cell cycle control + cell signaling

G0 phase

most of your cells are not in any of the cell cycle stages. They lose their ability to divide and enter a stage called G0, which is a permanent state and those cells will never divide again

Checkpoints

G1 checkpoint: most important checkpoint, pass this checkpoint if cell size is adequate, nutrients are sufficient, extracellular signals are present, and DNA is undamaged (mature cells do not pass this checkpoint and instead enter G0)

G2 checkpoint: pass this checkpoint if chromosomes have replicated successfully, DNA is undamaged, and activated MPF is present.

Metaphase checkpoint: pass this checkpoint if all chromosomes are attached to spindle apparatus

phosphorylation

protein phosphorylation is a rapid and reversible way to activate or inactivate a protein, allowing your cells to control which pathways are active and which are inactive.

protein kinases

protein kinases are enzymes and use ATP as a substrate. They each have a specific set of protein substrates, and the terminal phosphate of ATP is transferred to a protein substrate on serine/threonine and/or tyrosine residues.

Phosphorylation acts to change substrate protein conformation, and phosphorylation can activate or inactivate a protein

a kinase is an enzyme that catalyzes a specific reaction, and a phosphotase reverses the phosphorylation

How do kinases work as an on/off switch?

RB normally locks the regulatory transcription factors E2F and DP in an inactive state, preventing them from activating S-phase transcription. Kinases phosphorylates RB, inactivating the RB protein. E2F and DP can then drive transcription of genes for S phase.

What is at the core of cell cycle regulation and checkpoints

Cyclin dependent kinases (CDKs), and their enzymatic activity is tightly controlled by cyclins.

Cyclins bind to and activate CDKs to control progression through the cell cycle. CDKs phosphorylate target proteins involved in promoting cell division. Cyclins are degraded and CDKs are then inactivated. Cycle starts over again

A key feature of the cell cycle os control of cyclin accumulation

how the system of cyclin accumulation look

There are many CDKs and cyclins active during the cell cycle. Cyclins must accumulate separately for each checkpoint, and they activate CDK at peak accumulation.

how do cyclins accumulate

they accumulate in response to meeting checkpoint criteria. Growth factor signals activate some, then cell being big enough activates more, then mitochondria replication activates more and finally dNTP accumulation activates all. Now there’s enough CDK activity to trigger expression of genes for S phase. CDK amount is constant. Cyclin amount and CDK activity vary.

Cyclin accumulation to enter G2 checkpoint

Cyclin gets degraded after the G1 checkpoint. It reaccumulates in response to meeting new G2 checkpoint criteria. After CDKs get reactivated, there is enough activity to move into M phase

MPF

mitosis promoting factor. MPF was the first discovered CDK complex. MPF is the cyclin-CDK complex that drives the cell through the G2/M checkpoint. MPF activity is controlled by cyclin accumulation, and it drives the events of mitosis

How does MPF drive mitosis

It triggers the events that occur during mitosis through protein phosphorylation. this is true of all the cyclin/CDK complexes.

MPF is not just a checkpoint protein that allows the cell to move through mitosis. MPF drives the events of mitosis by directly and indirectly regulating the specific factors that carry out mitosis. This is true of other cyclin/CDK complexes that act at other checkpoints

why is cyclin degradation necessary

Cyclin degradation is critical so that the next cell needs to fulfill the next checkpoint criteria before progressing. Failure to degrade cyclins would result in promiscuous cell cycle progression, which could turn cancerous because it would be dividing without regulation.

No cyclin degradation = dividing without checkpoints which would be bad

How to degrade the right cyclin at the right time

targeted protein degradation/protein lysis.

Inactivating proteins is just as important for proper cell function as activating them in the first place. A common and permanent way to inactivate proteins is to specifically target them for proteolytic degradation

The proteasome

the proteasome is not specific for any protein sequence. It will degrade any ubiquitinated protein. It’s basically like a trash compactor and destroys what you put in. Cells use E3 ubiquitin ligase to target specific proteins for degradation, which grabs a specific substrate (cyclin) and E2 transfers ubiquitin to the substrate. The target is now tagged for degradation.

You have over 600 ubiquitin ligase genes to add ubiquitin to specific proteins. there are E3 ubiquitin ligases that specifically target cyclins.

How does MPF work with E3

MPF triggers activation of an E3 ubiquitin ligase that targets its own cyclin. In other words, activation of MPF triggers its own inactivation.

Why do cells need signaling

the activities of cells must be tightly linked to their environment. Ex: in multicellular organisms, cell type specification depends on signals that cell receives. Cell identity is acquired largely through cell signaling

General outline for cell signaling

signal - receptor - signaling intermediates - effectors - cell response

signal: factors outside the cell also known as ligands

receptor: protein in the cell that binds to the signal. Binding changes receptor activity.

Signaling intermediates: factors within the cell that are altered in response to receptor activation

effectors: the ultimate mediators of how the cell responds

regulatory transcription factors as effectors

Many signaling pathways act to control the activity of Regulatory Transcription Factors. When Reg TFs are the effectors for a pathway, then the consequence of signaling is to change gene expression patterns. Thus, much of the pattern of gene expression in a cell is the result of extracellular signals

metabolic enzymes as effectors

Cell signaling can also lead to changes in the activity of metabolic enzymes. When metabolic enzymes are the effectors for a pathway, then the consequence of signaling is to change in metabolism

The response that a cell has to a signal depends on which effectors get activated in that cell. The same signal can activate different effectors in different cell types. Several signals can sometimes create similar responses by activating common effectors

receptors

For every signal, there must be a receptor that binds to that signal. Typical receptors have an extracellular signal-binding domain, a transmembrane region, and a cytoplasmic signaling domain. Signal binding to the extracellular domain controls the activity of the cytoplasmic signaling domain

Lipid soluble vs cell surface receptors

Small nonpolar signaling molecules can freely pass through the plasma membrane and activate cytoplasmic receptors.

Polar signaling molecules cannot cross the plasma membrane and rely on cell surface receptors. These receptors have an intra and extracellular domain, and receptors with cytoplasmic protein kinase domains are a huge and varied family in plants and animals.

kinase and phosphotase

a kinase is an enzyme that catalyzes adding a phosphate group to a protein

A phosphatase reverses this phosphorylation. Phosphorylation can activate a protein but it can also inactivate it.

dimerization

Ligand binding changes receptor conformation, leading to dimerization. The kinase domains of dimerized receptors phosphorylate both each other and other targets. When the signal binds, shape and chemistry of the receptor changes and cross phosphorylation happens.

Inactive receptor tyrosine kinases have low affinity for each other, but when a signal binds, the kinases change shape and cross phosphorylate and are more attracted to each other.

Phosphorylation can activate or recruit signaling intermediates

Ras activation

In the MAPK pathway, receptor activation in turn activates Ras. Ras is a G protein. Its activity is controlled by whether it is bound to GDP (inactive) or GTP (active). For receptor signal transduction, the phosphorylated receptor brings a Ras activator to Ras at the plasma membrane.

Ras activator pulls out GDP, allowing GTP to replace it, which means there are 3 phosphates and G protein is actiated. Ras turns itself off by hydrolyzing a Pi, turning it back into GDP.

Activation by protein phosphorylation involves covalently adding a phosphate, and Ras activation involves the non-covalent binding of GTP.

Ras activating protein kinases

In the MAPK pathway, Ras activates a series of protein kinases. MAPKKK is activated by direct interaction with RasGTP – leading to conformational change. MAPKKK phosphorylates MAPKK, MAPKK phosphorylates MAPK

Active (phosphorylated) MAPK moves into the nucleus and activates transcription factors through phosphorylation

Once GTP gets hydrolyzed to become GDP again, phosphotase comes in and removes phosphates from all the different MAPKs to end the pathway

Why does signal transduction go through so many steps

Signal Amplification (turns a small signal into a large output)

Signal Branching to coordinate multiple responses for a single signal and to coordinate multiple signals

Signal Integration: Some cellular processes are regulated by multiple, different signals

Signal amplification

Some signaling steps are one-to-one activation (signal activating the receptor-kinase, Ras-GTP activating MAPKKK). At other steps, the signal in the cell can be amplified. This typically requires an enzyme that can create many products (e.g., a protein kinase). Ex: one signal can activate 100s of MAPKs

signal branching and signal integration

Signal branching occurs when a signaling component activates multiple downstream signaling components. This allows the cell to activate many processes in response to one signal.

Signal integration occurs when a signaling component responds to multiple signals. This allows the cell to coordinate its activity in response to a variety of signals