Module 8 - Receptor mediated cell signaling, metabolism Flashcards

1
Q

Describe the steps of RTK receptor signaling

A
  • growth factor binds to inactive RTK receptor
  • receptors dimerize and RTK becomes active
  • cytoplasmic tails of RTK are autophosphorylated
  • proteins bind to RTK phosphotyrosines
  • target proteins are phosphorylated
  • downstream signaling pathways are activated
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2
Q

Describe the steps of EGF receptor signaling through Ras activation

A
  • EGF binds to EGFR1
  • EGFR1 and EGFR2 dimerize and EGFR1 phosphoryltes the EGFR2 Tyr
  • conformational change leads to EGFR2 phosphorylating EGFR1 Tyr
  • GRB2 adaptor (an SH2 adaptor that also contains SH3) binds to phosphorylated Tyr residues
  • SOS (a GEF protein) binds to the SH2/SH3 adaptor
  • Ras (a G protein) binds to the SOS adaptor
  • GTP exchange for GDP activates Ras downstream signaling pathways
  • OR -
  • RasGAP stimulates GTPase in Ras and deactivates signaling
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3
Q

What is the difference between SH2 and SH3?

A

SH2 binds pTyr and Asn parts of the receptor

SH3 binds Pro parts of the SOS protein

(having both is what creates the bridge)

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4
Q

The Raf-MEK-ERK pathway is a type of…

A

EGF receptor signaling

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5
Q

What are the two kinds of EFG defects and how do they lead to cancer?

A

dominant gain of function mutations: one affected gene copy in the GTPase domain causes uncontrolled cell growth (oncogenes) by stimulating MAPK and being insensitive to GAP regulation

recessive loss of function mutations: two affected gene copies inactivate tumor suppressors

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6
Q

What kind of cancer is commonly associated with Ras mutations? How much? What mutations?

A

80% of pancreatic cancers

missense mutations G12D, G12V, and G12R which all decrease the GTPase activity of oncogenic Ras protein

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7
Q

Regarding GTP binding, GAP binding, and GTPase activity, what combinations of strong and weak produce normal response vs. cancer?

A

if all are strong, there will be normal response

if GTP is strong but GAP and GTPase are weak, there will be cancer (no regulation, only stimulated growth)

if GTP and GTPase are weak but GAP is strong, there will be cancer but not as bad (less regulation but also less growth)

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8
Q

Describe the structure of the insulin receptor

A

a2B2 tetrameric complex linked by disulfide bonds

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9
Q

Describe the insulin receptor signaling pathway through PI-3K activation

A
  • one molecule of insulin binds to the alpha subunit
  • conformational changes in the beta subunit activate intracellular kinase domains
  • autophosphorylation of tyrosines causes a final conformational change in the beta subunits
  • SPLIT:
  • one branch activates GRB2, SOS, and Ras for MAPK signaling and altered gene expression and cell division
  • Other branch is the Insulin specific pathway (cont. below)
  • phosphorylated tyrosine recruits and phosphorylates IRS
  • phosphorylated IRS binds to PI-3K
  • PI-3K signaling leads to glucose uptake and glycogen synthesis
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10
Q

What is the difference in SHC and IRS proteins recruited to the insulin receptor pathway?

A

SHC: recruited for MAPK pathway, binding domain is Asn-Pro-Gln-pTyr

IRS: recruited for PI-3K pathway, binding domain is Asn-Pro-Ala-pTyr

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11
Q

Describe the PI-3K pathway starting with activated PI-3K

A
  • PI-3K phosphorylates PIP2 to PIP3 (terminated by PTEN)
  • PIP3 recruits PDK1
  • PDK1 phosphorylates Akt
  • Akt phosphorylates downstream proteins and causes glucose uptake and glycogen synthesis in liver cells
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12
Q

What is the difference between IP3 and PIP3

A

PIP3 is 3, 4, 5
IP3 is 1, 4, 5

PI-3K phosphorylates PIP2 to PIP3

PLC breaks PIP2 into DAG and IP3

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13
Q

How do PDK1 and Akt stay at the membrane?

A

PDK1 and Akt have pleckstrin homology domains that bind to membrane associated PIP3 lipids in the insulin signaling pathway

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14
Q

TNF pathways do not involve any…

A

kinases

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15
Q

TNF receptor signaling initiates two pathways that lead to….
What determines the chosen outcome?

A

cell death (apoptosis) or cell survival

pathway and outcome is determined by relative abundance of downstream signaling proteins (FADD takes apoptotic pathway, TRAF2 takes cell survival pathway)

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16
Q

TNF is mediated by adaptors that have what types of domains?

A

death domains or death effector domains

17
Q

Describe TNF receptor signaling up to when the two pathways diverge

A
  • 3 molecules of TNF-a bind to the TNF receptor trimer
  • binding stimulates the exchange of SODDs for TRADDs (SODD inhibits signaling)
  • TRADD proteins initiate adaptor complex formation and downstream signaling (paths diverse at the level of TRADD)
18
Q

Describe the TNF receptor signaling starting when the two pathways diverge

A

Apoptotic pathway:
- DD and DED complexes assemble
- procaspase 8 autocleaves
- CASP8 cleaves procaspase 3
- CASP3 cleaves cellular proteins leading to cell death

Cell survival pathway:
- NIK/RIP mediate IKK phosphorylation
- IKK phosphorylates IKBa, activating p50/p65
- active p50/p65 form the active NFkB complex which moves to the nucleus
- NFkB increases expression of anti-apoptotic genes that inhibit CASP8 and CASP3 (stop apoptosis pathway)

19
Q

What is the structure of death domains of TNF?

A

six alpha helices

20
Q

How is CASP3 activated by CASP8?

A

CASP8 cleaves caspase 3 at Asp175 to a partially active procaspase 3

an inactive procaspase 3 finds another and noncovalent interactions form between the two subunits to form a partially active enzyme

procaspase 3 cleaves at Asp28 and Asp9 (extras off the ends)

two sets of procaspase subunits (p12 and p17) assemble into a heterotetramer to form a fully active CASP3

21
Q

What are nuclear receptors? What are the basic steps?

A

ligand regulated transcription factors that bind to specific DNA sequences in target genes and recruit coregulatory proteins to module transcriptional initiation rates

  • ligand binds
  • complex binds DNA
  • coregulatory proteins recruited and activate RNA polymerase
22
Q

What are the two types of nuclear receptors and their similarities and differences?

A

steroid and metabolite receptors

same:
- bind DNA specifically
- recruit regulatory proteins

different:
- DNA sequence is different (steroid bind inverted repeat sequences as homodimers, while metabolite bind direct repeat DNA sequences at heterodimers)
- steroid bind head to head while metabolite bind head to tail

23
Q

If two cell types are exposed to a steroid molecule but only one type had activated gene expression, what is the difference between the two cell types?

A

only one expresses the cognate steroid receptor

24
Q

Where do the zinc fingers on nuclear receptor homodimers bind?

A

cysteines in the major groove of DNA

25
Q

Define metabolic flux and what key factors determine the flux

A

rate at which metabolites are interconverted between reactants and products

  • availability of substrate (diet or stored reserves, Q mass action ratio)
  • level of enzyme activity (enzyme levels, catalytic activity, compartmentation/location)
26
Q

What is liver cell metabolism like before breakfast?

A

low insulin, high glucagon

degradation of glycogen to glucose, formation of glucose from gluconeogenesis

low glycolysis of glucose to pyruvate and low synthesis of glycogen from glucose

27
Q

What is liver cell metabolism like after breakfast?

A

high glucose

synthesis of glycogen from glucose (for storage) and breakdown of glucose by glycolysis into pyruvate (for energy)

low degradation of glycogen to glucose, and low gluconeogenesis of glucose

28
Q

What is the definition of metabolism?

A

biochemical reactions that turn chemical energy into work

29
Q

In the hierarchy of metabolic pathways, what are the 4 macromolecules, 6 primary metabolites, and 7 small biomolecules?

A

4 macromolecules: proteins, nucleis acids, carbohydrates, and lipids

6 primary metabolites: amino acids, nucleotides, fatty acids, glucose, pyruvate, and acetyl-CoA

7 small biomolecules: NH4+, CO2, NADH, FADH2, O2, ATP, and H2O

30
Q

How is dG’o calculated?
What does a negative or positive value indicate?

A

let reaction run until it reaches equilibrium

find concentrations of reactants and products at equilibrium and calculate Keq

plug Keq into dG qeustion and dG=0 (bc. equilibrium) and solve for dG’o

negative indicates the reaction is favorable in the direction written, positive indicates it is favorable in the reverse direction

31
Q

How do the values of dG and dG’o relate to metabolism?

A

dG is calculated from the mass action ratio (actual concentrations of reactants and products) because things are not at equilibrium in living systems

32
Q

How can unfavorable reactions be used in metabolism?

A

by linking them to a favorable reaction to create a net negative dG

33
Q

What is beneficial about protein complexes?

A

they increase the efficiency of coupled reactions through substrate channeling