All The Stuff Flashcards
(126 cards)
1
Q
What affects gene expression
A
PTM
Chromatin remodellers
Epigenetics (TF)
2
Q
What is a chromatin remodeller
A
It is a protein that can move the nucleosome out of the way for the transcription machinery to access the gene. It requires ATP
It can also work chromatin
But if works with TF to establish and maintain gene expression states
3
Q
Cell memory is achieved by
A
Using epigenetics markers such as Histone acetylation and DNA methylation
4
Q
What are PcGs
A
Polycomb group - epigenetic regulator that mark a gene off
Help maintain gene expression. It’s highly conserved
Help maintain SC fate in eukaryotes
5
Q
Establishment of gene pattern during embryonic development is via
A
Maternal deposition of mRNA
Pair rule
Segment polarity - off genes tag with PcG and on with TrxG
6
Q
Maintaining gene pattern is via
A
Transmission of pattern after disappearance of early factors
7
Q
Maintaining LT gene expression
Gene expression needs to be carefully regulated and maintained during diffentiation esp during what stage of development
A
Embryonic
8
Q
What genes must be on all the time to maintain pluripotency
A
OCT4 SOX2 Nanog
9
Q
What is the gene expressed in the trophectoderm after ICM is formed
A
CDX2
10
Q
Assays for NHEJ
A
- FACS to observe localisation of NHEJ proteins (ku, H2Ax, DNA pkcs
- Use direct assay (I-Scel)
- culture cells that have proteins expressing GFP in Brdu for real time observation
11
Q
Factors that result in human diseases
A
Environmental factors
Lifestyle
Genetics
Epigentics and imprinting
12
Q
What are inherited diseases
A
Inherited diseases are essential,y the inheritance of trait quite often determined by one or multiple genes (latter more common). I.e. They can be multi genic or monogenic
13
Q
Monogenic diseases are more rare. Why is that
A
It is rare because mutation often cause deleterious consequences and therefore are more susceptible to selective pressure
14
Q
Examples of monogenic diseases related to DDR proteins
A
Seckel syndrome - ATR/ATRIP FA- FANC genes AT - ATM, chk2 Bloom- BLM (helicase Werner - WRN Li fraumani - p53, chk2
15
Q
Naked virus DNA
A
Papilloma parvo adeno
16
Q
HPV genome and cancer type
A
Small Double stranded DNA circular and oripharygeal/ cervical
17
Q
Infection route of HPV
A
- Enter through abrasions in epidermis
- Infect basal cells and become quiescent (low viral expression
- Begin expressing protein as basal cell differentiate into other cells
- Expression of early proteins E7/6 makes cells enter cell cycle thereby promoting cell division and inhibiting apoptosis and inhibit host cell defence
- Expression of late structural proteins
- Assembly near cell surface and disseminate
18
Q
Function of E6 and E7
A
E7 will bind to hypophosohrykated pRB and result in release of E2F1 which promotes cell progression. However this will activate host cells defense response and so E6 will come in and inhibit host cel defense by tagging p53 for degradation via E3A6
19
Q
What other proteins can E6 inhibit
A
P53
MGMT (DNA transferase
P300 (HAT)
SSBR via decreasing ATM
20
Q
Adenovirus characteristics
A
Small dsDNA genome that is linear
Cause mild respiratory diseases
Good carcinogenesis model
21
Q
What does E1/2 protein do in host cell
A
Form replication centre and activate DDR response
22
Q
E1 and E7 can activate DDR checkpoints independent of each other (t/f
A
T
23
Q
Why does wild type adenovirus inhibit DDR
A
Because DNA virus replicate in the nucleus and that the viral genome can be recognised as the host cells own DSB. If the viral DNA is repaired by the DNA repair machinery, it will become too big for capsid packaging
24
Q
Why does virus activate DDR?
A
We don’t quite know but…
- Virus presence activate stress response which trigger DDR
- A standard antivirus mechanism in immunity
- Host cell recog viral DNA as own DSB
- Virus deliberately activate mechanism which may or may not help viral replication
25
mTOR1 and mTOR2 complex difference
1) contribute to cell growth via RhebGTPase (raptor protein and sensitive to rapamycin - promote growth via promoting ribosomal production and protein synthesis and inhibiting degradation of proteins
2) contains rictor protein and is insensitive to rapamycin - helps activate Akt
26
Rictor and raptor containing protein are ...
MTOR2/1
27
ICL Can be induced by
Endogenous reactive intermediates (acetaldehyde, formaldehyde)
- acetyalhyde intermediate of alcohol metabolism (alcohol dehydrogenase - DNA DNA crosslinks
- formaldehyde (histone and DNA demethylation intermediate; ADH5) - protein crosslinks
Exogenous - Drugs like cisplatin, alkylating agents
28
FA ICL repair can inhibit what pathway
NHEJ
29
Defect in FANC repair pathway is backup by which pathway
NHEJ but can cause toxic ending
30
How does ICL Pathaay work
ICL sensed when replication fork come across it during replication
Dissociation of CMG of the MCM complex will recruit FANCD2.I complex
Formation of core complex (fancACELG)
The FANCD2 complex is UBI by core complex and the UBI will be recognised by UBI binding nucleades which unhook DNA
Recruitment of specialised polymerase (REV1, ZETA) will resynthesis DNA by bypassing bulky lesions (thy have less restrictive active site to accommodate lesion). ICL is clipped and filled in
31
Strategies for anti angiogenic factors
1. Block VEGF receptor - herceptin (trastuzumab)
2. Block RTK (prevent autopi) - sunitinib (sutent)
3. Soluble receptor - aflibercept
4. Neutralising antibody - avastin/bevacizumab
32
Problem arise in what stages of the cell cycle for ICL lesion to be sensed
S phase when replication fork encounter lesion
33
If cell force to pull ICL apart will cause what type of consequences to the newly formed chromosomes
Anaphase bridge snap - forms micro nuclei and radial chromosome in FA
Can cause mitosis catastrophe where cells undergo NON-p53 mediated apoptosis
34
How does drinking and smoking cause foetal abnomalities
Formation of acetaldehyde and formaldehyde endogenously during alcohol and histone degradation can impair FA-ICL repair pathway and protein-DNA cross links resulting in cell death
35
Mechanism of SSBR
PARP bind to DNA ends
XRCC1/DNA Lig3 recruited
PNK Resection and pol b synthesis
Relocation by lig3
36
Tumour cell secretions and function
Proinflammatory cytokines - CSF1 recruit MP
Immunosuppressants
Tumour derived stimulating factor (cell priming)
S1P homing of lymphocyte and LPa to promote lymphocyte entry
37
Antitumour MP function
```
Antitumour
Cytotoxic
Recruited during acute inflammation
Kills tumour cells secrete proinflammatory cytokines (TNFa)
Produce ROS
Participate in Th1 immunity
```
38
M2 MP function
Pro-tumour development and found in most tumours
Secrets immunosuppressive cytokine IL10
Promote growth and tissue remodelling and also angiogenesis
Comes in during chronic inflammatory phase
39
What is DDR1 and function
Oncogenes TK that binds to collagen
| Ligand is collagen and it will autophosphorylate to drive survival and growth
40
Concept of coevolution of stroma with cancer
Stromatogenesis
Evolving of stroma due to tumour influences - stroma is primed by tumour cells which will facilitate stroma growth towards tumour cells liking
41
Principle of Analysing diseased human genes
1) find sequence that are close together as they as likely to be inherited together using genetic markers
2) the mutation shared by affected individuals through common descent will be surrounded by shared alleles at nearby loci
42
Means of tracking linkage using genetic markers
1) restriction enezyme markers - mutation can affect how the enzymes cut - less accurate
2) SNPs - single nucleotide polymorphism marker - illumina colours DNA bound to the probe and can compare to GWAS
3) genome sequencing of particular regions or target gene fragment
43
ZFN example
FOKI
44
What does FOKl recognise
Triplets
45
What does TALEN a stand for
Transcription activator like effector nucleases
46
What does TALEN target
One single nucleotide - more specific
47
RGEN Is what and an example of this is
RNA guided engineered nuclease
| CRISPR Cas9
48
The walburg effect
Cancer cells has altered metabolism and can increase lactate production in the presence of O2 to generate NADH
49
What are the two things that cancer cells love for energy production
Glucose and glutamate (support cell growth)
| *ALL -L-arginine
50
Why use glycolysis in cancer cells?
Irreversible damage to mitochondria energy production due to TCA cycle block (succinate dehydrogenase mutation and Malate enzyme mutation) - walburg effect to fuel glycolysis further
Changes to enzyme expression due to altered signals -cMyc PTEM HIF1
51
Tumour cells consumes so much energ that patient show what typical symptom
Cachexia (muscle wasting) - body goes into starvation mode
52
What is E1B55K
Part of E3 that can tag p53 for degration after complex binding to either E4/6
53
Effect of phosphorylation on histones
Position is important - alters H1 stability binding to nucleosome
Very high during mitosis
Condensation of chromatin - H3K9/27me + H3S10 or S28P
Opening of chromatin - H3K9/27 ace. + H3S10P
(On lysine residue)
54
What does TDT stand for and what does it do
Terminal deoxynucleotidyl transferase
| Add 1-3 nucleotides at junctional sites during VDJ recombination before NHEJ relegation to increase receptor diversity
55
MLL complex has what activity
It's a TrxG that has H3K4 methyltransferase activity which counteracts PcG activity
56
Death Luganda include
FAS ligand on T cells
| TNF receptor
57
Purpose of apoptosis
Regulate cell no.
Morphogenetic during embryonic development
Prevent abnormal cell proliferation thereby preventing cancer
Rid old cell to prevent accumulation of mutational events
58
CtlP binds to MRN to promote HR
T
59
ATR/ATRIP activation in response to DNA lesions that impede DNA replication. Is it directly activated by DSBs?
No, it is indirectly activated by DSB. RPA will bind to the damage DNA which recruits ATR/ATRIP. Hence ATR is activated after ATM to sustain checkpoint activation
60
RNF168 mutation results in what syndrome
RIDDLE
61
Ca dependent and independent binding of cell cell adhesion
Dependent - E-cad
| Independent - nectin
62
Oestrogen activated cells indirectly via
Transcription of proteins that produce autocrine activity to stimulate cell growth
63
Product of oestrogen transcription
IGF1 TGFa Progesterone
64
TAF1/2 are called
1- constitutive transcriptional activating function
| 2- ligand inductively transcription activating function
65
Often mutation in oncogenes are what type of mutation (gain or loss)
Gain of mutation with hotspots
66
Mutation of RAS often occurs on where
Missense on G12/13 Q61 which decreases GAP sensitivity (take off Pi)
67
What are protooncogenes
Cellular regulatory genes that positively regulate the cells whereby mutation of which can drive cancer (cell growth)
68
Gabetespid can inhibit hsp90 to inhibit what
To inhibit cell proliferation by destabilising p53
69
P14 function
Inhibit CDK4 and MDM2
70
P53 is what type of protein
Tetramer that can bind to DNA and drive transcription. Also a TSG that trigger cell cycle arrest and apoptosis in response to cellular stress
71
Neuro blastoma has amplification of what gene
CMYC (MYCN esp)
72
Resistance of tumour cells against alkylating agents
Normally combination
1) decrease entry or increase exit of agent
2) inactivation of agent in cell by expressing enzymes
3) increase DNA repair to overcome lesions produced by agent
73
Tumour cell produce LPA which does what
1) promote lymphocyte Homing - promote T/B cell entry to tumour cell resulting in depletion of lymphocyte in blood. Patient susceptible to infections
2) promote angiogenesis
3) promote tumour growth and formation
4) produce neuropathic pain
74
Function of S1P
Secreted by tumour cell to help retention of lymphocytes which results in lymphocytopenia
75
CAF produce what
Dense collagen matrix making ECM desmoplastic and hard for drug diffusion. Secrete MMP2 which promote tumour invasion by ECM breakdown
76
Hodgkin cells produce what to evade immune elimination
PDL1 - binds to T cell to prevent activation (Tc)
77
How does salt contribute to gastric cancer
High salt levels can directly damage gut wall which increase exposure to carcinogens. H. Pylori is also shown to be associated with salt-induced gastric cancer
78
Haem and gastric cancer
Haem can catalyse ROS formation which can result in the initiation of oxidative chain reaction (e.g. Lipid peroxidation).
Free haem is abundant in red meat and can also drive ENOS (endogenous nitrosocompound, carcinogen) formation
79
H pylori cause mainly what type of gastric cancer
Distal (non cardia) gastric cancer
80
Therapeutic options for p53
1) restore WT p53 activity by giving ARP246 - restore folding of mutant protein and sensitise them to cisplatin and doxorubicin
2) deplete p53 mutant by giving Ganetespid which binds to HSP90 (normally it stabilise p53 mutant) so now p53 is degraded due to MDM2 activity
81
INK4 esp p16/14
P16 inhibits CDK4/6
| P14 inhibits CDK4, MDM2 but mutation melanoma
82
Common mutation in RAS
98% hotspot in G12/13 Q61
83
Mutation in what oncogene result in glionlastoma
NRAS
84
Mutation in G12/13 and Q61 decrease sensitivity if what protein
GAP(takes Pi off)
85
Mutation in what causes neuroblastoma
MYCN (amplification
86
Hallmarks of cancer - 'SEE AIR' and what the term mean
Depicts means in which cancer use to survive and grow
```
Sustain proliferation signalling
Evade immune system
Enable replicative immortalisation
Angiogenesis
Invade and metastasis
Resist cell death
```
87
Imatinib (gleevec) MoA
Targets ATP binding site of ABL tyrosine kinase (competitive binding)
88
Avastin MoA
A neutralising Ab that binds to VEGF2 receptor
89
Herceptin MoA
Binds to EGFR to prevent downstream signalling
90
Imatinib binds to ATp binding site of ABL cytosolic TK to prevent
Phosphorylation of tyrosine residue of the substrate thereby preventing downstream signalling
91
95% haematological response for 18 months using imatinib
True
92
T315I is what type of mutation in what disease
Acquired substitution mutation of threorinine to isoleucine at position 315. Which is the ABL TK substrate binding domain. Mutation overcome by ponatinib that is less specific and can accommodate binding site change in CML refractory Patients
93
Resistance to imatinib mechanism
1) change drug binding affinity
| 2) alteration in binding site (conformation stability)
94
ARF246 does what to p53
Restore correct folding of mutant p53
| Increase sensitivity of chemo resistant cells to cisplatin and doxorubicin
95
The more hypoxic the tumour
The more likely it drives invasive and metastatic development
96
CDK activation requires
Binding of cyclin and subsequent dephosphorylation of the inhibitory phosphate
97
Metastasis is
A tumour deposit that is derived from but discontinued with the primary tumour
98
Anoikis def.
Apoptosis due to inadequate adherence of the tumour cells to the substratum
99
MTOR1 activates what TK achieve cell survival
Sk61 kinase
100
DIABLO complex does what
Aka SMAC. Released from MP and binds to IAF (inhibitory apoptotic factors) which prevent Caspase activation thereby preventing apoptosis
101
T(8;14)
Burkit
102
T(14;18)
Follicular lymphoma
103
T (15;17)
APML - Faggot cell present give ATRA/RA to allow differentiation
104
Fulvulserant
SERM that is a pure oestrogen antagonist
| Degrade ER
105
SNail and Clip and SLUG upregualtion causes
Down reg of Ecad
106
PDGF and Ang1 MoA
Stabilises pericyte at last stage of angiogenesis
| Ang1 also activate AKT which inhibits vessel modelling (antagonised by ang2
107
Ang2 and Ang1 function
Ang2 inhibits pi3k pathways and promote angiogenesis
| Ang1 promotes pi3k and thus promote anti-inflammation /antiapoptosis/ antipermeability
108
Rapamycin MoA and what it is use for
It is an immunosuppressant that is used to prevent organ transplant rejection
Works by inhibiting mTOR1(raptor containing protein) thereby preventing T/B activation by decreasing sensitivity to IL2
109
Beta catenin is tethered to E-cad, why is this important in EMT
Beta catenin is normally degraded via GSK3/APC/axin complex and loss of E-CAD or dissociation of Beta catenin is then allowed to translocate into nucleus and bind to TCF family to activate transcription
110
Structure of inositol phosphate
Inositol head
A phosphate attached to it
Glycerol backbone
2FA chain
111
What does SOS do
SOS is a GEF that adds GTP onto RAS
112
Is EMT reversible
Yes
113
Invasion of tumour cell needs
Invasion requires expression of proteolytic enzymes e.g. MMPs which breaks down ECM and invadopodia which are actin protrusion that act with the enzymes to degrade basement membrane and dense stroma
114
What is anoikis and its role in metastasis
Apoptosis due to inadequate adherence to substratum
| Cancer can detach from primary tumour mass to overcome this and prevent death
115
Cancer hijacks chronic inflammatory response via TF and use EMT to migrate. What TF especially does it use
SLUG, stimulated by TGFb and RTK activation
116
E selectin interact with what molecule to promote adherence
Integrin
117
Rare limiting step of metastasis is
Colonisation at secondary site
118
Models for non random metastasis are
1) anatomical model - route in which tumour cell travels determine metastatic site
2) seed and soil model - cancer cell express receptors that target site which can produce GF (or favourable destination - predetermined premetastatic niche
119
What does cancer do to avoid immmune activation
1) downregulate MHCI
2) express death ligand to inactivate T cells (FASL, PDL1, CTLA4)
3) immunosuppressive cytokine secretion (IL10) and stimulate proinflammatory cytokine production (TNFa)
4) recruit Treg
120
How does P53 regulate MDM2
After p53 action fulfilled, P53 will bind between exon 1 and 2 of the MDM2 gene and result in transcription of MDM2 (autoregulatory loop)
121
Mutation of p53 mostly occur in
Arg228 missense
122
Atm autophos at where
Ser1981
123
Telomere repetitive sequence
10-15kb with many TTAGGG repeats
124
Tumour cell hijack chronic inflammatory response via
SLUG transcription factor activated by TGFb and RTK activation
125
Gefitinib MoA
Inhibit EGFR TKD preventing auto Pi of receptor
| Used in NSCLC
126
SRC phosphorylase PTEN to inhibit PTEN
T
