begin of exam 3 stuff. signaling pathways for gene activity

Question 1

most famous oncogene? what are two mechanisms that cause it to stay on

Answer 1

Ras. if it is always on (always GTP loaded) then it can’t hydrolyze GTP or it can’t attach to a GAP to turn off

Question 2

long term signaling changes what for proteins?

Answer 2

it changes transcription

Question 3

what are the four types of signaling transduction?

Answer 3

protein kinase cascades: 1 = TGF beta, 2= cytokine receptor, 3= receptor tyrosine kinase, 4 = G protein-coupled receptors

Question 4

cytokine signaling: what should you think

Answer 4

jak signaling (just another kinase); these are critical to transcription factor activation

Question 5

TGF beta is?

Answer 5

simplest pathway, typically inhibitory, represses cell proliferation; receptor binds ligand and the first target is the transcription factor.

Question 6

how many steps between TGF beta and nucleus

Answer 6

receptor; transcription factor; DNA. 3

Question 7

transcritption factors usually reside __ in a __ form

Answer 7

cytoplasm; inactive

Question 8

what does transcrition factor do?

Answer 8

undergo a targeting trafficing event then go to the nucleus to do their job

Question 9

what are some ways you can activate a transcription factor (TF)

Answer 9

can disrupt ); can proteolytically cleave and allow the TF to go to the nucleus(NF kappaB)

Question 10

what does TGF beta stand for?

Answer 10

transforming growth factor

Question 11

receptor mediated endocytosis can regulate things by?

Answer 11

many receptors will be endocytosed and destroyed after they start the cascade. if you have a problem here, thats bad

Question 12

in general how does the TGF beta signal work?

Answer 12

what signal is secreted from cell, they are bound do be inactive. to be active you have to proteolytically process in extracellular matrix. [you can either destroy the propeptide or you can bring in another one to compete for interaction]

Question 13

what holds the TGF ligand together

Answer 13

disulfide

Question 14

what do rII and rIII do

Answer 14

3 has an extraplasmic part. its a shuttle. it collects things and keeps them until RII can come over and pick it up. that one has a protein kinase that is always on. it allows us to activate RI

Question 15

what does RI do when its turned on?

Answer 15

it doesn’t bond with a ligand, so it has to be turned on by RII but it is a serine threonine kinase. it phosphorylates Smads

Question 16

where are TF in relation to TGF beta?

Answer 16

smads (TF) are directly downstream

Question 17

how many smads are there

Answer 17

multiple
R-smad = receptor directly changed by TGF
I-smad = inhibitory nuclear transcription factor
Co-smad =

Question 18

does RIII have to play a role?

Answer 18

nope. it may not be required since this is a multipart receptor complex

Question 19

what keeps smad 3 in an autoinhibited form

Answer 19

protein protein interaction between smad3 and MH parts

Question 20

what happens when smad is changed by the RI complex

Answer 20

conformational change exposes an NLS

Question 21

what is an NLS

Answer 21

nuclear localization signal (usually basic charged amino acids. sometimes two stretches) it tells you where a protein should go

Question 22

what is the receptor for NLS

Answer 22

importin

Question 23

so to get into the nucleus smad hooks up with __ __ and __

Answer 23

co-smad 4, beta importin, NLS

Question 24

what process would inactivate TGF beta signaling

Answer 24

phosphorylation activates, so phosphatase will deactivate.

SnoN and Ski are inhibitors of the transcription factor complex

Question 25

what does ski stand for

Answer 25

sloan kettering institute. this guy was identified as a tumor inhibitor. its a supressor of the transcription factor complex by bringing in a histone deacetylase that leads to gene inactivation

Question 26

disruption of TGF beta results in?

Answer 26

cell transformation

example: pancreatic cancer has a deletion of co-smad4 so they can NOT inhibit gene transcription

Question 27

what is loss of TGF beta RI or RII associated with?

Answer 27

retinoblastoma, colon cancer, liver cancer

Question 28

TGF beta controls

Answer 28

cell proliferation and cell differentiation.

Question 29

if you lose the peptide hormone for miostatin, what happens

Answer 29

you get a buff bull

Question 30

when you see cytokine signaling, what should you think?

Answer 30

promotes cell growth and differentiation; activation of gene expression

Question 31

what is the cytokine signal

Answer 31

small polypeptide.

Question 32

examples of cytokines

Answer 32

prolactin, interferon alpha, and erytropoietin

Question 33

what does erythropoetin (epo) do

Answer 33

signal that you should make more red blood cells; PREVENTS cell death

Question 34

does the intracellular domain of the cytokine receptor have a kinase

Answer 34

NO. it is attached, however, to JAK (he IS a kinase). he is activated by phosphorylation (usually on tyr residues)

Question 35

how do you dock additional proteins on phosphorylation sites?

Answer 35

SH2 loves to bind phospho-tyr to a protein

Question 36

what is STAT

Answer 36

SH2 domain plus a dna binding domain. it dimerizes and goes to the nucleus and goes to work

Question 37

what is STAT 5 involved in

Answer 37

interacts with BCL-xL for programmed cell death (see apoptosis lecture) to INHIBIT programmed cell death

Question 38

how do you turn off JAK/STAT signalling

Answer 38

SHP1 dephosphorylates JAK. this is short term

SOCS destroy JAK by proteosome and polyubiquitization

Question 39

SOCS protein has two parts. what are they

Answer 39

the SH2 domain and SOCS box

Question 40

what is the famous cancer signalling pathway

Answer 40

receptor tyrosine kinase (RTK)- Ras-MAPK cascade

Question 41

how is RTK different from the other two signals

Answer 41

the kinase recruits a G protein to the cell surface and activates it (Ras in this case) which does another cascade through MAPK

Question 42

what do you HAVE TO KNOW

Answer 42

ras is typically mutated in most oncogenes (disruption of Gly12) this leads to a protein that is always GTP loaded that blocks the binding of a GAP and lock the ras in the active GTP-bound state

Question 43

what is her 2

Answer 43

human epidermal growth factor receptor 2

Question 44

what are the ligands for the RTK? what does that do to the receptor

Answer 44

peptide or protein hormones like NGF; dimerizes

Question 45

there is a battery of ___ and ___ for RTK

Answer 45

multiple ligands, multiple receptors, mix and match for different combos

Question 46

when you phosphorylate the receptor on the cytosol side, what gets recruited?

Answer 46

something with an SH2 domain. GRB2

Question 47

how do you turn on Ras with RTK?

Answer 47

GRB2 is the docks and is a recruiter of Ras and SOS. SOS is a GEF that is attracted to GRB2’s SH3 site

Question 48

what does ras do? what does that do?

Answer 48

activates Raf, it is autophosphorylated and a cascade of kinases are activated. Raf does MEK who does ERK who does

Question 49

what does the map kinase do

Answer 49

when phosphorylated it can go into the nucleus and phosphorylates other things to allow for a MULTIMERIC regulation to control early response genes. examples are C-Fos and C-Jun