BIOMG Lecture 15 - Cell Signaling Part 1

How many protein coding genes are in humans are devoted to cell signaling?

• Over 7,000 out of the around 21,000 protein coding genes in humans are devoted to cell signaling.

• Around ⅓ of genes in the human genome are dedicated to signaling!

When Do Signaling Pathways Begin?

• Signaling pathways begin when a signal binds to a receptor and triggers an intracellular signaling pathway that ends with effector proteins, which carry out the ultimate response(s) to the signal.

Upstream vs Downstream

• Upstream = earlier steps of the pathway

• Downstream = later steps of the pathway

Basic Pathway for External Cell Signals

Signaling cell(s) sends out a signaling molecule (ligand) which eventually binds to a receptor which is in or on the cell and this triggers an intracellular signaling pathway which passes on the signal to the effector which eventually produces the response in the target cell.

Effector Protein

• Effector protein is the protein that actually triggers the response from the signal rather than just passing the signal onto another protein in the intracellular signaling pathway.

• A protein that responds to a signal from another molecule, such as a receptor or signaling protein, to produce a specific cellular response. Effector proteins often function as enzymes or ion channels that regulate cellular activities, such as metabolism, gene expression, or cell movement.

• One out of many effector proteins can be activated by the same signal molecule in a process known as signal distribution.

Types of Extracellular Signaling Molecules or Mechanisms

• Extracellular signaling molecules (ligands) are diverse.

  • Proteins, peptides, amino acids, nucleotides, steroids, fatty acid derivatives, gases

  • There are also other forms of extracellular signaling that are not molecules or ligands and those include light (pupil dilates in response to amount of light) and mechanosensory signals (mechanical signals such as with Venus flytraps) 

Long and Short Range Signals

Long Range Signals: Endocrine and synaptic signaling

Short Range Signals: Paracrine, Autocrine, and Contact Dependent (Juxtacrine) signaling

Endocrine Signaling (Long Range)

• Endocrine Signaling is one form of long range signaling where ligands travel a long distance, usually through the bloodstream, to reach the target cell

  • Hormones, including epinephrine, insulin, estrogen, testosterone, and cortisol travel through the body via the bloodstream.

Synaptic Signaling (Long Range)

• Synaptic Signaling occurs specifically in neurons and involves the release of neurotransmitters in response to an electrical signal and this is another form of long range signaling

  • The axon of a neuron can be far away from the neuronal cell body. The axon terminates at specialized junctions called synapse.

  • Once activated, the neuron sends electrical impulses along the axon, leading to the release of neurotransmitters (signals) at the nerve terminal.

Paracrine Signaling (Short Range)

• Paracrine Signaling is an example of short range signaling. Almost like endocrine signaling but over a shorter range with the target cells being relatively near the signaling cell. 

  • A cell secretes a signal into the extracellular environment, which can be received by tis neighbors.

  • Paracrine signals are also known as local mediators and include histamine, nitric oxide, and growth factors.

Autocrine Signaling (Short Range)

• Autocrine Signaling is an example of short range signaling where a cell secretes its own signals that its own receptors bind with to produce a cellular response.

Contact Dependent (Juxtacrine) Signaling (Short Range)

• Contact Dependent Signaling (juxtacrine) is another example of short range signaling that occurs just between two or more cells but requires surface contact of a receptor in the target cell with the membrane bound signal molecule in the signaling cell.

  • A membrane bound signal binds to the membrane bound receptor in the adjacent cell.

Two Major Cellular Changes Caused by Signaling Pathways

Signals can either result in altered protein function or altered protein synthesis which is performed through changes in gene expression. Changes in protein synthesis from changes in gene expression require signals to enter the nucleus usually.

Altered protein function usually occurs in a shorter timespan than altered protein synthesis because altered protein synthesis requires change in gene expression.

Signal Speed

• Signals can act rapidly or slowly

• Fast cell reaction to signals can occur in a matter of seconds (or less than 1 second) to minutes.

• Slow cell reaction to signals can occur within a matter of minutes to hours.

• This is important since signal molecules activate intracellular signal pathways that depending on what the duties they perform lead to different forms of altered cytoplasmic machinery and thus altered cell behavior that sometimes must occur fast or slowly.

Fast Signal Speed

• Fast cell reaction to signals can occur in a matter of seconds (or less than 1 second) to minutes.

  • Fast responses to signaling occur when the pathway directly alters protein function within the cell. The proteins are already present in the cytoplasm, so switching them on or off can happen quickly and cause a near-immediate response.

Slow Signal Speed

• Slow cell reaction to signals can occur within a matter of minutes to hours.

  • Slow responses to signaling occur when the pathway directs changes in gene expression. Since this requires several steps of the central dogma to occur (transcription of the gene, processing of the mRNA, export of the mRNA from the nucleus, translating the protein, processing the protein, etc) there is a delay before there is a mature protein available to carry out the response to the original signal.

• This is important since signal molecules activate intracellular signal pathways that depending on what the duties they perform lead to different forms of altered cytoplasmic machinery and thus altered cell behavior that sometimes must occur fast or slowly.

Signal Response Changes or Differences

• The same signal can induce different responses in different target cells depending on the type of receptor available and the components of the intracellular signaling pathway.

• For example, acetylcholine ligand (signal molecule) has very different effects depending on the cells it interacts with.

• Acetylcholine can produce different effects in different cells with the same receptor or cells with different cells with different receptors for the same signaling ligand.

• When binding to a heart pacemaker cell acetylcholine produces a decreased rate of firing (decreased heart rate) but when binding to the same receptor in a salivary gland cell, acetylcholine causes the cell to undergo secretion.

• When binding to a separate receptor (not a heart pacemaker or salivary gland cell) such as a skeletal muscle cell, acetylcholine can cause contraction.

• The heart and salivary gland cells use the same receptor but respond differently, while skeletal muscle uses a different receptor.

• Information conveyed by the signal depends on how the target cells receives and interprets the signal (their developmental history and current state).

Summary of Signals

• Signals can be of different types.

  • Small or large molecules, light, mechanosensation, etc.

• Signals can act over a long or short range.

  • Endocrine, paracrine (autocrine), synaptic, contact dependent.

• Signals can act rapidly or slowly

  • Changes of protein function or gene expression.

• The same signal can induce different response.

  • Depending on the history and status of the target cell.

Signal Receptor Binding

• The signaling cell sends out signaling molecules (ligands) which bind to the receptors on the target cells.

• Receptors can be intracellular or on the cell surface.

• Steroid hormones regulate transcription too. They are small hydrophobic molecules that can pass through the plasma membrane.

• Cell surface receptors are membrane-bound and receive signals on the extracellular side of the plasma membrane.

• Intracellular receptors exist in the cytoplasm of the cell and receive signals that are able to diffuse through the plasma membrane (small, hydrophobic molecules).

Intracellular vs Cell Surface Receptors

• Intracellular Receptors:

  • Small hydrophobic signal molecules or steroid molecules can pass the lipid bilayer and bind to an intracellular receptor within the nucleus.

  • Intracellular receptors exist in the cytoplasm of the cell and receive signals that are able to diffuse through the plasma membrane (small, hydrophobic molecules).

• Cell Surface Receptors:

  • Larger, polar, or charged extracellular signal molecules must bind to cell surface receptor proteins and then those receptor proteins on the surface then send signals to intracellular signaling molecules. Thus, the signal molecule never needs to enter the cell.

  • Cell surface receptors are membrane-bound and receive signals on the extracellular side of the plasma membrane.

Steroid Hormone Signal Receptor Binding

• Steroid hormones regulate transcription too. They are small hydrophobic molecules that can pass through the plasma membrane.

  • Steroid hormones like cortisol can bind to nuclear receptor proteins (nuclear hormone receptors) inside of the cytoplasm. This binding of cortisol to the nuclear receptor protein causes a conformational change that activates the receptor protein.

  • The activated receptor-cortisol complex moves into the nucleus. Finally, the activated receptor cortisol complex binds to regulatory regions of the target gene and activates transcription.

  • Each hormone binds to a different receptor and each receptor acts at different sites in DNA. A given hormone usually regulates (activates or represses) different sets of genes in different cell types.

3 Different Parts of Signal Transduction Pathways

• Signal transduction pathways and responses involve 3 distinct parts.

  • Intracellular signaling pathways involve relaying, amplifying, integrating, and distributing signals from receptors.

  • Effectors produce alterations of gene expression, metabolism, cell cytoskeleton (shape or movement), etc.

  • Responses from signals may include cell division, growth, survival, migration, secretion, contraction, differentiation, apoptosis (programmed cell death), and activation or repression of the expression of particular genes, etc.

Signal Transduction

Signal transduction is the process of translating an extracellular signal into intracellular effectors that alter cell behavior. 

Since the extracellular signal can only bind to a receptor and cannot pass through the cell membrane it must be converted by the receptor into an intracellular signal that can be passed to relay/adaptor proteins.

Processes, Steps, or Functions of the Intracellular Signaling Pathway

• Intracellular signaling pathway contains multiple processes and functions.

  • After primary transduction, that signal can transform or be passed to other proteins in many different ways.

  • Primary transduction: The first step of signal transduction, in which an extracellular signal molecule binds its receptor and the receptor passes the signal across the plasma membrane into the cell. It happens before any relay, amplification, integration, or distribution of the signal.

  • The intracellular signaling pathway can relay the signal, can transduce (convert one signal to another) and amplify signals (2nd messenger), can integrate separate signals, can engage in either negative or positive feedback with earlier steps of the signaling pathway, and can distribute signals to different effectors for different responses.

Second Messengers

Second messengers are smaller molecules or ions that can be produced in large quantities which quickly amplify and spread a signal.

Types of Intracellular Signaling Molecules

• Intracellular signaling molecules include: proteases, lipids, 2nd messengers, lipids, other enzymes, kinases, phosphatases, GTP binding proteins, and adaptors.

• Many key intracellular signaling proteins act as molecular switches such as kinases and phosphatases which phosphorylate and dephosphorylate either to turn proteins on or off or GTPases (Ras, Ran, Rab, etc.) which can be turned on via GEF and turned off via GAP.

• For example, a signal could activate these proteins allowing them to transmit that signal further before becoming inactivated by a protein which turns them off preventing constant signaling (negative feedback).

Feedback regulation within Intracellular Signaling Pathways

• Feedback regulation within an intracellular signaling pathway can adjust the cell's response to a signal.

  • All or none responses are an example of positive feedback. A signal produces a response and that response gets amplified over time as there is positive feedback toward proteins that initially produce that response.

  • Responses that oscillate on and off are usually examples of negative feedback. A signal produces a response and that response decreases or disappears over time as there is negative feedback toward the proteins that initially produce that response.

  • Some key nomenclature in biological pathways: pointed arrows indicate activation, blunt ended lines indicate repression/inactivation.

  • Downstream components of the pathway will signal to upstream components to provide “feedback” on whether the pathway should continue signaling (positive feedback), or shut off (negative feedback). Regulation of the pathway, including feedback, is often carried out by molecular switches (proteins that can switch on or off).

Signal Integration

• Different ligands binding to different receptors on the cell's surfacer can produce different signaling pathways that each target the same protein, this protein integrates signals from multiple signal molecules on separate receptors to produce a singular cell response.

• For example signal A and signal D can both activate separate kinases (kinase 1 and kinase 2) which add 1 phosphate group each to the target protein, and only with both phosphate groups can the target protein produce a target response.

• Kind of the opposite of distribution as multiple inputs are funneled into one output.

Signal Distribution

• Distribution is when a signaling protein passes the signal onto several different targets at once, so a single signal can change multiple cell processes in parallel. Kind of the opposite of integration as one input is funneled into multiple outputs.

Diverse Responses from Multiple Signals Acting Upon a Cell

• Animal cells integrate and distribute multiple signals to produce diverse responses.

  • No signals usually result in apoptosis (programmed cell death)

  • Specific cell signal combinations result in cell survival.

  • Other cell signal combinations result in the cell to grow and divide.

  • Other cell signal combinations result in cell differentiation.

  • These are just some examples.

Extracellular Signaling

• Regulation of cell signaling also occurs outside of the cell.

• Extracellular signal molecules (ligands) can be regulated in four different ways. Namely by inactive to active precursor signaling molecules or signal proteins, extracellular enzymes degrading signals, signals being sequestered by the ECM, or signals being blocked from binding to their receptors by other ligands.

• Receptors can be regulated in three different ways. Namely they can be added or removed, they can be destroyed, and they can be turned on and off.

Regulation of Extracellular Signaling MOlecules

• Extracellular signal molecules (ligands) can be regulated in four different ways.

  • An inactive precursor to the signal protein can be cleaved to remove the inhibiting part allowing the protein active signal to bind to a cell surface receptor.

  • Extracellular enzymes can break the signal down into fragments ensuring it cannot initiate a signal transduction pathway.

  • Some extracellular signals can be sequestered or held by proteins and sugars in the extracellular matrix (the cage) prevented from binding to a receptor.

  • Some extracellular signals can be blocked from their receptors in a process similar to competitive inhibition where a similar molecule is bound instead.

Regulation of Extracellular Signaling Molecule Receptors

• Receptors can be regulated in three different ways.

  • Receptors can be added to or removed from the membrane in the process of endocytosis of vesicles via vesicle coat proteins and adaptor proteins. 

  • Receptors can be destroyed if they are sent to the lysosome for degradation also preventing them from functioning.

  • Receptors can also be turned on and off by the addition or removal of a phosphate group (phosphorylation). This changes whether a bound receptor actually sends out a signal.

Extracellular Signaling Example (Lefty and Nodal)

• Correct organization of the internal organs across the left right body axis depends on both positive and negative feedback.

• Negative feedback of nodal by lefty ensures that the right side doesn't receive any of the "this is left" signal.

• Positive feedback of nodal to itself ensures lots of the "this is left" signal is present on the left side.

• Nodal is a secreted protein that signals "this is the left side." It plays a crucial role in the developing embryo especially during organogenesis.

• Nodal and Lefty Protein Examples of Extracellular Signal Control

  • When the nodal signal is bound it induces an intracellular signaling pathway to an effector that acts in the nucleus to transcribe gene L. This transcription causes the gene expression of "left sided" genes.

  • When lefty is present, it blocks nodal signal from binding which prevents the transcription of gene L and thus "left sided" genes are not expressed.

Effects of a lose it experiment for lefty expression?

• There is no negative feedback of nodal by lefty to ensure that the right doesn’t receive any "this is left" signal.

• Since the right starts to receive a "this is left" signal in coordinate with the left receiving the same signal, both the left and right express the left organ signal.

• This results in left isomerism or two left sides which is often fatal for the developing organism.

Ways or Different Pathways Cell to Cell Communication in Animal Development is Mediated

• Cell to cell communication in animal development is mediated by only a small number of conserved signaling pathways, some of which are listed below.

  • Transforming growth factor B (TGFB), Fibroblast growth factor (FGF), Wnt, Hedgehog (Hh), Notch, Receptor tyrosine kinase (RTKs).

  • Yet despite the relatively small number of signaling pathways there is enormous diversity in animals.