Effector specificity- for a protein after receptor.Both protein A and B, will be considered effectors even though they can have different functions. They both can be present in different cell types.Opposite effects downstream are all mediated by receptors.Common features in signaling pathways are Kinases and Phosphatases. Kinase is a protein that adds a phosphate to another protein.There is a substrate protein in the inactive state. Kinases can add a phosphate group to any amino acid with an –OH group. The three amino acids that are capable of being phosphorylated are serine, threonine, and tyrosine. There are around 600 different kinases in humans. Binding depends on the amino acid surrounding the phosphorylation site. When a protein is phosphorylated, it is considered to be in the active state and on. In order to turn the protein off, the protein phosphatase cleaves off a phosphate group.Kinases are a series of enzymes that can be phosphorylated. Kinases become active when a phosphate group is added. A kinase in a cascade is when there are series of phosphorylation events.GTP Proteins are usually called G proteins or GTP-ases. Exist in off state when it is bound to GDP. The GEF will essentially change the confirmation of the G protein and cause the affinity for GDP to decrease and increases the affinity for GTP. The net result is that there is a swapping for GDP to GTP. When GTP is bound, this protein is considered to be in its active state. All GTP-ases have the ability to cleave off any terminal phosphate. GAP only exist for slow proteins.All these G proteins have switches on either side. The switch is what binds to the terminal phosphate. The terminal phosphate is bound by 2 specific amino acid switches. When the GTP is bound, the switches collapse. When only GDP is bound, the protein exist in a more comfortable state. When the terminal protein is bound, the switches are turned out. When it is only GDP, the switch is curled into itself. Mutations can occur where the switches are mutated and can cause cancer.Trimeric means that there are 3 subunits to the G protein.Monomeric means there is 1 subunit to the G protein.Intracellular second messengers are small molecules that serve two functions- can carry the signal throughout the cytoplasm and amplify the signal.Examples of second messenger- Calcium is 10,000 fold on outline of the cell. It can be higher on the outside of the cell. It can be stored in the mitochondria. As calcium levels are increased, it binds to two specific motifs known as EF hands (helix, loop helix). Calcium binds into the loop and the two alpha helixes cross each other. There is a massive confirmation change and the net result is that the conformation change allows the protein with the EF hand to bind to another protein.cAMP is cyclic AMP. It will be used to regulate protein kinases, to breakdown kinases activity, and open ion channels.DAG and IP3 are derivatives of Glycerol-3-Phosphate. It has long fatty acids. Glycerol is a 3 carbon molecule. On the third carbon, there is a polar head group. Phosphatidylinositol is almost always found on the cytoplasmic side of the membrane is and is used for cell signaling. Phospholipase C is an effector that cleaves phospholipids, cleaves between the oxygen and the phosphate.Parts of all G protein-coupled receptor systems are glycogen and fat metabolism, light and neurotransmission. All GPCR pathways have a receptor that has 7 transmembrane spanning domains, trimeric GTPase – lipid anchored proteins, effector in the plasma membrane, and feedback mechanisms. All have short term affects and will work on proteins that already exists.The receptors are GPCR receptors. An examples is the Beta-adrenergic receptor that has four cytoplasmic domains and seven transmembrane domains. The C3 and C4 loop are what bind to the G-proteins. Light binding induces a confirmation change in cytoplasmic domains. The C3 and C4 loops are now available for binding the G proteins.The G protein- alpha, beta, and gamma subunits. Beta and gamma are linked together, while alpha separates. Both can move laterally in the membrane. Trimeric has 3 subunits. Alpha subunits bind to GDP/GTP binding site, has a lipid anchor. Gamma and beta subunits always stay bond to each other. Binding anchor.When the signal comes in and binds to the receptor, there is a conformation change in the C3 and C4 cytoplasmic domain. The conformation change provides the docking cite for the alpha subunit of the G-protein. The receptor, when bound to ligand receptor acts as a GEF and allows removal of GDP and GTP to bind. Once GTP is bound to the G protein, it is in an active or on state and the GTP binding triggers dissociation of the alpha subunit. The alpha subunit now binds to an effector. Because they are GTPases, the G protein can hydrolyze its GTP meaning, phosphate will come off and the alpha subunit is bound to GTP, the 3 subunits (Alpha, Beta, Gamma) come back together. When the subunits come back together, the cycle is shut off.GPCR pathway proteins- receptor, G-protein, and effector. Effector proteins can be membrane bound ion channels, adenylyl cyclase which makes cyclic Amp, or phosphatase C which is DAG and IP3.GPCRs can regulate ion channels. The K+ channel is on the cell membrane. When Acetylcholine is signaled, the GDP is replaced with GTP. The gamma-beta subunit does the activity. It binds to the K+ channel, induces a conformation change, opens the channel up, and is one of the gated channels.G protein coupled receptors that activate or inhibit adenylyl-cyclase. Adenylyl-cyclase is the effector. Epinephrine and the B-adrenergic receptor cause the heart race to increase and increase contractions of the cardiac cells. The skeletal muscles require glucose, which can be seen by a massive increase of glucose.cAMP activates protein kinase A (PKA). PKA is a serine threonine kinase. PKA has a C subunit (catalytic), and R subunits which are regulators. Four cAMP molecules bind to sites on the regulatory subunits, releasing the catalytic subunits. The catalytic subunits are active kinases, so they are phosphorylate other proteins.03/10/2015Effector specificity- for a protein after receptor. Both protein A and B, will be considered effectors even though they can have different functions. They both can be present in different cell types.Opposite effects downstream are all mediated by receptors. Common features in signaling pathways are Kinases and