Rhea list of ChEBI terms representing the major species at pH 7.3.
Term not to be used for direct annotation
GO ribbon for eukaroytic cellular processes
A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact.
Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.
Note that this term should not be confused with 'GO:0140014 ; mitotic nuclear division'. 'GO:0000278 ; mitotic cell cycle represents the entire mitotic cell cycle, while 'GO:0140014 ; mitotic nuclear division' specifically represents the actual nuclear division step of the mitotic cell cycle.
The division of the cytoplasm and the plasma membrane of a cell and its partitioning into two daughter cells.
Note that this term should not be used for direct annotation. When annotating eukaryotic species, mitotic or meiotic cytokinesis should always be specified for manual annotation and for prokaryotic species use 'FtsZ-dependent cytokinesis ; GO:0043093' or Cdv-dependent cytokinesis ; GO:0061639. Also, note that cytokinesis does not necessarily result in physical separation and detachment of the two daughter cells from each other.
Combining with a virus component and mediating entry of the virus into the cell.
The chemical reactions and pathways resulting in the formation of a protein in the cytoplasm. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the protein.
Note that this term applies to translation performed by cytoplasmic ribosomes, which is distinct from translation performed by organellar ribosomes. For mitochondrial translation, consider GO:0032543 'mitochondrial translation' or its child terms.
Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
Note that this term is a direct child of 'biological_process ; GO:0008150' because some immune system processes are types of cellular process (GO:0009987), whereas others are types of multicellular organism process (GO:0032501).
An organ system process carried out at the level of a muscle. Muscle tissue is composed of contractile cells or fibers.
An organ system process carried out by any of the organs or tissues of the circulatory system. The circulatory system is an organ system that moves extracellular fluids to and from tissue within a multicellular organism.
An organ system process carried out by any of the organs or tissues of the renal system. The renal system maintains fluid balance, and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products. In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels; in other species, the renal system may comprise related structures (e.g., nephrocytes and malpighian tubules in Drosophila).
A process carried out by the organs or tissues of the respiratory system. The respiratory system is an organ system responsible for respiratory gaseous exchange.
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
Binding to an RNA molecule or a portion thereof.
Exportin-5 recognizes 3' overhang of pre-miRNA
Generation of force resulting in movement, for example along a microfilament or microtubule, or in torque resulting in membrane scission or rotation of a flagellum. The energy required is obtained either from the hydrolysis of a nucleoside triphosphate or by an electrochemical proton gradient (proton-motive force).
Extension of pseudopodia by myosin-X in a PI3K dependent manner
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
Catalysis of the reaction: GTP + H2O = GDP + H+ + phosphate.
hydrolase activity, acting on acid anhydrides, acting on GTP, involved in cellular and subcellular movement
heterotrimeric G-protein GTPase activity
protein-synthesizing GTPase activity, elongation
protein-synthesizing GTPase activity, initiation
protein-synthesizing GTPase activity, termination
signal-recognition-particle GTPase activity
heterotrimeric G-protein GTPase, alpha-subunit
heterotrimeric G-protein GTPase, beta-subunit
heterotrimeric G-protein GTPase, gamma-subunit
G alpha (s) auto-inactivates by hydrolysing GTP to GDP
Adenylate cyclase increases the GTPase activity of G alpha-olf
Adenylaye cyclase increases the GTPase activity of G alpha-olf
Adenylate cyclase increases the GTPase activity of Gi alpha
Endocytosis (internalization) of clathrin-coated vesicle
Translocation of TGN-lysosome vesicle to lysosome
Internalization of MHC II:Ii clathrin coated vesicle
GNAT1-GTP hydrolyses its bound GTP to GDP
G alpha (z) auto-inactivates by hydrolysing GTP to GDP
G alpha (i) auto-inactivates by hydrolysing GTP to GDP
G alpha (12/13) auto-inactivates by hydrolysing GTP to GDP
G alpha (q) auto-inactivates by hydrolysing GTP to GDP
P2Y purinoceptor 1 activates MAP kinase p38 alpha
trans-Golgi Network Lysosomal Vesicle Scission
80S:Met-tRNAi:mRNA:SECISBP2:Sec-tRNA(Sec):EEFSEC:GTP is hydrolysed to 80S:Met-tRNAi:mRNA:SECISBP2:Sec and EEFSEC:GDP by EEFSEC
39S subunit binds 28S subunit:mRNA:fMet-tRNA
TUFM hydrolyzes GTP and TUFM:GDP dissociates from 55S ribosome
Hydrolysis of GTP and dissociation of 28S and 39S subunits
Translocation of peptidyl-tRNA from A-site to P-site (and translocation of 55S ribosome by 3 bases along mRNA)
ASAP1 stimulates GTPase activity of ARF4
SRGAP2 stimulates RAC1 GTP-ase activity and ends FMNL1-mediated elongation of actin filaments
Rheb in the MTORC1 complex hydrolyses GTP
TBC1D20 stimulates GTPase activity of RAB1, resulting in hydrolysis of GTP
CYTH proteins stimulate ARF1 GTPase activity
ARHGAP35 stimulates RHOA GTPase activity
TBC RabGAPs accelerate GTP hydrolysis by RAB35
TBC1D2A accelerates GTP hydrolysis by RAB7
TBC1D15 accelerates GTP hydrolysis by RAB7
TBC1D16 accelerates GTP hydrolysis by RAB4A
TBC1D25 accelerates GTP hydrolysis by RAB33B
Dynamin-mediated GTP hydrolysis promotes vesicle scission
G alpha (i)i1/i2/i3 in G (i):RGS complex is inactivated
G alpha (z) in G alpha (z):RGS complex is inactivated
G alpha (q) in G (q):RGS complex is inactivated
RAS intrinsic GTPase activity hydrolyzes GTP to GDP
GBP1 hydrolyzes GTP forming GBP1 oligomers
ABCE1:ATP binds PELO:HBS1L-1:GTP:80S ribosome:non-stop mRNA:peptidyl-tRNA with nascent peptide and HBS1L-1:GDP is released
The action of a molecule that contributes to the structural integrity of a complex.
Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, accross or in between cells.
Some transporters, such as certain members of the SLC family, are referred to as 'carriers'; however GO uses carrier with a different meaning: a carrier binds to and transports the substance (see GO:0140104 molecular carrier activity), whereas a transporter forms some pore that allows the passing of molecules.
The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
Note that this term is intended to annotate gene products that are not attached to the cell surface. For gene products at the cell surface, consider annotating to external side of plasma membrane ; GO:0009897.
The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, 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; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
Not to be used for manual annotation. Please choose a more specific term: for bacteria, annotate to GO:0009274; peptidoglycan-based cell wall, for plants: annotate to GO:0009505 ; plant-type cell wall, for fungi: GO:0009277 ; fungal-type cell wall, and for archae, use GO:0030115 S-layer (see PMID:31214995).
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
The double lipid bilayer that encloses the nucleus, separating its contents from the cytoplasm. It consists of an inner and outer nuclear membrane, with an intermembrane space (20-40 nm wide, also called the perinuclear space) between them. The envelope is supported by the nuclear lamina and contains nuclear pore complexes, which regulate molecular transport.
That part of the nuclear content other than the chromosomes or the nucleolus.
A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore.
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. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
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.
Some anaerobic or microaerophilic organisms (e.g. Entamoeba histolytica, Giardia intestinalis and several Microsporidia species) do not have mitochondria, and contain mitochondrion-related organelles (MROs) instead, called mitosomes or hydrogenosomes, very likely derived from mitochondria. To annotate gene products located in these mitochondrial relics in species such as Entamoeba histolytica, Giardia intestinalis or others, please use GO:0032047 'mitosome' or GO:0042566 'hydrogenosome'. (See PMID:24316280 for a list of species currently known to contain mitochondrion-related organelles.)
A small lytic vacuole that has cell cycle-independent morphology found in most animal cells and that contains 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.
A vacuole to which materials ingested by endocytosis are delivered.
A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.
A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.
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).
A membrane-bound cytoplasmic organelle of the endomembrane system that further processes the core oligosaccharides (e.g. N-glycans) added to proteins in the endoplasmic reticulum and packages them into membrane-bound vesicles. The Golgi apparatus operates at the intersection of the secretory, lysosomal, and endocytic pathways.
Note that the Golgi apparatus can be located in various places in the cytoplasm. In plants and lower animal cells, the Golgi apparatus exists as many copies of discrete stacks dispersed throughout the cytoplasm, while the Golgi apparatus of interphase mammalian cells is a juxtanuclear, often pericentriolar reticulum, where the discrete Golgi stacks are stitched together to form a compact and interconnected ribbon, sometimes called the Golgi ribbon.
An intracellular non-membrane-bounded organelle comprising a matrix of coalesced lipids surrounded by a phospholipid monolayer. May include associated proteins.
Note that this term does not refer to vesicles, but instead to structures in which lipids do not necessarily form bilayers.
An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides.
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
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.
A cellular structure that forms the internal framework of eukaryotic and prokaryotic cells. The cytoskeleton includes 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.
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body.
Note that we deem cilium and microtubule-based flagellum to be equivalent. In most eukaryotic species, intracellular sub-components of the cilium, such as the ciliary base and rootlet, are located near the plasma membrane. In Diplomonads such as Giardia, instead, the same ciliary parts are located further intracellularly. Also, 'cilium' may be used when axonemal structure and/or motility are unknown, or when axonemal structure is unusual. For all other cases, please refer to children of 'cilium'. Finally, note that any role of ciliary proteins in sensory events should be captured by annotating to relevant biological process terms.
The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances.
generation of precursor metabolites and energy
The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by the origin recognition complex, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
DNA biosynthesis is only part of this process. See also the biological process terms 'DNA-dependent DNA replication ; GO:0006261' and 'RNA-dependent DNA replication ; GO:0006278'.
Activation of ATR in response to replication stress
The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Interchromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
The assembly or remodeling of chromatin composed of DNA complexed with histones, other associated proteins, and sometimes RNA.
establishment or maintenance of chromatin architecture
DNA replication-independent chromatin assembly
DNA replication-independent chromatin organization
DNA replication-independent nucleosome organisation
DNA replication-independent nuclesome assembly
transcription-coupled nucleosome assembly
The synthesis of an RNA transcript from a DNA template.
transcription from bacterial-type RNA polymerase promoter
Transcriptional activity of SMAD2/SMAD3:SMAD4 heterotrimer
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
regulation of cellular transcription, DNA-dependent
regulation of transcription, DNA-dependent
regulation of transcription, DNA-templated
regulation of gene-specific transcription
regulation of DNA-templated transcription
NOTCH4 Intracellular Domain Regulates Transcription
The chemical reactions and pathways involving tRNA, transfer RNA, a class of relatively small RNA molecules responsible for mediating the insertion of amino acids into the sequence of nascent polypeptide chains during protein synthesis. Transfer RNA is characterized by the presence of many unusual minor bases, the function of which has not been completely established.
The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
glycoprotein-specific chaperone activity
non-chaperonin molecular chaperone ATPase activity
protein complex assembly, multichaperone pathway
Formation of tubulin folding intermediates by CCT/TriC
N-glycan trimming in the ER and Calnexin/Calreticulin cycle
The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups.
cellular amino acid and derivative metabolic process
The chemical reactions and pathways involving compounds derived from amino acids, organic acids containing one or more amino substituents.
cellular amino acid derivative metabolic process
cellular amino acid derivative metabolism
cellular modified amino acid metabolic process
The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
The chemical reactions and pathways involving vitamins. Vitamin is a general term for a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body. Vitamins may be water-soluble or fat-soluble and usually serve as components of coenzyme systems.
The chemical reactions and pathways involving the nonmetallic element sulfur or compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione.
The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.
copper-induced intracellular protein transport
The directed movement of molecules between the nucleus and the cytoplasm.
Note that transport through the nuclear pore complex is not transmembrane because the nuclear membrane is a double membrane, and is not traversed.
The cellular catabolic process in which cells digest cellular materials, such as organelles and other macromolecular constituents, or non-self materials such as intracellular pathogens. Autophagy serves to provide essential nutrients under conditions of cellular stress; or can remodel intracellular structures during cell differentiation.
The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrion; includes mitochondrial morphogenesis and distribution, and replication of the mitochondrial genome as well as synthesis of new mitochondrial components.
mitochondrion organization and biogenesis
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures.
cytoskeletal organization and biogenesis
cytoskeleton organization and biogenesis
A microtubule-based process that results in the movement of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a peroxisome. A peroxisome is a small, membrane-bounded organelle that uses dioxygen (O2) to oxidize organic molecules.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a lysosome. A lysosome is a cytoplasmic, membrane-bounded organelle that is found in most animal cells and that contains a variety of hydrolases.
The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.
The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
Any cellular process that results in the specification, formation or maintenance of anisotropic intracellular organization or cell growth patterns.
establishment and/or maintenance of cell polarity
establishment and/or maintenance of cell polarization
establishment or maintenance of cell polarity
Binding to a protein component of a cytoskeleton (actin, microtubule, or intermediate filament cytoskeleton).
The chemical reactions and pathways resulting in the formation of glycoproteins, a protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide.
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.
A membranous cellular structure that bears the photosynthetic pigments in plants, algae, and cyanobacteria. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation.
A thylakoid is not considered an organelle, but some thylakoids are part of organelles.
A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell.
Note that this term should be used to annotate gene products in the organism undergoing the programmed cell death. To annotate genes in another organism whose products modulate programmed cell death in a host organism, consider the term 'modulation by symbiont of host programmed cell death ; GO:0052040'. Also, note that 'programmed cell death ; GO:0012501' should be used to refer to instances of caspase-independent cell death mechanisms, in the absence of further indications on the process taking place. At present, caspase-independent cell death is not yet represented in GO due to the lack of consensus and in-depth research on the topic. 'programmed cell death ; GO:0012501' may also be used to annotate gene products in taxa where apoptosis as defined in GO:0006915 does not occur, such as plants. You may also consider these specific children: GO:0097468 'programmed cell death in response to reactive oxygen species' (with descendants GO:0010421 'hydrogen peroxide-mediated programmed cell death' and GO:0010343 'singlet oxygen-mediated programmed cell death'), and GO:0009626 'plant-type hypersensitive response' and its children.
The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds.
The chemical reactions and pathways involving mRNA, messenger RNA, which is responsible for carrying the coded genetic 'message', transcribed from DNA, to sites of protein assembly at the ribosomes.
SLBP independent Processing of Histone Pre-mRNAs
The chemical reactions and pathways involving snRNA, small nuclear RNA, any of various low-molecular-mass RNA molecules found in the eukaryotic nucleus as components of the small nuclear ribonucleoprotein.
A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.
Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage.
Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
oxidoreductase activity, acting on other substrates
SUMF1 mediates the oxidation of cysteine to formylglycine, producing active arylsulfatases
Arachidonate is oxidised to 5S-HpETE by ALOX5
MARC1,MARC2 reduce N-hydroxylated compounds
Hydroperoxy reductase reduces 4(S)-Hp-17(S)-HDHA to RvD6
Hydroperoxy reductase reduces 7(S)-Hp-17(S)-HDHA to RvD5
Hydroperoxy reductase reduces 4(S)-Hp-17(R)-HDHA to AT-RvD6
Hydroperoxy reductase reduces 7(S)-Hp-17(R)-HDHA to AT-RvD5
Hydroperoxy reductase reduces 7(S),14(S)-diHp-DHA to 7-epi-MaR1
Hydroperoxy reductase reduces 7,17-diHp-DPAn-3 to RvD5n-3DPA
Lipoxygenase dehydrogenates 7(S),17(S)-diHp-DHA to 7S(8)-epoxy-17(S)-HDHA
Hydroperoxy reducatase reduces 14(S)-Hp-DHA to 14(S)-HDHA
Unknown sepiapterin synthase transforms PTHP to sepiapterin
Cob(I)alamin bound to MMACHC is oxidized to cob(II)alamin
Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
GSSeH combines with bGalNAc derivative to form GSSebGalNac
TRAF2 ubiquitinates cIAP1,2 in cIAP1,2:TRAF1:TRAF2:TRAF3:NIK
TSR3 transfers aminocarboxypropyl group from S-adenosylmethionine to N(1)-methylpseudouridine-1248 of 18SE rRNA yielding N(1)-methyl-N(3)-aminocarboxypropylpseudouridine-1248
Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
Partial proteolysis of antigen in phagolysosomes
Production of AA by iPLA2 upon FCGR activation
Phospholipid phosphatase 6 hydrolyses Presqualene diphosphate to presqualene monophosphate
QNG1 hydrolyzes queuosine 5'-monophosphate yielding queuine and ribose 5'-monophosphate
Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
PXLP-K278-PHYKPL tetramer hydrolyses 5PHL
TYW1:FMN:4Fe-4S transforms 1-methylguanosine yielding yW-187 (4-demethylwyosine) at nucleotide 37 of tRNA(Phe)
Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
GFUS dimer epimerises GDP-DHDMan to GDP-KDGal
Catalysis of the joining of two molecules, or two groups within a single molecule, using the energy from the hydrolysis of ATP, a similar triphosphate, or a pH gradient.
A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.
A physical, chemical, or biochemical process carried out by living organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism.
The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered.
Note that a signal is any variable property or parameter that serves to convey information, and may be a physical entity such as a gene product or small molecule, a photon, or a change in state such as movement or voltage change.
The cellular developmental process in which a relatively unspecialized cell, e.g. embryonic or regenerative cell, acquires specialized structural and/or functional features that characterize a specific cell. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
multicellular organismal protein catabolic process
This term refers to the breakdown of mature proteins. For cleavage events involved in generating a mature protein from a precursor, consider instead the term 'protein maturation ; GO:0051604' and its children.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix.
extracellular matrix organization and biogenesis
A structure that lies outside the plasma membrane and surrounds the entire cell or cells. This does not include the periplasmic space.
The outer membrane (of gram negative bacteria) or cell wall (of yeast or Gram positive bacteria) are defined as parts of this structure, see 'external encapsulating structure part'.
A structure lying external to one or more cells, which provides structural support, biochemical or biomechanical cues for cells or tissues.
A process in which an regulatory non-coding RNA molecule reduces expression of target genes. This can occur pre-transcriptionally by assembly of heterochromatin and prevention of transcription or co- or post-transcriptionally by targeting RNAs for degradation or by interfering with splicing or translation. This process starts once the inhibitory RNA molecule has been transcribed, and includes processing of the RNA such as cleavage, modifications, transport from the nucleus to the cytoplasm, loading onto the RISC complex, and the effect on transcription or translation.
regulatory ncRNA-mediated gene silencing
A molecular function exhibited by a protein that is covalently attached (AKA tagged or conjugated) to another protein where it acts as a marker, recognized by the cellular apparatus to target the tagged protein for some cellular process such as modification, sequestration, transport or degradation.
Use this term to annotate conjugated tags, not for conjugating enzymes. At the time of writing, all known gene products with this activity are ubiquitin-like, either based on overall sequence similarity or the presence of common motifs and structures.
A vesicle found in the cytoplasm of a cell.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of telomeres, terminal regions of a linear chromosome that include the telomeric DNA repeats and associated proteins.
organization of chromosome, telomeric region
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cell junction. A cell junction is a specialized region of connection between two cells or between a cell and the extracellular matrix.
Binding specifically to a substance (cargo) to deliver it to a transport vesicle. Cargo receptors span membranes (for instance the plasma membrane or the endoplasmic reticulum membrane), binding simultaneously to cargo molecules and coat adaptors, to efficiently recruit the cargo molecules to nascent vesicles.
receptor activity involved in receptor-mediated endocytosis
Notes: (1) For receptors binding a molecule but coupled to a signal transduction pathway, consider instead the term 'signaling receptor activity ; GO:0038023' and its children. (2) Cargo receptors transport substances by vesicular transport, not by transmembrane transport. For transmembrane transporters, consider instead the term 'transmembrane transporter activity ; GO:0022857'.
eNOS:Caveolin-1 complex binds to Nostrin
M6PR transports activated ARSA to the lysosome
CD320-mediated TCN2:RCbl uptake and delivery to lysosome
CUBN:AMN-mediated CBLIF:RCbl uptake and delivery to lysosome
LRP2-mediated uptake of extracellular CUBN:GC:25(OH)D
iRHOM2 transports ADAM17 from ER to the Golgi-network
iRHOM2 transports ADAM17:Zn2+ from Golgi to the plasma membrane
LRP2-mediated TCN2:RCbl uptake and delivery to lysosome
The series of events that restore integrity to a damaged tissue, following an injury.
A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis.
Binding to a histone, any of a group of water-soluble proteins found in association with the DNA of eukaryotic or archaeal chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in gene regulation and DNA replication. They may be chemically modified (methylated, acetlyated and others) to regulate gene transcription.
Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane.
Binding to a protein or a protein-containing complex to assist the protein folding process.
protein binding involved in protein folding
Note that a protein folding chaperone binds an unfolded protein to fold it. Do not confuse with unfolded protein holdase activity, which binds an unfolded protein and keeps it unfolded to deliver it to its final destination.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole.
microtubule-based flagellum organization
Note that we deem cilium and microtubule-based flagellum to be equivalent.
Any molecular function involved in the regulation of initiation, activation, perpetuation, repression or termination of polypeptide synthesis at the ribosome.
Functions in the storage of nutritious substrates.
Note that this term can be used in place of the obsolete terms 'storage protein ; GO:0005187' and 'storage protein of fat body (sensu Insecta) ; GO:0008041'.
The activity of a gene product that interacts with a receptor to effect a change in the activity of the receptor. Ligands may be produced by the same cell that expresses the receptor. Ligands may also be expressed at the plasma membrane of an adjacent cell (e.g. Notch ligands) or be secreted and diffuse extracellularly from their point of origin to the receiving cell (e.g. interleukins).
The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome.
Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another.
An organ system process carried out by any of the organs or tissues of the neurological system.
The process that involves the secretion of or response to endocrine hormones. An endocrine hormone is a hormone released into the circulatory system.
Any process leading to the attainment of the full functional capacity of a protein.
The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.
ATP hydrolysis coupled transmembrane transport
Transmembrane transport is the transport of a solute across a lipid bilayer. Note that transport through the nuclear pore complex is not transmembrane because the nuclear membrane is a double membrane and is not traversed. For transport through the nuclear pore, consider instead the term 'nucleocytoplasmic transport ; GO:0006913' and its children. Note also that this term is not intended for use in annotating lateral movement within membranes.
Miscellaneous transport and binding events
The cellular chemical reactions and pathways involving a nucleobase-containing small molecule: a nucleobase, a nucleoside, or a nucleotide.
nucleobase, nucleoside and nucleotide metabolism
nucleobase, nucleoside and nucleotide metabolic process
nucleobase-containing small molecule metabolic process
Phosphate bond hydrolysis by NUDT proteins
A compound molecular function in which an effector function is controlled by one or more regulatory components.
The binding activity of a molecule that brings together two or more molecules through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way.
4Fe-4S cluster assembles on NUBP2:NUBP1 scaffold
A system process carried out by any of the organs or tissues of the hepaticobiliary system. The hepaticobiliary system is responsible for metabolic and catabolic processing of small molecules absorbed from the blood or gut, hormones and serum proteins, detoxification, storage of glycogen, triglycerides, metals and lipid soluble vitamins and excretion of bile. Included are the synthesis of albumin, blood coagulation factors, complement, and specific binding proteins.
A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a 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.
The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex.
cellular protein-containing complex assembly
A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cell wall.
cell wall organization or biogenesis at cellular level
cellular cell wall organisation or biogenesis
cellular cell wall organization or biogenesis
A nitrogen compound metabolic process that contributes to the nitrogen cycle. The nitrogen cycle is a series of metabolic pathways by which nitrogen is converted between various forms and redox states; it encompasses pathways in which nitrogen is acted upon directly, such as nitrification, denitrification, nitrogen fixation, and mineralization.
A process in which a protein is transported to, or maintained in, a specific location in the plasma membrane.
Interacting selectively with one or more biological molecules in another (target) organism, initiating pathogenesis (leading to an abnormal, generally detrimental state) in the target organism. The activity should refer to an evolved function of the active gene product, i.e. one that was selected for. Examples include the activity of botulinum toxin, and snake venom.
Reactions triggered in response to the presence of another organism that act to protect the cell or organism from damage caused by that organism.
defence response incompatible interaction
defence response to pathogen, incompatible interaction
defense response, incompatible interaction
The binding by a cell-adhesion protein on a cell surface to an adhesion molecule on another cell surface or an external substrate, to mediate adhesion of the cell to the external substrate or to another cell.
protein binding involved in cell adhesion
Any process that reduces or removes the toxicity of a toxic substance. These may include transport of the toxic substance away from sensitive areas and to compartments or complexes whose purpose is sequestration of the toxic substance.
A molecular function regulator regulates the activity of its target via non-covalent binding that does not result in covalent modification to the target. Examples of molecular function regulators include regulatory subunits of multimeric enzymes and channels. Mechanisms of regulation include allosteric changes in the target and competitive inhibition.
This term should only be used in cases when the regulator directly interacts with the enzyme, but does not result in a covalent modification.
Combining with a virus component, and in cooperation with a nearby primary receptor, initiating a change in cell activity.
One of the two nuclear divisions that occur as part of the meiotic cell cycle.
A mitotic cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell.
The process of transcribing and translating the mitochondrial genome (mtDNA) to produce at least a subset of oxidative phosphorylation (OXPHOS) proteins, 2 rRNAs, and mitochondrial tRNAs, which are critical for ATP production. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
Catalytic activity that acts to modify a protein.
Catalytic activity that acts to modify DNA.
Catalytic activity that acts to modify RNA.
Directly binding to a specific ion or molecule and delivering it either to an acceptor molecule or to a specific location.
Note that a carrier moves with its substrate/cargo, while a transporter does not move with the cargo, but facilitates the change in localization.
STAR mediates CHOL translocation from cytosol to mitochondrial intermembrane space
MMADHC targets transport of cytosolic cob(II)alamin to mitochondria
cob(II)alamin is transferred from MMACHC:MMADHC:cob(II)alamin to MTRR:MTR
SERINC3,5,(1,2,4) transport L-Ser from cytosol to plasma membrane
A molecular function that controls the rate, timing and/or magnitude of gene transcription. The function of transcriptional regulators is to modulate gene expression at the transcription step so that they are expressed in the right cell at the right time and in the right amount throughout the life of the cell and the organism. Genes are transcriptional units, and include bacterial operons.
A molecular function required for core promoter activity that mediates the assembly of the RNA polymerase holoenzyme at promoter DNA to form the pre-initiation complex (PIC). General transcription factors (GTFs) bind to and open promoter DNA, initiate RNA synthesis and stimulate the escape of the polymerase from the promoter. Not all subunits of the general transcription factor are necessarily present at all promoters to initiate transcription. GTFs act at each promoter, although the exact subunit composition at individual promoters may vary.
Usage guidance: The distinction between general transcription factors and DNA-binding transcription factors is that the latter modulate the selection of which genes are expressed under specific conditions, while general transcription factors are the constitutive machinery required for transcription initiation.
general transcription initiation factor activity
Binding to a molecule and eliciting a change in the protein's activity in response to the intracellular level of that molecule.
Binding to a specific molecule to prevent it from interacting with other partners or to inhibit its localization to the area of the cell or complex where it is active.
eNOS:NOSIP translocation from caveolae to intracellular compartments
TCN1 binds correnoids in the circulation
A molecular function characterized by the coupling of ATP hydrolysis to other steps of a reaction mechanism to make the reaction energetically favorable, for example to catalyze a reaction or drive transport against a concentration gradient.
Note that this term represents a grouping class that includes all proteins that use ATP hydrolysis to drive a reaction; it is not meant to capture the ATP hydrolysis reaction itself. To annotate ATP hydrolysis, please use 'ATP hydrolysis activity ; GO:0016887'.
The chemical reactions and pathways involving carbohydrate derivative.
carbohydrate derivative metabolic process