Genome Dictionary - Genetics Glossary

3_ (pronounced three prime): One end of a DNA strand. The bases in a single strand of DNA are attached to each other through chemical bonds between their sugars. The five carbon atoms of the sugar (deoxyribose) are numbered 1 through 5. The bonds linking the bases together are between carbons 3 and 5. This means that each DNA strand will have an unbonded 3 carbon at one end and an unbonded 5 carbon at the other end. The two strands of the double helix are said to be antiparallel, meaning that one strand runs in the 5_ to 3_ direction while the complementary strand runs in the 3_ to 5_ direction.
5_ (pronounced five prime): One end of a DNA strand. The bases in a single strand of DNA are attached to each other through chemical bonds between their sugars. The five carbon atoms of the sugar (deoxyribose) are numbered 1 through 5. The bonds linking the bases together are between carbons 3 and 5. This means that each DNA strand will have an unbonded 3 carbon at one end and an unbonded 5 carbon at the other end. The two strands of the double helix are said to be antiparallel, meaning that one strand runs in the 5_ to 3_ direction while the complementary strand runs in the 3_ to 5_ direction.
Acquired genetic mutation: See: somatic cell genetic mutation
ACUC: Animal Care and Use Committee, assists in the development of proper mouse handling and technical skills.
Additive genetic effects: When the combined effects of alleles at different loci are equal to the sum of their individual effects.
See also: anticipation, complex trait
Adenine (A): A nitrogenous base, one member of the base pair AT (adenine-thymine).

It is a purine, i.e., a heterocyclic aromatic organic compound, consisting of a pyrimidine ring fused to an imidazole ring.

Adenine has a variety of roles in biochemistry including cellular respiration, in the form of both the energy-rich adenosine triphosphate (ATP) and the cofactors nicotinamide adenine dinucleotide (NAD) and flavin adenine dinucleotide (FAD), and in protein synthesis, as a chemical component of DNA and RNA.

It forms several tautomers, i.e., compounds that can be rapidly interconverted and are often considered equivalent.

Adenine is one of the two purine nucleobases used in forming nucleotides of the nucleic acids. In DNA, adenine binds to thymine via two hydrogen bonds to assist in stabilizing the nucleic acid structures. In RNA, which is used in the cytoplasm for protein synthesis, adenine binds to uracil.

Adenine forms adenosine, a nucleoside, when attached to ribose, and deoxyadenosine when attached to deoxyribose. It forms adenosine triphosphate (ATP), a nucleotide, when three phosphate groups are added to adenosine. Adenosine triphosphate is used in cellular metabolism as one of the basic methods of transferring chemical energy between chemical reactions.
See also: base pair, nucleotide
Affected relative pair: Individuals related by blood, each of whom is affected with the same trait. Examples are affected sibling, cousin, and avuncular pairs.
See also: avuncular relationship
Aggregation technique: A technique used in model organism studies in which embryos at the 8-cell stage of development are pushed together to yield a single embryo (used as an alternative to microinjection).
See also: model organisms
Allele: (From Greek allilos = "each other"). Alternative form of a genetic locus; a single allele for each locus is inherited from each parent (e.g., at a locus for eye color the allele might result in blue or brown eyes).

It is a viable DNA (deoxyribonucleic acid) coding that occupies a given locus (position) on a chromosome. Usually alleles are sequences that code for a gene, but sometimes the term is used to refer to a non-gene sequence. An individual's genotype for that gene is the set of alleles it happens to possess. In a diploid organism, one that has two copies of each chromosome, two alleles make up the individual's genotype. The word came from Greek allilos = "each other".

As an alternative form of a gene (in diploids, one member of a pair) it is located at a specific position on a specific chromosome.

Diploid organisms, such as humans, have paired homologous chromosomes in their somatic cells, which contain two copies of each gene. An organism in which the two copies of the gene are identical'sthat is, have the same allele'sis called homozygous for that gene. An organism which has two different alleles of the gene is called heterozygous. Phenotypes (the expressed characteristics) associated with a certain allele can sometimes be dominant or recessive, but often they are neither. A dominant phenotype will be expressed when at least one allele of its associated type is present, whereas a recessive phenotype will only be expressed when both alleles are of its associated type.

There are exceptions to the way heterozygotes express themselves in the phenotype. One exception is incomplete dominance (sometimes called blending inheritance) when alleles blend their traits in the phenotype. An example of this would be seen if, when crossing Antirrhinums'sflowers with incompletely dominant "red" and "white" alleles for petal color'sthe resulting offspring had pink petals. Another exception is co-dominance, where both alleles are active and both traits are expressed at the same time; for example, both red and white petals in the same bloom or red and white flowers on the same plant. Codominance is also apparent in human blood types. A person with one "A" blood type allele and one "B" blood type allele would have a blood type of "AB".

A wild type allele is an allele which is considered to be "normal" for the organism in question, as opposed to a mutant allele which is usually a relatively new modification.

(Note that with the advent of neutral genetic markers, the term 'allele' is now often used to refer to DNA sequence variants in non-functional, or junk DNA. For example, allele frequency tables are often presented for genetic markers, such as the DYS markers.) Also there are many different types of alleles.
See also: locus, gene expression
Allogeneic: Variation in alleles among members of the same species.
Alternative splicing: Different ways of combining a gene's exons to make variants of the complete protein
Amino acid: Any of a class of 20 molecules that are combined to form proteins in living things. The sequence of amino acids in a protein and hence protein function are determined by the genetic code.

An amino acid molecule contains both amine and carboxyl functional groups.

In biochemistry, the term amino acid refers to alpha-amino acids with the general formula H₂NCHRCOOH, where R is an organic substituent. In the alpha amino acids, the amino and carboxylate groups are attached to the same carbon, which is called the a�carbon. The various alpha amino acids differ in which side chain (R group) is attached to their alpha carbon. They can vary in size from just a hydrogen atom in glycine, through a methyl group in alanine, to a large heterocyclic group in tryptophan.

There are also artificial forms of alpha amino acids, with important roles in technology and industry, such as the chelating agents EDTA and nitriloacetic acid.

Alpha-amino acids are the building blocks of proteins. Proteins are formed by means of the condensation of amino acids to create a chain of amino acid "residues" linked by peptide bonds.

Proteins are defined by their unique sequence of amino acid residues, which constitutes their primary structure. Amino acids can be linked in varying sequences to form a great variety of proteins.

Living cells use twenty standard amino acids to synthesize proteins, and these are specified by the general genetic code. These amino acids are biosynthesized from other molecules, but organisms differ in which ones they can synthesize and which ones must be provided in their diet. The ones that cannot be synthesized by an organism are called essential amino acids.

In proteins, amon acids form short polymer chains called peptides, or longer chains either called polypeptides or proteins. The process of such formation from an mRNA template is known as translation.

The twenty amino acids that are encoded by the standard genetic code are called proteinogenic or standard amino acids. Other amino acids contained in proteins are usually formed by post-translational modification, which is modification after translation in protein synthesis. These modifications are often essential for the function or regulation of a protein.

The twenty standard amino acids are also used in the synthesis of proteins and other biomolecules, or oxidized to urea and carbon dioxide as a source of energy. Oxidation starts with the removal of the amino group by a transaminase.

Many types of non-protein amino acids have been found in nature, with marious functions in living organisms. Microorganisms and plants can produce uncommon amino acids.

Non-protein amino acids in humans, with biologically-important roles include Glycine, gamma-aminobutyric acid and glutamatem, which are neurotransmitters, and many amino acids which are used to synthesize other molecules, such as, tryptophan, a precursor of the neurotransmitter serotonin; glycine, which is a precursor of porphyrins like heme; arginine, which is a precursor of nitric oxide; carnitine, used in lipid transport within a cell; ornithine and S-adenosylmethionine, which are precursors of polyamines; homocysteine, an intermediate in S-adenosylmethionine recycling; hydroxyproline; hydroxylysine; sarcosine; and the thyroid hormones.

Amino acids have even been detected in meteorites suggesting that life may have arrived on earth from an extraterrestrial source.
Amplification: An increase in the number of copies of a specific DNA fragment; can be in vivo or in vitro.
See also: cloning, polymerase chain reaction
Analgesia: A type of drug that alleviates pain without rendering the lab animal unconscious.
Anesthesia: A type of drug that eliminates pain by rendering the lab animal unconscious or by blocing nerve sensation in a certain area of the body.
Animal model: See: model organisms
Annotation: Adding pertinent information such as gene coded for, amino acid sequence, or other commentary to the database entry of raw sequence of DNA bases.
See also: bioinformatics
Anterior: Anatomical term meaning toward the front of the body.
Anticipation: Each generation of offspring has increased severity of a genetic disorder; e.g., a grandchild may have earlier onset and more severe symptoms than the parent, who had earlier onset than the grandparent.
See also: additive genetic effects, complex trait
Antisense: Nucleic acid that has a sequence exactly opposite to an mRNA molecule made by the body; binds to the mRNA molecule to prevent a protein from being made.
Antisense strand is the DNA strand that serves as template for RNA polymerase during transcription. It is complementary in sequence to the sense strand.
See also: transcription
Apoptosis: Programmed cell death, the body's normal method of disposing of damaged, unwanted, or unneeded cells.
See also: cell
ARAC: Animal Research Advisory Committee.
Arrayed library: Individual primary recombinant clones (hosted in phage, cosmid, YAC, or other vector) that are placed in two-dimensional arrays in microtiter dishes. Each primary clone can be identified by the identity of the plate and the clone location (row and column) on that plate. Arrayed libraries of clones can be used for many applications, including screening for a specific gene or genomic region of interest.
See also: library, genomic library, gene chip technology
Aseptic: Free from most microorganisms.
Asphyxiation: Cessation of breathing and loss of consciousnes caused by excess CO₂ or lack of O₂.
Aspirate: Application of negative pressure to a syringe and needle in an attempt to withdraw fluid.
Assembly: Putting sequenced fragments of DNA into their correct chromosomal positions.
Autoradiography: A technique that uses X-ray film to visualize radioactively labeled molecules or fragments of molecules; used in analyzing length and number of DNA fragments after they are separated by gel electrophoresis.
Autosomal dominant: A gene on one of the non-sex chromosomes that is always expressed, even if only one copy is present. The chance of passing the gene to offspring is 50% for each pregnancy.
See also: autosome, dominant, gene
Autosome: A chromosome not involved in sex determination. The diploid human genome consists of a total of 46 chromosomes: 22 pairs of autosomes, and 1 pair of sex chromosomes (the X and Y chromosomes).
See also: sex chromosome
Avuncular relationship: The genetic relationship between nieces and nephews and their aunts and uncles.

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

Genome Dictonary

A