Term	Definition	Diagram/schematic (link or insert below)	Notes
Dimer
Dimerization
Phosphorylation	Biochemical process which adds the phosphate group to a molecule. / Reaction in which a phosphate group is covalently coupled to another molecule.
Kinase	It is an enzyme which catalyzes the transfer of a phosphate group, adds phosphate group
Phosphotase
GTPase	enzyme that converts GTP to GDP, the enzyme falls into 2 large families: large trimeric G proteins and small monomeric GTP binding proteins
Hydrolysis
Cytokine
cations	positively charged ions
anions	negatively charged ions
allostery	change in a protein’s conformation brought about by the binding of a regulatory ligand (at a site other than the protein’s catalytic site) or by covalent modification. the change in conformation alters the activity of the protein and can form the basis of directed movement.
apoptosis	form of programmed cell death, in which a suicide program is activated within within an animal cell, leading to rapid cell death mediated by intracellular proteolytic enzymes called capsases
arrestin	member of a family of proteins that contributes to GPCR desensitization by preventing the activated receptor from interacting with G proteins and serving as an adaptor to couple the receptor to clathrin-dependent endocytosis
bcl2	anti-apoptotic blc2 family protein of the outer mitochondria membrane that binds and inhibits pro-apoptotic bcl2 family proteins and prevents inappropriate activation of the intrinsic pathway of apoptosis
chromatin	complex of DNA, histones, and non-histone proteins found in the nucleus of a eukaryotic cell. the material of which chromosomes are made
clathrin	protein that assembles in a polyhedral cage on the cystolic side of a membrane so as to form a clathrin-coated pit, which buds off by endocytosis to form an intracellular clathrin-coated vesicle
dynein	large motor protein that undergoes ATP-dependent movement along microtubules
E2F protein	transcription regulatory protein that switches on many genes that encode proteins required for entry into the S phase of the cell cycle
early endosome	common receiving compartment with which most endocytic vesicles fuse and where internalized cargo is sorter either for return to the plasma membrane or for degradation by inclusion in a late endosome
effector cell	cell that carries out the final response or function in a particular process
endocytosis	uptake of material into a cell by an invagination of the plasma membrane and its internalization in a membrane-enclosed vesicle
enzyme	protein that catalyzes a specific chemical reaction
enzyme-coupled receptor	a major type of cell-surface receptor that has a cytoplasmic domain that either has enzymatic activity or is associated with an intracellular enzyme. in either case, the enzymatic activity is stimulated by an extracellular ligand binding to the receptor
equilibrium	sate in a chemical reaction where there is no net change in free energy to drive the reaction i neither direction. the ratio of product to substrate reaches a constant value at chemical equilibrium
executioner capsases	apoptotic capasaes that catalyze the widespread cleavage events during apoptosis that kill the cell
exocytosis	excretion of material from the cell by vesicle fusion with the plasma membrane; can occur constitutively or be regulated
extrinsic pathway	pathway of apoptosis triggered by extracellular signal proteins binding to cell-surface death receptors
Fas protein, receptor	trans-membrane death receptor that initiates apoptosis when it binds its extracellular ligand
Fas ligand	ligand that activated cell-surface death receptor, Fas, triggering the extrinsic pathway of apoptosis
general transcription factor	any of the proteins whose assembly at all promoters of a given type is required for the binding and activation of RNA polymerase and the initiation of transcription
GPCR kinase (GRK)	member of a family of enzymes that phosphorylates multiple serines and threonines on a GPCR to produce receptor desensitization
G protein (trimeric GTP-binding protein)	a trimeric GTP-binding protein with intrinsic GTPase activity that couples GPCRs to enzymes or ion channels in the plasma membrane
GPCR	a seven-pass cell-surface receptor that, when activated by its extracellular ligand, activates a G protein, which in turns activates either an enzyme or ion in the plasma membrane
Gq	a class of G protein that couples GPCRs to phospholipase C-beta to activate inositol phospholipid signaling pathway
growth factor	extracellular signal protein that can stimulate a cell to grow. they often have other functions as well, including stimulating cells to survive or proliferate. examples are epidermal growth factor (EGF) and platelet-derived growth factor (PDGF)
guanine nucleotide exchange factor (GEF)	protein that binds to a GTPase and activates it by stimulating it to release its tightly bound GDP, thereby allowing it to bind to GTP in its place
histone	one of a group of small abundant proteins, rich in arginine and lysine, that combine to form the nucelosome cores around which DNA is wrapped in a eukaryotic chromosomes
initiator capsases	apoptotic capsases that begin the apoptotic process, activating the executioner capsases
kinase cascade	intracellular signaling pathway in which one protein kinase, activated by phosphorylation, phosphorylates the next protein kinase in the sequence, and so on, relaying the signal onward
kinesin	member of one of 2 main classes of motor proteins that use the energy of ATP hydrolysis to move along microtubules
ion channel	transmembrane protein complex that forms a water-filled channel across the lipid bilayer through which specific inorganic ions can diffuse down their electrochemical gradients
ion-channel-coupled receptor (AKA transmitter-gated ion channel, AKA ionotropic receptor)	ion channel found at chemical synapses in the postsynaptic plasma membranes of nerve and muscle cells. opens only in response to the binding of a specific extracellular neurotransmitter. the resulting inflow of ions leads to the generation of a local electrical signal in the postsynaptic cell
K+ leak channel	K+-transporting ion channel in the plasma membrane of animal cells that remains open even in a ‘resting’ cell
late endosome	compartment formed from a bulbous, vacuolar portion of early endosomes by a process called endosome maturation; late endosomes fuse with one another and with lysosomes to form endolysosomes that degrade their contents
ligand	any molecule that binds to a specific site on a protein or other molecule
LTD - long-term depression	a long-lasting decrease in the sensitivity of certain synapses in the brain triggered by NMDA receptor activation. as the opposing process to LTP, it is thought to be involved in learning and memory
LTP - long-term potentiation	long-lasting increase in the sensitivity of certain synapses in the brain, induced by a short burst of repetitive firing in the presynaptic neurons
lysosome	membrane-enclosed organelle in eukaryotic cells containing digestive enzymes, which are typically most active at the acid pH found in the lumen of lysosomes
MAP kinase module (mitogen-activated protein kinase module)	an intracellular signaling module composed of 3 protein kinases, acting in sequence, with MAP kinase as the third. typically activated by Ras protein in response to extracellular signals
metabotropic receptors	neurotransmitter receptors that regulate ion channels indirectly through the activation of second-messenger molecules
mitogen	extracellular signal molecule that stimulates cells to proliferate
motor protein	protein that uses energy derived from nucleotides triphosphate hydrolysis to propel itself along a linear track (protein filament or other polymeric molecule)
myosin	type of motor protein that uses energy of ATP hydrolysis to move along actin filaments
nucleotides	nucleosides with one or more phosphate groups joined in ester linkages to the sugar moiety. DNA and RNA are polymers of nucleotides.
PIP2	membrane isnositol phosphplipid that is cleaved by phospholipase C into IP3 and diacylglycerol at the beginning of the inositol phospholipid signaling pathway. it can also be phosphorylated by PI 3-kinase to produce PIP3 docking sites for signaling proteins in the PI-3-kianse-Akt signaling pathways
phospholipids	the main category of lipids used to construct biomembranes. generally composed of 2 fatty acids linked through glycerol phosphate to one of a variety of polar groups
PIP3 (phosphoinositides	a lipid containing a phosphorylated inositol derivative. minor component of the plasma membrane, but important in demarking different membranes and for intracellular signal transduction in eukaryotic cells
phospholipase C (PLC)	membrane-bound enzyme that cleaves inositol phospholipids to produce IP3 and dicylglycerol in the inositol phospholipid signaling pathway. PLCbeta is activated by GPCRs bia specific G proteins, while PLCgamma is activated by RTKs
protein kinase	enzyme that transfers the terminal phosphate group of ATP to one or more specific amino acids of a target protein
PKC - phospholipase C	Ca2+ dependent protein kianse that, when activated by diacylglycerol and in increase in the concentration of cystolic Ca2+, phosphorylates target proteins on specific serine and threonine residues
polypeptide	linear polymer of amino acids, proteins are large polypeptides, and the 2 terms can be used interchangeably
primary structure	linear sequence of monomer units in a polymer, such as the amino acid sequence of a protein
positive feedback	control mechanism whereby the end product of a reaction or pathway stimulates its own production or activation
protein	major macromolecular constituent of cells, a linear polymer of amino acids linked together by peptide bonds in a specific sequence
protein kinase	enzyme that transfers terminal phosphate group of ATP to one or more specific amino acids of a target protein
protein translocator	membrane-bound protein that mediates the transport of another protein across a membrane
Rab cascade	an ordered recruitment of sequentially acting Rab proteins into Rab domains on membranes, which changes the identity of an organelle and reassigns membrane dynamics
Rab effectors	molecules that bind activated membrane-bound Rab proteins and act as downstream mediators of vesicle transport, membrane tethering, and fusion
Rab proteins	monomeric GTPase in the Ras superfamily present in plasma and organelle membranes in its GTP-bound state, and as a soluble cystolic protein in its GDP-bound state, involved in conferring specificity on vesicle docking
Ras protein	monomeric GTPase of the Ras superfamily that helps relay signals from cell-surface receptors to the nucleus, frequently in response to signals that stimulate cell division. named for the ras gene, first identified in viruses that cause rat sarcomas
Ras superfamily	large superfamily of monomeric GTPases (also called small GTP-binding proteins) of which Ras is the prototypical member
Ras GAPs	Ras GTPase-activating proteins; increase the rate of hydrolysis of bound GTP by Ras, thereby inactivating Ras
Ras GEFs	Ras guanine nucleotide exchange factors; stimulate the dissociation of GDP and the subsequent uptake of GTP from the cytosol, thereby activating Ras
Ras-MAP-kinase signaling pathway	intracellular signaling pathway that relays signals from activated receptor tyrosine kinases to effector proteins in the cell including transcription regulators in the nucleus
Rb gene	defective in both copies in individuals with retinoblastoma its protein product plays a central role in cell-cycle control
receptor	any protein that binds to a specific signal molecule (ligand) and initiates a response in the cell, some are on the cell surface, some are inside the cell
receptor serine/threonine kinase	cell-surface receptor with an extracellular ligand-binding domain and an intracellular kinase domain that phosphorylates signaling proteins on serine or threonine residues in response to ligand binding
receptor tyrosine kinase	cell-surface receptor with an extracellular ligand-binding domain and an intracellular domain that phosphorylates signaling proteins on tyrosine residues in response to ligand binding
receptor-mediated endocytosis	internalization of receptor-ligand complexes from the plasma membrane by endocytosis
recycling endosomes	organelle that provides an intermediate stage on the passage of recycled receptors back to the cell membrane, regulates plasma membrane insertion of some proteins
resting membrane potential	electrical potential across the plasma membrane of a cell at rest, i.e., a cell that has not been stimulated to open additional ion channels than those that are normally open
Rb protein	tumor suppressor protein involved in the regulation of cell division. mutated in the cancer retinoblastoma, and in many other tumors. its normal activity is to regulate the eukaryotic cell cycle by binding to and inhibiting the E2F proteins, thus blocking progression to DNA replication and cell division
Rho	member of Rho family of monomeric GTPases that regulate the actin and microtubule cytoskeletons, cell-cycle progression, gene transcription, and membrane transport
Rho family	family of monomeric GTPases within the Ras superfamily involved in signaling the rearrangement of the cytoskeleton, includes Rho, Rac
rhodopsin	seven-span membrane protein of the GPCR family that acts as a light sensor in rod photoreceptor cells in the vertebrate retina. contains light-sensitive prosthetic group retinol
scaffold protein	protein that binds groups of intracellular signaling proteins into a signaling complex, often anchoring the complex at a specific location in the cell
S-cdk	cyclin-cdk complex formed in vertebrae cells by an S-cyclin and the corresponding cyclin-dependent kinase (cdk)
S-cyclin	member of a class of cyclins that accumulate during late G1 phase and bind Cdks soon after progression through Start; they help stimulate DNA replication and chromosome duplication. levels remain high until late mitosis, after which these cyclins are destroyed
second messenger (small intracellular mediator)	small intracellular signaling molecule that is formed or released for action in response to an extracellular signal and helps to relay the signal within the cell. examples are cycling AMP, cyclin GMP. IP3, Ca2+
secondary structure	regular local folding pattern of a polymeric molecule; in proteins alpha helices and beta sheets
serine protease	type of protease that has a reacting serine in the active site
serine/threonine kinase	enzyme that phosphorylates specific proteins on serine or threonines
side chain	the part of an amino acid that differs between amino acid types. the side chains give each of the amino acid its unique physical and chemical properties
sister chromatids	tightly linked pair of chromosomes that arise from chromosome duplication during S phase. they separate during M phase and segregate into different daughter cells
smooth endoplasmic reticulum (smooth ER)	region of ER not associated with ribosomes. involved in detoxification reactions, Ca2+ storage, and lipid synthesis
SNARE proteins	members of a large family of transmembrane proteins present in organelle membranes and the vesicles derived from them. SNAREs catalyze the many membrane fusion events in cells. they exist in pairs - a v-SNARE in the vesicle membrane that binds specifically to a complimentary t-SNARE in the target membrane
S phase	period of a eukaryotic cell cycle in which DNA is synthesized
Src (Src protein family)	family of cytoplasmic tyrosine kinases that associate with cytoplasmic domains of some enzyme-linked cell-surface receptors that lack intrinsic tyrosine kinase activity. they transmit a signal onward by phosphorylating the receptor itself and specific intracellular signaling proteins on tyrosines
Start (restriction point)	important transition at the end of G1 in the eukaryotic cell cycle. passage through Start commits the cell to enter S phase. the term was originally used for this point in year cell cycle only; the equivalent in the mammalian cell cycle was called the restriction point. but now we use Start