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
that class.
Slots are inherited by a class from its parent classes. Usually this
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COMMENT: Refers to artificial cell components that are derived from disruptive cell biological techniques. The components are not present within any cells.
DEFINITION: Double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer, also includes associated proteins.
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.
COMMENT: 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: 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.
COMMENT: The term plastid membrane is a classification term for the inner and outer mitochondrial membranes. It does not include the intermembrane space.
DEFINITION: The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
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: Cytoplasmic organelles, spherical or oval in shape, that are bounded by a single membrane and contain oxidative enzymes, especially those utilizing hydrogen peroxide (H2O2).
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: A membrane-bound organelle that carries materials newly ingested by endocytosis. It passes many of the materials to lysosomes for degradation.
DEFINITION: Any small, fluid-filled, membrane-limited spherical organelle in the cytoplasm. Vesicle store, transport, or digest cellular products or wastes.
DEFINITION: Any vesicle associated with the Golgi complex and involved in mediating transport within the Golgi or between the Golgi and other parts of the cell.
DEFINITION: Small membrane-bounded organelle formed by pinching off of a coated region of membrane. Some coats are made of clathrin, whereas others are made from other proteins.
DEFINITION: A vesicle with a coat formed of the COPII coat complex proteins; COPII-coated vesicles are found associated with endoplasmic reticulum (ER) membranes at steady state, and are involved in ER to Golgi (anterograde) vesicle transport.
DEFINITION: A vesicle with a coat formed of the COPI coat complex proteins. COPI-coated vesicles are found associated with Golgi membranes at steady state, are involved in Golgi to endoplasmic reticulum (retrograde) vesicle transport, and possibly also in intra-Golgi transport.
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: The membrane-limited component of the Golgi apparatus which is typically flattened, usually with a central plate-like region which is often continuous with peripheral tubules and vesicles.
DEFINITION: Any double membrane structure including the intermembrane space that surrounds an organelle. In some cases, an organellar envelope may have more than two membranes.
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 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 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 plant cell wall that is still able to expand, permitting cell growth. Primary cell walls contain more pectin than secondary walls and no lignin is present.
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 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 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: A set of flattened disc-like sacs formed by the thylakoid membrane. They are interconnected and often arranged in stacks, and referred as grana.
DEFINITION: The Golgi cisterna closest to the endoplasmic reticulum; the first processing compartment through which proteins pass after export from the ER.
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: 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: 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 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: 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: A small, membrane-bounded organelle that uses dioxygen (O2) to oxidize organic molecules; contains some enzymes that produce and others that degrade hydrogen peroxide (H2O2).
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: 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 membrane-bounded organelle of eukaryotic cells that contains the chromosomes. It is the primary site of DNA replication and RNA synthesis in the cell.
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: The space enclosed by the double membrane of a chloroplast but excluding the thylakoid space. It contains DNA, ribosomes and some temporary products of photosynthesis.