L5-6: transcriptional responses to stress and infection

Question 1

environmental challenges to cells

Answer 1

DNA damage
infection
hypoxia
physical stress

Question 2

effector outcomes from environmental challenges

Answer 2

gene expression
repair
programmed death
immune response

Question 3

NF-kB

Answer 3

nuclear factor of kappa immunoglobulin light chain in B cells

Question 4

NF-kB function

Answer 4

response to external threat via expression regulation of target genes for survival/ recovery/ death induction

Question 5

RHD

Answer 5

rel homology domain
mediates DNA binding and dimerisation functions of NF-kB

Question 6

origin of p50/ p52

Answer 6

proteolytically processed from P105 / p100 precursor

Question 7

p100 precursor

Answer 7

inducible

Question 8

p105 precursor

Answer 8

constitutive

Question 9

2 sub families of NF-kB

Answer 9

Rel family
p105/p100

Question 10

relA

Answer 10

p65

Question 11

Rel family

Answer 11

C-terminal txn activation domain > txn activators

Question 12

p105/ p100

Answer 12

longer precursor proteins > protolytically cleaved to form active DNA - binding components
ankyrin repeats in C termini > IkB-like inhibitors

Question 13

NF-kB evolution

Answer 13

coincided w need for innate immunity
initially found in eukaryotes as single gene

Question 14

E3 ubiquitin ligase

Answer 14

76 amino acid
facilitates ubiquitin chain attachment to a target protein at Lysine
can form chains w self

Question 15

protein degradation

Answer 15

ATP-dependent process w 3 enzymes

Question 16

E3 ubiquitin ligase complex for proteasome recognition

Answer 16

26 Ub molecules sufficient for 26s proteasome recognition

Question 17

Ubiquitin proteasome pathway

Answer 17

Ub recognised by 26S proteasome complex
Ub attached at Lys to protein
degradation
Ub removed and linearized/ injected into proteasome core
digested to peptides
either broken down by peptidases > amino acids or used for antigen presentation

Question 18

NF-KB induction

Answer 18

inflam cytokines
bacterial products
viral proteins/ infection
DNA damage
cell stress

Question 19

what does NF-kB regulate

Answer 19

immune/ inflam response
stress response
cell survival and death
cell adhesion
proliferation

Question 20

where is NFkB retained?

Answer 20

cytoplasm in inactive form > bound to inhibitor protein IkB

Question 21

what happens when NFkB is stimulated

Answer 21

IkB phosphorylated and ubiquitin attached
26S proteasome degradation
free NF-kB translocates to nucleus

Question 22

IKK

Answer 22

IkB kinase

Question 23

IKK complex

Answer 23

3 sub-units:
IKK alpha
IKK beta (catalytic)
IKK delta/ NEMO (NF-kB essential modifier > regulatory)

Question 24

inhibitors of IkB kinase

Answer 24

IkB alpha
IkB beta b
IkB beta e
Bcl3

Question 25

characteristics of IKK inhibitors

Answer 25

Ankyrin repeat motifs in C termini PEST domain rich (proline/ glutamate/ serine/ threonine)

Question 26

alternative pathway for NF-kB activation

Answer 26

phosphorylates p100 cursor protein activates / partially processes to p52

Question 27

canonical vs non-canonical pathway for NF-kB activation

Answer 27

canonical activates p50RelA heterodimer non-canonical activates p52 relB heterodimer

Question 28

NF-kB responses

Answer 28

inflammation proliferation survival tumor promotion/ metastasis angiogenesis cell death/ anti proliferative effects

Question 29

NF-kB/ IKK gene knockout effects

Answer 29

apoptosis/ immunity/ inflammation cells abberantly nuclear (diseased) constitutive activity

Question 30

NF-kB binding site

Answer 30

imperfect palindrome\ > orientates NF-kB specifically

Question 31

what happens to NF-kB once it enters the nucleus?

Answer 31

kinases/ acetylases modify moderated txn response cooperates / antagonizes other txn factors

Question 32

promoter enhancers

Answer 32

regulate genes complex array of binding sites for variety of txn factors

Question 33

differential chromatin states at NFkB dependent genes

Answer 33

promoter enhancers can be inaccessible in cell, can recruit remodellers HAT/Swi/Snf CAT-dependent remodellers

Question 34

beta interferon

Answer 34

NFkB regulated gene produced in response to viral infection (and alpha) bind CSR for signalling cascade for activation of 50 anti-viral genes

Question 35

multimerisation of beta interferon enhancer

Answer 35

act as viral inducible promoter varying basal activity, responding to other inducers HMGI/HMGAI assisted

Question 36

interaction interface of enhanceosome complex

Answer 36

allows high affin recruitment of txn coactivators (p300/CBP)

Question 37

combination lock of NFkB

Answer 37

p50/ RelA complex at beta ifn enhancer

Question 38

basal transcription machinery

Answer 38

NFkB recruits to induce transcription