitrocellulose membrane onto the plate so that each colony contributes a small smudge of itself to the membrane, then treating the membrane with chemicals and heat, then washing the membrane with a labeled probe to find the specific DNA sequence. The smudges which are indicated by the probe are then compared back to the colonies on the plate. (from BioTech Dictionary) ILE (ISOLEUCINE)(I) One of the twenty naturally occurring amino acids. (from BioTech Dictionary) INTRON A noncoding sequence of DNA that is initially copied into RNA but is cut out of the final RNA transcript. (from National Human Genome Research Institute) IN SITU HYBRIDIZATION The base pairing of a sequence of DNA to metaphase chromosomes on a microscope slide. (from National Human Genome Research Institute) LEU (LEUCINE)(L) One of the twenty naturally occurring amino acids. (from BioTech Dictionary) LYS (LYSINE)(K) One of the twenty naturally occurring amino acids. (from BioTech Dictionary) 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. (from Human Genome Project Information) MET (METHIONINE)(M) One of the twenty naturally occurring amino acids. (from BioTech Dictionary) METAPHASE The phase of mitosis, or cell division, when the chromosomes align along the center of the cell. Because metaphase chromosomes are highly condensed, scientists use these chromosomes for gene mapping and identifying chromosomal aberrations. (from National Human Genome Research Institute) MITOSIS The process of nuclear division in cells that produces daughter cells that are genetically identical to each other and to the parent cell. (from Human Genome Project Information) MRNA Template for protein synthesis. Each set of three bases, called codons, specifies a certain protein in the sequence of amino acids that comprise the protein. The sequence of a strand of mRNA is based on the sequence of a complementary strand of DNA. (from National Human Genome Research Institute) NORTHERN BLOT A technique used to identify and locate mRNA sequences that are complementary to a piece of DNA called a probe. (from National Human Genome Research Institute). NUCLEOTIDE One of the structural components, or building blocks, of DNA and RNA. A nucleotide consists of a base (one of four chemicals: adenine, thymine, guanine, and cytosine) plus a molecule of sugar and one of phosphoric acid. (from National Human Genome Research Institute) NUCLEUS The central cell structure that houses the chromosomes. (from National Human Genome Research Institute) OLIGO Oligonucleotide, short sequence of single-stranded DNA or RNA. Oligos are often used as probes for detecting complementary DNA or RNA because they bind readily to their complements. (from National Human Genome Research Institute) PHE (PHENYLALANINE)(F) One of the twenty naturally occurring amino acids. (from BioTech Dictionary) POLYMER A polymer is formed from the fusion of two monomers which join completely without losing any small molecules. (from BioTech Dictionary). POLYPEPTIDE A protein or part of a protein made of a chain of amino acids joined by a peptide bond. (from Human Genome Project Information) PRO (PROLINE)(P) One of the twenty naturally occurring amino acids. (from BioTech Dictionary). PROMOTER a DNA sequence that enables a gene to be transcribed. The promoter is recognized by RNA polymerase, which then initiates transcription. (from Wikipedia). PROPHASE the first stage of meiosis the first stage of mitosis(from WordNet) PROTEIN A large complex molecule made up of one or more chains of amino acids. Proteins perform a wide variety of activities in the cell. (from National Human Genome Research Institute) 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. (from Human Genome Project Information) REPLICATION The process by which DNA copies itself before cell division. Unless mutation occurs, the new copy of DNA is identical to the original DNA. (from HOPES) RIBOSOME Cellular organelle that is the site of protein synthesis (from National Human Genome Research Institute) RNA A chemical similar to a single strand of DNA. In RNA, the letter U, which stands for uracil, is substituted for T in the genetic code. RNA delivers DNA's genetic message to the cytoplasm of a cell where proteins are made. (from National Human Genome Research Institute) SER (SERINE)(S) One of the twenty naturally occurring amino acids. (from BioTech Dictionary). SOUTHERN BLOT A technique used to identify and locate DNA sequences which are complementary to another piece of DNA called a probe. (from National Human Genome Research Institute). SPLICING The joining of separate strands of DNA or RNA. (from Wikipedia). TELOMERE The end of a chromosome. This specialized structure is involved in the replication and stability of linear DNA molecules. (from Human Genome Project Information) TELOPHASE the final stage of meiosis when the chromosomes move toward opposite ends of the nuclear spindle the final stage of mitosis(from WordNet) THR (THREONINE)(T) One of the twenty naturally occurring amino acids. (from BioTech Dictionary). THYMINE One of the four bases in DNA that make up the letters ATGC, thymine is the "T". The others are adenine, guanine, and cytosine. Thymine always pairs with adenine. (from National Human Genome Research Institute) TRANSCRIPTION the organic process whereby the DNA sequence in a gene is copied into mRNA; the process whereby a base sequence of messenger RNA is synthesized on a template of complementary DNA(from WordNet) TRANSCRIPTION FACTOR a protein that binds DNA at a specific promoter or enhancer region or site, where it regulates transcription. Transcription factors can be selectively activated or deactivated by other proteins, often as the final step in signal transduction. (from Wikipedia). TRANSLATION the process whereby genetic information coded in messenger RNA directs the formation of a specific protein at a ribosome in the cytoplasm. (from WordNet) 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. (from Human Genome Project Information) TRP TRYPTOPHAN)(W) One of the twenty naturally occurring amino acids. (from BioTech Dictionary). TYR (TYROSINE)(Y) One of the twenty naturally occurring amino acids. (from BioTech Dictionary). URACIL One of the four bases in RNA. The others are adenine, guanine, and cytosine. Uracil replaces thymine, which is the fourth base in DNA. Like thymine, uracil always pairs with adenine. (from National Human Genome Research Institute) VAL (VALINE)(V) One of the twenty naturally occurring amino acids. (from BioTech Dictionary).