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BMS 301 > Tumor Necrosis Factor - Dr Erdman > Flashcards

Tumor Necrosis Factor - Dr Erdman Flashcards

1
Q

what happen when homeostasis is disrupted?

A

> proliferation = cancer, autoimmune disease

> cell death = neurdegeneration, immunodeficiency

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2
Q

What is apoptosis

A
  • programmed cell death
  • maintain tissue homeostasis by balancing cellular life and death
  • when disregulated, cause premature cell loss
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3
Q

Features of apoptotic cells

A
  • membrane blebbing

* cellular shrinkage*condensation of chromatin

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4
Q

Explain the experiment that study the cell survival

A

FIRST EXPERIMENT
* victor hamburger
* chick embryo’s spinal cord ( motor neurons)
* remove limb bud
*number of motor neuron decrease dramatically in the limb of missing limb bud
* * conclusion **
limb bud is necessary for survival of sensory and motor neurons in the spinal cord

SECOND EXPERIMENT

  • extra limb bud transplanted
  • increase in the number of motor neurons

> > The neurotrophic hypothesis derived
- Target of innervation ( limb bud) secretes limiting survival factors (neurotrophic factor)- to generate a balance between the 1) size of organ, 2) the number of innervation

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5
Q

What is the neurotrophic hypothesis

A
  • Target of innervation ( limb bud) secretes limiting survival factors (neurotrophic factor)- to generate a balance between the 1) size of organ, 2) the number of innervation
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6
Q

How do we find out about the molecular basis of the neurotrophic factors?

A

experiment by cohen and montalcini

assay

  1. sympathetic ganglion extracted
  2. ganglion concentrated with cell bodies
  3. put some NGF
  4. observed axon growth
  5. later work to purify NGF

54: neurite outgrowth assay
60: NGF purified
69: NGF purified to homogeneity

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7
Q

What are Trk Receptor

A
  • Receptor tyrosine kinase
  • TrkA,B,C
  • Trk A binds to NGF
  • Trk B binds to BDNF
  • Trk C binds to NT-3

– this work shows that receptor tyrosine kinase not only regulate proliferation but also SURVIVAL (of neu=rite outgrowth )

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8
Q

Describe the experiment that proves Trk receptor can signal locally and retrogradely

A
  1. sympathetic neurons placed in petri dish with tight seal ( not allowing substance from outised to enter the soma area)
  2. in petri dish (PD)1 , put anti-NGF in soma… result = neurite failed to survived
  3. in PD 2 , put anti NGF in soma area. then put NGF in the neurite area. Result = neurite survived eventhough the soma received anti NGF
  4. suggestive that there is a retrograde transport mechanism of delivering NGF to the soma

CONCLUSION of the experiment

  1. Receptor can be endocytosed
  2. retrograde transport of the endosome ( containing the activated receptors)
  3. endosome receptor complex find other binding partner ( cell-body signalling speciic signalling components) to promote cell survival
  4. called signalling endosome
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9
Q

Explain signalling endosome

A
  • can be found in neurons
  • Ligand (NGF) bound to receptor (Trk A) in the –NEURITE– and become activated
  • the activated receptor in endosomed and known as signallling endosome
  • signalling endosome is retrogradely transported to the cell bodies
  • then binds to other signalling molecules ( such as cell-body specific signalling molecules)
  • promote cell survival
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10
Q

What the hell is p75

A

p75 LNTR / p75 LNGFR

  • p75 (L)ow affinity (N)euro(T)rophic (Re)eceptor
  • is NOT a receptor tyrosine kinase
  • founding member of the NGFR
  • contain the DEATH DOMAIN
  • Basically it is just historically important because people first discovered DEATH domain from p75. it is still a mystery~
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11
Q

TNF problem usually arise what problem

A

autoimmune disease

inflammatory disease

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12
Q

what structures are related to death domain?

A
  • Death DOmain
  • Death Effector DOmain (DED)
  • CARD domain
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13
Q

what will happen if you have FAS gene mutation

A
  • autoimmune disease
  • phenotype =
    a) increased proliferation of lymphocytes
    b) size increase in lymphoid organs like lymph nodes or spleen. non-malignant
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14
Q

what is a PTPN13?

A

Regulate membrane trafficking of FAS Receptor. so FAS R is now present at the CELL SURFACE

FAS R+ PTPN13 -> more FAS R at cell surface

overexpressed PTPN -> reduced FAS R in cell surface, cancerous cells ( no apoptosis )

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15
Q

FAS Rcan only exert it action when

A

it is in the cell surface ( regulated by PTPN13)

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16
Q

what happen when you have over expression of PTPN13

A

less FAS R on surface, become cancerous

17
Q

what is the structure of TNF alpha Ligand

A

Fas Ligand aka CD95 L is a transmembrane protein

classed as TNF -a

TRIMERIC

3 identical subunit

have JELLY ROLL STRUCTURE

18
Q

Describe the activation of the TNF receptor

A

the trimeric TNF-a causes TRIMERISATION of the FAS ligand

19
Q

What is the difference between the oligomerization of the RTK and TNFR?

A

the trimeric TNF-a (or FASL) will cause trimerisation of the TNFR (or FAS R)

the RTK will dimerize
-ligand will bind to each RTK (aka 1 ligand per RTK as oppose to 1 trimeric ligand per TNFR/ FASR)

20
Q

compare the RTK and TNFR/FASR clustering and intracellular domain changes

A

both will cluster (RTK dimerize, TNFR/FASR trimerize)

both oligomerization transduces signal by conformational change

in RTK, clustering of the Tyrosine Kinase Domain TKD cause transautophosphorylation, thus creating dosking site for SH2 and PLC gamma domain

in TNFR/FASR, trimerization causes clustering of the death domain, causing conformational change , thus creating a docking site for downstream signalling

21
Q

pre-ligand association domain

A

a theory

  • TNFR is a preformed trimer
  • like insulin
  • upon ligand binding, will have conformational change
22
Q

Describe the 2 model of activation of TNFR

A

a) TNFR have ligand binding domain, trimerisation is caused by trimeric ligand binding. not preformed
b) PLAD - pre ligand association domain, describe the idea that the PLAD domain assist in the formation of PREFORMED TNFR TRIMER. the proformed trimer is not active. can only be activated upon ligand binding . idea similar to insulin receptor

23
Q

p75 NTR binds to what

A

all (pro)-neurotrophin

24
Q

what effect does pro-neurotrophin and mature neurotrophin have on p75 NTR

A

proneurotrophin - cell death and degenration

neurotrophin - survival and neurite growth

25
Q

TNF super family are all membrane bound?

A

No. all of them are membrane bound but SOME of them have splice variant of soluble version

26
Q

TNFR superfamily

A
  • is much more complicated in terms of structure than RTKs
  • extracellular ligand binding domain are cycteine-rich
  • 2 subfamily ( with DEATH DOMAIN and without DD)
  • ones with DD are able to induce apoptosis
27
Q

Does phosphorylation takes place in TNF R?

A

NO in Death domain

–unlike in RTKs who will phosphorylate in the TKD upon TKD clustering and recpetor dimerization–

28
Q

Explain the extrinsic pathway of apoptosis

A
  1. (JUXTACRINE SIGNALLING) Fas L is membrane bound to other cell, usually immune cells such as T cells. But we also have splice variant of soluble TNF-a molecule
  2. TNFSF are trimeric, have jelly roll structures of beta sheets. Binds to corresponding TNFRSF.
  3. 2 ideas of TNFRSF activation, a) conventional. no ligand, no trimeric receptor. b) PLAD. Preformed Ligand Association Domain theory describe that the receptors are actually preformed trimers. But only activated upon ligand binding
  4. ligand binding > Receptor activation > conformational change in the DEATH DOMAIN
  5. death domain clustering upon receptor trimerisation, conformation change creates docking site for downstream signalling
  6. INSERT PICTURE HERE
  7. death domain in the FASR will bind to DeathDomain of FAS Associated Death Domain (FADD).
  8. FADD has DD and Death Effector Domain (DED)
  9. FASR DD binds to FADD DD
  10. FADD DED binds to DED on caspase 8/10 prodomain

11 INITIATOR caspase 8/10 have a) DED in the prodomainb) large a subunit c) small b subunit.

EEFECTOR caspase only have Large a subunit and s b subunit. does NOT have DED doamain in the prodomain. Prodomain will be cleaved by active caspase

12) 2 x L and 2 X S subunit of the same type of caspase becomes the active caspase
13. DED of initiator caspase will be cleaved. active initiator caspase allows for more effector caspase production by cleaving the prodomain of the effector caspase ( no DED )
14. a lot of caspase —» APOPTOSIS
15. effector caspase is NOT membrane bound/ FADD bound and does NOT have a DED in its prodomain

29
Q

Why do we have a lot of stages in a pathway

A
  1. amplifaction of signal (such as in RAS RAF MEK ERK )

2. more possible level of regulation

30
Q

How do we measure the activation of the caspase?

A

western blot

> look out for new band showing up ( caspase/protease)

> greater or lesser intensity

31
Q

type 1 cells vs type 2 cells in TNFR?

A

Type 1 cell&raquo_space; extrinsic only

Type 2 cell&raquo_space; extrinsic PLUS INTRINSIC pathway

32
Q

Describe type 2 cell in TNF R

A
  1. Caspase 8 cleaved Bid into truncated Bid (tBid)
  2. 2 tBid undergo myristoylation of N-terminal glycine by NMT and translocated to the mitochondria
  3. myristoylated tBido on the mitochondria facilitate recruitment of Bak, the protein that will form the pores that releases cytochrome c
  4. activation of a channel within the mitochondria so that cytochrome c can be released from the mitochondria
  5. Cytochrome c activate Apaf. Apaf have CARD domain. binding of cytochrome c to apaf will assemble a few Apaf into APOPTOSOME
  6. Apoptosome = molecular machinary to activate initiator caspase (procasoase 9)
  7. Apoptosome will cleave CARD domain on m the procaspase 9
  8. active caspase 9 activate procaspase 3
33
Q

What is the significance of truncated Bid

A

Bid -> tBid via cleavage by caspase 8&raquo_space;> creating new N terminus and C terminus (ye la kan dah cleave)

tBid translocate to the mitochondria and undergo myristoylation, the lipid modification where the N-terminal glycine is added with myristic acid by NMT N-myristoyltransferase.

this facilitate the recruitment of Bak, the protein that will form pores that release cytochrome c from the mitochondria

*New N terminal GLYCINE will be added Myristic acid by NMT (N- myristoyltransferase)

tBid undergo Myristoylation , a type of lipid modification.

34
Q

What is an apoptosome

A
  1. a structure formed by several Apaf with bound cytochrome c
  2. the CARD domain of the Apaf form the middle portion
  3. Apoptosome will cleave CARD domain from the procaspase 9
35
Q

What is other pathway of apoptosis by the FAS receptor?

A

NF-KB

FAS are activating the extrinsic, intrinsic and NFKB pathways

36
Q

How can we measure apoptosis

A
  1. Phosphatidyl serine (component of plasma membrane)

> in healthy cell, PS found only in the inner leaflet

> PS will flip from inner leaflet to outer leaflet in dying/ apoptotic cells

  1. Annexin5-FITC (annexin5 with fluoroform) added to the culture, annexin 5 will bind to PS.

> > the annexin5-FITC is not permeable, so cannot visualise those in the inner leaflet of healthy cells

  1. in healthy cell, no PS staining.

BMS 301 (5 decks)

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