Alu family the most common dispersed, repeated DNA sequence in the human genome. There are at least 750,000 Alu elements, each consisting of about 300 base pairs, accounting for 11% of human DNA. Each element is made up of two 130 base pair sequences joined head to tail with a 32 base pair insert in the right-hand monomer. Alu sequences are targeted by cohesins (q.v.). The family name is derived from the fact that these sequences are cleaved by restriction endonuclease Alu I. See human gene maps, repetitious DNA.
Alzheimer disease (AD) a multifactorial syndrome that causes a devastating decline in mental ability and is accompanied by the appearance of amyloid plaques in the cerebral cortex. These deposits were first observed in 1906 by a German physician, Alois Alzheimer, in brain tissue from a woman who had died of an unusual mental illness. Amyloid plaques contain aggregates of amyloid-beta-peptides (ApPs), and these are derived from an amyloid beta precursor protein (ApPP), which is encoded by a gene on human chromosome 21. Patients with tri-somy 21 (Down syndrome, q.v.) commonly develop AD by age 40. Familial, early-onset AD is often associated with mutations of genes that encode pre-senilins (PS1 and PS2). The genes for PS1 and PS2 are located at 14q24.3 and 1q42.1, respectively. The proteins they encode are made of 467 and 448 amino acids, respectively, and they contain seven to nine transmembrane domains. Both proteins are bound to membranes and play a role in cutting ApPP into ApPs, some of which are toxic. A gene homologous to the PS1 gene has been isolated from nematodes. See Appendix C, 1995, Sherrington, St. George-Hyslop et al., Schellenberg et al.; Caenorhab-iditis elegans, neuregulins (NRGs).
Amanita phalloides a poisonous mushroom which is the source of amatoxins and phallotoxins (both of which see). See Appendix A, Fungi, Basidiomycota.
amastigote See undulipodium.
amatoxins a group of bicyclic octapeptides that are among the poisons produced by Amanita phalloides (q.v.). These poisons inhibit transcription in eukaryotic cells because of their interaction with RNA polymerase II. However, they do not affect the RNA polymerases of mitochondria or chloroplasts. Alpha amanitin (formula, above) is an amatoxin most commonly used experimentally to inhibit transcription. See phallotoxins, RNA polymerase.
amaurosis blindness occurring without an obvious lesion in the eye, as from a disease of the optic nerve or brain. The term is sometimes found in the early descriptions of hereditary diseases leading to blindness (e.g., Leber congenital amaurosis). See Leber hereditary optic neuropathy (LHON).
amber codon the mRNA triplet UAG that causes termination of protein translation, one of three "stop" codons. The terms amber and ochre (q.v.) originated from a private laboratory joke and have nothing to do with colors.
Amberlite trade name for a family of ion-exchange resins.
amber mutation a mutation in which a polypep-tide chain is terminated prematurely. Amber mutations are the result of a base substitution that converts a codon specifying an amino acid into UAG, which signals chain termination. In certain strains of E. coli amber mutations are suppressed. These strains contain a tRNA with an AUC anticodon, which inserts an amino acid at the UAG site and hence permits translation to continue. See ochre mutation, nonsense mutation.
amber suppressor any mutant gene coding for a tRNA whose anticodon can respond to the UAG stop codon by the insertion of an amino acid that renders the gene product at least partially functional.
20 Ambystoma mexicanum
For example, a mutant tyrosine-tRNA anticodon 3'AUC would recognize 5'UAG, tyrosine would be inserted, and chain growth would continue.
Ambystoma mexicanum the Mexican axolotl, a widely used laboratory species. The urodele for which the most genetic information is available. It was in the nuclei of oocytes of this species that the giant lampbrush chromosomes (q.v.) were first observed. Ambystoma has 14 pairs of chromosomes, and a genome size of about 35 gbp of DNA. It is one of the few vertebrates able to regenerate entire body structures. See Appendix A, Animalia, Chordata, Verte-brata, Amphibia, Urodela; Appendix C, 1882, Flem-ming; neoteny, regeneration.
amelogenins highly conserved proteins that are secreted by ameloblasts and constitute 90% of the organic matrix in the enamel of teeth. The amelo-genins of humans come in a number of isoforms; the most common one contains 192 amino acids. The genes that encode amelogenins reside on the X and Y chromosomes. AMELX is at Xp22.22 and AMELY is at Yp11.2, and both are transcribed in the tooth buds of males. The X-linked gene contains 7,348 bases and the Y-linked gene 8,109. During forensic analyses, amelogenin primers from human X-Y DNA are often used in gender determination.
amelanogenesis imperfecta defects in the mineralization of teeth that affect the enamel layer. The teeth are small, pitted, and show yellow to brown discolorations. The condition often results from mutations in the genes that encode amelanogenins (q.v.).
amensalism a species interaction in which one is adversely affected and the other is unaffected.
Ames test a bioassay for detecting mutagenic and possibly carcinogenic compounds, developed by Bruce N. Ames in 1974. Reverse mutants to histidine independence are scored by growing his~ Salmonella typhimurium on plates deficient in histidine in the presence of the chemical (test) and in its absence (control).
amethopterin methotrexate (q.v.).
amino acid activation a coupled reaction catalyzed by a specific aminoacyl synthetase that attaches a specific amino acid (AA) to a specific transfer RNA (tRNA) in preparation for translation (q.v.).
amino acid attachment site the 3' end of a tRNA molecule to which an amino acid is covalently attached by an aminoacyl bond. See amino acid activation, aminoacyl-tRNA synthetases, transfer RNA.
amino acids aminocarboxylic acids that are components of proteins and peptides. They also occur in their free form or attached to transfer RNAs (q.v.). There are 20 different amino acids for which at least one specific codon exists in the DNA genetic code. These universal amino acids are illustrated on page 21. Their abbreviations and messenger RNA code designations are on page 22. Amino acids are joined together to form polypeptides. Polymers containing 50 or more amino acids are called proteins. All amino acids contain a central carbon atom (designated alpha) to which an amino group, a carboxyl group, and a hydrogen atom are attached. There is also a side chain or residue (R), and this gives each amino acid its characteristic properties. Note that proline is unique in that the alpha C and its amino group are incorporated into the side chain, which is in the form of a five-atom ring. At pH 7 the side chains of lysine, arginine, and histidine are positively charged and the side chains of aspartic acid and glu-tamic acid are negatively charged. Therefore, the net charge born by a protein is determined by the relative proportions of these five amino acids in it. Other amino acids control the shape of proteins. Amino acids like isoleucine, leucine, phenylalanine, and valine are repelled by water molecules and therefore tend to be found buried within the interior of the protein structure. See genetic code, peptide bond, translation.
amino acid sequence the linear order of the amino acids in a peptide or protein. See protein structure.
amino acid side chain a group attached to an amino acid, represented by R in the general formula for an amino acid:
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