S3 Flashcards
1
Q
dynamic instability
A
individual MTs do different things at different time (dont just grow at cc)
GTP cap
catastrophe
rescue
2
Q
critical concentration for assembly
A
an amount at which there is enough in solution to polymerize
plus end has lower critical concentration than minus end - polarity
MTs also need GTP, 37 degrees, Mg
3
Q
treadmilling
A
illusion of movement
one side grows while other side shrinks seen in vivo, not actual movement
4
Q
selective stabilization
A
proteins can bind to lattice to prevent dissasembly - important for cell polariation
Tau, MAP. double cortin, STOP, plectin, etc
5
Q
GTP hydrolysis and micrtotubules
A
all free tubulin is GTP-tubulin
adding to plus end forming GTP cap
then hydrolysis behind making GDP tubulin
catastrophe if GTP cap is lost,
rescue if cap comes back before dissasmbled
not technically necessary to form but without it cant dissassemble to do work
6
Q
microtubule based molecular motor proteinsd
A
get more work done than that stored in MTs ATPase dynein is retrograde toward minus end kinesin is anterograde toward plus end motor and cargo domain processivity
7
Q
tau
A
important for stabalizning MTs
absent in alzheimers
neruon specific
8
Q
katanin
A
cuts microtubule by pulling tubulin through hexamer pore
9
Q
microtubules
A
tubulin subunits hollow polar dynamic highly conserved railway for motor proteins
10
Q
actin filaments
A
actin subunits non holow polar dynamic highly conserved railways for motor protieints
11
Q
intermediate filaments
A
various kinds of intermediate filament subunits nonhollow non polar non dynamic diverse not a railway for motor proteins
12
Q
MT subunits
A
alpha beta dimer
free tubulin dimers
13
Q
MT polarity
A
alpha is minus end
beta is plus end
nothing to do with charge
14
Q
mitotic vs interphase microtubule org
A
both have centrosomes with minus ends and plus ends out
but Interphase has one in the center going out
mitotic has 2 on oposite ends
‘centralized foci’
15
Q
nucleation
A
getting new MTs started
has Lag without nucleation seed
less energetically favorable than elongation
needs MT nucleating elements to make favorable like centrosomes and basal bodies
16
Q
nucleating sites
A
in pericentriole matrix PCM around centrioles
rings of gamma tubulin
centrioles themselves only source of extracellular MTs
17
Q
cilia and flagella
A
short and long
9+2 arrangment
flagellar dyeinn
basal body is centriole that contacts cell membrane
18
Q
gamma tubulin
A
gamma turc is ring for nucleation sites
unclear if it binds to alpha or beta but it helps make polar proto filament
19
Q
cut and run
A
Mts break off centrosome then move for non centrosomal arrays like epithelial cells with apical and basal ends
20
Q
coverslip movement
A
kinesisn walks toward plus end to MT moves in dirextion of minus
Dynein walks toward minus end so plus end leads
21
Q
neuron MT patterns
A
dynien moves them into axon so plus end toward terminal
dendrite mixed because dynin moves in there then kinesins move it around
22
Q
axon branch formation
A
katanin cuts and tau gets phosphorylated while it moves to new branch
spastin cuts and tau stays on MT chunks that move to new branch
23
Q
actin filament growth and force on membranes
A
at cell concentrations actin is more stable in a filament so polymerization for brownian ratchet when it bends to allow another subunit then bends back working on the membrane
24
Q
myosin force generation cycle
A
attached and nucleotide free
ATP binds mysosin so it releases actin
ATP hydrolysis to ADP.Pi bound cocks forward
Pi release ADP bound and bound to actin while cocked forward
ADP release so nucleotide free again and bends back moving actin
25
conservation of actin
highly conserved in eukaryotes
26
human actin isoforms
5
muscle - smooth, skeletal, cardiac
cytoplasmic - beta, gamma
27
actin monomer
unusual subdomain structure
ATP binding sites
hydrolyzes and exchanges nucleotides slowly
28
actin filament
polar
subdomain 2 into 1-3 cleft
ATP hydrolysis is fast ier in filament than in monomer
29
in vitro actin assembly kinetics
nucleation slow and highly concentration dependent
elongation is fast and aysmetric - barbed + end is 1-3 cleft
pointed - end
30
[actin]eq
a fixed value that is the balance of forward and revere reactions
the critical concentration
31
buffering free actin
very little exists in cells
binds to beta-thymosin blocking both ends
most bins profilin which is a nucelotide exchange factor blocks elongation only on pointed end
32
growth on barbed end
beta thymosin blocks both ends
prolifin allows barbed end addition
almost all elongation this way
33
nucleation of actin
blocked by beta thymosin and or prolifin so nucleation is prevented in cells
34
nucleation factors for actin
needed to allow filaments to grow in the right place at the right time
35
actin elongation control
capping proteins to prevent elongation and depolarization like barbed end CapZ
elongation factors like formins, ENA/VASP control actin delivery and are capping protiens
36
actin disassembly
ATP hydrolysis destabalizes the filament meaning that ADP actin dominates away from barbed end
severing factors generate new pointed ends
capping proteins will arrest growth at barbed end while the unpcapped pointy end depolymerizes
37
lamellipodia
branched arrray
broad flat rapidly polymerizying protuisions in 2d environments
densely branched actin
38
lamellipodia assembly and disassembly
nucleated by Arp2/3 complex at membrane
WASp/Scar proteins activate Arp2/3
growing filaments pus mesh away from membrane into cell
agin filaments are enriched by ADP actin and targetted for recycling by coflin
depolarized gets grabbed and recharged by profilin
39
filopodia
parrallel bundled arrays
fast growing
nundling protein like fascin and a TIP complex
come from branched arrays
40
actin crosslinking
different bundling proteins result in different structures
alpha-actin - anti-parallel bundling factor
usually told apart by distance btwn filaments
41
myosin
actin binding motor
| walks toward barbed end
42
different myosin functions
same idea but differneent strucutre can be used for different cargo
43
stress fibers
have focal adhesions of actin but look similar to muscle
44
sarcomere
repeated in Skeletal muscle making it look striated
| like a stress fiber with overlapping actin and myosin and caps instead of focal adhesions
45
skeletal muscle regulation
troponin is bound to tropomyosin which blocks myosin from binding to actin but Ca comes and removes troponin so tropomyosin moves so myosins can do its thing
46
skeletal mucle triggering
t tubules send action potential
| sarcoplasmic reticulume then releases Ca
47
cell polarity
differences in shape and structure of cells
| asymmetry
48
regulated polarization
like lymphocyte becoming macrophage which is a direected homoestatic or immune response for migration and contact with other cells
49
T cells
2 poles and an axisl of polarity
migration
competition
asymmetric division
50
epitheilai cells
polarized protein diestribution between basal and apical ends
apical has actin and cell cell junction
Par6, Par3, APKC on apical side of junction
uses gradents and transporters to have nutrients flow through
cell cell junction dilineate transporter types
51
distribution of PAR proteins
Par3/Par6/aPKC
anterior side of asymmetric cell division
distal end of neve axon
leading end of cell migration
apical side of cell cell junction in epithelial cells
52
3 steps of cell migration
extension of leading edge
nuclear movement
tail contraction
53
migrating cell adhesion
```
extend
adhese
translocate
de adhese
focal adhesion kinase
```
54
distribution in C elegans
Mex5/mex6
Par3/6/aPKC
all anterior
55
symmetric vs asymmetrci
```
cadherin complex
zonular protein
apical marker/cadherin hole
if even amounts of above three then symmetrical
side with cadherin hole becomes NPC
```
56
2 axis of polarity
apical-basal
| planar cell
57
PCP mutants
disorginization
58
division of neural progentior cells
vertically = 2 NPC
| horizontal or angled = 1 NPC 1 neuron
59
Pro axon factors
PI3K
AKT
tau
PKB
60
pro dendrite
PTEN
| GSK-3 beta
61
planar cell polarity
2 axis: circunferential and radia
strucutres organs
downstream of wnt
62
posterior c elegants
pie1
par1,2
p-granules
63
wnt signaling
frizzled
disheveled
knock out experiments
gene transcription (canonical has beta catinin or calcium)
cytoskeleton remodeling for PCP has rho gtpase and JNK
64
why are there size limits in microscopy
visible wavelength, resolution
65
importance of tissue processing like fixation embedding sectioning
just to better visualize
66
importance of specialized illumination
better visualize
67
how to follow protein dynamics in living cells
fluroscence
68
light vs electron vs atomic force microscopy
biggest to smallest
69
compare images from atomic force microscopy, scanning electron microscopy, and transmission electron microscopy
d
70
refractive index
ratio of light in a vaccuum to light through medium
| used to match numerical aperture of a lens
71
limits of resolution
minimum that can be achieved given the limitations of the medium used for microscopy and what is used to produce the image
defined by distinguishing btwn two objects
72
photobleaching
overdoing the flourescence and destroying the flurophore
| photoprotective scavengars help
73
phototoxicity
hurting cells/samples by shining laser on i t
74
deconvolution microscopy
math enhances images
75
two photon microscopy
better than confocal
76
fluorescence resononance energy transfer FRET
multiple dyes used to map interactions
77
photoactivation
caged molecules remain unseen until catalytically freed
78
total internal reflection fluorescence
TIRF
used to amplify from 2D coverslip
light bounces at an angle
79
transmission electron m
shoots electrons through sampe to acheive 2 milllion x mag
wavelenght of electron is smaller than light
v inverse to w
ultra thin slicing
80
scannning electron m
cover sample with metal and shoot with electrons
| image based on scatter
81
atomic force microscopy
bounce laser off of tip of probe
measure deviations
can see individual atoms
82
visible light
0.4um to 0.7um
83
meiosis vs mitosis
meisosis has two stages ending in 4 haploid cells
| mitosis has its steps leading to 2 diploid cells
84
meiosis I vs mitosis
homologus chromosomes connect and exchange parts
| then pairs move to opposite sides
85
APC/C
something to do with metaphase anaphase checkpoint
| gets activated by cdc3- to help ubiquinate m cyclin-cdk and end metaphase
86
Cdk activating kinase
| and cyclin
get turned on by Cdc25 and off by wee1 kinase
| different versions G,s, M m is for m phase
87
phases of meisosis
```
pro
meta1
ana 1
telo 1
pro 2
meta 2
ana 2
telo 2
basically 2 division: first pairs of homolougs then sister chromatids
```
88
prophase I
homologuous recombination
| crossing over synaptonemal complexl
89
synaptonemal complex
combines two homologs with cohesisn and transverse filaments
90
cohesin
4 units making a ring around sister chromatids
| scc3-scc1 hook gets cleaved in anaphase
91
homologous recombination
homologous dna exchange parts
for repair
accurate separation because chiasmata between correct homo pairs
genetic diversity
92
chiasmata
happens after cross over when physically linked still
93
HR deficient
fail to form SC and dont get cross overs
94
separase in meiosis I
releases cohesin along the arms but cohesin near centromere is intact
95
nondisjunction
no crossover - unstable and random
distal cohesion - unstable and random
proximal crossover - reductional division in meisosi II (stuck)
so crossovers cant be random but must be medial
96
cross over interference
good thing?
two or more crossovers happen, so adjacnet events are located furthera apart than expected from random
but protects chiasmata
97
When can DSB happen
prophase I
98
spo11
catalyzes double strand breaks
part of large complex
so phosphorylation of Mer2 upregulates it
99
double strand break recombination model
```
resection
strand invation (Rad51)
synthesis
capture second end
synthesis
double holliday junction intermediate
cut both for resolution and either have crossover or non crossover
```
100
synthesisi dependent strand annealilng
syn
dissociat
anneal
get non crossover
101
Non crossover resultes
DSBR fits a lot but non crossovers appear at wrong time so maybe SDSA makes those
102
mitotci spindle
astral MTs
kinetochore MTs
interpolart MTs
103
astral MTs
stabalize centrosome
104
kinetochore
connect centrosome to homo
105
interpolar
stabalize entresomes to each other
106
3 stages of apoptotici cell removal
find me
eat me
anti inflammatory cytokines
107
procaspase activation
inactive procaspases have 2 celaveage sites
cleaveage activated by other active caspase so cascade
then dimerize
108
fas ligand model
extrinsic apoptotic pathway
fas ligand on killer lymphocyte binds to Fas death receptor leading to association of fas-associated death domain FADD and assembly of Death inducing signaling complex DISC which activates procaspase 8,10
death effector domain DED
Caspase activating and recruiting domain CARD
109
cytocrhome c
apoptotic stimulus relases from mitochondria
cc activates apaf1 (apoptotic protease activating factor)which has CARD domain and multimerizes to apoptosome
recruites procaspase 9 which gets executioner caspases
110
activation of intrinsic pathway
apoptotic stimuli like BH3 inactivates the anti-apoptotic Bcl2 protein allowing BH123 to dimerize on outermembrane of mito so cc can get out
111
scheme of mitochondria
basically bax/bak open a pore casuing cc and then mDNA to fall out
112
increased production of Bcl2 protein
after a survivial factor activates a receptor, transcription is upregulated making more bcl2 to block apoptosis
113
inactivation of proapoptotic BH3 only bcl2 protein
survival activates receptor activating AKt kinase whichactivates Bcl2 and inactivates Bad
blocking apoptosis
114
inactivation of IAPs
survival factor and receptor
| MAP kinase inactivates Hid which activates IAPs which i think block cc
115
inflammosome
causes inflammation kinda like DISC in apoptosome
ASC or apoptis asssociated speck like protein containing a caspase recruitment
activated by toxins to mobilize immune system, caspase 1 releases cytokines to recruit the A team
NALP3 and IPF3 are variants
116
necroptosis
causes immune response
necrosome with RIP3 kinase, caspase 8 activates
death from membrane osmolysis, energetic catastrophe, lipid peroxidation
117
start/restriction point
when cells decide to go from G1 to S
118
cyclin dependent kinase
depending on type of cyclin, will activate CDK for M or S phase
119
G1-CDK
cyclin D
| cdk4, cdk6
120
G1/S-CDK
cyclin E
| cdk2
121
S-Cdk
Cyclin A
| Cdk2,cdk1
122
M-CDK
cyclin B
| Cdk1
123
regulation of CDK
transcription
+/-p
Cdk inhibitors
ubiquitind dependent proteolysis
124
+/-P of Cdk
CAK cdk activating kinase
Wee1 +P inhibits
Cdc25 -P activates
125
Cdk inhibitors
p16, p21, p27
| bind to an inactivate the active cyclin-cdk complexes
126
ubiquitin dependent proteolysis
APC/C: Anaphase-promoting complex/cyclosome: ubiquitin ligase complex
gets turned on by Cdc20 which tags cyclin B for degredation to make meta to ana transition
127
SCF
Skp1-cullin-f-box ubiquitin ligase complex
| tags a Cdk inhibitor to promote S phase entry
128
S phase
DNA replication
| sister chromatid cohesion
129
M phase
mitosis
| cytokinesis
130
licensing factors
Cdc6
Cdt1
make sure chromosome duplication happens once only
131
prophase
chromosome condensation
kinetochore
two centrosomes already
132
prometaphase
nuclear envelope breaks down
mitotic spindle forms
centrosome at spindle poles
133
metaphase
chromosomes are attached to spindle MTs at kinetochore
| MTs line up signaling Met-anaphase transition
134
anaphase
sister chromatid separation
135
Telophase
chromosomes arrive at poles
chromosome decondensation
nuclear envelope reassembles
contractile ring starts to contract
136
cytokinesis
contractile ring creates cleavage
| telophase steps complete
137
which Cdk starts mitosis
M-CDK
| Cdk 1 and m-cyclin
138
condensin
protein for prophase condensation of chromosomes
139
breakdown of nuclear envelope
M-Cdk
140
parts of mitotic spindle
spindle poles
astral microtubules
kinetochore microtubules
interpolar microtubules
141
spindle poles
centers of microtubule nucleation with minus ends
142
astral MTs
radiate outward from the poles and contact the cell cortex to help position MS
143
kinetochore MTs
attach sisters at kinetochores
144
interpolar MTs
+ ends overlap making antiparallel array
145
centrosome duplication
G1/S-CDK
centrioles separate
act as templates
dont spread and duplicate until M phase
146
tension check
auroro B kinase phosphorylates Ndc80 when low tension and increases affinity for MT plus end so it can get pulled away
147
APC/C and separation
ubiquinates securin freeing separaste to cleave cohesin to separate sister chromatids
148
if choromosomes not properly attached to MS
Mad2 binds APC/C and inhibits so no separation
149
RhoA GTPase
assembly and contraction of contractile ring which uses actin and myosin II
150
extracellular promoters
mitogens - mitogen receptors
growth factors - RTKs and mTOR
survival factors
151
extracellular suppressors
Stress
| apoptotic signals
