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ICB - Cell Signalling > General Principles > Flashcards

General Principles Flashcards

1
Q

What is meant by receptor activation?

A

Information transfer across the membrane - an extracellular signal binds a membrane bound receptor

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2
Q

What is downstream signalling?

A

Information transfer within the cytosol, often via branching and conversion of different signalling pathways

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3
Q

What are the 5 types of cellular signalling?

A

Contact dependent, paracrine, autocrine, synaptic and endocrine

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4
Q

Describe contact dependent signalling.

A

Receptor on the surface of one cell receives a signal on the surface of another cell - there must be direct membrane to membrane contact between the cells.

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5
Q

Give an example of contact dependent signalling.

A

T cell receptor signalling - TCR on T cell recieves signal from peptide bound to MHC on the surface of an APC.

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6
Q

Describe paracrine signalling.

A

A cell secretes a diffusible signalling molecule which can be received by nearby target cells.

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7
Q

Describe autocrine signalling.

A

Cell responds to a diffusible signal that it released itself - signal acts upon the cell it was released from.

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8
Q

Describe synaptic signalling.

A

Neurotransmitter is released from the presynaptic terminal and diffuses across the synapse to receptors on the postsynaptic terminal.

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9
Q

Describe endocrine signalling.

A

Glands secrete hormones which are then distributed throughout the body, via the vascular system, in order to reach target cells.

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10
Q

Give an example of paracrine signalling.

A

Growth factor signalling in tumour cells

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11
Q

Give an example of endocrine signalling.

A

Adrenaline signalling at adrenergic receptors

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12
Q

Describe signalling by lipophilic signalling molecules.

A

Lipophilic signals can cross the cell membrane and are recognised by nuclear receptors - leads to transcription of a target gene.

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13
Q

How is the ECM involved in cell survival signalling?

A

Signals to survive are typically received by the extracellular matrix, meaning that the cell is okay and can carry on as it is. If there is a growth factor present, the response may be to grow and divide. Growth factors may act with the ECM in cases where the cell has adhered to the extracellular matrix. Some signals will result in cell differentiation or apoptosis - if epithelial cells have become withdrawn from the ECM.

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14
Q

Signalling is context dependent, what does this mean?

A

The extracellular signalling molecule itself carries little information. Information transfer and the final output depends on the cell type and receptors expressed, cell cycle status, and ECM attachment of the target cell.

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15
Q

How does acetylcholine signalling result in different outputs in different tissues?

A
  • In muscle- acetylcholine (neurotransmitter) stimulates contraction and is recognised by a ligand gated ion channel.
  • In the heart- acetylcholine results in a decreased rate of firing and is recognised by a GPCR.
  • In the salivary gland- acetylcholine is recognised by a GPCR and causes secretion of amylase.
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16
Q

How is information transferred from the activated receptor to the effector?

A

By changes in the states of downstream proteins - conformational changes, PTMs in the ON state, change in localisation, binding/dissociation of inhibitory molecules.

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17
Q

What are intracellular signalling molecules?

A

Either proteins that act as molecular switches (via PTMs etc.) or second messengers, e.g. cAMP, calcium ions and DAG.

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18
Q

Give an example of how a PTM can change the conformation or activity of an effector protein.

A

Phosphate groups on ser/thr can activate a protein.

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19
Q

What are the main ways in which a PTM can affect a downstream signalling protein?

A

Changes to conformation/activity, promotion or prevention of protein binding, different subcellular localisation (PTM targets protein to a different region), induce or prevent degradation.

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20
Q

How does the presence of a PTM promote or prevent binding of the next protein in the signalling pathway.

A

PTMs can act as binding sites for another protein. For example, only the phosphorylated protein is recognized by the second protein, which only binds in the presence of the PTM - the second protein reads whether the PTM is present or not

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21
Q

How can a change in subcellular localisation affect a signalling pathway?

A

some proteins are only active when in certain cellular compartments

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22
Q

Give an example of a PTM that would decrease protein stability.

A

Ubiquitination - used for tagging proteins for lysosomal degradation.

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23
Q

What is meant by a writer, eraser, reader system?

A

Writer - enzyme that adds a PTM
Eraser - enzyme that removes the PTM
Reader - protein domain that recognises the PTM (e.g. next protein in the pathway)

This allows the presence of the PTM to be used as a molecular switch.

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24
Q

Describe the writer, eraser, reader system that involves a tyrosine kinase.

A

Writer - tyr kinase, adds phosphate
Eraser - tyr phosphatase, removes phosphate
Reader - SH2 domains found in effector protein

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25
What are the two classes of protein kinases?
Ser/thr kinases and tyr kinases
26
Give examples of ser/thr kinases.
MAPK, CaMK and PKA
27
Give examples of tyr kinases.
Src and tyrosine receptor kinases
28
How many protein kinases are encoded by the human genome?
~500; 400 ser/thr, 100 tyr kinases
29
How many protein phosphatases are encoded by the human genome?
~140, split into pSer/Thr and pTyr phosphatases
30
Describe the on and off states of a GTPase.
Has GTP bound when active and GDP bound when inactive.
31
How can a GTPase be switched off quickly?
A GTPase Activator Protein (GAP) can be introduced and the signal will last for a shorter amount of time. GAPs stimulate the enzyme to hydrolyse the bound GTP to give GDP - inactivating the GTPase.
32
How can a GTPase be switched on quickly?
A Guanine Exchange Factor (GEF) is introduced and exchanges GDP for GTP. GEFs stimulate the enzyme to release its GDP, this becomes quickly replaced by a GTP which is present at high concentration in the cytosol.
33
Give an example of a family of monomeric GTPases.
Rho GTPases- with RhoGEFs and RhoGAPs. | Ras GTPases- with RasGEFs and RasGAPs, used in the Ras-MAP kinase pathway
34
What is a preformed signalling complex?
Commonly used scaffold proteins that bind all the required players in a pathway - along the scaffold in the correct order
35
What are activated receptor scaffolds?
this is an alternative to using a preformed signalling complex. Receptor acts as a scaffold with docking sites for each of the required players in the correct order - can only bind once the receptor has been actvated
36
Give an example of when activated receptor scaffolds are used.
In receptor tyrosine kinase signalling.
37
Describe the modular architecture of signalling proteins.
each have a combination of protein domains, allowing for complexity in signalling pathways - each domain has its own binding partners.
38
What do SH2 domains recognise?
pTyr
39
What do SH3 domains recognise?
proline rich regions
40
What do PH domains recognise?
phosphorylated inositol
41
What is the advantage of cooperative recognition?
increases affinity and specificity
42
How do multiple binding sites favour high affinity binding?
Receptor tail (or lipid) has multiple sites that can be phosphorylated. The reader will continually bind/unbind depending on its dissociation constant. If there are more binding sites nearby, it is more likely that the reader will rebind following dissociation.
43
How does membrane association increase the efficiency of binding?
As the signalling protein is membrane anchored, it is held in the correct orientation for interaction with other signalling proteins - there is more chance of productive collisions between the proteins.
44
Give an example of where a fast signalling response is required.
In the developing nervous system
45
Give an example of where a slower signalling response can be used.
During cell differentiation.
46
Describe a fast response.
Usually involves protein conformational changes or phosphorylation as a molecular switch.
47
When are slow signalling responses used and what is involved?
Involved in gene regulation and is used to change the cell's behaviour.
48
Describe a transient response.
Has fast turnover of signal mediators, negative feedback loops and allows adaptation.
49
Give an example of when adaptation is needed.
Eyes need to respond quickly to adapt to bright light.
50
Describe a longer lasting response.
Has switch-like behaviour, positive feedback loops - cell is instructed to do something that is not easily reversed.
51
What is the advantage of a switch-like response?
Ultrasensitivity - a small range of input strengths will result in a large output.
52
What is the advantage of signalling cascades?
Amplifies the response - a single receptor firing can result in a large output.
53
What is adaptation?
Allowed for by negative feedback - if a signal persists, adaptation means that it will eventually become unrecognisable.
54
Describe adaptation in the movement of bacteria.
Bacteria need to be able to adapt and move away from a chemorepellent signal. Bacteria need to be able to switch from tumbling to swimming motions rapidly.
55
How do bacteria respond to a chemorepellent signal?
1. Receptor detects chemorepellent 2. Activated receptor activates CheA which activates CheY by phosphorylation. 3. CheY switches rotation of flagellum – tumbling switched on - FAST 4. Methylase constitutively methylates the receptor which is only active when methylated. 5. Demethylase (CheB) removes methyl groups to inactivate the receptor and switch off tumbling - SLOW NEGATIVE FEEDBACK
56
What are some methods of adaptation?
Removal of receptor from the cell surface - either for storage in endosome or degradation in lysosome. Receptor or signalling molecule inactivation. Inhibitor production and sequential binding to prevent downstream signalling events.
57
How are oscillating behaviours generated?
Delay between responses in a negative feedback loop. Switching off the input eventually causes the feedback loop to switch off - at this point if the signal is still present the response output will increase again.
58
Describe the nature of the oscillations in oscillating signalling behaviours?
Usually unstable and of low amplitude
59
Give an example of stable oscillations.
Seen in the xenopus oocyte cell cycle - as the negative feedback loop is switched off (due to input inactivation) positive feedback loops activate CDK which activates the negative feedback - giving stable oscillations
60
When are logic gates used?
During signal integration
61
When is there a response at an AND gate?
There is only an output when both inputs A and B are present.
62
Describe the GBD/B motif AND gate.
GBD and B domains in N-WASP bind to the output domain - results in inhibition. Binding of Cdc42 to GBD and PIP2 to the B motif is needed to release the output domain (VCA - binds actin) to activate N-WASP Arp2/3 mediated actin polymerisation - requires both signals.
63
What happens in coherent feed forward loops?
Fast response and slow response branches converge at an AND gate. There is only an output if the slow branch hits the AND gate at the same time as the fast branch.
64
Give an example of a coherent feed forward loop.
Involving the Fos1 transcription factor. FAST - Erk MAPK phosphorylates Fos1 to stabilise it SLOW - phosphorylation of a transcription factor, activates Fos1 expression OUTPUT - Fos-mediated transcription of a target gene in order to get an output there must be a long pulse of input - increases the chance of signal integration. Without phoshphorylation by the fast branch, and Fos1 produced in the slow branch is rapidly degraded.

ICB - Cell Signalling (5 decks)

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