This section of the HTML version of the ontology contains the
class definitions of the ontology. Each class defines a type of
entity. A class is defined to have a set of slots, where each slot
defines attributes and properties that may be used by an instance of
Slots are inherited by a class from its parent classes. Usually this
HTML form of the ontology shows only the names of the slots at each
class, with links provided to the full definition of the slot in the
slot section of the ontology. However, when the definition of a slot
is changed within a class with respect to its parent, the full
definition of the slot is shown.
DEFINITION: Either of the inner and outer membranes, comprising the mitochondrial envelope. Note that the term mitochondrial membrane is a classification term for the inner and outer mitochondrial membranes. It does not include the intermembrane space.
some sources use the same term refer to nuclear envelope. We distinguish them. The term nuclear membrane is a classification term for the inner and outer nuclear membranes. It does not include the perinuclear space.
DEFINITION: A lipid bilayer that forms the outermost layer of the cell envelope of Gram-negative bacteria; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
DEFINITION: The Golgi cisterna farthest from the endoplasmic reticulum; the final processing compartment through which proteins pass before exiting the Golgi apparatus; the compartment in which N-linked protein glycosylation is completed.
DEFINITION: A placeholder for when it is not known in which space an object is located in.
This kind of situation can occur especially for protons or other compounds processed by
membrane-bound enzymes, because such systems may be hard to characterize experimentally.
DEFINITION: A variety of versatile proteins and polysaccharides that are secreted locally and assembled into an organized meshwork in close association with the surface of the cell that produced them. The matrix fills up the extracellular space.
DEFINITION: The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan.
DEFINITION: A protective structure outside the cytoplasmic membrane composed of peptidoglycan, a molecule made up of a glycan (sugar) backbone of repetitively alternating N-acetylglucosamine and N-acetylmuramic acid with short, attached, cross-linked peptide chains containing unusual amino acids; also called murein. As in, but not restricted to, the taxon Eubacteria (Bacteria, ncbi_taxonomy_id:2).
DEFINITION: The peptidoglycan layer of the Gram negative cell envelope. In Gram negative cells the peptidoglycan is relatively thin (approximately 2 nm) and is linked to the outer membrane by lipoproteins. In Gram negative cells the peptidoglycan is too thin to retain the primary stain in the Gram staining procedure and therefore cells appear red after Gram stain.
DEFINITION: A layer of peptidoglycan found outside of the cytoplasmic membrane. In Gram positive cells the peptidoglycan is relatively thick (approximately 40 nm) and retains the primary stain of the Gram procedure, thus cells appear blue after Gram stain. Gram positive cell walls often contain teichoic acids (acidic anionic polysaccharides) bound to the peptidoglycan.
DEFINITION: A rigid yet dynamic structure surrounding the plasma membrane that affords protection from stresses and contributes to cell morphogenesis. Major components are glycoproteins and peptidoglycans including mannoproteins, glucans and sometimes chitin. Enzymes involved in cell wall biosynthesis are also found in the cell wall. Note that some forms of fungi develop a capsule outside of the cell wall under certain circumstances; this is considered a separate structure. As in, but not restricted to, the fungi (Fungi, ncbi_taxonomy_id:4751).
DEFINITION: A more or less rigid membrane enclosing the protoplast of a cell and composed of cellulose and other organic and inorganic substances. As in, but not restricted to, the flowering plants (Magnoliophyta, ncbi_taxonomy_id:3398).
DEFINITION: A plant cell wall that is no longer able to expand and so does not permit growth. Secondary cell walls contain less pectin that primary cell walls. The secondary cell is mostly composed of cellulose and is strengthened with lignin.
DEFINITION: A discrete structure of a cell specialized to carry out a particular function, bounded by a membrane so that sets of enzymes can operate without interference from reactions occurring in other compartments.
DEFINITION: The acidocalcisome is a rounded, electron-dense organelle, rich in calcium and polyphosphate. It is acidic. It was originally discovered in Trypanosomes, but has been found in a substantial range of organisms. It might be the only organelle preserved between prokaryotes and eukaryotes. In Trypanosomes, it is in the vicinity of a contractile vacuole, which is implicated in controlling the cell's osmomolarity.
DEFINITION: A prelysosomal endocytic organelle defined by the time it takes for endocytosed macromolecules to be delivered. The time of delivery may vary ; for example, late endosomes are usually loaded 4-30 min after endocytic uptake in mammalian cells. late endosomes are more spherical than early endosomes and are mostly juxtanuclear, being concentrated near the microtubule organizing center. They are differentiated from early endosomes by their lower lumenal pH and different protein composition.
DEFINITION: The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
DEFINITION: The rough (or granular) endoplasmic reticulum (ER) has ribosomes adhering to the outer surface; the ribosomes are the site of translation of the mRNA for those proteins which are either to be retained within the cisternae (ER-resident proteins), the proteins of the lysosomes, or the proteins destined for export from the cell. Glycoproteins undergo their initial glycosylation within the cisternae.
DEFINITION: The smooth endoplasmic reticulum (ER) has with no ribosomes attached to it. The smooth is the recipient of the proteins synthesized in the rough ER. Those proteins to be exported are passed to the Golgi complex, the resident proteins are returned to the rough ER and the lysosomal proteins after phosphorylation of their mannose residues are passed to the lysosomes. Glycosylation of the glycoproteins also continues. The smooth ER is the site of synthesis of lipids, including the phospholipids. The membranes of the smooth ER also contain enzymes that catalyze a series of reactions to detoxify both lipid-soluble drugs and harmful products of metabolism. Large quantities of certain compounds such as phenobarbital cause an increase in the amount of the smooth ER.
DEFINITION: A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
DEFINITION: Any of a group of related cytoplasmic, membrane bound organelles that are found in most animal cells and that contain a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
DEFINITION: The glycosome is an organelle that is bounded by a single membrane and contains a dense proteinaceous matrix. It is mostly found in Trypanosomes and Leishmania. It contains the glycolytic enzymes.
DEFINITION: A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
DEFINITION: A subcellular organelle of plant cells surrounded by 'half-unit' or a monolayer membrane instead of the more usual bilayer. The storage body has a droplet of triglyceride surrounded by a monolayer of phospholipids, interacting with the triglycerides and the hydrophilic head groups facing the cytosol, and containing major protein components called oleosins.
Source: GOC:mtg_sensu, ISBN:0943088372
DEFINITION: Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.
DEFINITION: A membrane-enclosed sac that takes up most of the volume of a mature plant cell. Functions include storage, separation of toxic byproducts, and cell growth determination. Some sulfur bacteria also have large central vacuoles.
DEFINITION: A lytic vacuole that is maintained at acidic pH and has different tonoplast composition compared to the central vacuole. Found during leaf senescence and develops in the peripheral cytoplasm of cells that contain chloroplast.
DEFINITION: The contractile vacuole is an organelle that is bounded by a single membrane and is involved in osmoregulation. It is mostly found in protists like Trypanosomes, and in unicellular algae. Over several seconds, it grows by collecting excess water from the cytosol, and then shrinks by expelling the contents out of the cell.
DEFINITION: Secretory organelles, some 50 nm in diameter, of presynaptic nerve terminals; accumulate high concentrations of neurotransmitters and secrete these into the synaptic cleft by fusion with the 'active zone' of the presynaptic plasma membrane.
DEFINITION: A small subcellular vesicle, surrounded by a single-layered membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules.
DEFINITION: Long whiplike or feathery structures borne either singly or in groups by the motile cells of many bacteria and unicellular eukaryotes and by the motile male gametes of many eukaryotic organisms, which propel the cell through a liquid medium.
DEFINITION: Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
DEFINITION: A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis.
DEFINITION: An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.
DEFINITION: A placeholder needed for metabolites in some transport reactions that cross several membranes,
but where additional metabolites may also participate from an intermediate compartment,
which shall simply be called the middle compartment.
This section of the HTML version of the ontology contains the
slot definitions of the ontology. Each slot itself has several
properties such as documentation about that slot, a cardinality
(specifying the number of values that the slot may have), a value type
(specifying the data type of slot values), and a domain (specifying
the class(es) in which the slot is used).
The primary name by which an object is known to
scientists. Typically the name will be a standard name, or a widely used and familiar name.
In some cases arbitrary choices must be made when picking the Common-Name.
This slot lists the components of some physical assembly:
1. The subunits of a protein complex, a protein-RNA complex, and a
2. The genes within a genetic element, or the contigs of a genetic element
3. The genes and other DNA-Segments within a transcription unit
4. Entities witin the cell component ontology
5. The ion constituents in salts
The coefficient of each component (when known) is listed as an
annotation of the component value under the label coefficient.
When a modified protein is created to reflect a chemically modified
alternative form of the protein, if that protein is a complex, its subunit
structure need not be mirrored in the modified-protein frame. The
subunit structure should be defined only once, for the frame that
represents the unmodified form of the protein.
SURROUNDED-BY is used to describe topological relationships between
cellular compartments. We say X SURROUNDED-BY Y in two typical cases:
where a space Y is surrounded by a membrane X (example: the bacterial
cytosol is surrounded by the plasma membrane of the cell), and where a
membrane Y is surrounded by a space X (example: the bacterial inner
membrane is surrounded by the bacterial periplasmic space).
SURROUNDS is used to describe topological relationships between cellular
compartments. We say X SURROUNDS Y in two typical cases: where
a membrane X encloses a space Y (example: the plasma membrane of a
bacterial cell surrounds the cytosol), and where a space X encloses
a membrane Y (example: the bacterial periplasmic space encloses
the bacterial inner membrane).