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Proteins glossary & taxonomy
Evolving terminologies for emerging technologies

Suggestions? Comments? Questions?
Mary Chitty  MSLS
Last revised November 20, 2018 

Biology & chemistry term index:  Related glossaries include Biologics    Proteomics Protein informatics
Technologies Chromatography & electrophoresis
  Mass Spectrometry  NMR & X-ray crystallography  Protein Technologies   Sequencing 
  Biomolecules,  Expression, Protein categories   Protein Structure, Sequences, DNA & beyond

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 Acid Explorer, NCBI  Biochemical properties, Structure  and Chemistry, Common substitutions, Mutation analyzer,. Amino acid functional sites, Amino acids as ligands.

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,, 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

cytokine: The term lymphokine was originally used to denote products of lymphocytes,1 but Cohen et al.2 coined the word cytokine to emphasize the point that these factors need not be made by one specific cell source. This was an important insight, because many immunologically relevant cytokines are made by nonlymphoid cells. Later, the term interleukin was introduced to emphasize the importance of these factors in communication between leukocytes.3 Although this designation has remained in use, it is similarly inaccurate. Many of the polypeptides designated interleukins can also be made by or act on nonhematopoietic cells. Cytokines can be defined operationally as polypeptides secreted by leukocytes and other cells that act principally on hematopoietic cells, and whose effects include modulation of immune and inflammatory responses. However, there are clear exceptions to even this broad definition. Some definitions distinguish cytokines from hormones and growth factors, which act on nonhematopoietic cells. Thus, cytokines are typically characterized as factors made by more than one cell type and act locally, whereas hormones are secreted by specialized cells and act at a distance on a restricted set of target cells. Consequently, the boundary between cytokines and hormones is rather indistinct. In fact, classic hormones such as growth hormone (GH), prolactin (PRL) and erythropoietin (EPO) are clearly cytokines, as is one of the newest hormones, leptin, as evidenced by the type of receptor they bind and their modes of signaling. Cytokines and cytokine receptors John O'shea, ... Richard Siegel, in Clinical Immunology (Third Edition), 2008  Narrower terms: interleukins, lymphokines

enzymes: Pharmaceutical biology
glycosylation: Glycoscience
hormone: 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

 are a group of cytokines (secreted proteins and signal molecules) that were first seen to be expressed by white blood cells (leukocytes).[1] The function of the immune system depends in a large part on interleukins, and  rare deficiencies of a number of them have been described, all featuring autoimmune diseases or immune deficiency. The majority of interleukins are synthesized by helper CD4 T lymphocytes, as well as through  monocytes,  macrophages, and endothelial cells. They promote the development and differentiation of T and B lymphocytes, and hematopoietic cells. The term interleukin derives from (inter-) "as a means of communication", and (leukin) "deriving from the fact that many of these proteins are produced by leukocytes and act on leukocytes". The name is something of a relic, though (the term was coined by Dr Vern Paetkau, University of Victoria) it has since been found that interleukins are produced by a wide variety of body cells. Some interleukins are classified as lymphokines, lymphocyte-produced cytokines that mediate immune responses. Wikipedia accessed 2018 March 12
Broader term: cytokine, Related term: lymphokines

low-abundance proteins: Protein categories Related terms: depletion;
Laser Capture Microdissection; sample prep Technologies overview

lymphokines: a subset of cytokines that are produced by a type of immune cell known as a lymphocyte.[1] They are protein mediators typically produced by T cellsto direct the immune system response by signaling between its cells. Lymphokines have many roles, including the attraction of other immune cells, including macrophages and other lymphocytes, to an infected site and their subsequent activation to prepare them to mount an immune response. Circulating lymphocytes can detect a very small concentration of lymphokine and then move up the concentration gradient towards where the immune response is required. Lymphokines aid B cellsto produce , antibodies. Important lymphokines secreted by the T helper cell include:[2] Interleukin 2 , Interleukin 3, Interleukin 4, Interleukin 5, Interleukin 6, Granulocyte-macrophage colony-stimulating factor, Interferon-gamma,  Wikipedia accessed 2018 March 12

Lymphokines are cytokines produced by T cells (lymphocytes) of the immune system. Lymphokines act to attract additional immune cells to mount an immune response, for instance in stimulating B cells to generate antibodies against the invading pathogen. Nature Lymphokines  Broader term: cytokine Related term: interleukins

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
DNA Methylation Database,
Institut de Génétique Humaine (CNRS) Montpellier, France 
Related terms:
Functional genomics Post Translational Gene Silencing; Gene definitions epigenetics; Omes & omics epigenomics, epigenotype 

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.

Amides derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of  water. The term is usually applied to structures formed from a- amino acids, but it includes any amino carboxylic acid. IUPAC Compendium 
Related term: polypeptides

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 

polypeptides: Biomolecules   Protein categories


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.


protein engineering: Protein Technologies
protein expression: Expression genes & proteins   
protein family: Protein structure

protein isoprenylation:
A post- translational modification of proteins by the attachment of an isoprenoid to the C-terminal cysteine residue. The isoprenoids used, farnesyl diphosphate or geranylgeranyl diphosphate, are derived from the same biochemical pathway that produces cholesterol. MeSH, 1993 Broader term: post- translational modification

protein nomenclature: Nomenclature

protein superfamily: Protein structures
protein synthesis:
See transcription, translation. Sequences, DNA & beyond
protein therapeutics: Biologics

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

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,  carrier proteins, cellular proteins, chemokines, chromosome proteins, chimera protein, constitutive proteins, complex proteins, cytokines, designer proteins, DNA binding proteins, factitious proteins, fibrous proteins, fluorescent proteins, full-length proteins, fusion proteins, gatekeeper proteins, globular proteins, glycoproteins, GTP-binding proteins, heat shock proteins, growth factors, housekeeping proteins, hub proteins, hyperthermal proteins,  hypothetical proteins, immediate-early proteins, immunoglobulin iG, integral membrane proteins, interferons, low abundance proteins, luxury proteins, membrane proteins, membrane transport proteins, mitochondrial proteins, molecular chaperones, moonlighting proteins, mosaic proteins, naked proteins,  nuclear proteins, nucleoproteins, oligomeric proteins, orphan proteins, peripheral membrane proteins, peripheral proteins, polypeptides, polyproteins, probable proteins, proteases, protein complex,  protein RNA interactions, putative proteins, recombinant proteins, regulatory proteins, repressor proteins, RING finger proteins, secreted proteins, structural homology protein, structural proteins, transport proteins, truncation, ubiquitin’s, wild-type proteins, zinc finger proteins  Protein structures disordered proteins,multi- domain 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 

ubiquitin as a drug target, ubiquitin proteosome system: Drug targets

ubiquitination: Wikipedia 
Broader term: post- translational modification

wild-type proteins: Protein categories 

Proteins resources
IUPAC  International Union of Pure and Applied Chemistry, Compendium of Chemical Terminology: Recommendations, compiled by Alan D. McNaught and Andrew Wilkinson, Blackwell Science, 1997. "Gold Book" 6,500+ definitions.
IUPAC  International Union of Pure and Applied Chemistry, Glossary of Terms used in Bioinorganic Chemistry, Recommendations, 1997. 450+ definitions.
IUPAC  International Union of Pure and Applied Chemistry, Glossary for Chemists of terms used in biotechnology. Recommendations, Pure & Applied Chemistry 64 (1): 143-168, 1992. 200 + definitions.
NCBI Proteins
Proteins" Kimball's Biology Pages, John W. Kimball,
UNI-PROT KnowledgeBase keywords   Swiss Institute of Bioinformatics, Geneva Switzerland, European Bioinformatics Institute, Hinxton, UK, PIR Protein Information Resource, 2011

How to look for other unfamiliar  terms

IUPAC definitions are reprinted with the permission of the International Union of Pure and Applied Chemistry.

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