chitosan layer of spore wall

description: The second outermost layer of the spore wall, as described in Saccharomyces.


inner layer of spore wall

category: biolink:CellularComponent biolink:AnatomicalEntity biolink:PhysicalEssence biolink:OrganismalEntity biolink:SubjectOfInvestigation biolink:BiologicalEntity biolink:ThingWithTaxon biolink:NamedThing biolink:PhysicalEssenceOrOccurrent

description: Either of the two innermost layers of the spore wall, as described in Saccharomyces.


ascus lipid droplet

description: Any particle of coalesced lipids in an ascus or ascospore. May include associated proteins.


nucleus

description: 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.


nuclear envelope

description: The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space).


nuclear inner membrane

description: The inner, i.e. lumen-facing, lipid bilayer of the nuclear envelope.


lamin filament

description: Any of a group of intermediate-filament proteins that form the fibrous matrix on the inner surface of the nuclear envelope. They are classified as lamins A, B and C.


nuclear outer membrane

description: The outer, i.e. cytoplasm-facing, lipid bilayer of the nuclear envelope; continuous with the endoplasmic reticulum of the cell and sometimes studded with ribosomes.


nuclear envelope lumen

description: The region between the two lipid bilayers of the nuclear envelope; 20-40 nm wide.


annulate lamellae

description: Stacks of endoplasmic reticulum (ER) membranes containing a high density of nuclear pores, thought to form from excess nuclear membrane components, that have been described in a number of different cells. Annulate lamellar membranes are continuous with and embedded within the ER.


nuclear pore

description: A protein complex providing a discrete opening in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined.


nuclear lamina

description: The fibrous, electron-dense layer lying on the nucleoplasmic side of the inner membrane of a cell nucleus, composed of lamin filaments. The polypeptides of the lamina are thought to be concerned in the dissolution of the nuclear envelope and its re-formation during mitosis. The lamina is composed of lamin A and lamin C filaments cross-linked into an orthogonal lattice, which is attached via lamin B to the inner nuclear membrane through interactions with a lamin B receptor, an IFAP, in the membrane.


nucleoplasm

description: That part of the nuclear content other than the chromosomes or the nucleolus.


nucleolar ribonuclease P complex

description: A ribonuclease P complex located in the nucleolus of a eukaryotic cell, where it catalyzes the 5' endonucleolytic cleavage of precursor tRNAs to yield mature tRNAs. Eukaryotic nucleolar ribonuclease P complexes generally contain a single RNA molecule that is necessary but not sufficient for catalysis, and several protein molecules.


nuclear pre-replicative complex

description: A protein-DNA complex assembled at eukaryotic DNA replication origins during late mitosis and G1, allowing the origin to become competent, or 'licensed', for replication. The complex normally includes the origin recognition complex (ORC), Cdc6, Cdt1 and the MiniChromosome Maintenance (Mcm2-7) proteins.


replication fork

description: The Y-shaped region of a replicating DNA molecule, resulting from the separation of the DNA strands and in which the synthesis of new strands takes place. Also includes associated protein complexes.


alpha DNA polymerase:primase complex

description: A complex of four polypeptides, comprising large and small DNA polymerase alpha subunits and two primase subunits, which are capable of catalyzing the synthesis of an RNA primer on the lagging strand of replicating DNA and the subsequent synthesis of a small stretch of DNA. The smaller of the two primase subunits alone can catalyze oligoribonucleotide synthesis.


DNA replication factor A complex

description: A conserved heterotrimeric complex that binds nonspecifically to single-stranded DNA and is required for multiple processes in eukaryotic DNA metabolism, including DNA replication, DNA repair, and recombination. In all eukaryotic organisms examined the complex is composed of subunits of approximately 70, 30, and 14 kDa.


DNA replication factor C complex

description: A complex that loads the DNA polymerase processivity factor proliferating cell nuclear antigen (PCNA) onto DNA, thereby permitting processive DNA synthesis catalyzed by DNA polymerase. In eukaryotes the complex consists of five polypeptides.


name: nuclear origin of replication recognition complex

description: A multisubunit complex that is located at the replication origins of a chromosome in the nucleus.


RNA polymerase II, core complex

description: RNA polymerase II, one of three nuclear DNA-directed RNA polymerases found in all eukaryotes, is a multisubunit complex; typically it produces mRNAs, snoRNAs, and some of the snRNAs. Two large subunits comprise the most conserved portion including the catalytic site and share similarity with other eukaryotic and bacterial multisubunit RNA polymerases. The largest subunit of RNA polymerase II contains an essential carboxyl-terminal domain (CTD) composed of a variable number of heptapeptide repeats (YSPTSPS). The remainder of the complex is composed of smaller subunits (generally ten or more), some of which are also found in RNA polymerases I and III. Although the core is competent to mediate ribonucleic acid synthesis, it requires additional factors to select the appropriate template.


RNA polymerase III complex

description: RNA polymerase III, one of three nuclear DNA-directed RNA polymerases found in all eukaryotes, is a multisubunit complex; typically it produces 5S rRNA, tRNAs and some of the small nuclear RNAs. Two large subunits comprise the most conserved portion including the catalytic site and share similarity with other eukaryotic and bacterial multisubunit RNA polymerases. The remainder of the complex is composed of smaller subunits (generally ten or more), some of which are also found in RNA polymerase I and others of which are also found in RNA polymerases I and II. Although the core is competent to mediate ribonucleic acid synthesis, it requires additional factors to select the appropriate template.


transcription regulator complex

description: A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.


name: RNA polymerase transcription factor SL1 complex

description: A RNA polymerase I-specific transcription factor complex that contains the TATA-box-binding protein (TBP) and at least three TBP-associated factors including proteins known in mammals as TAFI110, TAFI63 and TAFI48.


transcription factor TFIID complex

description: A complex composed of TATA binding protein (TBP) and TBP associated factors (TAFs); the total mass is typically about 800 kDa. Most of the TAFs are conserved across species. In TATA-containing promoters for RNA polymerase II (Pol II), TFIID is believed to recognize at least two distinct elements, the TATA element and a downstream promoter element. TFIID is also involved in recognition of TATA-less Pol II promoters. Binding of TFIID to DNA is necessary but not sufficient for transcription initiation from most RNA polymerase II promoters.


transcription factor TFIIA complex

description: A component of the transcription machinery of RNA Polymerase II. In humans, TFIIA is a heterotrimer composed of an alpha (P35), beta (P19) and gamma subunits (P12).


transcription factor TFIIE complex

description: A transcription factor which in humans consists of a complex of two alpha and two beta chains. Recruits TFIIH to the initiation complex and helps activate both RNA polymerase II and TFIIH.


transcription factor TFIIF complex

description: A general transcription initiation factor which in humans consists of a heterodimer of an alpha and a beta subunit. Helps recruit RNA polymerase II to the initiation complex and promotes translation elongation.


transcription factor TFIIH holo complex

description: A complex that is capable of kinase activity directed towards the C-terminal Domain (CTD) of the largest subunit of RNA polymerase II and is essential for initiation at RNA polymerase II promoters in vitro. It is composed of the core TFIIH complex and the TFIIK complex.


chromatin silencing complex

description: Any protein complex that mediates changes in chromatin structure that result in transcriptional silencing.


anaphase-promoting complex

description: A ubiquitin ligase complex that degrades mitotic cyclins and anaphase inhibitory protein, thereby triggering sister chromatid separation and exit from mitosis. Substrate recognition by APC occurs through degradation signals, the most common of which is termed the Dbox degradation motif, originally discovered in cyclin B.


spliceosomal complex

description: Any of a series of ribonucleoprotein complexes that contain snRNA(s) and small nuclear ribonucleoproteins (snRNPs), and are formed sequentially during the spliceosomal splicing of one or more substrate RNAs, and which also contain the RNA substrate(s) from the initial target RNAs of splicing, the splicing intermediate RNA(s), to the final RNA products. During cis-splicing, the initial target RNA is a single, contiguous RNA transcript, whether mRNA, snoRNA, etc., and the released products are a spliced RNA and an excised intron, generally as a lariat structure. During trans-splicing, there are two initial substrate RNAs, the spliced leader RNA and a pre-mRNA.


U5 snRNP

description: A ribonucleoprotein complex that contains small nuclear RNA U5, a heptameric ring of Sm proteins, as well as several proteins that are unique to the U5 snRNP, most of which remain associated with the U5 snRNA both while the U5 snRNP is free or assembled into a series of spliceosomal complexes.


U7 snRNP

description: A ribonucleoprotein complex that contains the U7 snRNA and is required for the 3'-end processing of replication-dependent histone pre-mRNAs.


U2-type spliceosomal complex

description: Any spliceosomal complex that forms during the splicing of a messenger RNA primary transcript to excise an intron that has canonical consensus sequences near the 5' and 3' ends.


U1 snRNP

description: A ribonucleoprotein complex that contains small nuclear RNA U1, a heptameric ring of Sm proteins, as well as several proteins that are unique to the U1 snRNP, most of which remain associated with the U1 snRNA both while the U1 snRNP is free or assembled into a series of spliceosomal complexes.


U2 snRNP

description: A ribonucleoprotein complex that contains small nuclear RNA U2, a heptameric ring of Sm proteins, as well as several proteins that are unique to the U2 snRNP, most of which remain associated with the U2 snRNA both while the U2 snRNP is free or assembled into a series of spliceosomal complexes.


U4 snRNP

description: A ribonucleoprotein complex that contains small nuclear RNA U4, a heptameric ring of Sm proteins, as well as several proteins that are unique to the U4 snRNP, most of which remain associated with the U4 snRNA both while the U4 snRNP is free or assembled into the U4/U6 snRNP or into a series of spliceosomal complexes.


U6 snRNP

description: A ribonucleoprotein complex that contains small nuclear RNA U6, the Lsm2-8 heptameric ring complex, as well as several proteins that are unique to the U6 snRNP, most of which remain associated with the U6 snRNA both while the U6 snRNP is free or assembled into the U4/U6 snRNP or into a series of spliceosomal complexes.


U12-type spliceosomal complex

description: Any spliceosomal complex that forms during the splicing of a messenger RNA primary transcript to excise an intron; the series of U12-type spliceosomal complexes is involved in the splicing of the majority of introns that contain atypical AT-AC terminal dinucleotides, as well as other non-canonical introns. The entire splice site signal, not just the terminal dinucleotides, is involved in determining which spliceosome utilizes the site.


U4atac snRNP

description: A ribonucleoprotein complex that contains small nuclear RNA U4atac, a heptameric ring of Sm proteins, as well as several proteins that are unique to the U4atac snRNP, most of which remain associated with the U4atac snRNA both while the U4atac snRNP is free or assembled into the U4atac/U6atac complex or into a series of spliceosomal complexes.


U6atac snRNP

description: A ribonucleoprotein complex that contains small nuclear RNA U6atac, the Lsm2-8 heptameric ring complex, as well as several proteins that are unique to the U6atac snRNP, most of which remain associated with the U6atac snRNA both while the U6atac snRNP is free or assembled into the U4atac/U6atac snRNP or into a series of spliceosomal complexes.


U11 snRNP

description: A ribonucleoprotein complex that contains small nuclear RNA U11, a heptameric ring of Sm proteins, as well as several proteins that are unique to the U11 snRNP, most of which remain associated with the U11 snRNA both while the U11 snRNP is free or assembled into a series of spliceosomal complexes.


U12 snRNP

description: A ribonucleoprotein complex that contains small nuclear RNA U12, a heptameric ring of Sm proteins, as well as several proteins that are unique to the U12 snRNP, most of which remain associated with the U12 snRNA both while the U12 snRNP is free or assembled into a series of spliceosomal complexes.


chromosome

description: A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.


telomerase holoenzyme complex

description: Telomerase is a ribonucleoprotein enzyme complex, with a minimal catalytic core composed of a catalytic reverse transcriptase subunit and an RNA subunit that provides the template for telomeric DNA addition. In vivo, the holoenzyme complex often contains additional subunits.


polytene chromosome

description: A type of chromosome in a polyploid cell, formed when multiple copies of homologous chromosomes are aligned side by side to give a giant chromosome in which distinct chromosome bands are readily visible.


polytene chromosome chromocenter

description: A region at which the centric regions of polytene chromosomes are joined together.


polytene chromosome weak point

description: A region of the polytene chromosome where the diameter is considerably decreased, probably resulting from local differences in chromosome organization.


polytene chromosome puff

description: A swelling at a site along the length of a polytene chromosome, thought to be the site of active transcription.


polytene chromosome band

description: A stretch of densely packed chromatin along the polytene chromosome, visible as a morphologically distinct band.


polytene chromosome interband

description: A stretch of less tightly packed chromatin along the polytene chromosome, found between bands.


polytene chromosome ectopic fiber

description: A thread-like connection joining two regions of ectopically paired polytene chromosomes.


chiasma

description: A connection formed between chromatids, visible during meiosis, thought to be the point of the interchange involved in crossing-over.


recombination nodule

description: An electron dense structure that is associated with meiotic chromosomes.


early recombination nodule

description: An electron dense structure that is associated with meiotic chromosomes in leptotene or zygotene during meiosis I.


late recombination nodule

description: An electron dense structure that is associated with meiotic chromosomes in pachytene during meiosis I.


pericentric heterochromatin

description: Heterochromatin that is located adjacent to the CENP-A rich centromere 'central core' and characterized by methylated H3 histone at lysine 9 (H3K9me2/H3K9me3).


beta-heterochromatin

description: A diffusely banded region of heterochromatin located between euchromatin and alpha-heterochromatin in the polytene chromosome chromocenter; normally replicated during polytenization.


alpha-heterochromatin

description: A small, compact region of heterochromatin located in the middle of the polytene chromosome chromocenter, which undergoes little or no replication during polytenization.


intercalary heterochromatin

description: Any of the regions of heterochromatin that form a reproducible set of dense bands scattered along the euchromatic arms in polytene chromosomes.


perichromatin fibrils

description: Structures of variable diameter visible in the nucleoplasm by electron microscopy, mainly observed near the border of condensed chromatin. The fibrils are enriched in RNA, and are believed to be sites of pre-mRNA splicing and polyadenylylation representing the in situ form of nascent transcripts.


extrachromosomal circular DNA

description: Circular DNA structures that are not part of a chromosome.


extrachromosomal rDNA circle

description: Circular DNA molecules encoding ribosomal RNA that are replicated independently of chromosomal replication. These molecules originate in the chromosome but are excised and circularized, often by intramolecular homologous recombination between direct tandem repeats.


2-micrometer circle DNA

description: A plasmid commonly found in Saccharomyces, inherited in a non-Mendelian manner and often present in 100-400 copies.


nucleolus

description: 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.


nucleolus organizer region

description: A region of a chromosome where nucleoli form during interphase, and where genes encoding the largest rRNA precursor transcript are tandemly arrayed.


description: A ribonucleoprotein complex that contains an RNA molecule of the snoRNA family and associated proteins. Many are involved in a step of processing of rRNA molecules: cleavage, 2'-O-methylation, or pseudouridylation, but other RNA types can be targets as well. The majority fall into one of two classes, box C/D type or box H/ACA type, which are conserved across eukaryotes and archaea. Other members include the telomerase RNA and the ribonuclease MRP RNA.


RNA polymerase I complex

description: RNA polymerase I, one of three nuclear DNA-directed RNA polymerases found in all eukaryotes, is a multisubunit complex; typically it produces rRNAs. Two large subunits comprise the most conserved portion including the catalytic site and share similarity with other eukaryotic and bacterial multisubunit RNA polymerases. The remainder of the complex is composed of smaller subunits (generally ten or more), some of which are also found in RNA polymerase III and others of which are also found in RNA polymerases II and III. Although the core is competent to mediate ribonucleic acid synthesis, it requires additional factors to select the appropriate template.


cytoplasm

description: The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.


mitochondrion

description: 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.


mitochondrial envelope

description: The double lipid bilayer enclosing the mitochondrion and separating its contents from the cell cytoplasm; includes the intermembrane space.


mitochondrial outer membrane

description: The outer, i.e. cytoplasm-facing, lipid bilayer of the mitochondrial envelope.


name: mitochondrial outer membrane translocase complex

description: A large complex of the mitochondrial outer membrane that mediates transport of proteins into all mitochondrial compartments.


mitochondrial inner membrane

description: The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.


name: TIM23 mitochondrial import inner membrane translocase complex

description: The protein transport machinery of the mitochondrial inner membrane that typically transports proteins that possess a matrix-targeting N-terminal presequence. The TIM23 complex contains three essential Tim proteins: Tim17 and Tim23 are thought to build a preprotein translocation channel while Tim44 interacts transiently with the matrix heat-shock protein Hsp70 to form an ATP-driven import motor.


m-AAA complex

description: Protease complex of the mitochondrial inner membrane that is involved in mitochondrial protein turnover and in processing of proteins imported into mitochondria.


mitochondrial respirasome

description: The protein complexes that form the mitochondrial electron transport system (the respiratory chain), associated with the inner mitochondrial membrane. The respiratory chain complexes transfer electrons from an electron donor to an electron acceptor and are associated with a proton pump to create a transmembrane electrochemical gradient.


name: mitochondrial respiratory chain complex I

description: A protein complex located in the mitochondrial inner membrane that forms part of the mitochondrial respiratory chain. It contains about 25 different polypeptide subunits, including NADH dehydrogenase (ubiquinone), flavin mononucleotide and several different iron-sulfur clusters containing non-heme iron. The iron undergoes oxidation-reduction between Fe(II) and Fe(III), and catalyzes proton translocation linked to the oxidation of NADH by ubiquinone.


name: mitochondrial respiratory chain complex III

description: A protein complex located in the mitochondrial inner membrane that forms part of the mitochondrial respiratory chain. Contains about 10 polypeptide subunits including four redox centers: cytochrome b/b6, cytochrome c1 and an 2Fe-2S cluster. Catalyzes the oxidation of ubiquinol by oxidized cytochrome c1.


name: mitochondrial respiratory chain complex IV

description: A protein complex located in the mitochondrial inner membrane that forms part of the mitochondrial respiratory chain. Contains the 13 polypeptide subunits of cytochrome c oxidase, including cytochrome a and cytochrome a3. Catalyzes the oxidation of reduced cytochrome c by dioxygen (O2).


name: mitochondrial proton-transporting ATP synthase complex

description: A proton-transporting ATP synthase complex found in the mitochondrial membrane.


name: mitochondrial proton-transporting ATP synthase, catalytic core

description: The hexamer, comprising three alpha and three beta subunits, that possesses the catalytic activity of the mitochondrial hydrogen-transporting ATP synthase.


name: mitochondrial proton-transporting ATP synthase, central stalk

description: One of two stalks that connect the catalytic core of the hydrogen-transporting ATP synthase to the mitochondrial membrane-associated F0 proteins; rotates within the catalytic core during catalysis.


name: mitochondrial permeability transition pore complex

description: A protein complex that connects the inner and outer membranes of animal mitochondria and acts as a pore that can open transiently to allow free diffusion of solutes between the mitochondrial matrix and the cytosol. The pore complex is formed of the voltage-dependent anion channel (VDAC), the adenine nucleotide translocase (ANT) and cyclophilin-D (CyP-D).


mitochondrial intermembrane space

description: The region between the inner and outer lipid bilayers of the mitochondrial envelope.


mitochondrial matrix

description: The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.


gamma DNA polymerase complex

description: A DNA polymerase complex consisting of a large subunit, responsible for the catalytic activities, and a small accessory subunit. Functions in the replication and repair of mitochondrial DNA.


mitochondrial ribosome

description: A ribosome found in the mitochondrion of a eukaryotic cell; contains a characteristic set of proteins distinct from those of cytosolic ribosomes.


mitochondrial large ribosomal subunit

description: The larger of the two subunits of a mitochondrial ribosome. Two sites on the ribosomal large subunit are involved in translation: the aminoacyl site (A site) and peptidyl site (P site).


mitochondrial small ribosomal subunit

description: The smaller of the two subunits of a mitochondrial ribosome.


lysosome

description: 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.


lysosomal membrane

description: The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm.


primary lysosome

description: A lysosome before it has fused with a vesicle or vacuole.


secondary lysosome

description: Vacuole formed by the fusion of a lysosome with an organelle (autosome) or with a primary phagosome.


endosome

description: A vacuole to which materials ingested by endocytosis are delivered.


early endosome

description: A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.


late endosome

description: A prelysosomal endocytic organelle differentiated from early endosomes by lower lumenal pH and different protein composition. Late endosomes are more spherical than early endosomes and are mostly juxtanuclear, being concentrated near the microtubule organizing center.


multivesicular body

description: A type of endosome in which regions of the limiting endosomal membrane invaginate to form internal vesicles; membrane proteins that enter the internal vesicles are sequestered from the cytoplasm.


vacuole

description: 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.


vacuolar membrane

description: The lipid bilayer surrounding the vacuole and separating its contents from the cytoplasm of the cell.


vacuolar lumen

description: The volume enclosed within the vacuolar membrane.


autophagosome

description: A double-membrane-bounded compartment that engulfs endogenous cellular material as well as invading microorganisms to target them to the lytic vacuole/lysosome for degradation as part of macroautophagy.


peroxisome

description: 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.


peroxisomal membrane

description: The lipid bilayer surrounding a peroxisome.


name: extrinsic component of intraperoxisomal membrane

description: The component of the intraperoxisomal membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.


peroxisomal matrix

description: The volume contained within the membranes of a peroxisome; in many cells the matrix contains a crystalloid core largely composed of urate oxidase.


endoplasmic reticulum

description: 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).


Sec61 translocon complex

description: A translocon complex that contains a core heterotrimer of conserved alpha, beta and gamma subunits, and may contain additional proteins (translocon-associated proteins or TRAPs); in budding yeast the core proteins are Sec61p, Sbh1p, and Sss1p. The Sec61 translocon complex functions in cotranslational and posttranslational translocation events.


name: signal recognition particle receptor complex

description: A transmembrane heterodimeric protein located in the membrane of the rough endoplasmic reticulum. Both subunits contain GTPase domains with which signal recognition particle interacts. In the presence of GTP and SRP receptor, SRP is released from the ribosome-nascent chain complex.


name: signal recognition particle, endoplasmic reticulum targeting

description: A ribonucleoprotein particle of 325 kDa composed of a 7S (300 nucleotide) RNA molecule and a complex of six different polypeptides. This binds both to the N-terminal signal peptide for proteins destined for the endoplasmic reticulum as they emerge from the large ribosomal subunit and also to the ribosome. This binding arrests further translation thereby preventing the proteins from being released into the cytosol. The SRP-ribosome complex then diffuses to the endoplasmic reticulum where it is bound to the signal recognition particle receptor, which allows resumption of protein synthesis and facilitates the passage of the growing polypeptide chain through the translocon. Through a process involving GTP hydrolysis, the SRP-SRP receptor complex dissociates and SRP returns to the cytosol. Of the six polypeptides of SRP the 54 kDa subunit (SRP54) is the central player. It contains an N-terminal GTPase domain and a C-terminal domain that binds directly to the signal peptide and the SRP RNA. Examples of this component are found in Mus musculus, Saccharomyces cerevisiae and Arabidopsis thaliana.


signal peptidase complex

description: A protein complex that is located in the endoplasmic reticulum membrane and cleaves the signal sequence from precursor proteins following their transport out of the cytoplasmic space.


endoplasmic reticulum lumen

description: The volume enclosed by the membranes of the endoplasmic reticulum.


endoplasmic reticulum membrane

description: The lipid bilayer surrounding the endoplasmic reticulum.


smooth endoplasmic reticulum

description: The smooth endoplasmic reticulum (smooth ER or SER) has no ribosomes attached to it. The smooth ER 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.


rough endoplasmic reticulum

description: 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.


name: endoplasmic reticulum-Golgi intermediate compartment

description: A complex system of membrane-bounded compartments located between endoplasmic reticulum (ER) and the Golgi complex, with a distinctive membrane protein composition; involved in ER-to-Golgi and Golgi-to-ER transport.


Golgi apparatus

description: 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.


Golgi stack

description: The set of thin, flattened membrane-bounded compartments, called cisternae, that form the central portion of the Golgi complex. The stack usually comprises cis, medial, and trans cisternae; the cis- and trans-Golgi networks are not considered part of the stack.


Golgi lumen

description: The volume enclosed by the membranes of any cisterna or subcompartment of the Golgi apparatus, including the cis- and trans-Golgi networks.


Golgi medial cisterna

description: The middle Golgi cisterna (or cisternae).


Golgi-associated vesicle

description: 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.


cis-Golgi network

description: The network of interconnected tubular and cisternal structures located at the convex side of the Golgi apparatus, which abuts the endoplasmic reticulum.


trans-Golgi network

description: The network of interconnected tubular and cisternal structures located within the Golgi apparatus on the side distal to the endoplasmic reticulum, from which secretory vesicles emerge. The trans-Golgi network is important in the later stages of protein secretion where it is thought to play a key role in the sorting and targeting of secreted proteins to the correct destination.


lipid droplet

description: An intracellular non-membrane-bounded organelle comprising a matrix of coalesced lipids surrounded by a phospholipid monolayer. May include associated proteins.


centrosome

description: A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.


centriole

description: A cellular organelle, found close to the nucleus in many eukaryotic cells, consisting of a small cylinder with microtubular walls, 300-500 nm long and 150-250 nm in diameter. It contains nine short, parallel, peripheral microtubular fibrils, each fibril consisting of one complete microtubule fused to two incomplete microtubules. Cells usually have two centrioles, lying at right angles to each other. At division, each pair of centrioles generates another pair and the twin pairs form the pole of the mitotic spindle.


microtubule organizing center

description: 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.


spindle pole body

description: The microtubule organizing center in fungi; functionally homologous to the animal cell centrosome.


aster

description: An array of microtubules emanating from a spindle pole MTOC that do not connect to kinetochores.


spindle

description: The array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during mitosis or meiosis and serves to move the duplicated chromosomes apart.


intermediate layer of spindle pole body

description: Structure between the central and outer plaques of the spindle pole body.


inner plaque of spindle pole body

description: One of three laminate structures that form the spindle pole body; the inner plaque is in the nucleus.


central plaque of spindle pole body

description: One of three laminate structures that form the spindle pole body; the central plaque is embedded in the nuclear envelope.


outer plaque of spindle pole body

description: One of three laminate structures that form the spindle pole body; the outer plaque is in the cytoplasm.


half bridge of spindle pole body

description: Structure adjacent to the plaques of the spindle pole body.


actomyosin contractile ring

description: A cytoskeletal structure composed of actin filaments and myosin that forms beneath the plasma membrane of many cells, including animal cells and yeast cells, in a plane perpendicular to the axis of the spindle, i.e. the cell division plane. In animal cells, the contractile ring is located at the cleavage furrow. In budding fungal cells, e.g. mitotic S. cerevisiae cells, the contractile ring forms at the mother-bud neck before mitosis.


polar microtubule

description: Any of the spindle microtubules that come from each pole and overlap at the spindle midzone. This interdigitating structure consisting of antiparallel microtubules is responsible for pushing the poles of the spindle apart.


kinetochore microtubule

description: Any of the spindle microtubules that attach to the kinetochores of chromosomes by their plus ends, and maneuver the chromosomes during mitotic or meiotic chromosome segregation.


cytosol

description: The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.


steroid hormone aporeceptor complex

description: A protein complex consisting of a steroid receptor associated with nonreceptor proteins, minimally a dimer of Hsp90 and a monomer of hsp56/FKBP59; forms in the absence of bound ligand.


chaperonin-containing T-complex

description: A multisubunit ring-shaped complex that mediates protein folding in the cytosol without a cofactor.


hemoglobin complex

description: An iron-containing, oxygen carrying complex. In vertebrates it is made up of two pairs of associated globin polypeptide chains, each chain carrying a noncovalently bound heme prosthetic group.


heterotrimeric G-protein complex

description: Any of a family of heterotrimeric GTP-binding and hydrolyzing proteins; they belong to a superfamily of GTPases that includes monomeric proteins such as EF-Tu and RAS. Heterotrimeric G-proteins consist of three subunits; the alpha subunit contains the guanine nucleotide binding site and possesses GTPase activity; the beta and gamma subunits are tightly associated and function as a beta-gamma heterodimer; extrinsic plasma membrane proteins (cytoplasmic face) that function as a complex to transduce signals from G protein-coupled receptors to an effector protein.


fatty acid synthase complex

description: A multienzyme complex that catalyses the synthesis of fatty acids from acetyl CoA.


fatty-acyl-CoA synthase complex

description: A protein complex that possesses fatty-acyl-CoA synthase activity.


proteasome regulatory particle

description: A multisubunit complex, which caps one or both ends of the proteasome core complex. This complex recognizes and unfolds ubiquitinated proteins, and translocates them to the proteasome core complex.


proteasome core complex

description: A multisubunit barrel shaped endoprotease complex, which is the core of the proteasome complex.


ribosome

description: 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.


nuclear cap binding complex

description: A conserved heterodimeric protein complex that binds to the 5' terminal cap structure m7G(5')ppp(5')N of nascent eukaryotic RNA polymerase II transcripts such as pre-mRNA and U snRNA. The consists of proteins known as CBP20 and CBP80, binds to cap structures in the nucleus, and is involved in pre-mRNA splicing, 3'-end formation, and RNA nuclear export.


name: mRNA cleavage and polyadenylation specificity factor complex

description: A multisubunit complex that binds to the canonical AAUAAA hexamer and to U-rich upstream sequence elements on the pre-mRNA, thereby stimulating the otherwise weakly active and nonspecific polymerase to elongate efficiently RNAs containing a poly(A) signal.


name: mRNA cleavage stimulating factor complex

description: A protein complex required for mRNA cleavage but not for poly(A) addition.


mRNA cleavage factor complex

description: Any macromolecular complex involved in cleavage or polyadenylation of mRNA molecules.


name: eukaryotic translation initiation factor 2 complex

description: Complex of three heterogeneous polypeptide chains, that form a ternary complex with initiator methionyl-tRNA and GTP. This ternary complex binds to free 40S subunit, which subsequently binds the 5' end of mRNA.


name: eukaryotic translation initiation factor 2B complex

description: A multisubunit guanine nucleotide exchange factor which catalyzes the exchange of GDP bound to initiation factor eIF2 for GTP, generating active eIF2-GTP. In humans, it is composed of five subunits, alpha, beta, delta, gamma and epsilon.


name: eukaryotic translation initiation factor 3 complex

description: A complex of several polypeptides that plays at least two important roles in protein synthesis: First, eIF3 binds to the 40S ribosome and facilitates loading of the Met-tRNA/eIF2.GTP ternary complex to form the 43S preinitiation complex. Subsequently, eIF3 apparently assists eIF4 in recruiting mRNAs to the 43S complex. The eIF3 complex contains five conserved core subunits, and may contain several additional proteins; the non-core subunits are thought to mediate association of the complex with specific sets of mRNAs.


name: eukaryotic translation elongation factor 1 complex

description: A multisubunit nucleotide exchange complex that binds GTP and aminoacyl-tRNAs, and catalyzes their codon-dependent placement at the A-site of the ribosome. In humans, the complex is composed of four subunits, alpha, beta, delta and gamma.


nascent polypeptide-associated complex

description: A heterodimeric protein complex that can reversibly bind to ribosomes, and is located in direct proximity to newly synthesized polypeptide chains as they emerge from the ribosome.


cytoskeleton

description: 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.


axonemal dynein complex

description: A dynein complex found in eukaryotic cilia and flagella; the motor domain heads interact with adjacent microtubules to generate a sliding force which is converted to a bending motion.


muscle myosin complex

description: A filament of myosin found in a muscle cell of any type.


troponin complex

description: A complex of accessory proteins (typically troponin T, troponin I and troponin C) found associated with actin in muscle thin filaments; involved in calcium regulation of muscle contraction.


muscle thin filament tropomyosin

description: A form of the tropomyosin dimer found associated with actin and the troponin complex in muscle thin filaments.


striated muscle myosin thick filament

description: Bipolar filaments formed of polymers of a muscle-specific myosin II isoform, found in the middle of sarcomeres in myofibrils.


striated muscle thin filament

description: Filaments formed of actin and associated proteins; attached to Z discs at either end of sarcomeres in myofibrils.


cytoplasmic dynein complex

description: Any dynein complex with a homodimeric dynein heavy chain core that catalyzes movement along a microtubule. Cytoplasmic dynein complexes participate in many cytoplasmic transport activities in eukaryotes, such as mRNA localization, intermediate filament transport, nuclear envelope breakdown, apoptosis, transport of centrosomal proteins, mitotic spindle assembly, virus transport, kinetochore functions, and movement of signaling and spindle checkpoint proteins. Some complexes participate in intraflagellar transport. Subunits associated with the dynein heavy chain mediate association between dynein heavy chain and cargoes, and may include light chains and light intermediate chains.


dynactin complex

description: A 20S multiprotein assembly of total mass about 1.2 MDa that activates dynein-based activity in vivo. A large structural component of the complex is an actin-like 40 nm filament composed of actin-related protein, to which other components attach.


name: actin capping protein of dynactin complex

description: A heterodimer consisting of alpha and beta subunits that binds to and caps the barbed ends of actin filaments, nucleates the polymerization of actin monomers but does not sever actin filaments, and which is a part of the dynactin complex.


kinesin complex

description: Any complex that includes a dimer of molecules from the kinesin superfamily, a group of related proteins that contain an extended region of predicted alpha-helical coiled coil in the main chain that likely produces dimerization. The native complexes of several kinesin family members have also been shown to contain additional peptides, often designated light chains as all of the noncatalytic subunits that are currently known are smaller than the chain that contains the motor unit. Kinesin complexes generally possess a force-generating enzymatic activity, or motor, which converts the free energy of the gamma phosphate bond of ATP into mechanical work.


minus-end kinesin complex

description: Any complex that includes a dimer of molecules from the kinesin superfamily and any associated proteins, and moves towards the minus end of a microtubule.


plus-end kinesin complex

description: Any complex that includes a dimer of molecules from the kinesin superfamily and any associated proteins, and moves towards the plus end of a microtubule.


microtubule

description: Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.


microtubule associated complex

description: Any multimeric complex connected to a microtubule.


spindle microtubule

description: Any microtubule that is part of a mitotic or meiotic spindle; anchored at one spindle pole.


axonemal microtubule

description: A microtubule in the axoneme of a eukaryotic cilium or flagellum; an axoneme contains nine modified doublet microtubules, which may or may not surround a pair of single microtubules.


nuclear microtubule

description: Any microtubule in the nucleus of a cell.


cytoplasmic microtubule

description: Any microtubule in the cytoplasm of a cell.


intermediate filament

description: A cytoskeletal structure that forms a distinct elongated structure, characteristically 10 nm in diameter, that occurs in the cytoplasm of eukaryotic cells. Intermediate filaments form a fibrous system, composed of chemically heterogeneous subunits and involved in mechanically integrating the various components of the cytoplasmic space. Intermediate filaments may be divided into five chemically distinct classes: Type I, acidic keratins; Type II, basic keratins; Type III, including desmin, vimentin and others; Type IV, neurofilaments and related filaments; and Type V, lamins.


neurofilament

description: A type of intermediate filament found in the core of neuronal axons. Neurofilaments are heteropolymers composed of three type IV polypeptides: NF-L, NF-M, and NF-H (for low, middle, and high molecular weight). Neurofilaments are responsible for the radial growth of an axon and determine axonal diameter.


actin filament

description: A filamentous structure formed of a two-stranded helical polymer of the protein actin and associated proteins. Actin filaments are a major component of the contractile apparatus of skeletal muscle and the microfilaments of the cytoskeleton of eukaryotic cells. The filaments, comprising polymerized globular actin molecules, appear as flexible structures with a diameter of 5-9 nm. They are organized into a variety of linear bundles, two-dimensional networks, and three dimensional gels. In the cytoskeleton they are most highly concentrated in the cortex of the cell just beneath the plasma membrane.


Arp2/3 protein complex

description: A stable protein complex that contains two actin-related proteins, Arp2 and Arp3, and five novel proteins (ARPC1-5), and functions in the nucleation of branched actin filaments.


plasma membrane

description: The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.


name: potassium:proton exchanging ATPase complex

description: A protein complex that possesses hydrogen:potassium-exchanging ATPase activity; characterized in animal cells, where it maintains ionic gradients of K+ at the expense of ATP hydrolysis; The complex contains two obligatory subunits, the catalytic alpha subunit and a glycosylated beta subunit; two additional subunits, gamma and channel-inducing factor (CHIF), may also be present.


description: Sodium:potassium-exchanging ATPases are tetrameric proteins, consisting of two large alpha subunits and two smaller beta subunits. The alpha subunits bear the active site and penetrate the membrane, while the beta subunits carry oligosaccharide groups and face the cell exterior.


voltage-gated calcium channel complex

description: A protein complex that forms a transmembrane channel through which calcium ions may pass in response to changes in membrane potential.


acetylcholine-gated channel complex

description: A homo- or hetero-pentameric protein complex that forms a transmembrane channel through which ions may pass in response to acetylcholine binding.


interleukin-2 receptor complex

description: A protein complex that binds interleukin-2; comprises alpha, beta, and gamma subunits.


interleukin-3 receptor complex

description: A protein complex that binds interleukin-3; comprises an alpha and a beta subunit. The alpha chain is specific to the interleukin-3 receptor, whereas the beta chain is shared with the receptors for granulocyte-macrophage colony-stimulating factor and interleukin-5.


interleukin-5 receptor complex

description: A protein complex that binds interleukin-3; comprises an alpha and a beta subunit. The alpha chain is specific to the interleukin-5 receptor, whereas the beta chain is shared with the receptors for granulocyte-macrophage colony-stimulating factor and interleukin-3.


interleukin-6 receptor complex

description: A hexameric protein complex consisting of two molecules each of interleukin-6, interleukin-6 receptor alpha chain, and gp-130.


interleukin-9 receptor complex

description: A protein complex that binds interleukin-9; comprises an alpha and a beta subunit. The alpha chain is specific to the interleukin-9 receptor, whereas the beta chain is shared with the receptors for several other interleukins.


interleukin-13 receptor complex

description: A protein complex that binds interleukin-13; consists of two chains, interleukin-13 receptor alpha1 chain and interleukin-4 receptor alpha chain.


insulin receptor complex

description: A disulfide-bonded, heterotetrameric receptor complex. The alpha chains are entirely extracellular, while each beta chain has one transmembrane domain. The ligand binds to the alpha subunit extracellular domain and the kinase is associated with the beta subunit intracellular domain.


oncostatin-M receptor complex

description: A heterodimeric receptor for the cytokine oncostatin-M (OSM). In humans the receptor complex is made up of the gene products gp130 and OSMR-beta.


caveola

description: A membrane raft that forms small pit, depression, or invagination that communicates with the outside of a cell and extends inward, indenting the cytoplasm and the cell membrane. Examples include flask-shaped invaginations of the plasma membrane in adipocytes associated with caveolin proteins, and minute pits or incuppings of the cell membrane formed during pinocytosis. Caveolae may be pinched off to form free vesicles within the cytoplasm.


microvillus

description: Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments. Present in especially large numbers on the absorptive surface of intestinal cells.


brush border

description: The dense covering of microvilli on the apical surface of an epithelial cell in tissues such as the intestine, kidney, and choroid plexus; the microvilli aid absorption by increasing the surface area of the cell.


clathrin-coated pit

description: A part of the endomembrane system in the form of an invagination of a membrane upon which a clathrin coat forms, and that can be converted by vesicle budding into a clathrin-coated vesicle. Coated pits form on the plasma membrane, where they are involved in receptor-mediated selective transport of many proteins and other macromolecules across the cell membrane, in the trans-Golgi network, and on some endosomes.


cell-cell junction

description: A cell junction that forms a connection between two or more cells of an organism; excludes direct cytoplasmic intercellular bridges, such as ring canals in insects.


adherens junction

description: A cell-cell junction composed of the epithelial cadherin-catenin complex. The epithelial cadherins, or E-cadherins, of each interacting cell extend through the plasma membrane into the extracellular space and bind to each other. The E-cadherins bind to catenins on the cytoplasmic side of the membrane, where the E-cadherin-catenin complex binds to cytoskeletal components and regulatory and signaling molecules.


spot adherens junction

description: A small cell-cell adherens junction assembled during the cellularization stage of insect embyrogenesis; spot adherens junctions later fuse to form the zonula adherens.


zonula adherens

description: A cell-cell adherens junction which forms a continuous belt near the apex of epithelial cells.


fascia adherens

description: A cell-cell junction that contains the transmembrane protein N-cadherin, which interacts with identical molecules from neighbouring cells to form a tight mechanical intercellular link; forms a large portion of the intercalated disc, the structure at which myofibrils terminate in cardiomyocytes.


nephrocyte diaphragm

description: A specialized cell-cell junction found between nephrocytes of the insect kidney, which is adapted for filtration of hemolymph. The insect nephrocyte is anatomically and functionally similar to the glomerular podocyte of vertebrates.


septate junction

description: A cell-cell junction that forms a continuous band around each cell in an epithelium; within the septate junction the membranes of adjacent cells maintain a constant distance of approximately 15 nm; found in arthropods.


pleated septate junction

description: A septate junction in which regular arrays of electron-dense septae span the intermembrane space.


smooth septate junction

description: A septate junction that lacks the regular arrays of electron-dense septae found in pleated septate junctions.


gap junction

description: A cell-cell junction composed of pannexins or innexins and connexins, two different families of channel-forming proteins.


connexin complex

description: An assembly of six molecules of connexin, made in the Golgi apparatus and subsequently transported to the plasma membrane, where docking of two connexons on apposed plasma membranes across the extracellular space forms a gap junction.


bicellular tight junction

description: An occluding cell-cell junction that is composed of a branching network of sealing strands that completely encircles the apical end of each cell in an epithelial sheet; the outer leaflets of the two interacting plasma membranes are seen to be tightly apposed where sealing strands are present. Each sealing strand is composed of a long row of transmembrane adhesion proteins embedded in each of the two interacting plasma membranes.


focal adhesion

description: A cell-substrate junction that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments. In insects focal adhesion has also been referred to as hemi-adherens junction (HAJ).


muscle tendon junction

description: A cell-substrate junction found at the terminal anchorage site of skeletal muscle cells to tendons.


cilium

description: 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.


axoneme

description: The bundle of microtubules and associated proteins that forms the core of cilia (also called flagella) in eukaryotic cells and is responsible for their movements.


axonemal nexin link

description: A protein complex found in the axoneme of eukaryotic cilia and flagella. It forms interconnections between the microtubule outer doublets that surround the inner central pair of microtubules.


cellular bud

description: A protuberance from a cell of an organism that reproduces by budding, which will grow larger and become a separate daughter cell after nuclear division, cytokinesis, and cell wall formation (when appropriate). The daughter cell may completely separate from the mother cell, or the mother and daughter cells may remain associated.


cellular bud tip

description: The end of a cellular bud distal to the site of attachment to the mother cell.


cellular bud neck

description: The constriction between the mother cell and daughter cell (bud) in an organism that reproduces by budding.


mating projection

description: The projection formed by unicellular fungi in response to mating pheromone.


cell cortex

description: The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins.


septin ring

description: A tight ring-shaped structure that forms in the division plane at the site of cytokinesis; composed of members of the conserved family of filament-forming proteins called septins as well as septin-associated proteins. This type of septin structure is observed at the bud neck of budding fungal cells, at the site of cell division in animal cells, at the junction between the mother cell and a pseudohyphal projection, and also within hyphae of filamentous fungi at sites where a septum will form.


phosphatidylinositol 3-kinase complex

description: A protein complex capable of phosphatidylinositol 3-kinase activity and containing subunits of any phosphatidylinositol 3-kinase (PI3K) enzyme. These complexes are divided in three classes (called I, II and III) that differ for their presence across taxonomic groups and for the type of their constituents. Catalytic subunits of phosphatidylinositol 3-kinase enzymes are present in all 3 classes; regulatory subunits of phosphatidylinositol 3-kinase enzymes are present in classes I and III; adaptor proteins have been observed in class II complexes and may be present in other classes too.


name: phosphatidylinositol 3-kinase complex, class IA

description: A class I phosphatidylinositol 3-kinase complex that possesses 1-phosphatidylinositol-4-phosphate 3-kinase activity; comprises a catalytic class IA phosphoinositide 3-kinase (PI3K) subunit and an associated SH2 domain-containing regulatory subunit that is a member of a family of related proteins often called p85 proteins. Through the interaction with the SH2-containing adaptor subunits, Class IA PI3K catalytic subunits are linked to tyrosine kinase signaling pathways.


name: phosphatidylinositol 3-kinase complex, class IB

description: A class I phosphatidylinositol 3-kinase complex that possesses 1-phosphatidylinositol-4-phosphate 3-kinase activity; comprises a catalytic class IB phosphoinositide 3-kinase (PI3K) subunit and an associated regulatory subunit that is larger than, and unrelated to, the p85 proteins present in class IA complexes. Class IB PI3Ks are stimulated by G-proteins and do not interact with the SH2-domain containing adaptors that bind to Class IA PI3Ks.


6-phosphofructokinase complex

description: A protein complex that possesses 6-phosphofructokinase activity; homodimeric, homooctameric, and allosteric homotetrameric forms are known.


name: alpha,alpha-trehalose-phosphate synthase complex (UDP-forming)

description: A protein complex that possesses alpha,alpha-trehalose-phosphate synthase (UDP-forming) and trehalose-phosphatase activities, and thus catalyzes two reactions in trehalose biosynthesis. In the complex identified in Saccharomyces, Tps1p has alpha,alpha-trehalose-phosphate synthase (UDP-forming) activity, Tps2p has trehalose 6-phosphate phosphatase activity; Tps3p is a regulatory subunit, and an additional subunit, Tsl1p, may be present.


acetolactate synthase complex

description: A dimeric (a large and a small chain) or tetrameric (two large and two small chains) enzyme complex. Catalyzes the formation of acetolactate from pyruvate.


anthranilate synthase complex

description: A heterotetrameric enzyme complex made up of two components I and two components II. Catalyzes the formation of anthranilate, pyruvate and L-glutamate from chorismate and L-glutamine.


carbamoyl-phosphate synthase complex

description: A protein complex that catalyzes the formation of carbamoyl phosphate; comprises a small subunit that binds and cleaves glutamine, and a large subunit that accepts the ammonia group cleaved from glutamine, binds all of the remaining substrates and effectors, and carries out all of the other catalytic events.


cAMP-dependent protein kinase complex

description: An enzyme complex, composed of regulatory and catalytic subunits, that catalyzes protein phosphorylation. Inactive forms of the enzyme have two regulatory chains and two catalytic chains; activation by cAMP produces two active catalytic monomers and a regulatory dimer.


description: A heterodimeric enzyme, composed of an alpha and a beta subunit. Participates in the post-translational C-terminal modification of several small GTPases, allowing their targeting to the membrane.


name: calcium- and calmodulin-dependent protein kinase complex

description: An enzyme complex which in eukaryotes is composed of four different chains: alpha, beta, gamma, and delta. The different isoforms assemble into homo- or heteromultimeric holoenzymes composed of 8 to 12 subunits. Catalyzes the phosphorylation of proteins to O-phosphoproteins.


calcineurin complex

description: A heterodimeric calcium ion and calmodulin dependent protein phosphatase composed of catalytic and regulatory subunits; the regulatory subunit is very similar in sequence to calmodulin.


protein kinase CK2 complex

description: A protein complex that possesses protein serine/threonine kinase activity, and contains two catalytic alpha subunits and two regulatory beta subunits. Protein kinase CK2 complexes are found in nearly every subcellular compartment, and can phosphorylate many protein substrates in addition to casein.


name: DNA-dependent protein kinase-DNA ligase 4 complex

description: A large protein complex which is involved in the repair of DNA double-strand breaks and, in mammals, V(D)J recombination events. It consists of the DNA-dependent protein kinase catalytic subunit (DNA-PKcs), the DNA end-binding heterodimer Ku, the nuclear phosphoprotein XRCC4 or a homolog thereof, and DNA ligase IV.


glycine cleavage complex

description: A protein complex that catalyzes the reversible oxidation of glycine. In E. coli, it has four components: dihydrolipoamide dehydrogenase, glycine dehydrogenase (decarboxylating), lipoyl-GcvH-protein and aminomethyltransferase, also known as L, P, H, and T.


name: magnesium-dependent protein serine/threonine phosphatase complex

description: An intracellular enzyme complex that catalyzes the removal of serine- or threonine-bound phosphate groups from a wide range of phosphoproteins, including a number of enzymes that have been phosphorylated under the action of a kinase.


phosphorylase kinase complex

description: An enzyme complex that catalyzes the phosphorylation of phosphorylase b to form phosphorylase a.


protein farnesyltransferase complex

description: A protein complex that possesses protein farnesyltransferase activity.


description: An protein-containing complex which catalyzes of the transfer of a geranyl-geranyl group from geranylgeranyl pyrophosphate to a Rab protein. In mammals it is composed of an alpha and a beta subunit, and associates with an accessory protein Rep (Rab escort protein).


description: An enzyme complex that catalyzes the formation of hydroxypyruvate and alanine from serine and pyruvate.


description: An enzyme complex composed of 2-4 or more subunits, which usually contains nonheme iron and requires ATP for catalysis. Catalyzes the formation of 2'-deoxyribonucleoside diphosphate from ribonucleoside diphosphate, using either thioredoxin disulfide or glutaredoxin disulfide as an acceptor.


carbohydrate metabolic process

category: biolink:BiologicalProcess biolink:Occurrent biolink:OntologyClass biolink:BiologicalProcessOrActivity biolink:BiologicalEntity biolink:ThingWithTaxon biolink:NamedThing biolink:PhysicalEssenceOrOccurrent

description: The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.


polysaccharide metabolic process

description: The chemical reactions and pathways involving a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.


glycogen metabolic process

description: The chemical reactions and pathways involving glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues in alpha-(1->4) glycosidic linkage, joined together by alpha-(1->6) glycosidic linkages.


glycogen biosynthetic process

description: The chemical reactions and pathways resulting in the formation of glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues.


name: regulation of glycogen biosynthetic process

description: Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of glycogen.


glycogen catabolic process

description: The chemical reactions and pathways resulting in the breakdown of glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues.


name: regulation of glycogen catabolic process

description: Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of glycogen.


starch metabolic process

description: The chemical reactions and pathways involving starch, the most important reserve polysaccharide in plants. It is a glucan consisting of two components, amylose and amylopectin, which are both glucose homopolymers. Starch is synthesized as a temporary storage form of carbon and can be catabolized to produce sucrose.


starch catabolic process

description: The chemical reactions and pathways resulting in the breakdown of starch, the most important reserve polysaccharide in plants.


disaccharide metabolic process

description: The chemical reactions and pathways involving any disaccharide, sugars composed of two monosaccharide units.


sucrose metabolic process

description: The chemical reactions and pathways involving sucrose, the disaccharide fructofuranosyl-glucopyranoside.


sucrose biosynthetic process

description: The chemical reactions and pathways resulting in the formation of sucrose, the disaccharide fructofuranosyl-glucopyranoside.


sucrose catabolic process

description: The chemical reactions and pathways resulting in the breakdown of sucrose, the disaccharide fructofuranosyl-glucopyranoside.


lactose metabolic process

description: The chemical reactions and pathways involving lactose, the disaccharide galactopyranosyl-glucose.


lactose biosynthetic process

description: The chemical reactions and pathways resulting in the formation of lactose, the disaccharide galactopyranosyl-glucose.


lactose catabolic process

description: The chemical reactions and pathways resulting in the breakdown of lactose, the disaccharide galactopyranosyl-glucose.


trehalose metabolic process

description: The chemical reactions and pathways involving trehalose, a disaccharide that consists of two molecules of glucose and is isomeric with sucrose.


trehalose biosynthetic process

description: The chemical reactions and pathways resulting in the formation of trehalose, a disaccharide that consists of two molecules of glucose and is isomeric with sucrose.


trehalose catabolic process

description: The chemical reactions and pathways resulting in the breakdown of trehalose, a disaccharide that consists of two molecules of glucose and is isomeric with sucrose.


melibiose metabolic process

description: The chemical reactions and pathways involving melibiose, the disaccharide 6-O-alpha-D-galactopyranosyl-D-glucose.


melibiose catabolic process

description: The chemical reactions and pathways resulting in the breakdown of melibiose, the disaccharide 6-O-alpha-D-galactopyranosyl-D-glucose.


monosaccharide metabolic process

description: The chemical reactions and pathways involving monosaccharides, the simplest carbohydrates. They are polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides.


xylulose metabolic process

description: The chemical reactions and pathways involving xylulose, the ketopentose threo-2-pentulose.


xylulose catabolic process

description: The chemical reactions and pathways resulting in the breakdown of xylulose, the ketopentose threo-2-pentulose.


xylulose biosynthetic process

description: The chemical reactions and pathways resulting in the formation of xylulose, the ketopentose threo-2-pentulose.


fructose metabolic process

description: The chemical reactions and pathways involving fructose, the ketohexose arabino-2-hexulose. Fructose exists in a open chain form or as a ring compound. D-fructose is the sweetest of the sugars and is found free in a large number of fruits and honey.


fructose catabolic process

description: The chemical reactions and pathways resulting in the breakdown of fructose, the ketohexose arabino-2-hexulose.


fructose 6-phosphate metabolic process

description: The chemical reactions and pathways involving fructose 6-phosphate, also known as F6P. The D-enantiomer is an important intermediate in glycolysis, gluconeogenesis, and fructose metabolism.


name: fructose 2,6-bisphosphate metabolic process

description: The chemical reactions and pathways involving fructose 2,6-bisphosphate. The D enantiomer is an important regulator of the glycolytic and gluconeogenic pathways. It inhibits fructose 1,6-bisphosphatase and activates phosphofructokinase.


fucose metabolic process

description: The chemical reactions and pathways involving fucose, or 6-deoxygalactose, which has two enantiomers, D-fucose and L-fucose.


L-fucose biosynthetic process

description: The chemical reactions and pathways resulting in the formation of L-fucose (6-deoxy-L-galactose).


glucose metabolic process

description: The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides.


glucose catabolic process

description: The chemical reactions and pathways resulting in the breakdown of glucose, the aldohexose gluco-hexose.


glucose 1-phosphate phosphorylation

description: The process of introducing a phosphate group into glucose 1-phosphate to produce glucose bisphosphate.


UDP-glucose metabolic process

description: The chemical reactions and pathways involving UDP-glucose, uridinediphosphoglucose, a substance composed of glucose in glycosidic linkage with uridine diphosphate.


galactose metabolic process

description: The chemical reactions and pathways involving galactose, the aldohexose galacto-hexose. D-galactose is widely distributed in combined form in plants, animals and microorganisms as a constituent of oligo- and polysaccharides; it also occurs in galactolipids and as its glucoside in lactose and melibiose.


mannose metabolic process

description: The chemical reactions and pathways involving mannose, the aldohexose manno-hexose, the C-2 epimer of glucose. The D-(+)-form is widely distributed in mannans and hemicelluloses and is of major importance in the core oligosaccharide of N-linked oligosaccharides of glycoproteins.


D-ribose metabolic process

description: The chemical reactions and pathways involving D-ribose (ribo-pentose). As beta-D-ribofuranose, D-ribose forms the glycose group of all ribonucleosides, ribonucleotides and ribonucleic acids, and also of ribose phosphates, various glycosides, some coenzymes and some forms of vitamin B12.


name: 5-phosphoribose 1-diphosphate biosynthetic process

description: The chemical reactions and pathways resulting in the formation of 5-phosphoribose 1-diphosphate, also known as 5-phosphoribosyl-1-pyrophosphate.


name: 2-deoxyribose 1-phosphate biosynthetic process

description: The chemical reactions and pathways resulting in the formation of 2-deoxyribose 1-phosphate, the phosphorylated sugar 1-phospho-2-deoxyribose.


name: deoxyribose 1,5-bisphosphate biosynthetic process

description: The chemical reactions and pathways resulting in the formation of deoxyribose 1,5-bisphosphate, the diphosphorylated sugar 1,5-diphospho-2-deoxyribose.


name: 2-deoxyribose 1-phosphate catabolic process

description: The chemical reactions and pathways resulting in the breakdown of deoxyribose 1-phosphate, the phosphorylated sugar 1-phospho-2-deoxyribose.


deoxyribose 5-phosphate phosphorylation

description: The process of introducing a phosphate group into deoxyribose 5-phosphate to produce deoxyribose bisphosphate.


inositol metabolic process

description: The chemical reactions and pathways involving inositol, 1,2,3,4,5,6-cyclohexanehexol, a growth factor for animals and microorganisms.


inositol biosynthetic process

description: The chemical reactions and pathways resulting in the formation of inositol, 1,2,3,4,5,6-cyclohexanehexol, a growth factor for animals and microorganisms.


aminoglycan metabolic process

description: The chemical reactions and pathways involving aminoglycans, any polymer containing amino groups that consists of more than about 10 monosaccharide residues joined to each other by glycosidic linkages.


aminoglycan biosynthetic process

description: The chemical reactions and pathways resulting in the formation of aminoglycans, any polymer containing amino groups that consists of more than about 10 monosaccharide residues joined to each other by glycosidic linkages.


glycosaminoglycan biosynthetic process

description: The chemical reactions and pathways resulting in the formation of glycosaminoglycans, any of a group of polysaccharides that contain amino sugars.


description: The chemical reactions and pathways resulting in the formation of galactosaminoglycans, any of a group of polysaccharides that contain amino sugars derived from the galactose.


aminoglycan catabolic process

description: The chemical reactions and pathways resulting in the breakdown of aminoglycans, any polymer containing amino groups that consists of more than about 10 monosaccharide residues joined to each other by glycosidic linkages.


glycosaminoglycan catabolic process

description: The chemical reactions and pathways resulting in the breakdown of glycosaminoglycans, any one of a group of polysaccharides that contain amino sugars.


galactosaminoglycan catabolic process

description: The chemical reactions and pathways resulting in the breakdown of galactosaminoglycans, any of a group of polysaccharides that contain amino sugars derived from the galactose.


proteoglycan metabolic process

description: The chemical reactions and pathways involving proteoglycans, any glycoprotein in which the carbohydrate units are glycosaminoglycans.


chitin metabolic process

description: The chemical reactions and pathways involving chitin, a linear polysaccharide consisting of beta-(1->4)-linked N-acetyl-D-glucosamine residues.


chitin biosynthetic process

description: The chemical reactions and pathways resulting in the formation of chitin, a linear polysaccharide consisting of beta-(1->4)-linked N-acetyl-D-glucosamine residues.


chitin catabolic process

description: The chemical reactions and pathways resulting in the breakdown of chitin, a linear polysaccharide consisting of beta-(1->4)-linked N-acetyl-D-glucosamine residues.


chitin localization

description: A process in which chitin is transported to, or maintained in, a specific location.


amino sugar metabolic process

description: The chemical reactions and pathways involving any amino sugar, sugars containing an amino group in place of a hydroxyl group.


glucosamine metabolic process

description: The chemical reactions and pathways involving glucosamine (2-amino-2-deoxyglucopyranose), an aminodeoxysugar that occurs in combined form in chitin.


glucosamine biosynthetic process

description: The chemical reactions and pathways resulting in the formation of glucosamine (2-amino-2-deoxyglucopyranose), an aminodeoxysugar that occurs in combined form in chitin.


glucosamine catabolic process

description: The chemical reactions and pathways resulting in the breakdown of glucosamine (2-amino-2-deoxyglucopyranose), an aminodeoxysugar that occurs in combined form in chitin.


N-acetylglucosamine metabolic process

description: The chemical reactions and pathways involving N-acetylglucosamine. The D isomer is a common structural unit of glycoproteins in plants, bacteria and animals; it is often the terminal sugar of an oligosaccharide group of a glycoprotein.


description: The chemical reactions and pathways resulting in the formation of N-acetylglucosamine. The D isomer is a common structural unit of glycoproteins in plants, bacteria and animals; it is often the terminal sugar of an oligosaccharide group of a glycoprotein.


N-acetylglucosamine catabolic process

description: The chemical reactions and pathways resulting in the breakdown of N-acetylglucosamine. The D isomer is a common structural unit of glycoproteins in plants, bacteria and animals; it is often the terminal sugar of an oligosaccharide group of a glycoprotein.


description: The chemical reactions and pathways involving UDP-N-acetylglucosamine, a substance composed of N-acetylglucosamine, a common structural unit of oligosaccharides, in glycosidic linkage with uridine diphosphate.


description: The chemical reactions and pathways resulting in the formation of UDP-N-acetylglucosamine, a substance composed of N-acetylglucosamine, a common structural unit of oligosaccharides, in glycosidic linkage with uridine diphosphate.


description: The chemical reactions and pathways resulting in the breakdown of UDP-N-acetylglucosamine, a substance composed of N-acetylglucosamine, a common structural unit of oligosaccharides, in glycosidic linkage with uridine diphosphate.


mannosamine metabolic process

description: The chemical reactions and pathways involving mannosomine, 2-amino-2-deoxymannose; the D-isomer is a constituent of neuraminic acids as well as mucolipids and mucoproteins.


N-acetylmannosamine metabolic process

description: The chemical reactions and pathways involving N-acetylmannosamine, the acetylated derivative of mannosamine, 2-amino-2-deoxymannose.


description: The chemical reactions and pathways resulting in the formation of N-acetylmannosamine, the acetylated derivative of mannosamine, 2-amino-2-deoxymannose.


N-acetylmannosamine catabolic process

description: The chemical reactions and pathways resulting in the breakdown of N-acetylmannosamine, the acetylated derivative of mannosamine, 2-amino-2-deoxymannose.


N-acetylneuraminate metabolic process

description: The chemical reactions and pathways involving N-acetylneuraminate, the anion of 5-(acetylamino)-3,5-dideoxy-D-glycero-D-galacto-non-3-ulosonic acid.


description: The chemical reactions and pathways resulting in the formation of CMP-N-acetylneuraminate, a substance composed of 5-(acetylamino)-3,5-dideoxy-D-glycero-D-galacto-non-3-ulosonic acid in glycosidic linkage with cytidine monophosphate.


mannoprotein metabolic process

description: The chemical reactions and pathways involving a mannoprotein, a protein that contains covalently bound mannose residues.


mannoprotein biosynthetic process

description: The chemical reactions and pathways resulting in the formation of a mannoprotein, a protein that contains covalently bound mannose residues.


mannoprotein catabolic process

description: The chemical reactions and pathways resulting in the breakdown of a mannoprotein, a protein that contains covalently bound mannose residues.


hexitol metabolic process

description: The chemical reactions and pathways involving hexitols, any alditol with a chain of six carbon atoms in the molecule.


sorbitol metabolic process

description: The chemical reactions and pathways involving sorbitol (D-glucitol), one of the ten stereoisomeric hexitols. It can be derived from glucose by reduction of the aldehyde group.


sorbitol biosynthetic process

description: The chemical reactions and pathways resulting in the formation of sorbitol (D-glucitol), one of the ten stereoisomeric hexitols. It can be derived from glucose by reduction of the aldehyde group.


sorbitol catabolic process

description: The chemical reactions and pathways resulting in the breakdown of sorbitol (D-glucitol), one of the ten stereoisomeric hexitols. It can be derived from glucose by reduction of the aldehyde group.


uronic acid metabolic process

description: The chemical reactions and pathways involving uronic acid, any monocarboxylic acid formally derived by oxidizing to a carboxyl group the terminal hydroxymethylene group of either an aldose with four or more carbon atoms in the molecule, or of any glycoside derived from such an aldose.


glucuronate catabolic process

description: The chemical reactions and pathways resulting in the breakdown of glucuronate, any salt or ester of glucuronic acid.


UDP-glucuronate biosynthetic process

description: The chemical reactions and pathways resulting in the formation of UDP-glucuronate, a substance composed of glucuronic acid in glycosidic linkage with uridine diphosphate.


alcohol metabolic process

description: The chemical reactions and pathways involving alcohols, any of a class of compounds containing one or more hydroxyl groups attached to a saturated carbon atom.


ethanol metabolic process

description: The chemical reactions and pathways involving ethanol, CH3-CH2-OH, a colorless, water-miscible, flammable liquid produced by alcoholic fermentation.


ethanol catabolic process

description: The chemical reactions and pathways resulting in the breakdown of ethanol, CH3-CH2-OH, a colorless, water-miscible, flammable liquid produced by alcoholic fermentation.


octanol metabolic process

description: The chemical reactions and pathways involving octanol, the 8-carbon alcohol with the formula C8H17OH.


glycerol metabolic process

description: The chemical reactions and pathways involving glycerol, 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids.


glycerol-3-phosphate metabolic process

description: The chemical reactions and pathways involving glycerol-3-phosphate, a phosphoric monoester of glycerol.


(1->3)-beta-D-glucan metabolic process

description: The chemical reactions and pathways involving (1->3)-beta-D-glucans, compounds composed of glucose residues linked by (1->3)-beta-D-glucosidic bonds.


description: The chemical reactions and pathways resulting in the formation of (1->3)-beta-D-glucans, compounds composed of glucose residues linked by (1->3)-beta-D-glucosidic bonds.


(1->3)-beta-D-glucan catabolic process

description: The chemical reactions and pathways resulting in the breakdown of (1->3)-beta-D-glucans.


(1->6)-beta-D-glucan metabolic process

description: The chemical reactions and pathways involving (1->6)-beta-D-glucans, compounds composed of glucose residues linked by (1->6)-beta-D-glucosidic bonds.


description: The chemical reactions and pathways resulting in the formation of (1->6)-beta-D-glucans.


(1->6)-beta-D-glucan catabolic process

description: The chemical reactions and pathways resulting in the breakdown of (1->6)-beta-D-glucans.


substituted mannan metabolic process

description: The chemical reactions and pathways involving a mannan backbone composed of D-mannose unites, substituted with D-glucose and/or D-galactose units.


cellular aldehyde metabolic process

description: The chemical reactions and pathways involving aldehydes, any organic compound with the formula R-CH=O, as carried out by individual cells.


organic acid metabolic process

description: The chemical reactions and pathways involving organic acids, any acidic compound containing carbon in covalent linkage.


acetate metabolic process

description: The chemical reactions and pathways involving acetate, the anion of acetic acid.


acetyl-CoA metabolic process

description: The chemical reactions and pathways involving acetyl-CoA, a derivative of coenzyme A in which the sulfhydryl group is acetylated; it is a metabolite derived from several pathways (e.g. glycolysis, fatty acid oxidation, amino-acid catabolism) and is further metabolized by the tricarboxylic acid cycle. It is a key intermediate in lipid and terpenoid biosynthesis.


acetyl-CoA biosynthetic process

description: The chemical reactions and pathways resulting in the formation of acetyl-CoA, a derivative of coenzyme A in which the sulfhydryl group is acetylated.


name: acetyl-CoA biosynthetic process from pyruvate

description: The chemical reactions and pathways resulting in the formation of acetyl-CoA from pyruvate.


lactate metabolic process

description: The chemical reactions and pathways involving lactate, the anion of lactic acid.


pyruvate metabolic process

description: The chemical reactions and pathways involving pyruvate, 2-oxopropanoate.


name: generation of precursor metabolites and energy

description: 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.


gluconeogenesis

description: The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.


glycolytic process

description: The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.


glyoxylate cycle

description: A modification of the TCA cycle occurring in some plants and microorganisms, in which isocitrate is cleaved to glyoxylate and succinate. Glyoxylate can then react with acetyl-CoA to form malate.


pentose-phosphate shunt

description: The metabolic process in which glucose-6-phosphate is oxidized to form carbon dioxide (CO2) and ribulose 5-phosphate, coupled to reduction of NADP+ to NADPH; ribulose 5-P then enters a series of reactions that can yield biosynthetic precursors (ribose-5-phosphate and erythrose-4-phosphate) and glycolytic intermediates (fructose-6-phosphate and glyceraldehyde-3-phosphate).


tricarboxylic acid cycle

description: A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.


citrate metabolic process

description: The chemical reactions and pathways involving citrate, 2-hydroxy-1,2,3-propanetricarboyxlate. Citrate is widely distributed in nature and is an important intermediate in the TCA cycle and the glyoxylate cycle.


isocitrate metabolic process

description: The chemical reactions and pathways involving isocitrate, the anion of isocitric acid, 1-hydroxy-1,2,3-propanetricarboxylic acid. Isocitrate is an important intermediate in the TCA cycle and the glycoxylate cycle.


2-oxoglutarate metabolic process

description: The chemical reactions and pathways involving oxoglutarate, the dianion of 2-oxoglutaric acid. It is a key constituent of the TCA cycle and a key intermediate in amino-acid metabolism.


succinyl-CoA metabolic process

description: The chemical reactions and pathways involving succinyl-CoA, a compound composed of the monovalent acyl group 3-carboxypropanoyl, derived from succinic acid by loss of one OH group, linked to coenzyme A.


succinate metabolic process

description: The chemical reactions and pathways involving succinate, also known as butanedioate or ethane dicarboxylate, the dianion of succinic acid. Succinate is an important intermediate in metabolism and a component of the TCA cycle.


fumarate metabolic process

description: The chemical reactions and pathways involving fumarate, the anion of trans-1,2-ethenedicarboxylic acid, the diastereoisomer of maleate. It is a key intermediate in metabolism and is formed in the TCA cycle from succinate and converted into malate.


oxaloacetate metabolic process

description: The chemical reactions and pathways involving oxaloacetate, the anion of oxobutanedioic acid, an important intermediate in metabolism, especially as a component of the TCA cycle.


malate metabolic process

description: The chemical reactions and pathways involving malate, the anion of hydroxybutanedioic acid, a chiral hydroxydicarboxylic acid. The (+) enantiomer is an important intermediate in metabolism as a component of both the TCA cycle and the glyoxylate cycle.


name: regulation of carbohydrate metabolic process

description: Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving carbohydrates.


regulation of glycolytic process

description: Any process that modulates the frequency, rate or extent of glycolysis.


regulation of gluconeogenesis

description: Any process that modulates the frequency, rate or extent of gluconeogenesis, the formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.


energy reserve metabolic process

description: The chemical reactions and pathways by which a cell derives energy from stored compounds such as fats or glycogen.


fermentation

description: The anaerobic enzymatic conversion of organic compounds, especially carbohydrates, coupling the oxidation and reduction of NAD/H and the generation of adenosine triphosphate (ATP).


glycerol biosynthetic process

description: The chemical reactions and pathways resulting in the formation of glycerol, 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids.


ethanol biosynthetic process

description: The chemical reactions and pathways resulting in the formation of ethanol, CH3-CH2-OH, a colorless, water-miscible, flammable liquid produced by alcoholic fermentation.


NADH oxidation

description: A metabolic process that results in the oxidation of reduced nicotinamide adenine dinucleotide, NADH, to the oxidized form, NAD+.


acetaldehyde metabolic process

description: The chemical reactions and pathways involving acetaldehyde, a colorless, flammable liquid intermediate in the metabolism of alcohol.


oxidative phosphorylation

description: The phosphorylation of ADP to ATP that accompanies the oxidation of a metabolite through the operation of the respiratory chain. Oxidation of compounds establishes a proton gradient across the membrane, providing the energy for ATP synthesis.


name: mitochondrial electron transport, NADH to ubiquinone

description: The transfer of electrons from NADH to ubiquinone that occurs during oxidative phosphorylation.


name: mitochondrial electron transport, succinate to ubiquinone

description: The transfer of electrons from succinate to ubiquinone that occurs during oxidative phosphorylation, mediated by the multisubunit enzyme known as complex II.


name: mitochondrial electron transport, ubiquinol to cytochrome c

description: The transfer of electrons from ubiquinol to cytochrome c that occurs during oxidative phosphorylation, mediated by the multisubunit enzyme known as complex III.


name: mitochondrial electron transport, cytochrome c to oxygen

description: The transfer of electrons from cytochrome c to oxygen that occurs during oxidative phosphorylation, mediated by the multisubunit enzyme known as complex IV.


ferredoxin metabolic process

description: The chemical reactions and pathways involving ferredoxin, any simple, nonenzymatic iron-sulfur protein that is characterized by having equal numbers of atoms of iron and labile sulfur. Iron and sulfur atoms are present in one or two clusters of two or four atoms of each.


glycerophosphate shuttle

description: The process of transferring reducing equivalents from the cytosol into the mitochondria; NADH is used to synthesise glycerol 3-phosphate in the cytosol; this compound is then transported into the mitochondria where it is converted to dihydroxyacetone phosphate (DHAP) using FAD; DHAP then returns to the cytosol to complete the cycle.


name: nucleobase-containing compound metabolic process

description: Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.


name: regulation of nucleotide metabolic process

description: Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleotides.


name: regulation of purine nucleobase metabolic process

description: Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving purines.


name: regulation of pyrimidine nucleobase metabolic process

description: Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving pyrimidine nucleobases.


purine nucleobase metabolic process

description: The chemical reactions and pathways involving purine nucleobases, one of the two classes of nitrogen-containing ring compounds found in DNA and RNA, which include adenine and guanine.


purine nucleobase catabolic process

description: The chemical reactions and pathways resulting in the breakdown of purine nucleobases, one of the two classes of nitrogen-containing ring compounds found in DNA and RNA, which include adenine and guanine.


adenine catabolic process

description: The chemical reactions and pathways resulting in the breakdown of adenine, 6-aminopurine, one of the 5 main bases found in nucleic acids and a component of numerous important derivatives of its corresponding ribonucleoside, adenosine.


guanine catabolic process

description: The chemical reactions and pathways resulting in the breakdown of guanine, 2-amino-6-hydroxypurine, a purine that is one of the five main bases found in nucleic acids and a component of a number of phosphorylated guanosine derivatives whose metabolic or regulatory functions are important.


inosine catabolic process

description: The chemical reactions and pathways resulting in the breakdown of inosine, hypoxanthine riboside, a nucleoside found free but not in combination in nucleic acids except in the anticodons of some tRNAs.


deoxyinosine catabolic process

description: The chemical reactions and pathways resulting in the breakdown of deoxyinosine, hypoxanthine deoxyriboside.