final keywords Flashcards
(194 cards)
1
Q
nucleus
A
-compartmentalization of genome
-coordinate cellular activities
2
Q
nucleoid
A
prokaryotes, includes whole genome
3
Q
nucleolus
A
ribosome synthesis
4
Q
transcription factory
A
transcription factors are concentrated
5
Q
intrachromosomal channel
A
gene regulatory elements, activate other chromosomal genes
6
Q
nuclear speckle
A
mRNA splicing factors are concentrated
7
Q
nuclear matrix
A
-maintain nucleus shape
-anchor protein factors
8
Q
cytoskeleton components
A
-microtubules
-actin microfilaments
-intermediate filaments
9
Q
nuclear envelope
A
-barrier (cytoplasm/genome)
-spatially regulate gene regulation
10
Q
outer nuclear membrane
A
continuous with RER
11
Q
nuclear envelope lumen
A
continuous with ER lumen
12
Q
nuclear lamina
A
-mechanical support to nuclear envelope
-inner surface of nuclear inner membrane
13
Q
ABC nuclear lamins
A
related to proteins forming intermediate filaments in cytoskeleton
14
Q
nuclear pore complex
A
channels in nuclear envelope
-regulate nucleocytoplasmic trafficking
15
Q
nucleoporin
A
-Nups
-vesicle formation
16
Q
central scaffold
A
anchors NPC to nuclear envelope
17
Q
central channel
A
aqueous, FG nucleoporins, <40kDa size exlusion
18
Q
y-complex
A
-cytoplasmic ring
-nuclear ring
-composed of structural Nups
19
Q
cytoplasmic filament
A
Nups extending into cytoplasm from NPC
-cargo recognition and import
20
Q
nuclear basket
A
-linked to y-complex
-cargo import and export
21
Q
nuclear localization signal (classic & bipartite)
A
-target protein cytoplasm->nucleus
classic: + aa’s
bipartite: 2 stretches of basic aa’s, 7-10 aa spacer sequence
22
Q
karyoferins
A
receptor proteins to move macromolecules
-importin, exportin
23
Q
importin alpha
A
recognize and bind cargo with NLS
24
Q
importin beta
A
bind cytoplasmic filaments on NPC
25
ran-gtp
active form, high in nucleus
26
ran-gdp
inactive form, higher in cytoplasm
27
gef
GDP -> GTP
-nucleus
28
gap
GTP->GDP
-cytoplasm
29
nuclear export signal
nucleus->cytoplasm
-leucine-rich motif
30
cyclin
cytoplasmic, move to nucleus and activate CDKs when dephosphorylated
31
cell cycle components
G0, G1, S, G2, M
32
cyclin-dependent kinase
nucleoplasmic, phosphorylated and activated by cyclins
33
open vs closed mitosis
open: nucleus completely disassembled by metaphase, NLS proteins re-imported
closed: nuclear envelope remains intact
34
proteasome
degrade pre-existing cyclins
35
brightfield microscopy
undiffracted light focused by objective lens
36
deconvolution
remove background, higher contrast and clarity
37
resolution
separate two points that still remain identifiable as two points
-wavelength and NA
-better resolution=smaller #
38
fixation of samples
formaldehyde - crosslinks amino groups and proteins
39
microscopy artifacts
fixing sample kills and alters the cells you're viewing
40
microtome
embedding, sectioning with microtome, stained with dyes
41
fluorescence microscopy
visualize processes in living specimens
42
fluorescence methods
-autofluorescense (endogenous)
-immunofluorescense (dyed ab)
-autofluorescent proteins
43
confocal laser-scanning microscopy
-living sample, dynamic biological/cellular processes live
44
pinhole
emitted light focused through pinhole then viewed
45
focal place (z-stack)
single layer of light through sample, assembled into z-stack
46
photobleaching
no longer fluorescent
47
phototoxcity
react with oxygen to produce free radicals that damage membranes
48
super-resolution CLSM
10x better resolution than CLSM, visualize smaller structures
49
vesicle coat proteins
-select cargo proteins
-regulate vesicle formation and budding
50
biosynthetic pathway
ER-> golgi-> endosomes -> lysosomes
51
secretory pathways
1. constitutive (secretory vesicle)
2. regulated (secretory granules)
52
exocytosis
trafficking and fusion/release to PM
53
endocytosis
PM->endosomes->lysosomes
54
autoradiography
-secretory pathway
-radiolabelled amino acids
55
live-cell imaging
-autofluorescent proteins
56
subcellular fractionation
-separate and purify organelles using size/density
57
microsomes
fragments of ER membrane reform into spherical vesicles
58
equilibrium density gradient centrifugation
separate intact organelles on basis of density
-sucrose gradient
59
liposomes
spherical vesicles with phospholipid bilayer and aqueous centre
60
mutant phenotype analysis
observe vesicle trafficking by screening for mutant phenotypes
61
yeast sec mutants
secrete proteins at permissive temperature only
-proteins accumulate depending on altered step
62
endoplasmic reticulum components
tubules, cisternae, lumen
63
reticulons
regulate tubule/cisternae shape
64
er subdomains
rough ER, smooth ER, nuclear envelope, mitochondria & PM associated membranes, ER exit sites
65
signal recognition particle
binds ribosome during cotranslational translocation, halts translation
66
RER targeting signal sequence
8-15 hydrophobic amino acids
67
srp receptor
ER integral membrane protein, docks SRP, binds GTP
68
sec61 translocon aqueous channel components (2)
pore ring: 6 hydrophobic aa's
alpha-helix plug: swings open/shut
69
signal peptidase
cleave RER signal sequence
70
reticuloplasmins / ER molecular chaperones
properly fold protein transported to RER
71
transmembrane domain
alpha-helix 16-25 hydrophobic amino acids
72
type 1 TMD proteins
signal sequence, STA, Nin-Cout
73
type IV TMD proteins
multiple TMDs, STA&SA, Nin-Cout
74
stop-transfer anchor sequence
stop translocation through translocon
75
type 2 TMD proteins
no signal sequence, SA, Nout-Cin
76
type 3 TMD proteins
no signal sequence, SA, Nin-Cout
77
signal-anchor sequence
-halt translocation and serve as membrane anchor
78
positive-outside rule
positive amino acid residues always face cytosol (type 2- flipped)
79
glycosylation
addition of carbohydrate side chains
80
n-linked glycosylation
adding sugar monomers to terminal Asparagine (N) group
81
glycosyltransferases
synthesize core oligosaccharide
82
dolichol phosphate
first sugar is added to dolichol phosphate during glycosylation
-membrane anchor and carrier
83
tunicamycin
blocks first step of n-linked glycosylation, prevent proper folding
84
n-linked glycosylation sequence motif
-N-X-S/T-
85
glucosidases
cleave 2/3 terminal glucose units
86
protein disulfide isomerase
forms disulfide bonds between Cys
-promote proper folding
87
er protein quality control
reticuloplasmins mediate proper folding (BiP, calnexin)
88
mannosidase
removes one mannose unit from folded protein
89
uggt monitoring enzyme
glycosyltransferase - conformation sensing protein
-recognize hydrophobic residues
-add back single glucose unit to misfolded protein
90
p97 AAA ATPase
ERAD pathway - ATP hydrolysis to pull misfolded protein into cytosol
91
ubiquitin (mono vs poly)
mono: target proteins -> endosomes
poly: target for degradation by proteasome
92
PERK mediated unfolded protein response pathway
-active: dimerized
-phosphorylate and inactive eIF2 alpha
-decrease protein synthesis
93
ATF6 mediated unfolded protein response pathway
-TF domain cleave by golgi protease, move to nucleus
-upregulate reticuloplasmins
94
cop1/copII/clathrin coat proteins
cop1: golgi->ER
copII: ER->golgi
clathrin: golgi->endosomes / PM->endosomes
95
anterograde transport
forward ER->golgi
96
retrograde transport
backward golgi->ER
97
sar1
-COPII assembly
-GTPase
98
sec12
ER integral membrane protein, bind Sar1 during COPII assembly
-GEF (GDP->GTP)
99
sec23/sec24
strucural scaffolding & membrane curvature during COPII assembly
100
er-export sorting signal
di-acidic ER export signal
-asp-x-glu-
101
sec13/sec31
recruited by Sec23/24 during COPII assembly, mediate bending and scission
102
rab proteins vs rab effector
rab: lipid anchored, GTP-binding
effector: bind active rab, on target membrane
103
v-snares vs t-snares
v- transport vesicle membrane
t- target membrane
104
NSF & SNAP
ATP hydrolysis to unwind SNARE complex
105
er retrieval sorting signal (soluble vs membrane)
soluble: C-terminal -KDEL sequence
membrane: C-terminal di-lysine
106
KDEL receptor
binds -KDEL of escaped ER proteins, assemble to COPI coat
107
cis/medial/trans cisternae
golgi metabolism, polysaccharide synthesis
108
trans-golgi network
sorting station - clathrin coat assembly to endosomes
109
grasps
tethering proteins linking golgi subcompartments
110
alpha-mannosidase I
cis cisternae, remove 3 mannose sugars from core oligosaccharide
111
mannose-6-phosphate
sorting signal for lysosome, phosphorylated in cis cisternae
112
signal patch
M6P groups -> soluble lysosome protein targeting
113
n-acetylglucosamine phosphotransferase
recognize lysosome-destined proteins
114
cisternal maturation model
cis->medial->trans
115
COP1 function
move resident golgi proteins back to proper cisternae
116
lysosome
digestive organelle, degrade larger cell components
117
autophagy
degradation of large cell components by lysosome
118
acid hydrolyase
inside lysosome, active only at low pH
119
lysosome signal patch
M6P signal patch
120
m6p receptor
recognize and bind soluble M6P-bearing lysosomal destined proteins
121
clathrin-coated vesicle assembly
1. M6P receptor bind AP1 and GGA
2. GTP binding->bind Arf1
3. clathrin binds AP1/GGA, curve membrane and bud off
122
ap1/gga (ap complex)
-mediate cargo selection, clathrin linker
123
arf1
-GTPase, recruit AP1/GGA from cytoplasm during clathrin-coated assembly
-lipid anchored when GTP bound
124
clathrin assembly
triskelions (hexogon->pentagon = curvature)
125
dynamin
scission of clathrin coated vesicle, GTP-binding protein, form dynamin ring
126
gamma-gtp
non-hydrolyzable analog of GTP, continued dynamin ring polymerization = stalk
127
retromer transport vesicle
transport empty M6P receptors back to TGN, can also traffic to PM
128
receptor-mediated endocytosis
1. PM receptor binds ligand
2. AP2 coat binds, accumulate in clathrin coated pit enriched in phosphatidylinositol
3. vesicle budding and scission
129
constitutive secretion pathway
secretory vesicles , TGN->PM
130
phagocytosis
1. ab against foreign material made
2. opsonization - fab domain binds bacteria
3. fc receptors bind fc domain on ab
4. actin microfilament assembly ->pseudopod->phagosome
131
fc receptor
on leukocyte to bind ab on opsonized bacteria
132
fc domain
on opsonized bacteria/ab
133
pseudopod/phagosome
changes in shape of leukocyte uptaking bacteria to degrade
134
bulk phase endocytosis
non specific uptake of materials into small vesicles
135
ap2 binding domains
-PI(4,5)P2
-PM receptors
-clathrin
136
clathrin-coated pit
formed during receptor mediated endocytosis by binding AP2
137
phosphatidylinositol (4,5) P2
lipid microdomain - recruit AP2 with bound ligand receptors to clathrin coated pit
138
multivesicular body
inward budding of vesicles into late endosome interior
139
ESCRT machinery
mediate cargo selection to MVB and inward vesicle budding
140
Hrs
ESCRT machinery, mono-ubiquinated, mediate inward budding and scission into MVB lumen
141
Vps4 ATPase
disassembles ESCRT complex in MVB
142
HIV gag protein
similar to ESCRT Hrs, mono-ubiquinated, mediate vesicle formation for virus particles
143
endosymbiont theory
first eukaryotic ancestor was engulfed prokaryote
144
organelle biogenesis
protein targeting, membrane assembly, morphology, motility, replication, degradation, inheritance
145
semi-autonomous
replication controlled by nuclear and organelle genome
146
mitochondria components
outer/inner membrane, intermembrane, matrix
147
mitochondrial network
long, interconnected set of tubules
148
mitochondrial fusion
1. ER subdomain MAM constrict site
2. Drp1 form Drp ring with cardiolipin
3. GTP hydrolysis constricts ring and cell splits
149
mitochondrial fusion
1. Mfn1/2 bind with Bak and Bax
2. phospholipase d converts cardiolipin->phosphatidic acid (membrane curves)
3. OPA1 and GTP fuses inner membranes
150
organelle homeostasis
rates of fission vs fusion, control number, size and connections in network
151
drp1
uses GTP hydrolysis to constrict mitochondrial for fission
152
cardiolipin
microdomain in mitochondrial OM, helps fission and is converted to phosphatidic acid in fusion
153
mitofusions (mfn1, mfn2)
-GTPase cytoplasmic domain, protein interaction domain
-form tethering complex in mitochondrial fusion
154
bak and bax
mitochondrial OM proteins - help OM fusion
155
phospholipase d
converts cardiolipin -> phosphatidic acid to allow mitochondrial fusion
156
phosphatidic acid
mitochondrial OM curvature inward
157
opa1
use GTP to promote inner mitochondrial membrane fusion
158
prohibition
ensures OPA1 only fuses other membranes - prevent self-fusion
159
matrix targeting sequence
-20-50 aa long
-N terminus, + aa's one side, (S/T) hydroxylated other side
160
cytosolic molecular chaperones
recognize mitochondrial matrix destined proteins
161
cytosolic hsp70
cytoplasmic molecular chaperone, recognize mitochondrial matrix destined proteins
162
mitochondrial rna cloud
mRNAs encoding mitochondrial proteins enriched in cytoplasm surrounding mitochondria
163
import receptor complex
recognize & bind matrix targeting signal on mitochondrial OM
164
tom20 / tom22
form import receptor complex on mitochondrial OM
165
tom40
forms general import pore and transmembrane channel in mitochondrial membrane
166
tim23 / tim17
form mitochondrial inner membrane channel
167
membrane contact sites
between general import pore and inner membrane channel in mitochondrial membrane
168
matrix processing protease
cleave matrix targeting signal in mitochondrial matrix
169
matrix hsp70
bind protein entering mitochondrial matrix, bound to Tim44
170
tim44 (molecular motor)
uses ATP to pull protein into mitochondrial matrix
171
h+ electrochemical gradient
[H+]intermembrane>[H+]matrix, drives mitochondrial protein transport
172
matrix molecular chaperones
uses ATP hydrolysis to fully fold protein in mitochondrial matrix
173
chloroplasts
plant cell organelle, site of photosynthesis
174
photosynthesis
CO2+H2O+sunlight->sugars+ATP
175
chloroplast components
inner/outer membranes, intermembrane, envelope, thylakoids, stroma
176
stromules
connect chloroplasts
177
chloroplast fission
1. FtsZ1/2 form FtsZ ring with ARC3, MinD/E
2. ARC6 links z-ring to membrane
3. PDV1/2 bind ARC5 - PD-ring
4. GTP hydrolysis->cell splits
178
FtsZ1 / FtsZ2
form FtsZ ring at chloroplast division site
179
ARC3, MinD & MinE
position FtsZ proteins during chloroplast division
180
ARC6
links FtsZ ring to inner chloroplast membrane during division
181
plastid dividing machinery
interact with ARC5/6, form PD-ring and uses GTP hydrolysis to divide chloroplast
182
PD-ring
formed by ARC5
183
stromal import sequence
-N-terminus
-hydroxylated (S/T) and hydrophobic aa's
184
TOC/TIC chloroplast complex
recognize and bind chloroplast stromal import sequence with GTP
185
stromal processing enzyme
cleave stromal import sequence in chloroplast stroma
186
hsp93
stromal chaperone protein, recognize and bind incoming protein, uses ATP to pull protein into stroma
187
thylakoid targeting sequence
revealed when stromal import sequence is cleaved
188
SRP-dependent chloroplast targeting pathway
1. chloroplast signal recognition particle binds thylakoid sequence and SRP receptor
2. translocate through membrane via thylakoid Sec61-like translocon
189
pH-dependent chloroplast targeting pathway
1. protein fully folded in stroma
2. di-Arg sequence binds unique receptor
3. pH gradient pulls protein stroma->thylakoid
190
chloroplast signal recognition particle
recognize and bind thylakoid-targeting signal
191
chloroplast SRP receptor
bind SRP and GTP to translocate protein stroma->thylakoid
192
thylakoid Sec61-like translocon
translocate protein stroma->thylakoid
193
thylakoid lumenal protease and molecular chaperones
remove thylakoid-targeting sequence and fully fold protein
194
di-arginine-containing thylakoid targeting sequence
pH dependent thylakoid translocation pathway, fully folded protein
