Quiz 5 Flashcards
(119 cards)
1
Q
2 biochemical mechanisms of epigenetic gene regulation
A
DNA methylation histone modification
2
Q
epigentics is inheritance of
A
gene states
3
Q
for epigenetics alternate gene states are heritable through
A
mitosis
4
Q
3 mechanisms to confer heritable gene expression states
A
- DNA Methylation 2. Histone Covalent Modifications 3. Chromatin Remodeling Complexes
5
Q
where does DNA methyltransferase attach methyl group
A
position 5 of cystein in CpG dinucleotides
6
Q
what percentage of CpG dinucleotides in genome are methylated?
A
70
7
Q
what is function of the methyl group added?
A
provides structure/recognition for other proteins
8
Q
t/f methylation patterns are maintained during DNA Replication
A
t
9
Q
what enzyme does methylations
A
DNA methytransferase
10
Q
which Dna methylase does de novo, which does maintenance
A
DNMT 3a, 3b DNMT1
11
Q
DNMT1 only knows how to put a methyl group in what orientation
A
diagonally
12
Q
What helps DNMT1 recognize where to methylates
A
CpG repeats are palindromic
13
Q
what part of histones is modified in histone modification
A
tails
14
Q
6 histone modifications
A
acetylation methylation ubiquitination sumoylation ADP-ribosylation
15
Q
P/CAF and CPB do what?
A
histone acetyltransferases
16
Q
SWI/SNF does what
A
chromatin remodeling complex
17
Q
how many bp around histones
A
147
18
Q
4 examples of epigenetic inheritance and regulation
A
X Chromosome inactivation Genomic Imprinting Tissue-Specific Gene Regulation Cancer Epigenetics
19
Q
How is genomic imprinting established?
A
imprinted genes are protected from genome-wide demethylation that occurs during early development
20
Q
when does imprinting occur
A
development of germ cells in female/ale
21
Q
primordial germ cells are imprinted based on
A
gender of embryo
22
Q
imprints from prior generation and X inactivation are inherited by which cells: somatic, germline, both
A
somatic cells
23
Q
which cell type establishes new imprints
A
germ cells
24
Q
DNA methylation generally enhanced or repressed transcription?
A
repressed
25
Histone Acetylation occurs on which position of which AA acid
amino group of the side chain lysines residues in the tails of histones
26
Histone methylation at arginine in general correlates to (activated/repressed) gene transcription
active
27
Histone methylation at lysine in general correlates to (activated/repressed) gene transcription
both
28
chromatin remodeling (activated/repressed) gene transcription
remodeling complex can result in repression or activation
29
how many genes become silenced in germ cells b/c of gender specific genomic imprinting
70
30
what's faster necrosis or apoptosis
apoptosis
31
2 major DNA breakdown steps by # of bases
1- DNA breaks down into 50 to 300kb pieces 2-internucleosmal cleavage of DNA into oligos in multiples of 180 to 200 bases
32
What enzymes lead to internucleosomal cleavage of DNA
Ca and MG dependent endonucleases
33
4 Differences b/2 Necrosis and Apoptosis
1. Apoptosis doesn't rupture cell 2. There is not tissue damage in apoptosis 3. Cell corpses are gotten rid of in apoptosis by phagocytosis whereas they are gotten rid of by inflammatory response in necrosis 4. Apoptosis is rapid ie minutes vs hours
34
how many apoptotic cells/ day
50-70 billion
35
4 examples where apoptosis occurs
1. embryonic development 2. Hormone dependent involution 3. death of immune cells 4. death of cells induced by cytotoxic T cells
36
5 features of apoptotic cells
1. Cell size decreases 2. Chromatin condenses 3. DNA is fragmented 4. Pronounced blebbing of plasma membrane 5. Phagocytosis
37
Intrinsic cell death is stimulated by what 3 things
withdrawal of cytokines withdrawal of growth factors damage from radiation or free radicals
38
What stimulates Extrinsic cell death
Fas/Fas-Ligand interactions at cell surface
39
Is intrinsic/Extrinsic used by Cytotoxic T-Cells
extrinsic
40
what is Fas
tumor necrosis factor that activates death programs
41
what is signal for intrinsic pathway
loss of hormones, growth factors, or cytokines that suppress death programs
42
What are the adaptors in intrinsic pathway
Apaf-1 associates with caspases and activates them to initiate cell destruction
43
what does apaf stand for
apoptotic protease activating factor
44
what is adaptor for extrinsic pathway
FADD..activated Fas receptor associates with FADD as an adaptor molecule to transmit its signal inside the cell. FADD activates caspases to initiate cell destruction
45
what does FADD stand for
Fas Associated protein with Death Domain
46
Which are the initiating caspases
Ced 8&9
47
Which are the executin caspases
Ced 3,6,7
48
how are initiator caspases activated
aggregation by assocating with an adaptor protein (FADD or Apaf-1)
49
how are execution caspases activated
cleavage by initiating caspases
50
3 main targets of execution caspases
proteins involved in transcription, DNA replication, and DNA repair
51
which phospholipid signals phagocytosis
phosphatidyl serine
52
what enzyme makes plasma membrane asymmetric
scramblase
53
CED-1 is necessary for what
binding to apoptotic cells
54
Bcl-2 family does what
regulates apoptosis
55
pro survival members of of Bcl-2 family have what domain
BH1 and BH2
56
which BH domain seems to be the killer domain
BH3
57
how do pro-survival Bcl-2 family members actually promote survival 2 ways
-they bind to Apaf-1 to prevent it from activating caspases -bind to pro-apoptoic family members and prevent them from forming pores that releasing cytochrome C
58
what is cytochrome c's role in apoptosis
activates Apaf-1
59
is Bad active when phosphorylated/ unphos
unphos
60
what are caspases
cellular proteases
61
where do caspases cut
carboxyl side of aspartic acid
62
5 constituents of the apoptotic program
signal adaptors regulators caspases scramblase/phagocytosis
63
adaptors act by
recognizing apoptotic signal and aggregating/activating initiating caspase enzymes
64
Bcl-2 family associated w/ intrinsic or extrinsic
intrinsic
65
which AA is in hte active site of Caspase
cysteine
66
what mechanically activates caspases
cut off autoinhiibtory domain
67
how much time does it take for caspases to act
30-60 minutes
68
5 methods of Cdk regulation
1.Cyclin association 2. Phosphorylation 3. Dephosphorylation 4. Cyclin kinase inhibitors 5. Cyclin subunit proteolysis
69
what does Cdc25 do?
removes inhibitory phosphorylation on Cdk
70
What does Ink4 family do?
block Cdk kinase activity
71
What does CKI family do?
block Cdk kinase activity
72
what classificationof protein is APC
anaphase promoting complex--ubiquitin ligase in M-phase
73
SCF does what?
ubiquitin ligase in a cell cycle phases except M-phase
74
draw cell cycle loop w/ Cyclins and Cdk's
75
how does INK 4 family inhibit
how does CKI family inhibit
does not allow cyclin to bind
does not allow ATP to bind
76
2 roles of cyclins
activate kinase
control substrate specificity
77
Mcm does what
helicase activity
78
S phase entry
79
DNA replication control
80
which cyclin promotes movement into mitosis
B and A
81
What are two targets of APC
cyclin B
separation of sister chromatids
82
Anaphase sister chromatid separation
APC/C ubiquinates securin
Separase is active and cleaves
83
4 Major Checkpoints
DNA dmage (G1 arrest)
Unreplicated DNA (S arrest)
DNA Damage (G2 arrest)
Improper spindle formation (M arrest)
84
DNA Damage checkpoint for G1/S transition on/off default
off
85
how does DNA damage G1/S checkpoint work?
DNa dmage, phosphorylates p53, p53 transcription factor for p21, p21 inhibits cdk2/cyclin E complex
86
Spindle checkpoint is on/off default
on
87
Mad2 works at which checkpoint
function of Mad2
spindle separation
if MT is not connected to kinetochore then APC is inhibited and cyclin B isn't active
88
2 methods to make DNA replication control unidrectional
Cdc 6 is destoryed
ORC can't recurit MCM when phosphorylated
89
M phase is driven mostly by which cdk/cyclin combo
B /cdk1
90
exit form mitosis is driven mostly by
APC
91
Cell Cycle Stage and Chemotherapy agent used
1. G1--DNA Damage---Cisplatin
2. S--Unreplicated DNA--DNA Pol or Topo inhibitors
3. G2-Replication Erros--none
4. M--Chromosome Alignment--Taxol and Colcemid
92
peripheral membrane proteins can be removed by
mild extraction w/ high salt or pH
93
integral membranes proteins are extracted by
disrupting the membrane w/ detergent
94
t/f flipping of integral membrane proteins occurs
f
95
Moderate concentrations of cholesterol in the membrane
imparts increased/decreased fluidity to the membrane
increased
96
High concentrations of cholesterol in the membrane causes increased/reduced fluidity at
normal temperatures, but can protect the membrane from drastic (increases/losses) of fluidity at low
temperatures.
reduced
losses
97
cytosolic [Na] high or low?
low
98
cytosolic [Ca] high or low?
low
99
cytosolic [K] high or low?
high
100
4 categories of membrane proteins q
1. Structural
2. Enzymes
3. Receptors
4. Transporters/Channels
101
4 major membrane transport systems
1. Ion pumps
2. ABC transporters
3. Antiport/Symport
4. Uniports/Channels
102
Mechanism for Ion Pumps
couple change in affinity and conformation
103
MDR is what and what kind of transporters
multidrug resistance protein
ABC trasporters
104
TAP is what and what kind of transporters
transporter associated w/ antigen presentation
ABC transporter
105
CFTR is what and what kind of transporters
CF transmembrane conductance regulator
ABC transporters
106
NO generated from which AA
arginine
107
4 essential features of signaling pathways
1. Reversibility
2. Signal cascades
3. Cross-talk
4. Feedback
108
4 classes of receptors
GPCR
ion channels
receptor kinase
receptor enzyme
109
SH2 is what
domainof Grb2 that recgonizes activated Recptor tyrosine kinase
110
What active Gq activate and what does that do
phospholipase C
catalyzes the conversion of phophatidylinositol 4,5 bisphosphate (PIP2) to diacylglycerl and inositol triphospate (IP3)
111
What does IP3 do?
rleases Ca from ER
112
What does diacylglycerol do?
activates C-kinase which goes on to phosphoylate cell protein
113
what activates diacylgylcerol
Ca
114
TGF\_ B activation results in
inhibtion of hte cell cycle
115
How do cAMP signals turn off?
phosphodiesterase eliminates cAMP
116
How do Map Kinase signals turn off?
MAP K Phosphatase
117
How do Ca signals turn off?
Ca eliminated from cytoplasm
118
how does phototransduction turn off
Arrestin releases retinal and retinal inactivates rhodopsin
119
