Cell Signaling and Signal Transduction - Handout 14

In these cascades of relay, second messengers, and kinase reactions, the number of molecules activated is actually multiplied at each step. The binding of one signal to one receptor can activate 10 effector molecules, each of which activates 100 kinases. This is rapid amplification, not just a chain reaction.

Amplification in terms of signal transduction pathways.

The amplified cascade is limited and often brief, controlled by enzymes that inactivate.

Control in terms of signal transduction pathways.

Signal can move from receptor to other parts of the cell including turning on genes.

Dispersion in terms of signal transduction pathways.

A particular signal molecule binds only to specific receptor proteins.

Explain Specificity in terms of signal transduction pathways.

One very important second messenger is cyclic AMP (cAMP). When a hormone binds to its membrane receptor, a G-protein that is associated with the receptor is activated; G-proteins are proteins separate from receptors that are found in the cell membrane. When a hormone is not bound to the receptor, the G-protein is inactive and is bound to guanosine diphosphate, or GDP. When a hormone binds to the receptor, the G-protein is activated by binding guanosine triphosphate, or GTP, in place of GDP. After binding, GTP is hydrolysed by the G-protein into GDP and becomes inactive. The activated G-protein in turn activates a membrane-bound enzyme called adenylyl cyclase. Adenylyl cyclase catalyzes the conversion of ATP to cAMP. cAMP, in turn, activates a group of proteins called protein kinases, which transfer a phosphate group from ATP to a substrate molecule in a process called phosphorylation. The phosphorylation of a substrate molecule changes its structural orientation, thereby activating it. These activated molecules can then mediate changes in cellular processes. The effect of a hormone is amplified as the signaling pathway progresses. The binding of a hormone at a single receptor causes the activation of many G-proteins, which activates adenylyl cyclase. Each molecule of adenylyl cyclase then triggers the formation of many molecules of cAMP. Further amplification occurs as protein kinases, once activated by cAMP, can catalyze many reactions. In this way, a small amount of hormone can trigger the formation of a large amount of cellular product. To stop hormone activity, cAMP is deactivated by the cytoplasmic enzyme phosphodiesterase, or PDE. PDE is always present in the cell and breaks down cAMP to control hormone activity, preventing overproduction of cellular products

Give two examples, one with phosphatases and one with cAMP deactivation to tell how cells achieve "control" over their signal transduction responses.

The cyclic AMP (cAMP) initiates a response in two different types of enzymes. The cAMP phosphorylates (adds phosphate through hydrolysis to a protein) these two enzymes. The addition of phosphate causes one enzyme to increase its production while the addition of phosphate causes the the other enzyme to halt its work.

How could the same type of signal, like epinephrine, trigger different responses in different cells?

In order to detect a signal (that is, to be a target cell), a neighbor cell must have the right receptor for that signal.

In order to respond to a specific signal, a cell must have what?

Ligand (chemical messenger) attaches → Receptor (either on cell surface or for INTERcellular transduction or within the cell for INTRAcellular transduction)→ Receptor reacts to the ligand in some way (i.e. changing its shape to open an ion channel or initiating phosphorylation) → Secondary messengers are then initiated by the receptor protein's change causing a chain reaction which can lead to some sort of cellular response. Receptors and ligands come in many forms, but they all have one thing in common: they come in closely matched pairs, with a receptor recognizing just one (or a few) specific ligands, and a ligand binding to just one (or a few) target receptors. This specificity ensures that when receptors and ligands bind, they will initiate a certain response.

List the components of signal transduction pathways, and tell how they interact to produce specificity and diversity of cell responses.

A signal molecule outside the cell (the "first messenger") binds to a membrane receptor, affects a relay system and effector molecules, triggers activation of secondary messengers and cascades of chemical reactions inside the cell.

Signal transduction

Intracellular receptors are receptor proteins found on the inside of the cell, typically in the cytoplasm or nucleus. In most cases, the ligands of intracellular receptors are small, hydrophobic (water-hating) molecules, since they must be able to cross the plasma membrane in order to reach their receptors. For example, the primary receptors for hydrophobic steroid hormones, such as the sex hormones estradiol (an estrogen) and testosterone, are intracellular. When a hormone enters a cell and binds to its receptor, it causes the receptor to change shape, allowing the receptor-hormone complex to enter the nucleus (if it wasn't there already) and regulate gene activity. Hormone binding exposes regions of the receptor that have DNA-binding activity, meaning they can attach to specific sequences of DNA. These sequences are found next to certain genes in the DNA of the cell, and when the receptor binds next to these genes, it alters their level of transcription. Many signaling pathways, involving both intracellular and cell surface receptors, cause changes in the transcription of genes. However, intracellular receptors are unique because they cause these changes very directly, binding to the DNA and altering transcription themselves.

Tell how signal transduction pathways can cause activation and changes in protein conformation leading to changes in gene expression

Adrenaline, also known as epinephrine, is a hormone (produced by the adrenal gland) that readies the body for short-term emergencies. When epinephrine binds to its receptor on a muscle cell (a type of G protein-coupled receptor), it triggers a signal transduction cascade involving production of the second messenger molecule cyclic AMP (cAMP). This cascade leads to phosphorylation of two metabolic enzymes— that is, addition of a phosphate group, causing a change in the enzymes' behavior. The first enzyme is glycogen phosphorylase (GP). The job of this enzyme is to break down glycogen into glucose. Glycogen is a storage form of glucose, and when energy is needed, glycogen must be broken down. Phosphorylation activates glycogen phosphorylase, causing lots of glucose to be released. The second enzyme that gets phosphorylated is glycogen synthase (GS). This enzyme is involving in building up glycogen, and phosphorylation inhibits its activity. This ensures that no new glycogen molecules are built when the current need is for glycogen to be broken down. Through regulation of these enzymes, a muscle cell rapidly gets a large, ready pool of glucose moelcuels. The glucose is available for use by the muscle cell in response to a sudden surge of adrenaline—the "fight or flight" response.

Using an example, like epinephrine, tell how the binding of one signal molecule could activate several types of responses in a cell (e.g., open ion channels, activate cytosol enzyme, turn on gene)

Different combinations of specific receptor subunits, relay systems, second messengers and kinases, can produce a huge variety of different specific cell responses.

Diversity in terms of signal transduction pathways.

•Specificity •Diversity •Dispersion •Amplification •Control

What are features of signal transduction pathways?

A general term for signaling molecules that bind specifically to other molecules (such as receptors).

What are ligands?

Receptors come in many types, but they can be divided into two categories: intracellular receptors, which are found inside of the cell (in the cytoplasm or nucleus), and cell surface receptors, which are found in the plasma membrane.

What are the two categories of ligand (chemical messenger) receptors of cells?

When a cell is damaged, unneeded, or potentially dangerous to an organism, it may undergo programmed cell death, or apoptosis. Apoptosis allows a cell to die in a controlled manner that prevents the release of potentially damaging molecules from inside the cell. Cells that undergo apoptosis go through a different and much more orderly process. They shrink and develop bubble-like protrusions (technical name: "blebs") on their surface. The DNA in the nucleus gets chopped up into small pieces, and some organelles of the cell, such as the endoplasmic reticulum, break down into fragments. In the end, the entire cell splits up into small chunks, each neatly enclosed in a package of membrane. What happens to the chunks? They release signals that attract debris-eating (phagocytic) immune cells, such as macrophages. Also, the fragments of the dying cell display a lipid molecule called phosphatidylserine on their surface. Phosphatidylserine is usually hidden on the inside of the membrane, and when it is on the outside, it lets the phagocytes bind and "eat" the cell fragments. Apoptosis removes cells during development. It also eliminates pre-cancerous and virus-infected cells, although "successful" cancer cells manage to escape apoptosis so they can continue dividing. Apoptosis maintains the balance of cells in the human body and is particularly important in the immune system.

What happens to cells in apoptosis? When is this "programmed cell suicide" advantageous?

Gap junctions in animals and plasmodesmata in plants are tiny channels that directly connect neighboring cells. These water-filled channels allow small signaling molecules, called intracellular mediators, to diffuse between the two cells. Small molecules, such as calcium ions Ca​2+, are able to move between cells, but large molecules like proteins and DNA cannot fit through the channels without special assistance. The transfer of signaling molecules transmits the current state of one cell to its neighbor. This allows a group of cells to coordinate their response to a signal that only one of them may have received. In plants, there are plasmodesmata between almost all cells, making the entire plant into one giant network.

What is the common function of gap junctions and plasmodesmata? How do they differ?

A phosphatase is an enzyme that removes a phosphate group from its substrate by hydrolysing phosphoric acid monoesters into a phosphate ion and a molecule with a free hydroxyl group.

What reaction does protein phosphatase catalyze?

•An external signal molecule binds a membrane receptor protein, changing its conformation. •This change in the receptor protein affects membrane relay and effector proteins that immediately activates second messengers. (eg, G protein relay system) •Second messengers are small, non-protein molecules such as cyclic AMP and Ca++ ions. Second messengers are released in the cytoplasm. • Protein kinases (enzymes that phosphorylate proteins, using ATP) activate other kinases. • A cascade of phosphorylation steps activates many processes and reactions in the cell at once. • In many systems, certain activated proteins enter the nucleus and regulate gene transcription.

Basic essential steps of signal transduction pathways

Cyclic adenosine monophosphate (cyclic AMP or cAMP), a small molecule made from ATP. In response to signals, an enzyme called adenylyl cyclase converts ATP into cAMP, removing two phosphates and linking the remaining phosphate to the sugar in a ring shape. Once formed cAMP works as a secondary messenger that can activate an enzyme called protein kinase A (PKA), enabling it to phosphorylate its targets and pass along the signal. cAMP signaling is turned off by enzymes called phosphodiesterases, which break the ring of cAMP and turn it into adenosine monophosphate (AMP).

Cyclic AMP is formed from what and serves as what in signal transduction?

One of the most common tricks for altering protein activity is the addition of a phosphate group to one or more sites on the protein, a process called phosphorylation. Phosphate groups can't be attached to just any part of a protein. Instead, they are typically linked to one of the three amino acids that have hydroxyl (-OH) groups in their side chains: tyrosine, threonine, and serine. Adding a phosphate group attaches a big cluster of negative charge to the surface of the protein. This negative charge may attract or repel amino acids within the protein itself, changing its shape. Because a protein's function depends on its structure, changing the shape of the protein may alter its ability to work as an enzyme, either increasing or decreasing activity. Alternatively, phosphorylation may provide a docking site for an interaction partner (say, one with a bunch of positive charges), or prevent another partner from binding. In general, phosphorylation isn't permanent. To flip proteins back into their non-phosphorylated state, cells have enzymes called phosphatases, which remove a phosphate group from their targets. The transfer of the phosphate group is catalyzed by an enzyme called a kinase, and cells contain many different kinases that phosphorylate different targets.

Describe the chemical processes of protein phosphorylation and de-phosphorylation. What kind of reaction does a protein kinase enzyme catalyze

One unique example of paracrine signaling is synaptic signaling, in which nerve cells transmit signals. This process is named for the synapse, the junction between two nerve cells where signal transmission occurs. When the sending neuron fires, an electrical impulse moves rapidly through the cell, traveling down a long, fiber-like extension called an axon. When the impulse reaches the synapse, it triggers the release of ligands called neurotransmitters, which quickly cross the small gap between the nerve cells. When the neurotransmitters arrive at the receiving cell, they bind to receptors and cause a chemical change inside of the cell (often, opening ion channels and changing the electrical potential across the membrane). The neurotransmitters that are released into the chemical synapse are quickly degraded or taken back up by the sending cell. This "resets" the system so they synapse is prepared to respond quickly to the next signal.

Describe the sequence of events at a chemical synapse that allows a signal to be transmitted from a pre-synaptic cell to a post-synaptic cell

Cells typically communicate using chemical signals. These chemical signals, which are proteins or other molecules produced by a sending cell, are often secreted from the cell and released into the extracellular space. There, they can float - like messages in a bottle - over to neighboring cells. Not all cells can "hear" a particular chemical message. In order to detect a signal (that is, to be a target cell), a neighbor cell must have the right receptor for that signal. When a signaling molecule binds to its receptor, it alters the shape or activity of the receptor, triggering a change inside of the cell. Signaling molecules are often called ligands, a general term for molecules that bind specifically to other molecules (such as receptors). The message carried by a ligand is often relayed through a chain of chemical messengers inside the cell. Ultimately, it leads to a change in the cell, such as alteration in the activity of a gene or even the induction of a whole process, such as cell division. Thus, the original intercellular (between-cells) signal is converted into an intracellular (within-cell) signal that triggers a response. Cell-cell signaling involves the transmission of a signal from a sending cell to a receiving cell. However, not all sending and receiving cells are next-door neighbors, nor do all cell pairs exchange signals in the same way. There are four basic categories of chemical signaling found in multicellular organisms: paracrine signaling, autocrine signaling, endocrine signaling, and signaling by direct contact. The main difference between the different categories of signaling is the distance that the signal travels through the organism to reach the target cell.

Explain different ways cells communicate with each other, contrasting target cell receptors according to their location in the cell (plasma membrane or intracellular) and their function.

•Intercellular is a signal between cells. Cell-surface receptors are membrane-anchored proteins that bind to ligands on the outside surface of the cell. In this type of signaling, the ligand does not need to cross the plasma membrane. So, many different kinds of molecules (including large, hydrophilic or "water-loving" ones) may act as ligands. A typical cell-surface receptor has three different domains, or protein regions: a extracellular ("outside of cell") ligand-binding domain, a hydrophobic domain extending through the membrane, and an intracellular ("inside of cell") domain, which often transmits a signal. The size and structure of these regions can vary a lot depending on the type of receptor, and the hydrophobic region may consist of multiple stretches of amino acids that criss-cross the membrane. •Intracellular is a signal within a cell. In most cases, the ligands of intracellular receptors are small, hydrophobic (water-hating) molecules, since they must be able to cross the plasma membrane in order to reach their receptors. For example, the primary receptors for hydrophobic steroid hormones, such as the sex hormones estradiol (an estrogen) and testosterone, are intracellular.When a hormone enters a cell and binds to its receptor, it causes the receptor to change shape, allowing the receptor-hormone complex to enter the nucleus (if it wasn't there already) and regulate gene activity. Hormone binding exposes regions of the receptor that have DNA-binding activity, meaning they can attach to specific sequences of DNA. These sequences are found next to certain genes in the DNA of the cell, and when the receptor binds next to these genes, it alters their level of transcription.

Intercellular signal vs intracellular signal.

When a ligand binds to a cell-surface receptor, the receptor's intracellular domain (part inside the cell) changes in some way. Generally, it takes on a new shape, which may make it active as an enzyme or let it bind other molecules. The change in the receptor sets off a series of signaling events. For instance, the receptor may turn on another signaling molecule inside of the cell, which in turn activates its own target. This chain reaction can eventually lead to a change in the cell's behavior or characteristics. The molecules that relay a signal are often proteins. However, non-protein molecules like ions and phospholipids can also play important roles. Proteins can be activated or inactivated in a variety of ways. However, one of the most common tricks for altering protein activity is the addition of a phosphate group to one or more sites on the protein, a process called phosphorylation. Phosphate groups can't be attached to just any part of a protein. Instead, they are typically linked to one of the three amino acids that have hydroxyl (-OH) groups in their side chains: tyrosine, threonine, and serine. The transfer of the phosphate group is catalyzed by an enzyme called a kinase, and cells contain many different kinases that phosphorylate different targets. Phosphorylation often acts as a switch, but its effects vary among proteins. Sometimes, phosphorylation will make a protein more active (for instance, increasing catalysis or letting it bind to a partner). In other cases, phosphorylation may inactivate the protein or cause it to be broken down.In general, phosphorylation isn't permanent. To flip proteins back into their non-phosphorylated state, cells have enzymes called phosphatases, which remove a phosphate group from their targets.

List the series of steps by which a signal molecule (the "first messenger") that stays outside the cell can lead to the activation (phosphorylation) of proteins inside the cell.

Many signaling pathways cause a cellular response that involves a change in gene expression. Gene expression is the process in which information from a gene is used by the cell to produce a functional product, typically a protein. It involves two major steps, transcription and translation. Transcription makes an RNA transcript (copy) of a gene's DNA sequence. Translation reads information from the RNA and uses it to make a protein. Signaling pathways can target either or both steps to alter the amount of a particular protein produced in a cell. We can use the growth factor signaling pathway as an example to see how signaling pathways alter transcription and translation. This growth factor pathway has many targets, which it activates through a signaling cascade that involves phosphorylation (addition of phosphate groups to molecules). Some of the pathway's targets are transcription factors, proteins that increase or decrease transcription of certain genes. In the case of growth factor signaling, the genes have effects that lead to cell growth and division. One transcription factor targeted by the pathway is c-Myc, a protein that can lead to cancer when it is too active ("too good" at promoting cell division). The growth factor pathway also affects gene expression at the level of translation. For instance, one of its targets is a translational regulator called MNK1. Active MNK1 increases the rate of mRNA translation, especially for certain mRNAs that fold back on themselves to make hairpin structures (which would normally block translation). Many key genes regulating cell division and survival have mRNAs that form hairpin structures, and MNK1 allows these genes to be expressed at high levels, driving growth and division. Notably, neither c-Myc nor MNK1 is a "final responder" in the growth factor pathway. Instead, these regulatory factors, and others like them, promote or repress the production of other proteins. that are more directly involved in carrying out cell growth and division. ​

Through what steps can a signal from outside the cell serve to activate a gene?