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MIMS > Cell Signalling And Protein Sorting > Flashcards

Cell Signalling And Protein Sorting Flashcards

1
Q

How many cells are in the body

A

10^13

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2
Q

How thick is the plasma membrane

A

2 molecules thick

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3
Q

How do lipophilic substances pass across the plasma membrane (PM)

A

They dissolve in the PM and so can pass through it

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4
Q

How do channels work

A

Allow materials to flow downhill into or out of a cell

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5
Q

What does it mean for production if chemical signals are lipophilic

A

They must be made on demand as they cannot be retained

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6
Q

What do transporters do

A

Export chemical signals from cytosol across PM

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7
Q

Give 3 ways for cells to receive a signal (ie get across the PM)

A

Lipophilic pass through the PM to reach intracellular targets

Extracellular messenger may be recognised by a binding site in a channel (to open or close it) and the flux of ions across PM changes

Allosteric PM-spanning protein (where intracellular side of protein changes shape)

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8
Q

3 ways to send our cellular information

A

Diffusion across PM

transporters

Vesicles

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9
Q

How is the nucleus separated from the cytosol

A

By a double membrane penetrates by nuclear pores

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10
Q

What is the ER and what does it contain

A

Endoplasmic reticulum

A lumen where proteins mature and Ca2+ is stored

The ER also contributes to lipid and steroid synthesis

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11
Q

Why is rough ER rough

A

It is studded with ribosomes

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12
Q

Describe the Golgi apparatus

A

Stacks of tubules linked to the ER

it has an important role in maturation/ glycosylation of proteins and their dispatch

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13
Q

What are almost all proteins encoded by

What is the exception

A

Nuclear genes

Those encoded by the small mitochondrial genome

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14
Q

What is the overall process of making proteins

A

Their DNA is transcribed into mRNA which is processed in the nucleus before export through the nuclear pores. Within the cytosol, mRNA provides the template for synthesis of proteins by ribosomes

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15
Q

How many genes are mitochondrial

A

37

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16
Q

How can disease caused by defects in mitochondrial genes be avoided

A

Use an enucleated egg from a surrogate with normal mitochondria to serve as the host for parent’s DNA/nucleus

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17
Q

Where do most proteins begin there life

Then what happens

A

On a cytosolic ribosome

Address labels in the primary structure dispatch proteins to different destinations

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18
Q

How do fully folded proteins re-enter the nucleoplasm

A

Nuclear localisation signals allow them to move Through nuclear pores

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19
Q

If the protein does not stay in the cytosol or go to the nucleoplasm, what happens to them

A

They must cross a membrane and therefore must stay unfolded

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20
Q

What is post translation targeting and where does it occur

A

When the protein has been fully translated but doesn’t fully fold until it has crossed the membrane

Mitochondria and peroxisomes

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21
Q

What is co-translational targeting

A

When proteins destined for the ER are dispatched before translation is complete

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22
Q

What is a NLS

A

A nuclear localisation signal: a stretch of 6 +/ve residues anywhere in the primary sequence, recognised by importin

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23
Q

How can nuclear translocation be regulated

A

By unmasking a NLS

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24
Q

How do proteins reach the peroxisome

When does this go wrong

A

The C terminal sequence (Serine-Lysine-Leucine) is recognised by PTS1 receptors and guides it to peroxisome membrane

In Zellweger Syndrome, when the PTS1 is non functional

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25
Q

Why is mitochondrial targeting complex

A

There are 4 destinations:

Inner and outer membranes, intermembrane space, and matrix

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26
Q

How do cells target for mitochondrial matrix proteins

A

N-terminal amphipathic helix is recognised by a chaperone protein

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27
Q

Is targeting for peroxisomes and mitochondria reversible

A

No

It is irreversible

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28
Q

How is co-translational targeting used for proteins to the ER

A

A hydrophobic signal sequence at the N terminal (for luminal proteins) or internally (for integral membrane proteins) is recognised by a large protein-RNA complex

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29
Q

What are ER proteins from co translational targeting recognised by

A

Signal Recognition Particle (SRP)

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30
Q

What happens when SRP recognises a protein

A

The protein’s translation stops so SRP-nascent peptide chain can associate with the SRP receptor on the ER membrane

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31
Q

What does the SRP receptor associate with? What does it do when this has happened?

A

Translocon (a protein channel in the ER membrane)

Checks the signal sequence of the peptide

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32
Q

What happens once the SNP receptor has checked the peptide

A

The nascent peptide chain is inserted into the translocon and SRP is released for reuse.
Protein synthesis continues, threading the growing protein through the translocon

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33
Q

What is important when the nascent peptide is inserted into the translocon

A

It is the right orientation as this cannot be changed later

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34
Q

The translocon continues to survey the growing protein. What is it looking for and what happens if it is found?

A

Stretches of hydrophobic residue

Retained in the translocon to be formed into membrane spanning domains

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35
Q

What happens when the growing peptide emerges into the ER lumen

A

It is further scrutinised and a protease cleaves any N terminal signal sequence.
Chaperone proteins pull it into the lumen and help it fold and help form disulphide bonds for example

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36
Q

Give a summary of co-translational targeting of proteins to ER

A

Recognition of signal peptide by SRP

SRP stops translation

SRP conveys peptide to SRP receptor in ER

SRP is recycled while translation continues and protein is pulled into lumen to be defined and checked

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37
Q

What happens to faulty proteins in the ER

What proportion are faulty

A

They must be removed as they may aggregate/ clog the system

> 30% of all ER proteins are sent for degradation

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38
Q

How are faulty proteins removed from the ER

A

ERAD allows them to be sent back to the cytosol through a pore associated with ubiquitin ligases

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39
Q

How are faulty proteins marked for degradation

A

Ubiquitin ligase attaches ubiquitin to Lys residues on the protein

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40
Q

What is defective in Parkinson’s disease

A

Parkin- a subunit of ubiquitin ligase

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41
Q

What is the most common cause of Cystic fibrosis

A

CFTR is degraded by ERAD before it reaches the PM where it should modulate Cl- transport

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42
Q

How is ΔF508 treated

A

Drugs help the CFTR avoid ERAD and reach the PM

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43
Q

What does cytomegalovirus do

A

Hijacks ERAD pathway by expressing a protein that associates with MHC (which usually indicates that a cell is infected)
By targeting MHC for degradation, the virus remains undetected

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44
Q

What happens to proteins that were folded and N- glycosylated in the ER

A

Collected into COPII vesicles and conveyed to the cis Golgi, where the sugar structures are modified

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45
Q

What happens in the Golgi to proteins destined for lysosomes

A

The sugars are modified to include mannose-6-phosphate (M6P)

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46
Q

How does all trafficking from the ER occur

A

In vesicles

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47
Q

What is one of the most important organelle identity label?

Describe it

A

Rabs

Small G proteins that are active when GTP is bound and inactive with GDP bound

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48
Q

Describe rab cycle

A

Rab-GDP is recruited by an intracellular membrane but only activated if the membrane has the correct proteins for GDP to swap for GTP.
when another organelle recognises the rab-GTP it will hydrolyse it if it has the correct proteins. This hydrolysis releases the rab and GDP for the cycle to restart

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49
Q

Other than rabs, what else provides identity labels

A

Lipids

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50
Q

What do COPII proteins do

A

Bind to a specific Cytosolic sequence of proteins in the ER membrane, collecting them into clusters to be cut off as small vesicles coated in COPII

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51
Q

What happens to COPII vesicles

A

They travel along microtubules to the cis Golgi and shed the COPII coat to reveal their identity labels

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52
Q

Why must the COPII cost be shed

What do SNARE proteins do

A

COPII must fuse with cis Golgi but not other organelles

Mediate fusion of 2 organelles by drawing their membranes close together

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53
Q

What do COPI do

A

COPI vesicles carry cargo from Golgi back to the ER

The cargo is recognised by a KDEL sequence which binds to a KDEL receptor.

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54
Q

What is the sequence after the KDEL binds to the KDEL receptor

A

Cargo is concentrated, pinched off into vesicles, uncoated for recognition and then the vesicles fuse with the membrane

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55
Q

What sorts protein to different destinations

A

Trans Golgi

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56
Q

How are proteins destined for lysosomes recognised

When do they detach from this

A

M6P

When they reach the late endosomes, there is a low pH causing the M6P receptors to dissociate and the cargo passes on to the lysosomes

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57
Q

What happens to the M6P receptor when it is dissociated

A

Sorted into vesicles and returned to the trans Golgi

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58
Q

What is Gaucher disease

How can it be treated

A

An enzyme is missing meaning M6P receptors are imperfectly targeted

An M6P modifies form of the enzyme can be given and it will be endocytosed by the M6P receptor and delivered to lysosomes

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59
Q

What are the common themes in protein trafficking

A

Segregation of cargo and coating
Vesicle formation and transport
Uncoating and recognition
Fusion

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60
Q

What is familial hypercholesterolemia

What causes it

A

Where plasma cholesterol levels are too high

Mutation in LDL receptors so LDL is trapped in the ER and there is no signal sequence

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61
Q

What is “bad cholesterol “

A

LDL

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62
Q

How is LDL taken up

A

LDL receptors bind to ApoB-100 component of LDL
Cytosolic side of receptor interacts with AP2 which interacts with clathrin
Clathrin gathers the LDL receptor and cargo into a clathrin Coated pit which is trafficked to endosomes
In the acidic endosome lumen, LDL dissociates from the receptor and and LDL passes to lysosomes where ApoB-100 is degraded

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63
Q

Where do protein trafficking pathways begin and converge

A

In the ER
or at the PM

Both converge at the Golgi

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64
Q

What are the only signals that enter the cell to regulate activity

A

Lipophilic signals

All other signals are specifically recognised at the extracellular surface of the membrane spanning receptor and the signal is transmitted inside the cell

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65
Q

2 ways that extracellular signal recognition transmits a signal to the interior

A

Receptor forms an ion channel

Allosteric proteins, which transmit conformational changes

66
Q

What mediates the faster form of intercellular communication

A

Ion channels (they might allow several million ions to pass downhill each second)

67
Q

What part of the cell does the ion fluxes of APs affect?

A

Membrane potential, NOT intracellular activity

68
Q

How is intracellular activity regulated in a neuron

A

Membrane potential changes must be transduced into Ca2+ which enters the cell

69
Q

What are nicotinic ACh receptors in muscle permeable to

What do they respond to

A

Na+ and K+

ACh

70
Q

How is myasthenia gravis

A

Drugs that interact with nicotinic ACh receptors

71
Q

Where are GABA and glycine receptors found and what are they permeable to?

A

CNS

Cl- permeable

72
Q

What js the common structure of voltage gated cation channels

A

24 membrane spanning regions around a central pore

73
Q

For Na+ and Ca2+ channels what is the channel formed from

What about for K+

A

A single protein

4 proteins

74
Q

Describe the selectivity filter of Ca2+ channels

A

2 Ca binding sites which both can bind to Ca tightly

When both are occupied, electrostatic repulsion between them causes one to be dislodged

75
Q

How are Ca channels selective against monovalent cations

A

The repulsion would not be enough to dislodge the other bound Ca

76
Q

How do VG Ca channels close

A

Residues at the Cytosolic tip of the pore linking helix come together like the top of a teepee, occluding the channel

77
Q

How are VG Ca channels opened

A

A voltage sensor moves outwards when the membrane depolarises
This pulls on a short Cytosolic helix that links the voltage sensor to the TMD forming the pore
This twists the pore helices, opening up the ‘teepee’

78
Q

Give some general features of signalling pathways (4)

A

Allostery
Amplification
All steps are reversible
Integration

79
Q

What is an easy means of reversibly regulating activity

How often is this used

A

Phosphorylation

50% of all cellular proteins are phosphorylated

80
Q

How common is tyrosine phosphorylation

A

rare, but important (0.05%)

81
Q

How many tyrosine kinases in man

A

85

82
Q

How is receptor tyrosine kinase activated?

What happens after activation ?

A

Activation begins with binding of dimeric extracellular signal, which causes the receptor to dimerise

Dimerisation activates Cytosolic tyrosine kinase, allowing each subunit of receptor to trans-phosphorylate Tyr residues on the other
This allows the proteins which can bind to phospho-Tyr to dock here and be recruited for signalling complexes

83
Q

What is the insulin receptor structure?

What happens when insulin binds?

A

Dimeric

Re-arranges dimer so intracellular tyrosine kinase is activates to cause trans-phosphorylation

84
Q

What happens after trans-phosphorylation in an insulin receptor

A

IRS-1 is recruited by phospho-Tyr
IRS-1 is further phosphorylated to provide docking sites for other proteins, such as PI3K
Active PI3K phosphorylates PIP2 to give PIP3 which is the scaffold for further recruitment

85
Q

What does PIP3 do

A

Recruits Akt2 and PDK1, which both phosphorylate Ser and Thr

Recruitment to PM, causes Akt2 to change shape and becomes a substrate for PDK1 so at PM PDK1 phosphorylates Akt2

86
Q

When is Akt2 maximally active

Why

A

In fed cells stimulated by insulin

It is phosphorylated by PDK1 after insulin binds and is further phosphorylated by mTORC2 which is activated only in the fed state

87
Q

What does Akt2 do when activated

A

It causes further phosphorylation, leading to stimulation of glycogen synthesis, inhibition of glucose synthesis, and insertion of glucose transporters into the PM

88
Q

2 classes of allosteric receptors

A

GCPRs and tyrosine kinase receptors

89
Q

How do active GPCRs work

A

Catalyse activation of G proteins by causing them to release the GDP the have bound in the inactive state and replace it with GTP
The active GTP bound G protein then signals onwards

90
Q

What features does the sequence from cAMP to activation of glycogen phosphorylase show

A

Amplification
Integration (cAMP both stimulates glycogen breakdown and inhibits glycogen synthesis)
Protein phosphorylation

91
Q

What did Rodbell serendipitously show

A

That both ATP and GTP were required to allow liver membranes to make cAMP

92
Q

What can be used to treat HIV using GPCRs

A

Maraviroc binds to the recognition site of CCR5 chemokine receptor so I cant bind to HIV coat proteins

HIV cannot then infect the T cells

93
Q

What must HIV do before infecting cells

A

It’s coat proteins are recognised by a co-receptor in the host membrane, comprising a chemokine receptor (a GPCR) and a CD4 receptor (in T lymphocytes)

94
Q

What does vasopressin do

A

Controls V2 receptor (a GPCR) which controls water reabsorption in the Kidney

95
Q

How does the V2 receptor control water reabsorbtion

What does mutation cause

A

Through cAMP, causing insertion of water channels into the PM of collecting tubules

Congenital Nephrogenic Diabetes Insipidus

96
Q

What does TSH do

What can mutations cause

A

Stimulates release of hormones from the thyroid

Constitutive activation of TSH receptor leading to hyperthyroidism

97
Q

Is GDP dissociation from inactive G protein slow

A

Yes very slow

98
Q

How do GPCRs assist G protein activation

A

Active GPCRs speed up GDP dissociation so GTP can bind instead

They are exchange catalysts

99
Q

Why is the dissociation of GDP an important step in G protein activation

Where can this be seen

A

Rate limiting step

Boys with mutated G protein (in αs ) so GDP binds weakly, leading to spontaneous activation -> cool testes -> precocious puberty

Unless GDP dissociation is slow there is nothing for the GPCR to control

100
Q

How are GPCRs exchange catalysts

A

Reduce AE of GDP dissociation from G protein for activation

Can activate many G proteins in its life time

101
Q

How are G proteins deactivated

A

Intrinsic GTPase acts on a molecular clock. It will hydrolyse the GTP to deactivate the G protein

102
Q

What contributes to reward effects of alcohol consumption in alcoholics

How do they signal

A

Stimulation of dopamine and GABAb receptors (GPCRs)

Through G protein Gi

103
Q

What is the i for in Gi

A

Inhibit (inhibits cAMP formation)

104
Q

What does RGS6 do

A

Enhances the GTPase activity of Gi

105
Q

How are alcoholic mice different

What does this mean

A

RGS6 is up regulated so more intense stimulation is required for same effect

106
Q

What treatment may help alcoholics

A

RGS6 knockout mice do not become alcoholic so drugs which inhibit RGS6 might treat alcoholics

107
Q

Structure of G proteins activated by GPCRs

A

Trimeric

βγ subunits are inseparable and anchored to PM
α subunits bind and hydrolyse GTP
GDP is held by an inactive α in a pocket so GDP cannot escape

108
Q

What does cholera do

A

Modifies αs to block GTPase activity resulting in over production of cAMP in gut endothelium

109
Q

How does whooping cough occur

A

Pertussis toxin covalently modifies αi uncoupling G protein from GPCR

110
Q

How do GCPRs promote G protein activity

A

Opening deep pocket containing GDP

111
Q

What dictates whether a G protein is active

A

The 3rd P group on the guanine pushes apart Thr and Gly

112
Q

What are the consequences of GTP binding and the trimeric G protein dissociating

A

GPCR is separated and can now activate another protein

The α-GTP and βγ can now regulate their effectors (α-GTP acts GTPase)

113
Q

How is ACh related to GPCRs ?

A

ACh stimulates GPCRs in the heart

The response is mediated by the dissociation of subunits of Gi that slows heart rate and reduces force of contraction

114
Q

What is the structure of a GPCR

What happens when activated

A

Extra cellular N terminus
7 TMDs
Cytosolic C terminus

Extracellular signal stimulates N and a cleft opens between Cytosolic ends of TMDs 3,5,6, and 7 where the α subunit of the G protein can insert, causing the GDP to be released

115
Q

Are intracellular messengers usually restricted?

A

Yes they are usually restricted to the cell in which they were made

Different GCPRs converge to regulate intracellular activity through a limited repertoire of intracellular messengers

116
Q

How is cAMP made

What is its most important target

A

Made from ATP by adenylyl Cyclases (AC) and inactivated by phosphodiesterases (PDEs)

Protein kinase A (PKA)

117
Q

How many forms of AC are there

How are they activated and respond

A

9

Stimulated by G protein sub unit αs-GTP
different responses to other intracellular signals (including Ca2+)

118
Q

What are most PDEs inhibited by

A

Caffeine and theophylline (used to treat severe asthma)

119
Q

What is the target for Ciloztazol,

A

PDE3 to treat obstructed peripheral arteries

120
Q

What does PDE3 do

A

It breaks down cAMP to AMP

It is found in vascular smooth muscle and is stimulated by PKA (cAMP therefore stimulates its own breakdown)

121
Q

Give the structure of PKA

A

Tetramer: 2 Regulatory subunits which each bind 2 cAMP molecules
2 catalytic subunits which phosphorylate protein substrates
Each regulatory subunit contains a pseudo-substrate domain

122
Q

How do PKA molecules work

How is their work undone

A

When R binds cAMP the subunits fall apart and the blocked active site (from the pseudo substrate) is revealed allowing the real protein to be phosphorylated

Protein phosphatases

123
Q

What are AKAPs

A

Scaffold proteins that anchor R subunit on PKA

A Kinase Anchoring Protein

124
Q

Give the structure of cGMP

A

Made by guanylyl cyclases

Degraded by PDEs and is mediated by PKG

125
Q

What is the target of viagra

A

PDE5 which selectively degrades cGMP

126
Q

How does Viagra work (in relation to cGMP)

A

Prevents degradation of cGMP in blood vessels of the penis, causing dilation and accumulation of blood

127
Q

What is the substrate in the PLC pathway

What intracellular messengers does it provide

A

PIP2

DAG
IP3
PIP2 itself regulates ion channels so decrease in [PIP2] after PLC is a signalling mechanism

128
Q

How is DAG an intracellular messenger

How is it deactivated

A

Remains in PM to activate PKC

Phosphorylation

129
Q

What are phorbol esters

Why

A

Tumour promoting molecules

Look like DAG and activate PKC but cannot be degraded

130
Q

Describe IP3

How is it deactivated and what is the final step of this degradation

A

Water soluble
Enters cytosol and stimulates Ca release from ER

By dephosphorylation
IP3 into inositol

131
Q

What happens to deactivated products of PLC

A

Reunited and synthesised back into PIP2

132
Q

What is used to treat bipolar? Why?

A

Lithium ions

Blocks degradation of IP1 to inositol
Blocking this reduces PLC signalling in over active brain areas by preventing reformation of PIP2

133
Q

How is PLC (phospholipase 3) pathway activated

A

By GCPRs or PTKs

134
Q

What did Roger Tsien develop

A

Ca indicators

135
Q

How are Ca signals developed

How does this change as stimulus increases

A

As Ca spikes

Frequency increases

136
Q

What are Ca spikes good for?

A

Protect cells from damaging effects of excessive increases in Cytosolic [Ca]

Allow digital signalling

Spatially organised Ca signals allow Ca from different sources to be delivered to different targets

137
Q

Adipose tissue does not have glycerol kinase. What does this mean?

A

If glucose is low then glycerol-3-phosphate will be low. FFA cannot be re esterified and will be exported

138
Q

Name an enzyme adipose releases

A

AMPK

139
Q

What causes RAS to exchange GDP for GTP

A

SOS

140
Q

Are λ phage vectors only used with cDNA libraries

A

No

141
Q

Name a protein that recognises specific DNA sequences using its α helices

A

Fos- Jun

142
Q

Name a monoclonal antibody that binds to EGFR

A

Cetuximab

143
Q

What is linkage

A

When a pair of genes do not demonstrate independent segregation

144
Q

Describe what happens when insulin binds to its receptor (up to PIP3)

A

Insulin receptor is a dimer and when insulin binds the dimer rearranges so trans phosphorylation of the tyrosine residues can occur.

Now IRS1 can bind to the receptor and be phosphorylated. IRS1 is now the docking site

PI3K binds to IRS1. PI3K is now active and can phosphorylate PIP2 to PIP3

145
Q

Which subunit of PI3K allows it to bind to IRS1

A

it’s p85 adaptor subunit

146
Q

After insulin has bound to its RTK and PIP3 has been made, what happens

A

PIP3 recruits Akt2 and PDK1 to the PM.

At the PM, Akt2 changes shape to become a substrate for PDK1. Akt2 is thus phosphorylated by PDK1 and mTORC2

Now that Akt2 is activate, it can recruits GLUT4 to the PM and increase glycogen synthesis

147
Q

What are the actions of Akt2

A

Recruit GLUT4 to PM

Increase FOXO activity which inhibits gluconeogenesis

Reduce activity of glycogen synthase kinase, thereby increasing glycogen synthesis

148
Q

Where does the G protein insert Into the 7 TMDs of the GPCR

A

Between the cytosolic ends of TMDs 3,5,6

149
Q

Which G protein subunit has GTPase activity

A

α

150
Q

Name 2 diseases related to Rab

A

Charcot Marie Tooth disease (rab7 mutation)

Legionnaire’s Disease (bacterial modifies rab1 to divert ER to a vacuole)

151
Q

Which domain in GRB2 binds to the activates RTK

A

AH2 domain

152
Q

What does RAF do

A

It is a protein kinase that is activated by binding to a small G protein

153
Q

Name a amino acid directly involved in the urea cycle

A

Arginine

154
Q

Give 4 glucogenic and 4 ketogenic amino acids

A

Ketogenic: tyrosine, leucine, tryptophan, isoleucine

Glucogenic: arginine and glutamine (these both make glutamate, which makes α ketoglutarate); methionine (which makes succinyl CoA) and phenylalanine (which makes fumarate)

155
Q

How is HSL activated

A

phosphorylation by PKA activated by adrenaline

156
Q

What is AKAP

A

Scaffold proteins that associate with PKA

157
Q

What does PLC do

A

Phospholipase C

Hydrolysis PIP2 into IP3 and DAG

158
Q

Which amino acid forms an isopeptide bond between ubiquitin and target protein

What is the ubiquitin ligase

A

Internal lysine

E3 enzyme

159
Q

What is trisomy 18

A

Edward’s syndrome

160
Q

What causes Leber Hereditary Optic neuropathy

A

A mitochondrial disease with matrilineal heritage

161
Q

What is KDEL

A

C terminal sequence that ensures nascent soluble proteins are retained in the ER

K- lysine
D - aspartic acid
E - glutamate
L - leucine

MIMS (12 decks)

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