Cell Bio final Exam review- Cell Signaling

Extracellular signals

Signals, normally small molecules that bind to receptors, that control all aspects of cell behavior, such as, metabolism, movement, proliferation, differentiation, and survival

(Ex. the regulation of glycogen breakdown by the small molecule epinephrine/adrenaline)

Generally activate and finish within a short period of time (~15-20min)

Signals get sent from one cell to another (form of communication between cells) → one cell type talking to another cell type

The process of passing a signal involves many different molecules and changes, such as phosphorylation, proteins, break down of molecules, etc.

(Ex. regrowth of tissue during wound healing → blood platelets release PDGF at the site of a wound during blood clotting → regrowth of the damaged tissue)

Cellular responses elicited by these signals occurs through cell signaling cascades

Commonly called the first messenger

Epinephrine / adrenaline

A small molecule and hormone generated by the adrenal glands that binds to receptors to start a signaling pathway that produces ATP and glucose giving the body a “jolt” of energy

Normally binds to receptors on muscle cells

PDGF (Platelet derived growth factor)

An extracellular growth factor that stimulates the proliferation of fibroblasts

Helps with the process and signaling pathway involved in the regrowth of tissue during wound healing

Gets released by blood platelets at the site of a wound during blood clotting, allowing for the regrowth of damaged tissue

Platelet

A small portion of cell that has been “pinched” off of the main part of the cell

Doesn’t contain a nucleus, however it can still function and release molecules such as growth factors

Small enough so that it can squeeze into tight spaces such as blood vessels

Often the first “blood cells” released when you get a cut because they release growth factors that help with the wound healing process

Have the ability to communicate with other cells, such as fibroblasts

Release PDGF at the site of a wound during blood clotting allowing for the regrowth of damaged tissue

Fibroblasts

A type of cell that has that ability to secrete collagen and perform other functions that create clots, stopping bleeding, often when someone is cut

Often in communication with platelets during the signaling process of regrowth during wound healing

Cell signaling cascades

A process that produces cellular responses elicited by extracellular signals

Molecular mechanisms through which extracellular signals are detected by cells and converted into a response

There are 4 different “modes” of this cell-cell process

Pathways that happen within short periods of time → turn on and off quickly due to the presence of phosphatases

Second messenger

Signaling molecules that help in cell signaling pathways that are located inside of the cell

Small intracellular molecules that are altered (chemically or locally) in response to activation of a cell surface receptor (ex. ATP is altered into cAMP) → leading to a response

Its alteration further transduces a signal (ex. cAMP activates many enzymes, leading to a response)

Typically small molecules, such as calcium, cAMP, and acetylcholine

Signaling molecules

Molecules responsible for starting cell signaling cascades

Act as a means of communication between cells

Can be first or second messengers (extracellular or intracellular)

At least 12% of human genes encode for these molecules

The extracellular molecules that are sent by one cell, modulate the behavior of the target cells

Direct cell-cell signaling

One of the 4 different modes of cell-cell signaling in which both of the cells in communication are communicating directly through transmembrane proteins bound to the surface

The ligand and the receptor are both membrane bound, so the cells must be in relatively close contact to one another or touching each other allowing one cell to signal to the other cell

Ex. ephrins

Endocrine signaling

One of the 4 different modes of cell-cell signaling and one of the three types of signaling by secreted molecules in which a small molecule is generated in a cell somewhere in the body, enters the circulatory system, and then has an effect on a target cell in another part of the body

Ex. epinephrine/ adrenaline → a small signaling molecule is produced in the adrenal gland → enters the blood stream → exits the blood stream and effects muscle cells throughout the body

Paracrine signaling

One of the 4 different modes of cell-cell signaling and one of the three types of signaling by secreted molecules in which the two cells are relatively close, so the signaling molecule does not have to enter the bloodstream

Ex. a synapse in a neurotransmitter binds to a neurotransmitter receptor (close together)

Autocrine signaling

One of the 4 different modes of cell-cell signaling and one of the three types of signaling by secreted molecules in which the cell that secretes the signal molecule also acts as the target molecule

The signal molecules being released in this type of signaling are normally growth factors

Allows immune system cells to divide, expand, and make more antibodies

Commonly occurs in the immune system and in B cells

Structure of steroid hormones and cholesterol signal molecules

4 ring structure → allows for diffusion through membrane (the receptors for all of these signals are NOT at the cell surface, they are inside of the cell, so they must be able to diffuse through the membrane)

Short unsaturated (CH) portion

Some have transporters that allow them to move more efficiently across the membrane

Similarities and derivatives from cholesterol allow for easy diffusion through the membrane

smaller molecules can be packaged into vesicles

Nuclear receptors

A family of transcription factors bound to and regulated by steroid hormones, thyroid hormones, vitamin D3, and retinoic acid

Ultimately end up in the nucleus, regulating transcription

Bind ligands, activate transcription, and then bind to DNA

Contain domains for DNA binding, transcriptional activation, and ligand binding (specific receptors bind to specific ligands) → each of these different things are regulated by different hormones

Glucocorticoid receptor and glucocorticoid

A major signaling pathway example of a nuclear receptor and its specific ligand

This receptor is normally found in the cytosol when its inactive (isolated from the DNA in the nucleus) → when the specific ligand is present, it can diffuse through the membrane, bind to its receptor, cause dimerization of its receptor, and enter the nucleus → once in the nucleus, the specific receptor-ligand complex recruits a coactivator (HAT protein) and binds to the DNA, which allows for the activation and regulation of transcription of individual genes

One example of how hormones can regulate transcription

HAT protein

A coactivator protein recruited by the active glucocorticoid receptor-ligand complex

Acetylates histones, relaxes DNA, and makes it more likely likely for DNA to be transcribed

Thyroid hormone receptor

A major signaling pathway example of a nuclear receptor and its specific ligand

The receptor is always in the nucleus located at the DNA site → when not active, it associates with an HDAC

Binds DNA regulatory sequences within target genes independent of ligand binding → leads to gene regulation

In the absence of a hormone (ligand), the receptor interacts with corepressors (HDACs), causing transcription to be repressed

When the hormone (ligand) is present, the hormone can diffuse through the nuclear membrane and bind to the receptor → its binding induces a conformational change in the receptor, causing a release of corepressors and the interaction with coactivators, causing transcription to be activated

HDAC

A co-repressor protein complex that deacetylates DNA, keeping it condensed, and stopping it from being transcribed

Associates with the inactive version of the thyroid hormone receptor

Common small signaling molecules

nitric oxide, glutamate, acetylcholine, GABA, an auxin, cAMP

an auxin

The most common small signaling molecule in plants

Growth factors

Larger proteins that play key roles in regulating animal cell proliferation during embryonic development and in adult organisms

Can act as signaling molecules

The binding to the outside of a cell activates cell surface receptors, triggering a cascade of reactions inside of the cell

Can function as dimers

Ex. epidermal growth factor (EGF)

G Protein-Coupled Receptor (GPCR)

The largest family of receptor proteins with ~1000 members

Includes receptors for hormones, neurotransmitters, growth factors, and smell, sight, and taste receptors

Its structure includes a ligand-binding domain on the outside, allowing different signals to come in from the outside, carbohydrates on the outside, and a GEF domain inside of the cell

Has a 7 transmembrane structure

When a ligand binds to this receptor, a conformational change is caused in the transmembrane domain, allowing for the GEF domain to be activated, ultimately activating the receptor → allows for the start of a signaling pathway

(In some, less common, scenarios, when a ligand binds to this receptor it can also inhibit certain pathways)

Couples up with heterotrimeric G proteins

GEF

A G-protein complex that “bumps” off GDP from a G-protein, binding to GTP, and leading to activation of the G protein

Makes up part of the G protein-coupled receptor structure

G proteins

Proteins that were discovered during studies of hormones that induce cAMP synthesis and glycogen breakdown (ex. epinephrine/adrenaline pathway)

They require GTP for their hormonal activation of adenylyl cyclase, meaning they require GTP in order to activate the pathways that they were discovered to activate

Dependent on GTP

Also known as GTP-binding proteins

Acts as an intermediary in adenylyl cyclase activation

Couples up with G protein receptors

Activity of these proteins is regulated by GTP/GDP binding (GTP= active form → GDP= inactive form)

Many of these proteins connect receptors to distinct targets (many different specific signaling pathways with specific signals and specific receptors → ex. epinephrine/ glycogen metabolism pathway)

In addition to enzyme regulation, these proteins can also regulate ion channels (ex. action of the neurotransmitter acetylcholine on heart muscle) → they can either depolarize or hyperpolarize a membrane depending on the channel its opening

Heterotrimeric GTP-binding (G) proteins

The type of G proteins that bind to G protein-coupled receptors

Made up of 3 different G proteins

Made up of an alpha, beta, and gamma subunit

Only the alpha subunit of the protein actually binds GTP

Considered inactive when they are bound to GDP

Considered active when a ligand binds to a receptor, causing the GEF domain to bind GTP to the alpha subunit → alpha, beta, and gamma subunit dissociate from the receptor and the alpha subunit goes on to activate adenylyl cyclase (the beta and gamma subunits help with this as well, but they do not rely on GTP for this)

(HOWEVER → sometimes the binding of a ligand to GPCR can lead to inhibition of adenylyl cyclase)

There are ~21 different alpha, 6 different beta, and 12 different possible gamma subunits in humans → combinations of these subunits together respond differently depending on the receptor and ligand, and will have different targets (ex. some target adenylyl cyclase, and some do not)

Alpha subunit of heterotrimeric G proteins

One of the three subunits making up heterotrimeric G proteins that is the only subunit that actually binds GTP

Acts as a GTPase along with a GAP protein to hydrolyze GTP back to GDP and inactivate the heterotrimeric G protein back to its inactive form → works too slowly on its own, so the GAP protein helps to speed up the process

GS

G proteins that lead to the stimulation (activation) of adenylyl cyclase

GI

G proteins that lead to the inhibition or inactivation of adenylyl cyclase

GAP

Proteins that hydrolyze GTP, turning it to GDP, and often inactivating the molecule it was bound to

Acts as a GTPase

When working with other GTPases, speeds up the process of GTP hydrolysis

Works with the alpha subunit of heterotrimeric G proteins and GPCRs to speed up the process of GTP hydrolysis

Ex. RGS proteins

cAMP

A small signaling molecule

Plays important roles in many signaling cascades (ex. cascade in which this molecule activates enzymes such as cAMP protein dependent kinase)

An easy to make molecule, however it doesn’t last a long time (gets broken down into AMP quickly in cascades)

Activates the epinephrine signaling pathway after being generated by adenylyl cyclase, ultimately leading to the production of glucose

Often binds to protein kinase A in signaling pathways, freeing up the catalytic subunit, which then activates glycogen phosphorylase, ultimately leading to glucose production

Plays important roles in regulating cell proliferation, survival, and differentiation → these processes normally occur through the regulation of gene expression

The main target of this enzyme is a transcription factor called CREB

Caffeine

A drug that acts as a cAMP phosphodiesterase inhibitor

Stops the breakdown of cAMP, meaning it causes increased production of glucose in the epinephrine signaling pathway

cAMP phosphodiesterase

An enzyme formed by adenylyl cyclase in certain pathways

Its main job is to break down cAMP

Gets inhibited by caffeine

Phosphorylase kinase

A substrate often found in signaling pathways with cAMP

Gets activated through phosphorylation by the catalytic subunit of protein kinase A, and then activates glycogen phosphorylase, ultimately leading to glucose production

Glycogen phosphorylase

The enzyme found at the end of the epinephrine, glycogen metabolism pathway that ultimately breaks down the glycogen into glucose

Gets activated through phosphorylation by activated phosphorylase kinase

1. Signal amplification

2. Reversibility

2 characteristics used to describe the epinephrine glycogen metabolism pathway

1. Describes the pathways ability to produce hundreds of thousands of glucose molecules per molecule of epinephrine → at each step of the signal pathway, more and more molecules are being produced

2. Describes the pathways ability to “turn-off” after its been activated → does this through phosphatases and cAMP phosphodiesterase

Protein kinase A (PKA)

One of the major enzymes in the epinephrine glycogen metabolism pathway

Made up of 4 subunits, including 2 catalytic subunits and 2 regulatory subunits

Binds 4 molecules of cAMP, two on each of the two regulatory subunits

Gets activated by cAMP and goes on to activate phosphorylase kinase through phosphorylation, ultimately leading to the production of glucose

Plays important roles in regulating cell proliferation, survival, and differentiation → these processes normally occur through the regulation of gene expression

Regulates many transcription factors

The main target of this enzyme is a transcription factor called CREB (has the ability to phosphorylate CREB)

Has two substrates (never functions in isolation) → always ATP and whatever the target protein is that it is modifying

Activation of this type of protein and signaling pathways involving this type of protein get turned on and off very quickly due to protein phosphorylation being rapidly reversed by protein phosphatases, which terminate responses initiated by receptor activation of these proteins

Some families of these types of proteins are also phosphatases (reverse phosphorylation)

First messengers

Signaling molecules that communicate with the outside of the cell, usually with cell surface receptors

CREB (cAMP Response Element Binding Protein)

A transcription factor and the major target of cAMP and PKA signaling

Binds to CRE

Gets regulated by phosphorylation by PKA in the nucleus which leads to its activation → when it’s phosphorylated it recruites a coactivator (HAT), allowing for its regulation of transcription and different target genes

Many genes targeted by this transcription factor are involved in regulating cell proliferation, survival, and differentiation

CRE (cAMP Response Element)

A short DNA sequence that binds CREB

Rhodopsin

A specific type of GPCR found in the photoreceptor in retinal rod cells in eyes, responsible for pupil dilation in response to light

Has a specific small molecule that binds to the receptor, causing the GPCR to change conformation, activate different channels, and lead to the response of pupil dilation

Muscarinic acetylcholine receptor

A specific GPCR that binds acetylcholine in order to regulate heart muscles

Normally found on heart muscle cells

Regulated by neurons

Acetylcholine gets released from the neuron → the acetylcholine binds to the specific GPCR, opening a potassium channel, causing the membrane to hyperpolarize, and leading to less calcium in the cell (potassium flows out of the cell)→ this relaxes the heart muscle cell

This is an example of GI (G protein inhibitory pathway) (adenylyl cyclase is being inhibited)→ regulates heart rate

In this example, the beta/gamma subunit is doing the activating rather than the typical alpha subunit of the G protein

Norepinephrine

A signaling molecule similar to epinephrine that binds to B-adrenergic receptors and leads to the opening of voltage gated calcium channels via phosphorylation, which enhances muscle contraction, increasing heart rate (does the opposite of the muscarinic acetylcholine receptor)

B-Adrenergic receptor

A specific GPCR that binds norepinephrine, which leads to to the opening of voltage-gated calcium channels via phosphorylation, which enhances muscle contraction, increasing heart rate (does the opposite of the muscarinic acetylcholine receptor)

Allows for calcium to enter the cell, increasing muscle contraction

Receptor protein-tyrosine kinases (RTKs)

A type of kinase and receptor for most growth factors that controls cell proliferation and survival

There are 59 of this type of receptor in humans, and they all share a common structural organization

They are single transmembrane domain receptors → consist of an N-terminal extracellular ligand-binding domain (specific to the specific ligand), a single transmembrane alpha-helix domain (20-25 amino acids), and a C-terminal cytoplasmic domain with protein-tyrosine kinase activity (has the ability to add phosphates to other proteins at tyrosine residues)

This receptor commonly regulates the cell cycle as well as commonly gets mutated, meaning that it is likely for mutations in these kinds of receptors to lead to cancer

Ex. EGF receptor, insulin receptor, PDGF receptor

Has the ability to phosphorylate other molecules of its own kind (autophosphorylation), which allows for signals to be transmitted within the cell

Many of the ligands (growth factors) for this type of receptor function as dimers → dimerization is key to activation

Activation of this kind of receptor begins with receptor dimerization

Insulin receptor

A specific type of RTK receptor for insulin in which its structure is a dimer made up of 2 subunits (alpha & beta) which are held together by disulfide bonds

The only RTK receptor “pre-built” as a dimer

Autophosphorylation

A process that happens in response to receptor dimerization in which two receptors get so close to one another that they start phosphorylating each other

This process can happen at multiple different parts of the receptor leading to the activation of different parts of the receptor

If this process occurs at the tyrosine kinase domain of the receptor → the purpose is to increase kinase activity

If this process occurs at the C terminus of the receptor → it provides the receptor a docking site for other proteins to recognize the phorylation domain, allowing them to interact with the receptor, only when it is phosphorylated → allows for signals to be transmitted within the cell

1. Increases kinase activity (at the tyrosine kinase domain)

2. Creates binding sites for other molecules (at the C terminus) → allows for signals to be transmitted inside of the cell

The 2 main effects of phosphorylation include:

Non-receptor tyrosine kinases

Kinases that stimulate intracellular tyrosine kinases with which they are non-covalently associated

Receptors that do NOT have tyrosine kinase domains built into their structure work with these separate proteins that are tyrosine kinases in order to function (2 proteins bound together, trying to achieve the same goal as a regular RTK receptor)

Belong to the cytokine receptor superfamily of receptors

Get recruited by cytokine receptors

Mediates intracellular signaling

Belong to the Src family of kinases

Cytokine receptor superfamily

A family of receptors that includes receptors for most cytokines (interleukins, interferons) and some polypeptide hormones (growth hormone, prolactin)

These receptors do NOT have tyrosine-kinase domain activity → they recruit non-receptor tyrosine kinases

These structure of these receptors are like receptor tyrosine kinases, but the cytosolic domains have no catalytic activity

The ligands to these receptors cause dimerization of the receptors, autophosphorylation, and then activation of a pathway

Ex. non-receptor tyrosine kinases

Interleukins

A molecule that is part of the cytokine receptor superfamily that is found in the immune system, responsible for signaling to different cells in the blood and in the immune system

JAK/STAT Pathway

A specific signaling pathway in which the ligand is a cytokine which binds to a cytokine receptor on the cell surface → the receptors dimerize, autophosphorylate, increase JAK protein activity, phosphorylate the C terminal domain, and provide a scaffold for proteins (ex. STAT proteins) → these STAT proteins then get closer to each other, dimerize, get phosphorylated by the non-receptor tyrosine kinase, go to the nucleus, and then activate transcription

STAT proteins (signal transducers and activators of transcription)

Proteins with the specific job of transducing signals and activating transcription

In the JAK/STAT pathway, these proteins are bound to non-receptor tyrosine kinases, where they dimerize, get phosphorylated by the non-receptor tyrosine kinase, go to the nucleus, and then activate transcription

Contain SH2 domains

Janus Kinase (JAK) family

A family of kinase that includes non-receptor tyrosine kinases associated with cytokine receptors

Key targets of these kinases are STAT proteins

Important in the JAK/STAT pathway

SH2 domains (sarc-homology domain)

'“Puzzle piece”-like structures on STAT proteins where the proteins fit together when forming a dimer

Src family

A specific family of kinases that plays key roles in signaling downstream of cytokine receptors, receptor tyrosine kinases, antigen receptors on B and T lymphocytes, and receptors involved in cell-cell and cell-matrix interactions (ex. cadherins & integrin)

Non-receptor tyrosine kinases belong to this family

Integrins

Cell surface, transmembrane proteins that integrate information from the extracellular matrix to the cell

Detect changes in the extracellular matrix and talk to molecules such as focal adhesion kinases

Sends messages to the cell from the extracellular environment when there is a change in the extracellular environment

Attach cells to the extracellular matrix

Serve as receptors that activate intracellular signaling pathways

Integrin signaling

A signaling pathway specific to integrins and the extracellular matrix, in which integrins serve as receptors that activate intracellular signaling pathways

Often used to send signals from the extracellular environment to the cell

If there is a change in the extracellular environment, integrins detect the changes in the extracellular matrix, communicate with focal adhesion kinases, which then recruit molecules such as Src, which change molecules such as actin-binding proteins by phosphorylating them, which in turn, change the actin cytoskeleton

This signaling mechanism occurs very quickly

Focal adhesions

Parts of the cytoskeleton in which the actin cytoskeleton is holding the cell onto the plate

Focal adhesion kinase (FAK)

Kinases specifically for focal adhesions of the actin cytoskeleton

A type of non-receptor tyrosine kinase

Recruits molecules such as Src in integrin signaling pathways in order to change the actin cytoskeleton

General signaling pathway outline

Stimulus (ligand/growth factor) → transmembrane domain (receptors) → inside cell → activation of small GTP-binding proteins → upstream kinases (amplification) → MAP kinase → Response

Due to amplification, the molecules at the beginning of the pathway are functionally more consequential for the pathway → if there is a mutation in one of the starting molecules, it is likely that the whole cell will become cancerous due to amplification

GTP-binding proteins

Small proteins vital to most signaling pathways that depend on whether or not they are bound to GTP

When they are bound to GTP, they are active

When they are bound to GDP, they are inactive

To go from their inactive to active state, they get help from GEF proteins

They are able to go from their active to inactive state themselves, as they act as GTPases, with the help of GAP proteins, which speed up the process

Ex. Ran, EIf2, Eef2, Eef1

MAP kinases (mitogen activated protein kinases)

A specific type of kinase that directly affects and regulates mitosis and cell division

Regulates the cell cycle

Plays an important role in cell proliferation

ERK MAP kinase pathway

A specific key pathway in regulating animal cell proliferation

Common in human cancers

Growth factor → Ras → Raf → Mek → Erk → proliferation, differentiation, cell survival (MEMORIZE)

Growth factors activate Ras, which gets localized to the plasma membrane by prenyl groups (lipid anchors), Ras gets regulated by GEFs and GAPs, which then activates the upstream kinases starting with Raf via protein-protein interactions, which then phosphorylates and activates the next upstream kinase, MEK, which then phosphorylates and activates the MAP kinase ERK, ERK then phosphorylates a variety of proteins involved in cell proliferation, leading to the ultimate response

The signal is constantly getting amplified as it goes down the pathway

Pathways such as this one help cells divide, proliferate, and survive

Ras

A small GTP binding protein important to the ERK MAP kinase pathway

When bound to GDP, it’s inactive, when bound to GTP, it’s active → goes from inactive to active using a GEF protein → goes from active to inactive with the help of GAP proteins

In the ERK MAP kinase pathway, gets localized to the plasma membrane by prenyl groups

Often found to cause human cancer when there are issues with regulation by GEFs and GAPs → if GAPs are not working correctly and this protein is constantly activated, could lead to excess cell division → this protein is at the top of a cell signaling pathway that controls cell proliferation, so there are high chances that it would cause cancer if a mutation were to happen

Mutations in many human cancers keep this protein in its active GTP-bound state

Mutations in genes that code for this protein found in cancers inhibit GTP hydrolysis, so the proteins remain in continuously in their active GTP-bound form, driving proliferation of cancer cells

Mutations in these genes are found in ~25% of all human cancers, including ~50% of colon cancers

The best mechanism of activation of these proteins in response to growth factors is activation through RTKs → activation of RTKs, recruitment of GEF by SH2 domain → growth factor binds to RTKs causing them to dimerize and become activated, they then phosphorylate the kinase domain, increasing their activity, and they phosphorylate the C terminal domain providing the scaffold for SH2 domain containing proteins to bind, the SH2 domain then recruits a GEF protein, which then activates the Ras protein

Raf

A specific kinase; the first kinase found in the ERK MAP kinase pathway

Gets activated by Ras via protein-protein interactions, then grabs ATP and its substrate, MEK → phosphorylates and activates MEK

MEK kinase

The second upstream kinase of the ERK MAP kinase pathway

Acts a serine threonine and tyrosine kinase

Gets activated by the first upstream kinase in the pathway, Raf, through phosphorylation

Phosphorylates and activates the MAP kinase, ERK

ERK

A MAP kinase important to the ERK MAP kinase pathway

Gets phosphorylated and activated by the MEK upstream kinase in the pathway, phosphorylates a variety of proteins involved in cell proliferation, and then ultimately causes the response

Determines the fate of whether or not the cell is going to divide at the end of the pathway

Works on many different targets, including transcriptional targets, that help to regulate cell proliferation

Contains a serine and a tyrosine site allowing MEK to phosphorylate it

Regulates transcription of many genes via regulation of transcription factors (recruits other transcription factors for help - ex. Elk-1/SRF complex) → amplifies a signal to increase the transcription of many genes

Phosphorylates the Elk-1/SRF transcription factor complex, allowing it to regulate transcription of many genes

Elk-1/SRF (serum response factor) complex

A transcription factor complex regulated by ERK kinase

When cells were treated with this transcription factor, it started rapidly inducing ~100 genes almost immediately (immediate early genes) → many of these genes were transcription factors themselves (cascade of transcription factors that will go on to regulate many different genes)

Binds to DNA at the SRE sequence to regulate genes through phosphorylation by ERK (This whole pathway had to start as the ERK MAP kinase pathway in order for ERK to be available to phosphorylate this transcription factor complex)

Immediate early genes

Genes that when treated with growth factors begin to change or get turned on almost immediately (within an hour)

Many of these types of genes are transcription factors and create cascades of transcription factors in which they go on to regulate many different genes

The goal of many of these genes is regulate mitosis and cell proliferation by pushing the cell cycle forward

Ex. the genes treated with Elk-1/SRF complex transcription factor

SRE (serum response element)

The 6 base pair sequence of DNA that the Elk-1/SRF transcription factor complex binds to

Scaffold proteins

Large proteins that hold molecules specific to specific signaling pathways in place next to each other, allowing the pathway to move along quickly

Ex. these (KSR) proteins would hold Raf, MEK, and ERK together, allowing Ras to quickly find the molecules and allow for the ERK MAP kinase signaling pathway to start and finish quickly

Allow signaling pathways to happen so quickly because necessary molecules do not need to “look” for each other in the cytosol → they are already associated with each other and neighbors due to being held in place by these proteins

Can also hold together GPCRs and their associated G proteins

These proteins can be regulated, which can also affect pathways (molecules can be brought closer or farther apart, affecting the speed of the pathway)

These proteins keep the molecules in close proximity even when they are inactive, so that when they become active they can find each other within seconds

KSR

A specific type of scaffold protein that organizes ERK and its upstream activators, Raf and MEK, into a signaling pathway

PI 3-kinase/Akt signaling pathway

A specific type of signaling pathway that involves the production of a phospholipid as a second messenger

Considered a “survival pathway” because signaling pathways downstream from this pathway can lead to apoptosis OR to cell proliferation and cell survival depending on the events of the cascade

PIP2 (phosphatidylinositol phospholipid) is phosphorylated by PI 3-kinase, turning it into PIP3 a second messenger, which then attracts proteins and changes their behavior (specifically, usually Akt) → Akt (or other target) gets activated through phosphorylation by mTORC2 and PDK1, allowing Akt to activate other targets (such as FOXO)

The version of this pathway that targets for GSK-3 regulates global translation via eIF2B (the normal pathway inhibits GSK-3 rather than activates it)

This signaling pathway can also regulate translation via regulation of the mTOR pathway (another target of Akt)

Growth factor → cell surface receptor → PI 3-kinase → PIP2 → PIP3 (second messenger) → Akt → various targets

asymmetrically between the inner and outer leaflets

Phospholipids are distributed _________ of the plasma membrane (EXAM QUESTION)

PIP2 (Phosphatidylinositol)

One of the specific types of phospholipids that exists in low quantities in the plasma membrane and plays key roles in cell signaling

Can be modified through phosphorylation by PI 3-kinase, turning it into PIP3

Associated with 3 phosphate groups

PIP3

The phosphorylated version of PIP2 and THE second messenger in the PI 3-kinase/Akt signaling pathway

A small molecule that’s inside the cell that has been modified, and changes the behavior of other proteins within the cell → second messenger

Associated with 4 phosphate groups

The key target of this second messenger is Akt kinase

Binds to Akt at its PH domain by its sticky phosphates

PI 3-kinase

A specific kinase that phosphorylates PIP2 in the PI 3-kinase/Akt signaling pathway

Plays major roles in cell proliferation and survival

Mutations that over-activate this kinase contribute to some human cancers

Mutations are common in this kinase because it is at the beginning of the signaling pathway, so if it has a mutation, it will get amplified as it goes down the signaling pathway, and likely lead to cancer

This kinase is activated and regulated downstream of GPCRs and RTKs

There are different family members of this kinase that are each slightly different depending on if they are associated with GPCRs or RTKs → they have different mechanisms of activation → allows activation of the pathway in response to different extracellular stimuli → ALL family members phosphorylate PIP2, turn it into PIP3, and create a second messenger for the cell (all family members have the same function)

Recruitment of this kinase to activated RTKs stimulates the activity of the kinase

Akt

A specific serine-threonine kinase and the key target of PIP3 in the PI 3-kinase/Akt signaling pathway

Plays a major role in cell survival

One of the biggest hubs of kinase activity in cells → has many different targets

Binds PIP3 via its PH domain

Gets activated by a 2 step process by 2 different kinases (mTORC2 & PDK1) → gets phosphorylated at the plasma membrane by these kinases, leading to its activation → can then go on to activate its own targets (ex. molecule that induces apoptosis, or transcription factors, or GSK-3- translation regulation)

It’s three main targets are proteins leading to apoptosis, transcription factors (FOXO), and GSK-3

Its key transcription factor is FOXO → the default pathway to cell death (if no growth factors) → if growth factors, FOXO is sequestered by protein 14-3-3, keeping the cell alive

Pleckstrin homology (PH) domain

A domain found on many proteins that interacts with sticky phospholipids of other molecules, allowing them to bind

Ex. Akt and PIP3 binds together through the sticky phospholipids on PIP3 binding to this domain on Akt

mTORC2

One of the 2 kinases that activates Akt through phosphorylation at the plasma membrane

Phosphorylates Akt at one sight and completes half of Akt’s phosphorylation

Exists in a complex-like structure

Made up of many different proteins that affect its activity and substrate specificity

(upstream)

PDK1

One of the 2 kinases that activates Akt through phosphorylation at the plasma membrane

Phosphorylates Akt at one sight and completes half of Akt’s phosphorylation

Apoptosis

Programmed cell death

FOXO

The key transcription factor target of Akt in the PI 3-kinase/Akt signaling pathway (default pathway of this cascade)

A transcription factor that activates the transcription of genes that inhibit cell proliferation and induce cell death → leads to apoptosis (IN THE ABSENCE OF GROWTH FACTORS)

If there ARE growth factors present → Akt phosphorylates this transcription factor, causing it to get sequestered by the binding of protein 14-3-3, stopping it from reaching and transcribing apoptosis genes, and allowing the cell to survive

Protein 14-3-3

A sequestering protein that binds to the transcription factor FOXO in the presence of growth factors in the PI 3-kinase/Akt signaling pathway

Causes FOXO to be sequestered (isolated) in the cytosol, stopping it from binding to DNA and activating transcription of apoptosis genes, allowing the cell to survive

GSK-3 (glycogen synthase kinase)

One of the 3 main targets of Akt in the PI-kinase/Akt signaling pathway

A serine-threonine kinase that gets phosphorylated by Akt, making it INACTIVE

Phosphorylates eIF2B when active, stopping it from initiating translation

Loss of growth factors = activation of this kinase → when active, this kinase regulates numerous targets (including eIF2B) → phosphorylates eIF2B, stopping it from being able to initiate transcription

Presence of growth factors = inhibition of this kinase → global translation proceeds (eIF2B is NOT phosphorylated)

Plays important roles in regulating metabolism (glycogen metabolism), translation factor eIF2B (translation initiation), and transcription factors

The regular PI 3-kinase/Akt signaling pathway inhibits this kinase rather than activates it (growth factors inhibit it)

eIF2B

A translation initiation factor and a GEF protein that is regulated by GSK-3 kinase

Regulates translation initiation of proteins

Becomes inactive when GSK-3 phosphorylates it, becomes active when GSK-3 is not able to phosphorylate it

eIF4E

A translation initiation factor whose main job is to bind to the 5’ methyl cap of the mRNA

Is in association with a sequestering protein called 4E-BP

Regulated by the mTOR pathway

Gets regulated by mTORC1 in the mTOR pathway through phosphorylation of its binding protein, 4E-BP

REQUIRED to initiate translation (if mRNA does not have a 5’ methyl cap, translation cannot start because this translation initiation factor wont be able to recognize the mRNA as needing to be translated)

mTOR pathway

A signaling pathway that regulates the translation initiation factor eIF4E

The main goal of this pathway is to regulate translation and autophagy

A “back-up” pathway to the GSK-3 pathway target of Akt → very similar to the GSK-3 pathway and has the same goal (regulation of global translation) → both pathways are downstream from Atk, initially coming from the PI 3-kinase/Akt signaling pathway

Utilizes the same kinase enzyme that is used to activate Akt (mTORC1/2), however the complex is just made up of different proteins (complex 1 instead of complex 2)

mTORC1 inhibits the eIF4E binding protein (4E-BP) by phosphorylating it, stopping it from being able to inhibit eIF4E, allowing it to carry out translation by binding to the 5’ methyl cap of mRNA

This same pathway also regulates autophagy → if translation is turned, autophagy will most likely be turned on in order to save energy and recycle materials → when cells are starved of nutrients, mTORC1 activity decreases → this stimulates autophagy and allows cells to degrade nonessential proteins so the amino acids can be reused

2 main goals: regulation of translation factors and regulation of autophagy

mTORC1

A kinase enzyme complex that is important for the activation of the mTOR translational regulation signaling pathway

Made up of many different proteins that affect its activity and substrate specificity

(downstream)

Regulates global translation via phosphorylation of eIF4E-binding protein (4E-BP)

This kinase inhibits the eIF4E binding protein (4E-BP) by phosphorylating it, stopping it from being able to inhibit eIF4E, allowing it to carry out translation by binding to the 5’ methyl cap of mRNA

This kinase also inhibits protein degradation by regulation of autophagy → when cells are starved of nutrients, the activity of the kinase decreases, stimulating autophagy and allowing cells to degrade nonessential proteins so the amino acids can be reused

4E-BP (eIF4E binding protein)

A sequestering protein that is associated with translation initiation factor eIF4E, which normally inhibits eIF4E, stopping it from being able to initiate translation

Allows for the regulation of eIF4E in the mTOR signaling pathway by getting phosphorylated by mTORC1

Gets inhibited by mTORC1, stopping it from being able to inhibit eIF4E

In the absence of growth factors, this protein inhibits eIF4E, stopping it from being able to initiate translation

When growth factors are present, this protein is inhibited by being phosphorylated by mTORC1, stopping eIF4E from being inhibited, and allowing it to initiate translation

Autophagy

The cell’s process of saving and recycling energy

Regulated by the mTOR pathway of the PI 3-kinase/Akt signaling pathway → when cells are starved of nutrients, mTORC1 activity decreases, stimulating this process to start and allowing cells to degrade nonessential proteins so the amino acids can be reused

TGF-B Receptor signaling pathway

A specific type of signaling pathway that includes two types of serine/threonine kinase polypeptides (type I & II) that form dimers

TGF-B ligand binding enables type II polypeptides to activate type I via phosphorylation → the activated type I receptor the phosphorylates an R-Smad protein which binds a co-Smad protein, forming a dimer and allowing it to enter the nucleus where it can regulate transcription → the Smad complex binds DNA, regulating target gene transcription

This signaling pathway regulates cell proliferation, differentiation, and apoptosis, and is essential in development, wound healing, and immunity

Homo-dimers

Dimers made up of 2 of the same molecules

They are both regulated the same way

Hetero-dimers

Dimers made up of 2 different molecules, or 2 similar molecules with different properties (ex. one is phosphorylated the other is not)

TGF-B

A ligand specific to the TGF-B receptor signaling pathway

Binds to TGF-B receptors that are considered hetero-dimers, starting the signaling pathway

TGF-B receptors

The receptors specific to the TGF-B receptor signaling pathway

Made up of 2 different types of serine/threonine kinase polypeptides that come together to a hetero-dimer (each subunit is called type I and type II)

The type II subunit phosphorylates the type I subunit, allowing it to recruit an R-Smad protein and phosphorylate and dimerize it, which allows it to bind to a co-smad, forming a dimer and allowing it to regulate transcription

R-Smad

One of the proteins important to the TGF-B receptor signaling pathway

Gets phosphorylated by the active type I receptor, allowing it to bind the co-Smad protein, which then allows the proteins to form a dimer, enter the nucleus, and regulate transcription

When in their dimer, these proteins bind DNA, regulating target gene transcription

co-Smad

One of the proteins important to the TGF-B receptor signaling pathway

Binds to the previously phosphorylated R-Smad protein, which forms a dimer allowing it to enter the nucleus and regulate transcription

When in their dimer, these proteins bind DNA, regulating target gene transcription

Wnt signaling pathway

A specific signaling pathway that regulates cell proliferation, differentiation, and embryonic development

The ultimate goal of this pathway is to regulate transcription

This pathway includes a Wnt ligand, a frizzled receptor, and a co-receptor called LRP

When there is no Wnt ligand present → B-catenin levels are kept low by the destruction complex (when there is no ligand present, there is an active destruction complex) → the destruction complex phosphorylates B-catenin, targeting it for ubiquitination → it is then degraded by the proteasome, preventing it from being able to regulate and initiate the transcription of the Wnt target gene (degradation = no regulation of transcription)

When the Wnt ligand is present → Wnt binds to the frizzled receptor and LRP co-receptor on the cell surface → LRP then recruits many other proteins (including the destruction complex) → a protein called disheveled gets recruited by the frizzled receptor → the recruiting of these protein complexes by the receptor and co-receptor, inactivate the complexes, stopping them from being able to phosphorylate and ubiquitinate B-catenin → this allows B-catenin to accumulate in the cytoplasm, stabilize, and enter the nucleus, where it then forms a complex with Tcf, switching it to a transcriptional activator

(Similar to the IkB pathway in that molecules get phosphorylated first and then ubiquitinated)

A critical signaling pathway for limb development

Frizzled

The receptor specific to the Wnt signaling pathway

When the Wnt ligand binds to this receptor, it recruits the disheveled protein, helping the LRP co-receptor to inactivate the destruction protein complex, and allow for the activation of the rest of the signaling pathway