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proteins glossary & taxonomy
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amino acid receptors: Cell surface proteins that bind amino acids and trigger changes which influence the behavior of cells. Glutamate receptors are the most common receptors for fast excitatory synaptic transmission in the vertebrate central nervous system, and GAMMA- AMINOBUTYRIC ACID and glycine receptors are the most common receptors for fast inhibition. MeSH, 1993 amino acid sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining protein conformation. MeSH, 1966-1999 Related terms: Sequencing sequence homology amino terminus: Narrower term: N-terminus. Compare carboxyl terminus. amino terminus domain: In protein-protein interactions, the N-terminal domain binds to specific DNA sequences. [S. Fields and O. Song “Novel genetic system to detect protein- protein interactions” Nature 340:245-246 July 20 1989 amino acids: Organic compounds that generally contain an amino (-NH2) and a carboxyl (-COOH) group. Twenty alpha- amino acids are the subunits which are polymerized to form proteins. MeSH A building block of proteins. There are 20 different kinds of amino acids; a protein consists of a specific sequence of amino acids. NIGMS amino acids- number of: The great majority of the now classical twenty amino acids have been on the scene for more than a century. Threonine was the last to be discovered in 1936. There was a scoop in 1986 though when it was discovered that the UGA codon could produce a new amino acid altogether: selenocysteine. Selenocysteine, the 21st amino acid, is found in archaea, eubacteria and animals. And why is it new and not simply a modified cysteine? Because it has its own tRNA which is like granting it a passport. Similarly, in May 2002, the existence of a 22nd amino acid was reported: pyrrolysine. Pyrrolysine was found in the sequences of three enzymes which participate in the production of methane in the archaeon Methanosarcina barkeri: mono-, di- and trimethylamine methyltransferases. Like selenocysteine, it is coded from a stop codon, though this time the UAG or amber codon, and sports its own tRNA. Life's jokers, Vivienne Baillie Gerritsen, Bio.com, 2002 The "classical" amino acids are naturally occurring ones. Others have been synthesized. Related term: proteins - numbers of cell surface receptors: Cell surface proteins that bind signalling molecules external to the cell with high affinity and convert this extracellular event into one or more intracellular signals that alter the behavior of the target cell (From Alberts, Molecular Biology of the Cell, 2nd ed, pp693- 695). Cell surface receptors, unlike enzymes, do not chemically alter their ligands. MeSH, 1994 characterization - protein: Some of the information that can be gathered from a protein chip based characterization includes: post translational modification: phosphorylation, glycosylation, biotinylation, ADP-ribosylation (Cardone et al. 1998) C-terminal sequencing, epitope (binding site) mapping (Hinshelwood et al. 1999) . [what is this from?] Broader term: characterization Biomolecules C-terminus: The residue that has a free carboxyl group, or at least does not acylate another amino acid residue, (it may, for example, acylate ammonia to give -NH-CHR-CO-NH2), is called C-terminal. IUPAC Bioinorganic “amino acid residue in a polypeptide” Also called the carboxyl terminus. carboxyl terminus: See C terminus. Contrast with N-terminus. carboxyl terminus domain: In protein- protein interactions, the C- terminal domain contains acidic regions necessary to activate transcription factors. S Fields and O Song “Novel genetic system” Nature 340: 245-246 July 20 1989 CDR Complementarity Determining Region:
Three regions (CDR1; CDR2
and CDR3) of amino acid sequence in the IMMUNOGLOBULIN
VARIABLE REGION that are highly divergent. Together the CDRs from the
light and heavy immunoglobulin chains form a surface that is complementary
to the antigen. These regions are also present in other members of the
immunoglobulin superfamily, for example, T-cell receptors (
RECEPTORS, ANTIGEN, T-CELL). MeSH 2001 cross-annotation: Comparing gels of similar samples and the information attached to them for verification based solely upon mobility enzymes: Pharmaceutical
biology inclusion bodies: Insoluble aggregates of misfolded proteins which must be solubilized and refolded into an active form to be functional. inteins: Sequences,
DNA & beyond methylation:
Attachment of methyl groups (-CH3) to DNA most commonly at cytosine residues. May be involved in regulation of gene expression. Also may prevent some restriction endonucleases from cutting DNA at their recognition sites.
Schlwindlein N-terminus:
The residue in a peptide that has an amino group
that is free, or at least not acylated by another amino acid residue (it
may, for example, be acylated or formylated), is called N-terminal; it
is the N-terminus. IUPAC Bioinorganic Also called the amino terminus. peptidome, peptidomics: -Omes & -omics phosphorylation: A process involving the transfer of a phosphate group (catalyzed by enzymes) from a donor to a suitable acceptor;. IUPAC Bioinorganic Broader term: post- translational modifications poly A: A group of adenine ribonucleotides in which the phosphate residues of each adenine ribonucleotide act as bridges in forming diester linkages between the ribose moieties. MeSH, 1976 polyadenylation: The addition of a tail of polyadenylic acid (POLY A) to the 3' end of mRNA (RNA, MESSENGER). Polyadenylation involves recognizing the processing site signal, (AAUAAA), and cleaving of the mRNA to create a 3' OH terminal end to which poly A polymerase (POLYNUCLEOTIDE ADENYLTRANSFERASE) adds 60- 200 adenylate residues. The 3' end processing of some messenger RNAs, such as histone mRNA, is carried out by a different process that does not include the addition of poly A as described here. MeSH, 2002 During the maturation of messenger RNA, about 200 adenosine nucleotides are added in a polyadenylation reaction at the 3' end. These are not coded by the corresponding gene. In certain cases there are multiple alternative polyadenylation sites in the primary transcript. This was first observed in adenoviruses [127 - 131]. In cellular genes many alternative polyadenylation sites have also been found [see 132 for review]. Alternative polyadenylation sites usually involve the untranslated trailer sequence in the messenger RNA, but they can also involve translated sequences, and in this case they can affect the structure of the encoded protein. Thus multiple polyadenylation sites are one mechanism whereby a single gene can control the synthesis of more than one polypeptide. Petter Portin in "The Origin, Development and Present Status of the Concept of the Gene: A Short Historical Account of the Discoveries" Univ. of Turku, Finland, Current Genomics, 2000 http://www.bentham.org/cg/sample/cg1-1/Portin.pdf polypeptides: Biomolecules Protein categories prenylation: Attachment of an isoprenoid to the C-terminal cysteine residue. SWISS-PROT keywords http://www.expasy.ch/cgi-bin/get-entries?KW=Prenylation primary structure: In the context of macromolecules such as proteins, the constitutional formula, usually abbreviated to a statement of the sequence and if appropriate cross- linking of chains. IUPAC Compendium See also amino acid sequence. proteasome:
Breaking
down unneeded proteins — a task equal in importance to synthesizing new
proteins — is accomplished by the orderly action of several multiprotein
complexes. At the heart of this process is a multiprotein complex called the
proteasome. Proteasomes: The Machines of Life, DOE Genomes to Life,
US http://genomics.energy.gov/gallery/systems_biology/detail.np/detail-18.html protein nomenclature: Nomenclature protein transport: The process of moving proteins from one cellular compartment (including extracellular) to another by various sorting and transport mechanisms such as gated transport, protein translocation, and vesicular transport. MeSH, 2001 All new proteins in the cell have a tag on them, telling whether the protein is to be sent out of the cell or to a special part in the cell. By comparing tags from known proteins the scientist can find out where an unknown protein will be located. PhD programme in Medical Bioinformatics, Karolinska Institutet http://www.cbb.ki.se/fmb/leaflet.pdf proteins: Naturally occurring and synthetic polypeptides having molecular weights greater than about 10,000 (the limit is not precise). IUPAC Compendium Polymers of amino acids linked by peptide bonds. The specific sequence of amino acids determines the shape and function of the protein. MeSH Proteins provide the critical link between genes and disease, and as such are the key to understanding of basic biological processes including disease pathology, diagnosis, and treatment. The pervasiveness of protein function and their potential for therapeutic intervention are attracting increasing attention from the pharmaceutical and biotechnology industries.
Proteins are the main catalysts, structural elements, signaling messengers
and molecular machines of biological tissues. David Eisenberg et al. “Protein
function in the post-genomic era” Nature 405: 823-826, 15 June 2000 Narrower terms: Cell
biology cell cycle proteins, cellular protein
complexes; Protein categories
antifreeze proteins, basic
proteins, , checkpoint control proteins, factitious proteins, fusion proteins, gatekeeper proteins, heat shock
proteins, housekeeping proteins, hydrophobic proteins, hypothetical proteins,
immediate- early proteins, low- abundance proteins, luxury proteins, membrane
proteins, mitochondrial proteins, oncogene proteins, orphan proteins,
polypeptides, probable proteins, protein kinases, putative proteins, secreted
proteins, therapeutic proteins, trans- acting proteins, tumor- suppressor proteins, wild- type
proteins, zinc finger proteins; Protein
structures disordered proteins, membrane proteins, molecular chaperones,
mosaic proteins, multi- domain proteins, oligomeric proteins, protein families,
protein superfamily proteins - numbers of: Nobody is sure how many naturally occurring proteins will eventually be identified. The precise number of genes will take some years to identify. The extent of alternative splicing is now known to be more than originally expected, before the draft version of the Human Genome Project was published. Post- translational modifications further increase the number of proteins. residue: When two or more amino acids combine to form a peptide, the elements of water are removed, and what remains of each amino acid is called an amino acid residue. IUPAC Bioinorganic Related terms C-terminus, N-terminus ubiquitin: Wikipedia
http://en.wikipedia.org/wiki/Ubiquitin Bibliography
How to look for other unfamiliar terms IUPAC definitions are reprinted with the permission of the International Union of Pure and Applied Chemistry. |
