in this talk we're going to learn about different aspects of cell signaling all cells have developed mechanisms to monitor and respond to physical and chemical changes around their environment regardless of what kind of a cell it is for example a unicellular organism has developed mechanisms to communicate and influence another unicellular organism's behavior and this happens through the process of cell signaling in the case of multicellular organisms the cells have to communicate with each other and function as a unit the cells are able to communicate with each other as well as sense molecules around their environment through the process of cell signaling this communication between cells occurs through molecules that are present on a cell surface or that are secreted into the environment the cells are able to sense these molecules that are on a cell surface or secreted to the environment and they respond to the presence of these molecules using different proteins and this process is in a nutshell cell signaling a signaling pathway begins when an extracellular signaling molecule called as a ligand binds to the receptor in the figure shown to the right the ligand is shown by the small red circle and this ligand binds to a receptor and this receptor is a protein that is present on the cell the binding of the ligand to the receptor allows the cell to sense the presence of the ligand in the environment once the ligand binds to the receptor the receptor is activated and it activates the signaling pathway the signaling pathway comprises of proteins that are activated in the pathway some of the proteins that are shown here are in the box below words are called as the intracellular signaling proteins these are proteins that are present inside the cell and are normally present in an inactive state which means they cannot perform their functions they have to be activated to perform their functions and this happens only when the receptor becomes active finally we have the effector proteins that are activated by the signaling proteins these effector proteins are proteins that can mediate a specific outcome in the figure that is shown to the right the different effector proteins that have been shown are proteins that are metabolic enzymes and hence can alter metabolism or they can be transcription regulatory proteins and thus alter the expression of genes or they can be cytoskeletal proteins that allow the cell to change its shape or allows the cell to move in a specific direction bottom line is the presence of the ligand generates a cellular response which can be in many different forms so now let's look a little bit more about the extracellular membrane signal molecules or the ligands these signal molecules can either be on a membrane or they can be secreted into the environment these ligands can act on nearby cells or on cells that are far away let us first look at ligands that are bound to the membrane and hence can be sensed by cells only when there is direct cell contact so when we look at the figure in the right the signaling cell has the extracellular signal molecule or the ligand which is attached to the membrane of the signaling cell for this ligand to be detected by the target cell the receptor in the target cell has to have a direct contact with the signaling cell this kind of a mechanism where the a target cell is able to sense a membrane-bound signaling molecule or ligand through direct contact is seen in the development and generation of many immune responses and this will be something that will be studied more in detail in an immunology class we can also have ligands that are secreted by cells and when the cell secretes the ligand the ligand can be sensed by the cell itself or by cells that are nearby or around or by cells that are far away from the cell that is secreting the ligand when you have a scenario where a cell that secretes the ligand also has receptors to bind to the ligand and hence response to the ligand such type of a signaling mechanism is called autocrine signaling in another instance you can have a signaling cell that is secreting a ligand as shown on the bottom figure and the ligand that is secreted by the signaling cell is not sensed by that signaling cell itself however there are cells nearby or neighboring cells that have receptors that can bind to the ligand and this is an example of paracrine signaling another example of a signaling mechanism is endocrine signaling where there is a cell that secretes the ligand which is called as the endocrine cell and the ligate that is secreted in an example can enter the bloodstream of a multicellular organism and can travel to far away distances and be sensed by target cells that have the appropriate receptor these target cells are far away from the endocrine cell and hence such signaling is called endocrine signaling a perfect example of endocrine signaling is the sensing of hormones by the appropriate target cells a special type of signaling is also called a synaptic signaling which is actually a type of paracrine signaling and in the case of synaptic signaling there are always neurons that are involved and the signaling occurs in a region called as a synapse you will learn more about synaptic signaling when we learn about the nervous system and how nerve signaling occurs now that we look at different receptor different ligands we're not going to look at what exactly are receptors so receptors are proteins that are present on the target cell that will sense or bind to the ligands the receptors will have a binding site that is specific to the ligand and it should be remembered that the only way the cell knows that a ligand is present is because it has a receptor that can bind to it if a cell does not have a receptor for a specific ligand it will be unable to respond or sense that ligand and hence it's as if the ligand is not there at all receptors can be present on the cell surface or they can be intracellular receptors here let's look at a cell that has an extracellular receptor and the extracellular receptor is shown in the box this extracellular receptor is usually recognizing hydrophilic ligands and these hydrophilic ligands cannot pass through the plasma membrane of the cell and hence we have the extracellular or the cell surface receptor proteins if you have a ligand that has the ability to pass the plasma membrane and enter the cell by itself then normally it is sensed by receptors that are present inside the cell or by intracellular receptors in this example we are showing an intracellular receptor that is present in the nucleus of a cell it should be noted that these intracellular receptors can be in the cytoplasm also many cell surface receptors are transmembrane proteins there are different types of transmembrane receptors that are present on cells an example of one of them are the channel linked receptors channel linked receptors can be chemically gated ion channels these ion channels will open only when a chemical binds to that channel protein so in the figure we are able to see a channel protein that is closed and hence ions are not able to pass through this ion channel however when a ligand binds to the ion channel for example a neurotransmitter there is a conformational change in the ion channel that allows it to open up and ions can then flow through it g-protein-coupled receptors are transmembrane receptors that are found in the cell membrane or plasma membrane of many cells these g protein couple receptors are associated with an intracellular protein called as the g protein when g-protein-coupled receptors bind to ligands on the extracellular part of the cell they undergo a conformational change which results in the activation of the g-proteins when the proteins become active they can activate other kinds of proteins like ion channels or enzymes and thus they can play a role in signal transduction enzyme-coupled receptors are transmembrane proteins that are associated with an enzymatic activity in the case of enzyme-coupled receptors they're able to bind to ligands on the extracellular side and the enzymatic activity is associated in the intracellular part when the enzyme coupled receptors bind to a ligand then in some cases they have intrinsic enzymatic activity and that intrinsic enzymatic activity becomes active upon ligand binding in some cases the receptor itself does not have any enzymatic activity but it has the ability to associate with enzymes inside the cell and this association is able to activate the enzymes when a ligand binds to the enzyme-coupled receptor once the ligand binds to the receptor then that information has to be passed inside the cell this is normally done by recruiting intracellular proteins to the plasma membrane this can be done in a variety of ways one example is where you can have certain proteins that have binding sites where other proteins can bind and thus they are able to brought closer to the plasma membrane another way is to generate certain types of phospholipids like in this case we are making phosphorylated inositol phosphates and these phosphorylated inositol phosphates like pip 3 can then form binding sites for other proteins and thus protein protein or protein lipid interactions play an important role in the recruitment of proteins to the plasma membrane now how exactly do proteins bind and interact to other proteins and this is normally mediated by domains domains are parts of a protein that have their own specific functions and can fold independently of the protein there are many domains that are involved in allowing proteins to interact with one another an example of one such domain is the sh2 domain which is the sarcomology 2 domain when a protein that has this specific domain has the ability to bind to other proteins that have phosphorylated tyrosines another domain is the phosphotyrosine binding domain or the ptb domain and this domain and once again allows proteins to bind to phosphorylated tyrosines the phosphorylated tyrosines that are recognized by sh2 domains and by ptb domains have different types of amino acids surrounding the phosphorylated tyrosines another domain is the plextron homology domain or ph domain that can bind to special phosphorylated lipids present on the plasma membrane like the phosphorylated inositides another domain that allows proteins to interact with one another are the sh3 domain or the sarcomology 3 domain this is a domain that binds to proline rich peptide sequences that are present in proteins a lot of these domains play a role in the cell signaling process because they promote protein protein interactions as shown in the figure that to the right these domain-mediated protein-protein interactions can result in the formation of multi-protein signaling complexes these multi-protein signaling complexes can be assembled using proteins like scaffold proteins or adapter proteins scaffold proteins are proteins that are phosphorylated at multiple sites and thus we can see that in this figure where a kinase is able to phosphorylate a protein at multiple sites and these phosphorylated sites are able to form binding sites for other proteins to be recruited usually proteins with sh2 or ptb domains are able to associate with the scaffold proteins adaptive proteins are proteins that have several signaling modules or domains that can interact with other proteins let us take the example of the adapter protein grab 2. grab 2 has two sh3 domains that are able to bind to proline rich regions in another protein for the example of sas greb2 also has an sh2 domain and this sh2 domain is able to bind to phosphorylated tyrosine residues that are present in other proteins and this way grep 2 is able to form an interaction with different types of proteins and bring them closer together and thus grab 2 is an example of an adapter protein protein function can be regulated in different ways one way is by the binding to other proteins for example we have already looked at how ligand binding is able to activate receptors another way that proteins can be activated is through binding to guanine nucleotides like gtp proteins can also be activated by post-translational modifications that can act as molecular switches phosphorylation is an example of a post-translational modification which involves the addition of phosphate groups ubiquitination is another example where the protein ubiquitin is added the first way a protein can be activated is through phosphorylation phosphorylation is the process of adding a phosphate group two amino acids of a protein normally phosphate groups can be added to serine threonine or tyrosine residues phosphate groups are obtained from atp and there are specific enzymes whose job is to add phosphate groups to proteins these proteins are called or these enzymes are called kinases and kinases hence are the proteins or the enzymes that will add phosphate groups to proteins and when the protein has the phosphate group it can be functionally active if you have a functionally active protein and that activity is due to the presence of a phosphate group then that protein can be rendered inactive by removing that phosphate group the removal of phosphate groups is done by a different set of enzymes called phosphatases phosphatases are able to remove the phosphate group so that the protein now lacks the phosphate group and hence is now functionally inactive this phosphorylation can act as a switch to determine whether a protein is active and functional or not it should be noted that though phosphorylation is usually associated with activation of protein function that is not always the case as there are examples where phosphorylation has been associated with inhibition of protein function likewise even though de-phosphorylation is usually associated with the activation of protein function that is not always the case another way to regulate protein activity is through ubiquitination ubiquitin is a cytosolic protein which has a c-terminal glycine this glycine at the c-terminal end of ubiquitin can be covalently attached to lysine residues in proteins this results in ubiquitination proteins like receptors as shown in the figure can be mono or diubiquinated in the figure we are seeing a receptor that has been ubiquitinated at two places and hence it is diubnated and this ubiquitination then results in that protein to go into endosomes which will ultimately fuse with the lysosome and result in an appropriate fate of the protein like degradation of the protein in addition to mono and die ubiquitination polyubiquiti polyubiquitination can also occur polyubiquitination is the addition of ubiquitin to existing ubiquitin that has been attached to a protein as shown in the figure this edition of additional ubiquitin molecules can happen on the lysine 48 residue or the lysine 63rd residue of the previous ubiquitin when ubiquitins are added at lysine 48 then that protein that has undergone polyubiquitination is tagged for degradation by the proteosome in the proteosome it will be degraded into shorter peptides and thus the protein is then degraded by the cell another outcome of polyubiquitination when it occurs on lysine 63 is that it can form these scaffolds that form binding sites for other proteins as shown in the figure in this figure we are able to see a polyubiquitinated chain and this polyubiquitin chain can form binding sites for the protein tach1 such polyubiquin scaffolds are seen in tlr and nlr signaling which play important roles in immune system another way protein activity can be controlled is through the binding of a nucleotide which is the guanine nucleotide triphosphate proteins that have a gtpa's activity can bind to gtp a gtpa's activity is basically the ability to hydrolyze gtp to gdp which is the guanine nucleoside that has two phosphates attached to it a lot of times the protein that is bound to gtp is in its active and functional form however when the gtp is hydrolyzed to gdp the protein is inactive so in many cases a protein will have gdp associated with it and will be in the functionally inactive position when a ligand binds to the receptor and the receptor gets activated you can have proteins called guanine nucleotide exchange factors that can mediate the exchange of gdp to gtp and now the protein that has the gtp bound to it is functionally active when this protein needs to be rendered inactive the gtp has to be hydrolyzed there are proteins called the gtpa's activating proteins or gaps whose function is to help a protein hydrolyze the gtp so that the gtp loses a phosphate and you end up with the protein bound to the gdp and thus the presence of gtp or gdp determines whether a protein is active or not signaling pathways get activated when the ligand binds to its appropriate receptor in this scenario the ligand is called as the first messenger during the process of signal transduction inside the cell second messengers are produced these second messengers are small molecules that are formed inside the cell in response to the presence of the ligand binding to the receptor in the picture shown an example of a second messenger is the calcium ions which are localized in the endoplasmic reticulum of the cell when a ligand binds a receptor the ion channels that are able to regulate the flow of calcium inside the cytoplasm will open up and this results in a flood of calcium ions inside the cytoplasm calcium is a second messenger because it is a small molecule that was formed inside the cell and its entry into the cytoplasm was in response to the presence of the cell signaling that was triggered by the ligand second messengers have the ability to diffuse throughout the cell the way the calcium ion does and in the process they're able to bind to other proteins and activate them these proteins that are activated can then interact with other proteins and in turn activate them thus second messengers help in the propagation as well as the amplification of the signaling cascade there are different types of second messengers that are made in a cell some examples are cyclic amp which is made by the enzyme adenylate cyclase another second messenger is diacyl glycerol which is made by the action of phospholipase c beta phospholipase c beta is able to cleave the phosphatidyl inositol four fibers phosphate which is a phospholipid to produce two second messengers and one of them is diacylglycerol diacylglycerol is one of the few second messengers that are membrane bound inositol 145 phosphate which is also called as ip3 is the second product that is produced when phospholipase c beta cleaves the phosphatidyl inositol four fibers phosphate calcium is also a second messenger and it is an ion that is normally stored in the endoplasmic reticulum it is released into the cytosol by ion channels nitric oxide is an example of another second messenger that is made by the enzyme nitric oxide synthase it is a second messenger that is a gas and hence it is easy for nitric oxide to leave the cell and thereby play roles in neighboring cells also signaling pathways are activated so that the cell is able to respond to the environment the outcome of signaling pathways include the activation of transcription factors that in turn can start activating or repressing certain genes and thus gene expression is regulated by signaling pathways signaling pathways can also activate certain enzymes that are involved in metabolism and that way anabolic and catabolic pathways can be regulated by signaling pathways the cytoskeleton can also undergo rearrangement when signaling pathways are activated and thus cell shape or motility is regulated by signaling pathways we're now going to look at an example of a signal transduction pathway in this case we're going to see how the hormone insulin is able to ensure that glucose is converted to glycogen and thus the glucose levels present in your blood are tightly regulated the whole process begins when the insulin binds to the receptor so in the figure we can see the insulin molecule and the insulin molecule will bind to the insulin receptor and this will cause a conformational change in the receptor this conformational change in the receptor will activate a kinase function that is present in the receptor and the receptor will end up phosphorylating itself once the receptor phosphorylates itself the receptor is active and can phosphorylate other molecules however these molecules have to come close to the receptor in order for the receptor to phosphorylate them for that the phosphorylated tyrosines present on the receptor will form binding sites for proteins like the insulin response protein as shown in the box in the figure the insulin response protein is able to bind to the phosphotyrosines present on the insulin receptor and this allows the insulin response protein to become active through the subsequent activation of other types of proteins finally we will have an enzyme become active which is the enzyme glycogen synthase the function of glycogen synthase is to take glucose and add them together or covalently attach them together to form glycogen and thus the insulin hormone is able to promote the enzymatic activity of glycogen synthase thereby converting glucose to glycogen and this is shown in the box in the figure where we can see glucose being converted into glycogen through the activity of glycogen synthase thus the insulin receptor is able to have or the presence of the insulin and detection of insulin through the insulin receptor is able to have an altered metabolic effect where now glucose is being converted to glycogen in case you have two less glucose and don't want it to be converted to glycogen then this whole process or pathway can be deactivated by simply de-phosphorylating the proteins and by also dephosphorylating the receptor and this will terminate the pathway another example of a signal transduction pathway is shown in this figure where we're looking at cytokines which are secreted ligands and they're normally made by cells when they are infected by pathogens these cytokines are released or secreted by the infected cells as a way to alert the immune system and to alert the neighboring cells that there is a pathogen in the vicinity the cytokine as shown here is detected by the cytokine receptors that are present in the cells these cytokine receptors then undergo a conformational change and allow and this conformational change allows the kinase to associate with the receptor and allows the kinase to be active the activated kinase can now phosphorylate the receptor to generate docking sites for other proteins and one of these proteins is called as the stat protein which is a signal transducer and activator of transcription the stat proteins are come in close contact with the kinase and they get phosphorylated the phosphorylation of the stat protein renders them as active and the stat proteins can interact with one another in the phosphorylated state and enter the nucleus once the stat proteins enter the nucleus they can bind to dna and increase the transcription of specific genes because the stat proteins are transcription factors the transcription factor ability of the stat proteins is kept inactive until they get phosphorylated and the phosphorylation happens only when a ligand is present the stat proteins will allow the expression of specific genes whose job is to protect cells from other pathogens they can also be used to activate the immune cells who can then come and help in clearing the pathogen another example of a signal transduction pathway that uses second messenger is shown in this figure in this case we have the hormone adrenaline which functions as the ligand and it binds to its receptor that is present on the cell surface right next to this receptor is a protein called as a g protein and the g protein normally has gdp associated with it however when the ligand binds the receptor the gdp of the g protein is exchanged to gtp and now the g protein becomes active the activated g protein can activate the enzyme adenylyl cyclase and this is the enzyme that will produce the second messenger cyclic amp cyclic amp is a soluble molecule and it can diffuse throughout the cytoplasm and it can activate many different kind of proteins and the example here shows the protein protein kinase a protein kinase a is normally present in an inactive state however when cyclic amp is present it binds to protein kinase a and protein kinase a is now functional and can phosphorylate other proteins since it is a kinase when protein kinase a is in the active state due to the presence of cyclic amp the protein kinase a can go ahead and phosphorylate transcriptional regulators and make these transcriptional regulators active once the transcriptional regulators are active they can now bind to the dna sequences and cause the transcription of specific genes thus the adrenaline that is present in the extracellular environment is enabling the cell to respond by transcribing specific genes through the action of the receptor and the second messenger with this we come to the end of our talk where we learned about what ligands are and what receptors are in the context of cell signaling we learned about the different types of signaling like direct direct cell interaction autocrine paracrine endocrine as well as synaptic signaling we also learned about the recruitment of proteins and the role of domains in protein protein interactions we learned about the regulation of protein activity and the role of second messengers in cell signaling finally we looked at the outcomes of signaling pathways and saw a few examples of signaling cascades in action