MT Exams Flashcards
(110 cards)
1
Q
Tools involved in Short Patch BER
A
Pol β lyase, DNA Ligase III, XRCC1
2
Q
XRN2
A
Exonuclease involved in RNA Pol II separation from template
3
Q
Tools involved in Long Patch BER
A
Pol 𝜀, β, δ, DNA Ligase I, PCNA
4
Q
Tools involved in NER
A
XPC-HR23B
XPA, XPB, XPD
XPG, XPF-ERCC1
RPA
DNA Ligase III
Pol 𝜀, 𝜅, 𝛿
5
Q
TLS Polymerase
A
Pol 𝛿, PCNA, Pol N
6
Q
Fanconi Anaemia genetic links
A
FANCD1
FANCQ
Rad51C
FANCN
FANCJ
7
Q
FA Tools in Pathway
A
Convergence of replication forks,
FANCM,
FANCL (FANCD2 and FANCI)
FANCP (SLX4)
SNM1A
Pol Ζ
8
Q
Driver Cyclin
A
D
9
Q
Mitosis CDK
A
CDK1, Cyclin B
10
Q
G1 to S Cyclin
A
E
11
Q
Wee1
A
inhibitory kinase
12
Q
CAK
A
activating kinase
13
Q
Cdc25
A
activating phosphatase
14
Q
INK, CIP
A
CDK inhibitory proteins
15
Q
APC/C
A
MCC prevents chromosome separation by inhibiting APC/C ubiq. ligase function
16
Q
MDM2
A
Ubiq ligase for p53. When damage P p53 it separates from MDM2 making it more stable
17
Q
ATR pathway
A
ssDNA - Chk1 - Wee1 - inhibits CDKs
18
Q
ATM pathway
A
dsDNA - Chk2 - inhibits Cdc25 - inhibits CDKs
19
Q
SPRTN
A
enzyme required to repair DPCs by removing DPC at start of the replication fork
20
Q
PRP40
A
Splicing factor
21
Q
What P Serine 2
A
P-TEFβ
CDK12
22
Q
What P Serine 5 and Serine 7
A
TFIIH
CDK7
23
Q
Kinases which P dsDNA break in H2A.X modification
A
DNA-PK
ATM
24
Q
SAM
A
Used to install DNA methyl groups on cytosine
25
How are unmodified CpGs protected from DNMT1
CXXC domain on DNMT1
- restricts access of catalytic domain
- occurs in promoter regions
26
TDG
Recognises site for demethylation and excises the base leaving an abasic site
27
Readers of DNA modifications
Unmethylated CpGs = CXXC and MBD1 domains
Methylated CpGs = MBD domain
28
DNMT3B DNA modifications in disease
ICF1
(immunodeficiency)
29
DNMT2A DNA modifications in disease
AML
30
MECP2 Reader - DNA modifications in disease
Rett syndrome
(neurological)
31
Function of ALK enzymes
Reverse effects of DNMT1
32
Tools required for MMR
MutS
MutL complex (MLH1, PMS2)
RPA
Exo1 and RFC
DNA Pol 𝛿
DNA Ligase I
33
ORC6 mutation - DNA Replication Disorder
Meier Gorlin Syndrome
34
Van Esch O'Driscoll Mutation
Complete degradation of Pol A1
35
XLPDR Mutation
Pol A1 deficiency
36
DNA Pol E lesions in endonuclease
P286R
V411L
37
IMAGe Syndrome Mutation
Pol E pathogenic variant - CDKN1C/p57 (neg reg of cell prolif.)
38
MDP
Loss of Motif A in Pol D
39
Additional Firing Factors
GINS, CDC45
40
MCM10
With Hydrolysis converts inactive CMG into active CMG
41
Tools for Okazaki Fragment Processing
Pol 𝛿, RNAse H, Fen1, DNA Ligase
42
Termination tools
Dia2, MCM7, p97, TopII
43
Sic1/p27
Binds to S-CDK activity and inactivates it
44
CTCF
binding factor that binds to insulators
important cofactor on cohesin rings
45
CSK
RASSF1A Co-P with SRC
46
RISC
Regulates the selective degradation of mRNA transcripts
- miRNAs that hybridise perfectly = cleaves and marks UTR for degradation
- miRNAs that hybridise imperfectly = RISC protein blocks translation
47
lncRNA
Long non-coding RNA
- regulate translation
- cover AUG codons which prevents translation of RNA molecule
- lncRNA binds to AUG which influence selectivity of ribosomal binding
48
H3K9
Repressed histone marks
49
NANOG, SOX2, OCT4
Embryonic stem cell markers
These genes are NOT associated with LADs
50
H2A.X P site
Serine 139
51
Modifiers of H2A.X P
ATM, ATR, DNA-PK - all kinases
52
Readers of H2A.X P
MDC1
53
Erasers of H2A.X P
Phosphates
Cdc25 is degraded after P for the activation of the checkpoint
54
Most common Ubiq linkage types
K11, K4
55
Monoubiq chain type linkage type
K63
55
RINGs involved in dsDNA DDR
RNF8 and RNF168
56
RNF18-UBC13
Promotes K63 linked polyubiq - recognised by RNF168
57
Nedd8
allows Ub transfer in Cullin Ring Ligases
58
MLN4924
Inhibitor of Nedd8
59
Types of SCF
FBXW, FBXL, FBXO
60
FBXW1
βTrCp1
61
FBXW11
βTrCp2
62
How do FBXW recognise substrates
DSGXXS motif
63
CDC20
recognises RXXL motif
64
CDH1
recognises KEN motif
65
What type of chains do APC/C assemble
K11
66
APC/C-CD20
Degrades glue holding chromosomes together
Early mitosis and mid-mitosis
67
APC/C-CDH1
Degrades everything that starts cell cycle
After anaphase
During mitotic exit
G1 phase
68
Cyclin F
Master regulator of G2/M transition
Turns off S phase events
69
When does Cyclin F accumulate
G2
70
What corresponds with Cyclin-F
Degradation of RRM2
71
RRM2 function
RNA --> DNA
72
Function of Cyclin F in terms of RRM2
Cyclin/CDK P T33
Cyclin F recognises RRM2 via RXI
Tagged for degradation in G2/M
Blocks end of S phase
73
Substrates of Cyclin F
EXO1
E2F1
74
53BP1
DDR factor involved in NHEJ
75
Stress responses towards EIF2a
PTEN
HRI
GCN2
PKI
76
Brn2 function
Anti-apoptotic protein
mutually exclusive from MITF
Suppresses cell death - allows time for dysfunctional factors to be fixed
77
Pathways that turn on Brn2 expression
B-catenin
Pax3
MAPK
78
Shc
adaptor protein for TK
79
Grb2
adaptor protein for TK
80
SMAD
Substrate for TGF-B
SMAD-4 mutations upregulated in cancer
81
inhibitory SMADs
6 and 7
82
Impact of SMADs on TGFB singalling
Can trigger MAPK or cytoskeletal response once bound to TGFB
Can lead to tumour progression or regression
83
What type of enzyme linked receptor is associated with TGFB
Serine/Threonine Kinase
84
What type of enzyme linked receptor is associated with JAK-STAT
Tyrosine Kinase
85
How are JAK/STAT Tyr Kinases activated
Cytokines - TPO, IFN
Growth Hormones - EPO
86
What determines STAT specifity
SH2 domain
87
Mutation involved with TPO signalling
V617F
CALR
88
Scaffold protein for Hippo signalling
MST2
89
Proteins involved in Hippo signalling
LATS1 and MOB1 - when P - binds to YAP/TAZ
90
YAP/TAZ inside nucleus
TEAD --> oncogenic transcription
91
Hippp signalling in terms of mechanosensing
F-actin prevents LATS from P YAP/TAZ - cell proliferation
92
Hippo and Wnt signalling
P of YAP/TAZ --> remains in cytosol
Binds to B-catenin - prevents its accumulation - no stiffness - decreased Wnt signalling - cell cycle progression
DOES NOT OCCUR WHEN THERE IS DECREASED HIPPO/RASSF1A ACTIVITY
93
Intrinsic Apoptosis pathway protein involved in activation of apoptosome
APAF1
- cytochrome C binds
94
DISC
extrinsic apoptosis pathway
complex consisting of ligand and receptor
95
what ligands promote extrinsic apoptosis pathway
Fas and TNF-a
96
Caspases associated with intrinsic apoptosis pathway
9
97
Caspases associated with extrinsic apoptosis pathway
8/10
98
Initiation complex formed in Macroautophagy
ULK1
ATG13
ATG101
99
Bafilomycin
prevents autophagosome and lysosome fusion
100
chloroquine
prevents autophagosome and lysosome fusion
101
Ferroptosis Inhibitors
Ferrostatin - ROS inhibitor
DFO - Fe inhibitor
102
Ferroptosis Inducers
System X inhibitor - Elastin
GPX4 inhibitor - RSL3
103
NCOA4
Helps Fe from ferritin go into autophagosome during ferritinophagy
104
What do MTST2 and RASSF1A recruit at NE
RAN and XPO6
105
SRP
SIGNAL RECOGNITION PROTEIN
nascent protein detects hydrophobic segment during biogenesis of membrane proteins
106
Subcomplexes involved in COP II formation
Sec13,31,23,24
107
Transmembrane sensors in UPR
IRE1, PERK, ATF6
108
Binding protein for IRE1
XPB1 - pro survival
109
