Slide set 9

Question 1

Intracellular signaling pathway activated by an extracellular signal molecule

Answer 1

1. Signal molecule binds to a receptor protein in plasma membrane of target cell (on cell surface)
2. Receptor activates 1 or more intracellular signaling pathways
   
   1. involves a series of signaling proteins
3. 1 or more of the intracellular signaling proteins alters activity of effector proteins
   
   1. this alters the behavior of the cell

Question 2

types of effector proteins

Answer 2

transcription regulators, ion channels, components of metabolic pathways, or parts of the cytoskeleton

Question 3

contact-dependent signaling

Answer 3

requires cells in membrane-membrane contact

Question 4

paracrine signaling

Answer 4

local mediators (molecules secreted into extracellular space)

released into extracellular space and act on neighboring cells

Question 5

synaptic signaling

Answer 5

neurons transmit signals electrically along their axons and release NTs at synapses

synapses are often located far away from neuronal cell body

Question 6

Endocrine signaling

Question 7

autocrine signaling

Answer 7

signaling and target cells are same cell type

EX: cancer

Question 8

cell-surface receptors

Answer 8

• most signal molecs are hydrophilic (Can’t cross target cell’s plasma membrane)
• bind to signal molecule extracellularly
• binding changes target cell in some way

Question 9

intracellular receptors

Answer 9

• small signal molecs diffuse across plasma membrane
• bind to receptor proteins in cytosol OR nucleus
• signal molecs are hydrophobic and poorly soluble in aqueous solns
• molecs are transported into blood and extracellular fluids while bound to carrier proteins
  
  • dissociate from carried proteins before entering target cell

Question 10

how do cells decide on the appropriate cellular response

Answer 10

integrate MULTIPLE SIGNALS

if a cell doesn’t receive the required survival signals, its undergoes apoptosis (cellular suicide)

some extracellular signals are inhibitory

Question 11

cell surviving vs growing and dividing

Answer 11

depends on PI-3-Kinase/Akt/mTOR pathway

Question 12

Survival pathway

Answer 12

PI-3-Kinase-Akt signaling pathway: survival, growth, and division

Question 13

IGF’s

Answer 13

insulin-like growth factor (IGF) signal proteins

stimulate animal cells to survive and grow

bind to specific RTKs that active PI-3-Kinase to produce PI(3,4,5)P₃

PI(3,4,5)P₃ recruits 2 protein kinases to plasma membrane via their PH domains (Akt and PDK1)

Akt is now active and phosphorylates target proteins at plasma membrane, cytosol, and nucleus

target cells now have enhanced cell survival and growth!

Question 14

PDK1 aka

Answer 14

phosphoinositide-dependent protein kinase

Question 15

Akt aka

Answer 15

protein kinase B (PKB)

Question 16

survival pathway

Answer 16

1. Extracellular survival signal activates an RTK
2. RTK recruits and activates PI 3-kinase
3. PI-3-kinase produces PI(3,4,5)P₃ (a docking site for 2 serine-threonine kinases with PH domains)
   
   1. Akt and PDK1 are brought into proximity at plasma membrane
4. Akt is phosphorylated on a serine by a third kinase (mTOR in complex 2)
   
   1. this alters conformation of Akt so it can be phosphorylated on a threonine by PDK1
5. PDK1 activates Akt
6. active Akt dissociates from plasma membrane and phosphorylates target proteins (EX: Bad protein)
7. Bad holds one or more apoptosis-inhibitory proteins (of Bcl2 family) in an inactive state
8. phosphorylated Bad releases inhibitory proteins
   
   1. they now block apoptosis and thus promote cell survival
9. phosphorylated Bad is bind to ubiquitous cytosolic protein 14-3-3 which keeps bad out of action

Question 17

Bad protein

Answer 17

• targeted by Akt for phosphorylation
• Bad holds one or more apoptosis-inhibitory proteins (of Bcl2 family) in an inactive state
• phosphorylated Bad releases inhibitory proteins
• they now block apoptosis and thus promote cell survival
• phosphorylated Bad binds to ubiquitous cytosolic protein 14-3-3 to become inactive
• active Bad = phosphorylated
• inactive Bad = bound to ubiquitous cytosolic protein 14-3-3

Question 18

survival vs growth pathways

Answer 18

Without extracellular growth factor

• Tsc2 (a Rheb-GAP) keeps Rheb inactive AND mTOR in complex 1 is inactive: there is no cell growth!

With extracellular growth factor

• active Akt phosphorylates and inhibits Tsc2 (promotes activation of Rheb)
• active Rheb (Rheb-GTP) helps activate mTOR in complex 1: stimulates cell growth

Question 19

Tsc2 aka

Answer 19

tuberous sclerosis protein 2

1 component of a heterodimer composed of Tsc1 and Tsc2

mutations in either gene encoding them causes tuberous sclerosis (genetic disease) that causes benign tumors that contain abnormally large cells

Question 20

A response to a signal depends on…

Answer 20

the specific cell type AND cohort of proteins that the cell expresses for detection and relay of the signal

Question 21

types of cell-surface receptors

Answer 21

cell-surface receptors: act as signal transducers by converting an extracellular ligand-binding event into intracellular signals that alter behavior of target cell

ion-channel-coupled receptors

G-protein-coupled receptors

enzyme-coupled receptors

Question 22

ion-channel-coupled receptors

Answer 22

aka transmitter-gated ion channels/ionotropic receptors

rapid synaptic signaling btwn nerve cells and other electrically excitable target cells (nerve and muscle cells)

mediated by small number of NTs that transiently open or close and ion channel formed by the protein to which they bind

the NTs briefly change ion permeability of plasma membrane and change excitability to postsynaptic target

most ion-channel-coupled receptors belong to a large family of homologous, multipass transmembrane proteins!

Question 23

G-protein-coupled receptors

Answer 23

indirectly regulate activity of a separate plasma-membrane-bound target protein (either an enzyme or an ion channel)

a trimeric GTP-binding protein (G protein) mediates interaction between activated receptor and this target protein

activation of target protein can change concentration of 1 or more small intracellular signaling molecules (if target protein is an enzyme)

OR

it can change ion permeability of the plasma membrane (when target is an ion channel

Question 24

Enzyme-coupled receptors

Answer 24

either act as enzymes or associate directly with enzymes that they activate

usually single-pass transmembrane proteins with ligand-binding site outside the cell and catalytic or enzyme-binding site inside

majority are protein kinases or associated with protein kinases (phosphorylate specific sets of proteins in the target cell when activated

Question 25

Intracellular molecular switches

Answer 25

Signaling by phosphorylation: * a protein kinase covalently adds a phosphate from ATP to signaling protein * a protein phosphatase removes the phosphate * \*some signaling molecules are activated by dephosphorylation rather than by phosphorylation Signaling by GTP binding: * GTP-binding protein is induced to exchange its bound GDP for GTP (this activates the protein) * protein then inactivates itself by hydrolyzing its bound GTP to GDP

Question 26

Allostery

Answer 26

proteins can shift between two or more slightly different conformations

Question 27

RTKs aka (also what are they an example of)

Answer 27

Receptor tyrosine kinases (RTKs) example of an enzyme-coupled receptor!

Question 28

different RTK families

Answer 28

* different RTKs have different extracellular domains * RTKs all have an intracellular tyrosine kinase domain

Question 29

Activation of RTKs

Answer 29

dimerization! * in the absence of extracellular signals, most RTKs are monomers (internal kinase domain is inactive) * binding of ligand brings 2 monomers together to form a dimer * the close proximity in the dimer leads the 2 kinase domains to phosphorylate each other (this has 2 effects!) * 1) phosphorylation at some tyrosines in the kinase domains promotes the complete activation of the domains * 2) phosphorylation at tyrosines in other parts of the receptors generates docking sites for intracellular signaling proteins (results in formation of large signaling complexes that can then broadcast signals along multiple signaling pathways)

Question 30

what protein domain recognizes phosphorylated tyrosines

Answer 30

SH2 domain! it's a general protein domain SH2 domains bind to a phosphotyrosine residue and an amino acid side chain by changing the binding site of the amino acid side chain, the domain can have specificity for different proteins

Question 32

scaffold proteins

Answer 32

enhance specificity of signal transduction scaffolds bind to **activated receptors** and can be bound by multiple other downstream signaling proteins this **limits** what proteins can be activated, which **increases specificity** this also keeps the signaling molecules in **close proximity**, so rxn can have **faster rate**

Question 33

different types of scaffold complexes

Answer 33

1. preformed scaffold complex 1. receptor and some intracellular signaling proteins it activates in sequence are preassembled into a signaling complex on the inactive receptor by a large scaffold protein 2. scaffold complex only forms after signal arrives 1. signaling complex assembles transiently on a receptor only after binding of an extracellular signal molecule has activated the receptor 2. activated receptor phosphorylates itself at multiple sites, which then act as docking sites for intracellular signaling proteins

Question 34

modified lipids as docking sites for complex formation

Answer 34

assembly of signaling complex on phosphoinositide docking sites * activation of a receptor = increased phosphorylation of specific phospholipids (phosphoinositides) in the adjacent plasma membrane * these are then docking sites for specific intracellular signaling proteins (they can now interact with one another)

Question 35

conserved interaction motifs

Answer 35

often act as part of adaptor complexes certain domains bind to specific docking sites

Question 36

SH2 and PTB domains

Answer 36

bind to phosphorylated tyrosines in a specific peptide sequence

Question 37

SH3 domains

Answer 37

bind to short, proline-rich amino acid sequences

Question 38

PH domains

Answer 38

bind to charged head groups of specific phospholipids

Question 39

signal relay after RTK activation

Answer 39

how an RTK activates Ras 1. Grb2 recognizes a specific phosphorylated tyrosine on the activated receptor by means of an SH2 domain 2. recruits Sos by means of 2 SH3 domains 3. Sos stimulates the inactive Ras protein to replace its bound GDP by GTP 4. now Ras is active and signal is relayed downstream

Question 40

Sos

Answer 40

Son-of-sevenless sevenless = an RTK Sos = a Ras-GEF

Question 41

RTK aka

Answer 41

receptor tyrosine kinase

Question 42

signal relay after RTK activation (MAP)

Answer 42

MAP kinase module activated by RAS 1. MAP kinase kinase kinase (Raf): Ras recruits Raf to plasma membrane and helps activate it 2. Raf activates MAP kinase kinase (Mek) which activates MAP kinase (Erk) 3. Erk phosphorylates a variety of downstream proteins (including other protein kinases) 1. EX: transcription regulators in nucleus 4. Resulting changes in protein activity and gene expression cause complex changes in cell behavior

Question 43

MAP aka

Answer 43

mitogen-activated protein

Question 44

ways in which signal pathways vary

Answer 44

1. response timing (milliseconds to days) 2. sensitivity to extracellular signal 3. dynamic range 4. persistence 5. signal processing (switch-like, oscillations, etc) 6. integration 7. coordination

Question 45

response timing

Answer 45

* Slow responses: increased cell growth + division * slow bc they involve changes of gene expression and synthesis of new proteins * Fast responses: changes in cell movement, secretion, or metabolism * fast bc they don't change transcription * can involve rapid phosphorylation of effector proteins in cytoplasm * synaptic responses mediated by changes in membrane potential are even quicker * some signaling systems have rapid and slow responses * allows quick response while preparing slower long term response

Question 46

signal integration

Answer 46

extracellular signals A and B activate diff intracellular signaling pathways each leads to phosphorylation of protein Y, but at diff sites Protein Y is only activated when both sites are phosphorylated (signal A and B must be simultaneously present) A and B are called coincidence detectors

Question 47

coincidence detectors

Answer 47

2 signals that are required to be present simultaneously to elicit a response