17 Cell Communication

One striking feature of living organisms is their ability to sense and respond to the environment (see examples in Figure 17.1). Place a plant in a sunny window, and over time, you will observe the leaves turning towards the sun. If you’ve gotten cuts or scrapes on your skin, you saw these eventually healed as new cells replaced the damaged ones. If you’ve found yourself in dangerous situation, you may remember the heightened awareness, faster reflexes, and other changes that occurred in response. Plant growth towards sunlight, wound healing, and the “fight or flight” response are all examples of coordinated activity among many cells of an organism in response to specific stimuli.

One note before we continue: in this chapter, we will focus on cell communication that occurs in multicellular organisms, and in human cells more specifically. However, all organisms, even single-celled bacteria, sense specific environmental cues and respond accordingly. For example, when nutrient availability changes, some bacteria alter their gene expression to change their metabolism (see the chapters on gene regulation for more details).

Chapter Outline

Section 17.1 General Cell Communication Principles

Section 17.2 Signal Transduction Mechanisms

Section 17.3 Types of Receptors

Section 17.4 Model for the In-class Activity

Section 17.1 General Cell Communication Principles

The focus of this chapter is basic principles of cell communication involving chemical signals, although some cells can respond to other stimuli, such as light. A signal, or ligand, released by a signaling cell serves as the message (Figure 17.2, leftmost cell). The message can only be sensed by a cell with a receptor protein with the correct shape and chemical properties to bind to the ligand (Figure 17.2, top right cell) and generate a cellular response. A cell without the correct receptor, such as the one in the bottom right of Figure 17.2, will not respond to this ligand.

Once the ligand binds to the receptor, a change in the receptor’s shape leads to a cellular response in the cell with the receptor (responding cell). This process typically requires many signal transduction proteins, which are recruited by the activated receptor and act in sequence to cause the cellular response (Figure 17.3). Depending on the functions of the signal transduction proteins, the cellular response might be a change in gene expression (Figure 17.3, response to ligand 1), other specific chemical reactions (Figure 17.3, response to ligand 2), cell movement, cell division, or some other change in the cell. After the signal is received, signaling must be terminated to allow the cell to respond to a new signal. Signal termination involves the reversal of signaling steps – the ligand is removed from the receptor, the receptor is inactivated, and all proteins affected by signal transduction are returned to their original state.

As we go through different examples of common signaling pathways, you should look for and note commonalities of signaling pathways. Every pathway has a signal, receptor, and a cellular response. For chemical signals, physical interactions (binding) with the receptor leads to a change in receptor shape, which allows the receptor to pass on the signal. In most cases, signal transduction proteins are activated by physical interactions or chemical modifications that change the shape of signal transduction proteins. Look for these changes in shape and think about how you would describe the cause of any changes you see. In most drawings of signaling pathways, arrows show the sequence of steps and may also be used to indicate chemical reactions and molecule movements. Oftentimes, though, arrows just indicate that a molecule at one step of the pathway activates another molecule in a later step. It’s up to you to explain how this activation occurs! Finally, because signaling needs to be terminated, make sure you can describe what needs to happen to “reset” the components of the signaling pathway.

While there are many different types of signaling pathways, a small number of which will be explored here, let’s first focus on what they all have in common. All signaling pathways involve a specific type of ligand binding to a specific type of receptor. This binding is specific because only a ligand with the correct properties will be able to form a high affinity interaction with the receptor. The ligand and receptor each must have compatible functional groups to form intermolecular forces such as hydrogen bonding, ionic bonding, and LDFs. Furthermore, the binding of ligand to the receptor leads to a change in the receptor’s shape (receptor activation). Remember that receptors are proteins, and thus their tertiary structure (shape) is determined by intermolecular forces (IMFs) between amino acids (see Figure 6.6b). When the ligand binds, these interactions shift slightly, causing changes in shape that activate the receptor. This change in shape is needed for the receptor to cause the cellular response.

To bind to specific receptors and elicit specific cellular responses, ligands come in a variety of shapes, sizes, and chemical properties (Figure 17.4). Some ligands are mostly nonpolar, and easily cross cell membranes to find their receptors (Figure 17.4a). However, most ligands are too polar (Figure 17.4b) or also too large (Figure 17.4c) to cross the plasma membrane, and thus remain outside the cell. To cause a cellular response, these polar ligands interact with receptors that span the plasma membrane. These receptors have portions sticking out of the cell to bind to ligands, and portions that extend into the cytosol to interact with proteins there to pass along with signal.

Section 17.2 Signal Transduction Mechanisms

Most receptors for cell signaling are in the cell’s plasma membrane, since most ligands are polar and remain outside of the cell. Thus, to communicate the presence of ligand outside the cell, the receptor must change shape to be activated (receptor activation), as described previously. This change in receptor shape is crucial for the receptor to then activate proteins or cause other changes inside the cell. There are several signal transduction mechanisms commonly used to activate proteins in these pathways, and all of these involve physical interactions that cause signal transduction proteins to change shape in a manner associated with activation.

G Proteins

One common component of signal transduction pathways is called a G protein. These proteins are so named because they are always non-covalently bound to the nucleotide GDP (guanine diphosphate) or GTP (guanine triphosphate). The structures of these nucleotides are shown in Figure 17.5a. Importantly, the G protein’s shape is different depending on which nucleotide it binds. In Figure 17.5b, the models show the Ras G protein backbone, and regions marked in green indicate amino acids in different positions between the GTP- and GDP-bound forms, which allows the G protein’s function to differ as well.

Figure 17.5c shows the steps of activating and inactivating the G protein. When bound to GDP, the G protein is inactive and not participating in signal transduction. However, when the G protein interacts with a protein called a Guanine nucleotide exchange factor, or GEF, this causes GDP to unbind from the G protein. Since the cytosol has high concentrations of GTP, a molecule of GTP quickly binds to the G protein and changes the shape of the G protein. This process, called GDP to GTP exchange, is part of signal transduction in response to receptor activation, though the details vary from pathway to pathway. However, in all pathways, the G protein bound to GTP has a different shape, than the GDP-bound form, allowing interactions with different proteins. Through forming protein-protein interactions with proteins such as kinases or adenylyl cyclase (described below), the active G protein causes further signal transduction.

Shortly after being activated, the G protein inactivates itself by hydrolyzing its bound GTP to GDP, releasing inorganic phosphate (P_i) as a result. This intrinsic GTPase activity of the G protein is enhanced by binding to a GTPase activating protein, or GAP. Once again bound to GDP, the G protein returns to its inactive shape and no longer causes signal transduction (Figure 17.5c).

Phosphorylation

Another very common mechanism of signal transduction is phosphorylation, or the addition of a phosphate group to a protein. Most often, this occurs when an enzyme called a kinase transfers a phosphate from ATP to another protein, which we will refer to as the protein target in this generic example (Figure 17.6a). The products of this reaction are ADP and a phosphorylated protein. In some pathways, kinases are activated by interactions with active G proteins. Notice that the kinase, being an enzyme, is not consumed in the reaction, and is able to repeat the phosphorylation reaction many times and produce many phosphorylated proteins as a result.

Importantly, this reaction is a covalent modification of the protein target, typically targeted to amino acids with hydroxyl function groups. Go back to the amino acid structures shown in Chapter 2–which amino acids are most likely to be modified by kinase? Consider also the effect of this modification. What are the properties of the hydroxyl functional group, and what interactions do amino acids with this functional group form? Adding a phosphate group to a protein means adding two full negative charges–how will this affect interactions among amino acid side chains?

As shown in Figure 17.6, the phosphorylated protein has an altered shape that allows it to interact with different molecules than the unphosphorylated form. Depending on the specific change, phosphorylation could either increase or decrease the function of the protein. If phosphorylation activates the protein target, in signal termination, a phosphatase that removes the phosphate from the protein target will return the target to its previous shape and function. Conversely, if dephosphorylation activates a protein target, a kinase phosphorylating the protein would inactivate it.

Let’s expand upon a point mentioned earlier–in a phosphorylation reaction, the kinase enzyme is not consumed, but rather continues to phosphorylate proteins as long as the kinase remains active. As shown in Figure 17.7, one active kinase could affect the activity of many protein targets (pink rectangles) through phosphorylation. Imagine these protein targets are also kinases that are activated by phosphorylation. When activated, these kinases phosphorylate a different set of protein targets (blue triangles). This series of phosphorylation reactions is an example of signal amplification, in which one active protein activates more than one protein that can then carry out the next step in signal transduction. In Figure 17.7, a single activated kinase results in 9 activated proteins at the end of the cascade, helping to ensure a robust cellular response to the signal.

cAMP, a Second Messenger

In some signaling pathways, signal transduction involves the accumulation of specific molecules in the cytosol of cells. Cyclic adenosine monophosphate (cAMP) is a common second messenger, so-called because cAMP in the cell indicates the presence of the ligand, the first message, bound to its receptor. cAMP is formed by the enzyme adenylyl cyclase, which is activated by protein-protein interactions with an active G protein (see the later section on G protein-coupled receptors for more context. As shown in Figure 17.8, adenylyl cyclase removes two phosphates ATP and forms another bond between the phosphate and the ribose sugar to form cAMP. Because one active adenylyl cyclase can produce many molecules of cAMP, this is another example of amplification in signal transduction. To terminate the signal, a different enzyme, cAMP phosphodiesterase, hydrolyzes a bond between the phosphate and the ribose sugar on cAMP to form AMP.

Section 17.3 Types of Receptors

Now that we have explored different signaling mechanisms inside the cell, let’s turn our attention to different types of receptors. Some receptors are found inside cells, but most are in the plasma membrane.

Intracellular Steroid Hormone Receptors

Intracellular receptors such as steroid hormone receptors are found either in the cytosol or in the nucleus of cells. These receptors can interact with and respond to ligands released by other cells because the ligands are overall nonpolar and easily cross cell membranes. Steroid hormone receptors are activated by interacting with steroid hormones like testosterone or estrogen, and the activated receptor itself causes the cellular response, so no signal transduction proteins are needed.

Figure 17.9 shows a model of the estrogen signaling pathway, in which estrogen binds to its receptor located in the nucleus. Once the estrogen receptor binds estrogen, a dimer of two estrogen-estrogen receptor complexes binds to specific DNA sequences. The complex bound to DNA then recruits RNA polymerase to carry out transcription, so the cellular response is gene expression. In this pathway, the estrogen-estrogen receptor complex acts as a positive transcription factor (for a refresher on transcription factors, refer to Chapter 4: Gene expression I).

Ligand-gated Ion Channels

Figure 17.10 shows another simple cell signaling mechanism, the ligand-gated ion channel, which is in the plasma membrane of cells. The presence of a specific ligand activates the receptor, which opens a channel and allows specific ions to flow down their concentration gradients across the membrane. Many neurotransmitters, which are chemical signals used for communication between cells of the nervous system, are ligands for these types of ion channels. Note that in the case of the ion channel and other cell-surface receptors, the ligand remains outside of the cell, yet causes a cellular response inside the cell, due to changes in the receptor shape caused by ligand binding.

G Protein-Coupled Receptors

One of the largest families of receptors, responsible for most of our senses, regulation of body functions, and the mediator of the fight-or-flight response, is another type of cell-surface receptor called G protein-coupled receptor (GPCR). GPCRs get their name because each receptor ls associated with a G protein (Figure 17.11). This type of G protein has three parts, or subunits, named alpha (α), beta (β), and gamma (γ). The α subunit is the portion that binds to GDP or GTP.

When the ligand is absent, the GPCR and its associated G protein are also inactive (Figure 17.11a). The ligand binding activates the receptor, and the new shape of the receptor allows it to act as a GEF, causing GDP to GTP exchange to activate the G protein (Figure 17.11b). When active, the G protein subunits separate into α and β/γ components to cause further signal transduction. In some cases, the α subunit separates from the GCPR to form a protein-protein interaction with adenylyl cyclase, activating the production of the second messenger cAMP (Figure 17.11c). Going one step further, a molecule of cAMP interacts with and activates a specific kinase called Protein Kinase A, which in turn can phosphorylate many protein targets to generate the cellular response.

Comparing the GCPR pathway to the two receptor pathways discussed previously, you may be wondering why there are so many different proteins and steps in these pathways. While having many steps adds to the complexity, this provides opportunities for cells to amplify signals to ensure a robust cellular response. For example, after the active G protein separates from the receptor, new G proteins can associate with and be activated by the receptor, and in turn activate more adenylyl cyclase enzymes. The production of cAMP and the phosphorylation reactions carried out by Protein Kinase A are additional points of signal amplification, since many cAMP molecules are produced by one active adenylyl cyclase enzyme, and multiple phosphorylated proteins are produced by each active Protein Kinase A.

Receptor Kinases

The last type of receptor we will discuss is the receptor kinase family of receptors, also known as receptor tyrosine kinases or RTKs. These receptors regulate gene expression and cell division, and are particularly important in embryonic development and in the formation of cancer. When no ligand is present, these receptors are found as monomers in the plasma membrane, not interacting with any other proteins (Figure 17.12a). When ligand is present, two receptor monomers are brought together to form a dimer that is now activated (Figure 17.12b). One part of the receptor that is inside the cell is a kinase enzyme that transfers phosphates from several ATP molecules to other intracellular parts of both receptors in the dimer. The phosphorylated receptor (Figure 17.12c) is now fully activated and can cause further signal transduction for the cellular response, which often involves changes in gene expression. The next section will describe examples of the signal transduction that follows activation of receptor kinases.

While we have discussed each of these types of receptors individually, cells typically have many different types of receptors to respond to many different types of signals (Figure 17.13).  Each type of receptor typically activates distinct sets of proteins, but there can be overlap among these pathways. Additionally, we can see that pathways converge on key cellular responses, such as apoptosis (programmed cell death), gene expression, and proliferation (cell division), indicating how extracellular signals influence key cellular behaviors.

Section 17.4 Model for the In-class Activity

The major theme for unit 3 is cancer, which is the uncontrolled division of cells. In most eukaryotic cells, but especially in multicellular eukaryotes like us, the process of cell division is tightly regulated. Normally, cell division only occurs in response to specific signals, called growth factors, that are sent from other cells. Growth factors are small proteins that bind to and activate receptors of the receptor kinase family. Later chapters will introduce more of the biology of cancer, and to prepare for the foundation for understanding the changes that lead to cancer, we will study a receptor kinase pathway in more depth.

Figure 17.14 shows the key proteins in the absence (left side) or presence (right side) of growth factor ligand. Other than the growth factor ligand, notice that all proteins are present in both scenarios. What is different is their status – all inactive when ligand is absent, and active when ligand is present. As we go through the figure, please note all changes that occur as you consider how you would explain to someone else what is happening and why those things happen. In this representation, key steps are indicated with numbers and marked in the order in which they occur. Solid arrows indicate activations–one protein or step activating the next protein or step—and dashed arrows indicate molecule movements. Steps 2, 6, and 8 are phosphorylation reactions, but the model does not show the details of what is actually happening. Review Figure 17.6, and for each of these reactions, determine which protein is the active kinase, which protein is the target, and the role of ATP, and draw out the full chemical reaction to show what is happening at each of these steps.

When ligand is present, this causes the first change—receptor kinase monomers form a dimer and phosphorylate each other. The phosphorylated receptor has different properties due to the phosphates that are now bound, which allows for new interactions with several small scaffolding proteins that we have combined in this representation as adaptor. After interacting with and being activated by the active receptor, the adaptor interacts with Ras, a G protein. Remember, you can identify G proteins because they are always bound to either GDP or GTP. Importantly, Ras is a single subunit, so it is a different type of G protein than the G protein observed in the GPCR pathway.

In its active shape bound to the phosphorylated receptor, the adaptor acts as a GEF for Ras, causing the GDP-to-GTP exchange, which converts Ras into its active form. Active Ras G protein continues the signal transduction by interacting with a protein called MapKK. What kind of protein is MapKK? Well, in Figure 17.14, we can see that MapKK activates MapK (indicated by the arrow marked #6), and that active MapK now has a phosphate. We know that enzymes that add phosphates to proteins are kinases, so MapKK is a kinase (review 17.6 for the the full reaction). In fact, “MapK” stands for mitogen-activated protein kinase, a protein that is commonly activated in several types of signaling pathways including those involved in causing cell division. Thus, MapKK is the kinase for the MapK, which is also a kinase. Once activated, MapK has a different shape that allows it to move into the nucleus and phosphorylate pos TF (positive transcription factor), which causes pos TF to bind to DNA and recruit RNA polymerase to cause gene expression.

Just as in the GPCR pathway, there are ample opportunities for signal amplification in the receptor kinase pathway: active adaptor can activate multiple Ras G proteins, active MapKK can activate many MapK proteins, and active MapK can activate many pos TF proteins. Thus, a small amount of ligand can lead to a strong change in gene expression and potentially cause the cell to divide.

Because activation of receptor kinases could result in cell division, signaling steps that are not correctly terminated could lead to excessive or inappropriate cell division. While not shown in Figure 17.14, there are GTPase activating proteins (GAPs) to inactivate Ras, and phosphatases that remove the phosphates that were added by kinases. These steps are crucial so that signaling for cell division is correctly coordinated among cells. With this knowledge, you might anticipate (correctly!) that some forms of cancer are linked to specific mutations that disrupt signal termination in this pathway.

To help prepare you to think through the implications of specific mutations in this pathway, consider what would happen if the ligand were no longer present, yet a mutation causes one of the termination steps to not occur. Thus, a protein that should have been inactivated now remains active in the absence of ligand, and in turn continues to activate the next steps of the pathway. Based on our model, this would lead to the cellular response of gene expression. The cell with the mutation would have more gene expression than a typical cell without the mutation.