Principles of cell signalling - info transfer 2

What is meant by signalling specificity?

Precise protein–protein interactions connect proteins in signalling pathways and ensure that signals are passed to the correct targets.

How can protein interactions be mediated by broad interaction surfaces?

Proteins interact through complementary-shaped surfaces on their structures. These interfaces determine which proteins can bind to one another.

Why is understanding protein interaction interfaces important in drug development?

A drug can be designed to bind to a protein interaction surface and disrupt a signalling pathway.

How can protein interactions be mediated by short, linear peptides?

A short, linear peptide sequence on one protein fits into a corresponding groove on the surface of its binding partner.

How long are the short linear peptide sequences involved in many protein interactions?

Approximately 4–8 amino acids.

What is often true of the linear motifs involved in protein interactions?

The linear motif or sequence is usually conserved.

How can post-translational modifications regulate protein–protein interactions?

Some interaction domains recognise changes in a protein's state. A binding partner may only interact with the protein after it receives a particular post-translational modification.

What is an example of a protein interaction domain that recognises a post-translational modification?

An SH2 domain recognises and binds phosphorylated tyrosines.

When might two proteins only interact after one has been phosphorylated?

When the phosphorylation creates a binding site recognised by a domain on the second protein, such as an SH2 domain.

What can happen to a signalling interaction when a post-translational modification is removed?

The binding interaction can stop because the recognition site is no longer present.

What is signal diversification?

One incoming signal can produce multiple different downstream signalling outputs.

How can one protein generate two different signalling outputs?

A protein can carry two separate post-translational modifications, allowing two different proteins to bind and activate separate branches of signalling.

How can growth factor receptors produce signal diversification?

A single ligand binding to the outside of a growth factor receptor can lead to extensive diversification of signalling inside the cell.

What is signal integration?

The integration of multiple signals so that a cell only passes on a signal when several conditions have been met.

How can signalling proteins act as decision-making systems?

Their activation can depend on the presence, timing or combination of several different signals.

How can suppressor proteins regulate signal integration?

A suppressor protein holds another protein inactive until the required signals cause a conformational change that releases the inhibition.

In the example involving three signalling sites, when is the inactive protein allowed to produce an output?

Only when all three sites are occupied by signals, causing the suppressor protein to undergo a conformational change and permit the output.

How can a kinase be kept inactive before receiving the appropriate signals?

Its catalytic domain is held inactive by another region of the enzyme that blocks its activity.

How can calcium and lipid signals activate an inhibited kinase?

Calcium and lipid signals bind to the kinase, causing a conformational change that moves the inhibitory segment away from the catalytic region.

Why must intracellular information transfer be amplified?

Amplification allows small signals to produce cellular responses, while random fluctuations or noise can be filtered out.

What is a primary messenger?

The original signalling molecule or ligand that initiates a signalling pathway.

What are second messengers?

Small, non-protein signalling mediators that relay signals from receptors to intracellular responses.

Are all intracellular signalling mediators proteins?

No. Most are proteins, but small non-protein mediators called second messengers are also important.

Give examples of small non-protein signalling mediators.

Calcium ions (Ca²⁺), lipid-derived mediators such as inositol trisphosphate (IP3), and cyclic nucleotides such as cAMP and cGMP.

How do small non-protein mediators transfer information within cells?

They signal through rapid changes in their concentration and location within the cell.

Why are small non-protein mediators useful for intracellular signalling?

They are highly mobile, can move throughout the cell, and can produce fast, distant and amplified signal transduction.

Why can small non-protein mediators diffuse more rapidly and further than proteins?

Their smaller size allows them to move more easily through the cell.

How does the movement of a kinase compare with the movement of cAMP and calcium?

A kinase may move only around 10 microns and is often more anchored near its target. cAMP can move further, while calcium can move even further.

How can small non-protein mediators amplify a signal?

They can be produced or released in large numbers, allowing a small initial input to generate many signalling molecules.

What happens when an input activates a synthetic enzyme involved in producing signalling mediators?

The enzyme can work much more quickly and produce large quantities of signalling mediators.

What determines the intracellular concentration of most small non-protein signalling mediators?

The balance between their production and their destruction or elimination.

Why must signalling mediators be rapidly degraded or eliminated?

Their activity needs to be limited in time so that signalling pathways do not continue indefinitely.

What could happen if signalling mediators are not properly eliminated?

Signalling pathways may remain active for too long, potentially contributing to disease.

What is meant by the balance between synthesis and degradation of a signalling mediator?

Its intracellular concentration depends on the rate at which it is produced compared with the rate at which it is destroyed or eliminated.

What happens to the intracellular concentration of a mediator when its synthesis and degradation rates are equal?

Its concentration remains constant.

How can changing the synthesis rate of a mediator affect its intracellular concentration?

Increasing or decreasing synthesis while degradation remains unchanged can alter the mediator's concentration.

How can changing the degradation rate affect the concentration of a signalling mediator?

Decreasing degradation allows the mediator to accumulate, while increasing degradation reduces its concentration.

How can signalling pathways generate complex temporal and spatial patterns of mediator concentrations?

They can alter the rates of mediator synthesis and degradation, changing how much mediator is present and how its concentration changes over time and across the cell.

How do small non-protein signalling mediators exert their effects?

They bind to downstream effector proteins.

Which enzyme synthesises cAMP?

Adenylyl cyclase.

Which enzyme degrades cAMP?

cAMP phosphodiesterase.

What are the inputs and downstream targets of cAMP signalling?

Inputs include G protein-coupled receptors (GPCRs). Downstream targets include kinases, channels and GEFs.

Which enzyme synthesises cGMP?

Guanylyl cyclase.

Which enzyme degrades cGMP?

cGMP phosphodiesterase.

What can act as inputs to cGMP signalling?

Nitric oxide, rhodopsin and receptor guanylate cyclase.

What are the downstream targets of cGMP?

Kinases and channels.

Which enzyme produces inositol triphosphate (IP3)?

Phospholipase C (PLC).

How is IP3 eliminated?

By dephosphorylation.

Where is IP3 located, and what are its inputs and downstream targets?

It is intracellular. Its inputs include receptor tyrosine kinases and GPCRs, and its downstream target is the IP3 receptor.

Which enzyme produces diacylglycerol (DAG)?

Phospholipase C (PLC).

How is DAG eliminated?

By phosphorylation.

Where is DAG located, and what are its inputs and downstream targets?

DAG is membrane-restricted. Its inputs include receptor tyrosine kinases and GPCRs, and its downstream targets include kinases.

Which enzyme produces phosphoinositides such as PIP2?

PI kinase.

How are phosphoinositides such as PIP2 eliminated?

By PI phosphatases.

Where are phosphoinositides located, and what are their inputs and downstream targets?

They are membrane-restricted. Their inputs include receptor tyrosine kinases and GPCRs, and their downstream targets include kinases and many PH domains.

How is intracellular calcium produced or released into the cytosol?

Through calcium channels, release from intracellular stores and influx into the cell.

How is intracellular calcium removed or sequestered?

Through Ca²⁺-ATPase pumps and calcium-sequestering proteins.

What are the downstream targets of calcium signalling?

Channels, kinases, enzymes, calmodulin and cytoskeletal proteins.

How is nitric oxide (NO) synthesised?

By nitric oxide synthase (NOS).

How is nitric oxide eliminated?

Through reaction with oxygen and heme binding.

Where can nitric oxide act, and what regulates its production according to the notes?

It can act both intracellularly and intercellularly. Its production is associated with Ca²⁺/calmodulin and phosphorylation.

What is the downstream target of nitric oxide signalling?

Guanylyl cyclase, which leads to cGMP production.

Which statement best describes how SH2 domains contribute to signalling specificity? A. They degrade phosphorylated proteins. B. They recognise and bind phosphorylated tyrosines. C. They synthesise cyclic nucleotides. D. They remove phosphate groups from proteins.

Correct answer: B. SH2 domains recognise and bind phosphorylated tyrosines, allowing protein interactions that depend on post-translational modification.

A protein has two separate post-translational modifications, each recognised by a different binding partner. What signalling principle does this demonstrate? A. Signal degradation. B. Signal diversification. C. Signal termination. D. Signal sequestration.

Correct answer: B. The two modifications allow different proteins to bind, producing separate downstream signalling branches from one incoming signal.

Which statement best describes signal integration? A. One signal activates every intracellular protein. B. A signal is only passed on when several conditions or signals are met. C. Signalling mediators are produced without regulation. D. All signalling proteins are permanently active.

Correct answer: B. Signal integration allows the cell to make a decision based on multiple inputs.

A kinase is held inactive by an inhibitory segment. Calcium and a lipid signal bind and cause the inhibitory segment to move away from the catalytic region. What happens? A. The kinase becomes active. B. The kinase is degraded. C. The kinase loses its catalytic domain. D. The kinase becomes a second messenger.

Correct answer: A. The conformational change removes inhibition of the catalytic region, activating the kinase.

Which of the following are small non-protein signalling mediators? (Select all that apply.) A. Ca²⁺. B. cAMP. C. cGMP. D. IP3. E. A kinase.

Correct answers: A, B, C and D. Calcium, cyclic nucleotides and IP3 are small non-protein signalling mediators. A kinase is a protein.

Why can small non-protein mediators produce rapid and distant signalling? A. They are larger than proteins. B. They are highly mobile and diffuse rapidly. C. They are permanently attached to membranes. D. They cannot be degraded.

Correct answer: B. Their small size allows them to diffuse more rapidly and further than larger molecules.

Which statements about the intracellular concentration of small signalling mediators are correct? (Select all that apply.) A. It depends on the balance between production and elimination. B. Equal production and elimination rates maintain a constant concentration. C. Their concentration cannot be altered by changing degradation. D. Their concentrations can generate temporal and spatial patterns.

Correct answers: A, B and D. Concentrations depend on synthesis and degradation, and changes in these rates can generate complex temporal and spatial patterns.

Which enzyme synthesises cAMP? A. Guanylyl cyclase. B. Adenylyl cyclase. C. Phospholipase C. D. Phosphodiesterase.

Correct answer: B. Adenylyl cyclase synthesises cAMP.

Which enzyme degrades cAMP? A. cAMP phosphodiesterase. B. PI kinase. C. Nitric oxide synthase. D. Guanylyl cyclase.

Correct answer: A. cAMP phosphodiesterase degrades cAMP.

Which signalling mediators are produced by phospholipase C (PLC)? (Select all that apply.) A. IP3. B. DAG. C. cAMP. D. cGMP.

Correct answers: A and B. PLC produces IP3 and DAG.

Which statement correctly compares IP3 and DAG? A. Both are synthesised by adenylyl cyclase. B. IP3 is intracellular, whereas DAG is membrane-restricted. C. IP3 is degraded by phosphorylation, whereas DAG is degraded by dephosphorylation. D. Both are degraded by cAMP phosphodiesterase.

Correct answer: B. IP3 is intracellular and eliminated by dephosphorylation, while DAG is membrane-restricted and eliminated by phosphorylation.

Which enzyme produces phosphoinositides such as PIP2? A. PI kinase. B. PLC. C. Adenylyl cyclase. D. Nitric oxide synthase.

Correct answer: A. PI kinase produces phosphoinositides, which are eliminated by PI phosphatases.

Which processes contribute to the regulation of intracellular calcium levels? (Select all that apply.) A. Calcium entry through channels. B. Release from intracellular stores. C. Removal by Ca²⁺-ATPase pumps. D. Calcium sequestration by proteins.

Correct answers: A, B, C and D. Calcium levels are controlled by the balance between release or entry and removal.

Which enzyme synthesises nitric oxide? A. Nitric oxide synthase. B. Guanylyl cyclase. C. Adenylyl cyclase. D. Phospholipase C.

Correct answer: A. Nitric oxide synthase (NOS) produces nitric oxide.

What is the downstream target of nitric oxide signalling? A. Adenylyl cyclase. B. Guanylyl cyclase. C. PI kinase. D. cAMP phosphodiesterase.

Correct answer: B. Nitric oxide acts on guanylyl cyclase, leading to cGMP production.

Explain how protein interaction surfaces contribute to signalling specificity.

Protein interaction surfaces have specific shapes that determine which proteins can bind. These interactions connect proteins in signalling pathways and ensure that signals are passed to appropriate partners.

Explain how post-translational modifications can act as molecular switches in signalling.

A modification such as phosphorylation can create a binding site recognised by another protein. The interaction occurs only while the modification is present, and can stop when the modification is removed.

Explain how one incoming signal can produce multiple intracellular outputs.

A signalling protein can carry multiple post-translational modifications. Different proteins recognise these modifications and bind, allowing separate signalling pathways to be activated.

Explain how a suppressor protein can ensure that a signalling response occurs only when several conditions are met.

The suppressor holds a signalling protein inactive. Only when the required signals bind and cause a conformational change is the inhibition released and an output produced.

Explain the importance of amplification in intracellular signalling.

Amplification allows a small initial signal to generate a large response. Small non-protein mediators can be produced in large quantities and diffuse rapidly, helping transmit signals over greater distances.

Compare the movement of proteins and small non-protein signalling mediators.

Small non-protein mediators diffuse faster and further than larger proteins. A kinase may be relatively anchored and move only around 10 microns, whereas cAMP can move further and calcium further still.

Explain why signalling mediator concentrations must be tightly controlled.

Their concentrations depend on production and elimination. Rapid degradation limits how long they remain active and prevents signalling pathways from continuing indefinitely.

Explain how changes in synthesis and degradation can alter signalling mediator concentrations.

Increasing synthesis raises mediator concentration, while decreasing synthesis lowers it if degradation remains unchanged. Reducing degradation allows accumulation, whereas increasing degradation lowers the concentration.

Describe the synthesis, degradation and targets of cAMP.

cAMP is synthesised by adenylyl cyclase and degraded by cAMP phosphodiesterase. It is produced in response to GPCR signalling and acts on kinases, channels and GEFs.

Describe the synthesis, degradation and targets of cGMP.

cGMP is synthesised by guanylyl cyclase and degraded by cGMP phosphodiesterase. Inputs include nitric oxide, rhodopsin and receptor guanylate cyclase. Its targets include kinases and channels.

Compare IP3 and DAG in terms of synthesis, degradation and location.

Both are produced by PLC. IP3 is intracellular and eliminated by dephosphorylation, while DAG is membrane-restricted and eliminated by phosphorylation.

Describe how intracellular calcium concentration is regulated.

Calcium enters through channels or is released from intracellular stores. It is removed by Ca²⁺-ATPase pumps and calcium-sequestering proteins. Its downstream targets include channels, kinases, enzymes, calmodulin and cytoskeletal proteins.

Describe nitric oxide signalling.

Nitric oxide is produced by nitric oxide synthase. It can act intracellularly or intercellularly and is eliminated through reactions with oxygen and heme binding. It acts on guanylyl cyclase, leading to cGMP production.