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mcb2050 > final keywords > Flashcards

final keywords Flashcards

1
Q

nucleus

A

-compartmentalization of genome
-coordinate cellular activities

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2
Q

nucleoid

A

prokaryotes, includes whole genome

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3
Q

nucleolus

A

ribosome synthesis

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4
Q

transcription factory

A

transcription factors are concentrated

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5
Q

intrachromosomal channel

A

gene regulatory elements, activate other chromosomal genes

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6
Q

nuclear speckle

A

mRNA splicing factors are concentrated

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7
Q

nuclear matrix

A

-maintain nucleus shape
-anchor protein factors

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8
Q

cytoskeleton components

A

-microtubules
-actin microfilaments
-intermediate filaments

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9
Q

nuclear envelope

A

-barrier (cytoplasm/genome)
-spatially regulate gene regulation

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10
Q

outer nuclear membrane

A

continuous with RER

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11
Q

nuclear envelope lumen

A

continuous with ER lumen

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12
Q

nuclear lamina

A

-mechanical support to nuclear envelope
-inner surface of nuclear inner membrane

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13
Q

ABC nuclear lamins

A

related to proteins forming intermediate filaments in cytoskeleton

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14
Q

nuclear pore complex

A

channels in nuclear envelope
-regulate nucleocytoplasmic trafficking

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15
Q

nucleoporin

A

-Nups
-vesicle formation

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16
Q

central scaffold

A

anchors NPC to nuclear envelope

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17
Q

central channel

A

aqueous, FG nucleoporins, <40kDa size exlusion

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18
Q

y-complex

A

-cytoplasmic ring
-nuclear ring
-composed of structural Nups

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19
Q

cytoplasmic filament

A

Nups extending into cytoplasm from NPC
-cargo recognition and import

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20
Q

nuclear basket

A

-linked to y-complex
-cargo import and export

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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

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22
Q

karyoferins

A

receptor proteins to move macromolecules
-importin, exportin

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23
Q

importin alpha

A

recognize and bind cargo with NLS

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24
Q

importin beta

A

bind cytoplasmic filaments on NPC

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25
Q

ran-gtp

A

active form, high in nucleus

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26
Q

ran-gdp

A

inactive form, higher in cytoplasm

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27
Q

gef

A

GDP -> GTP
-nucleus

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28
Q

gap

A

GTP->GDP
-cytoplasm

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29
Q

nuclear export signal

A

nucleus->cytoplasm
-leucine-rich motif

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30
Q

cyclin

A

cytoplasmic, move to nucleus and activate CDKs when dephosphorylated

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31
Q

cell cycle components

A

G0, G1, S, G2, M

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32
Q

cyclin-dependent kinase

A

nucleoplasmic, phosphorylated and activated by cyclins

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33
Q

open vs closed mitosis

A

open: nucleus completely disassembled by metaphase, NLS proteins re-imported
closed: nuclear envelope remains intact

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34
Q

proteasome

A

degrade pre-existing cyclins

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35
Q

brightfield microscopy

A

undiffracted light focused by objective lens

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36
Q

deconvolution

A

remove background, higher contrast and clarity

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37
Q

resolution

A

separate two points that still remain identifiable as two points
-wavelength and NA
-better resolution=smaller #

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38
Q

fixation of samples

A

formaldehyde - crosslinks amino groups and proteins

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39
Q

microscopy artifacts

A

fixing sample kills and alters the cells you’re viewing

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40
Q

microtome

A

embedding, sectioning with microtome, stained with dyes

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41
Q

fluorescence microscopy

A

visualize processes in living specimens

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42
Q

fluorescence methods

A

-autofluorescense (endogenous)
-immunofluorescense (dyed ab)
-autofluorescent proteins

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43
Q

confocal laser-scanning microscopy

A

-living sample, dynamic biological/cellular processes live

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44
Q

pinhole

A

emitted light focused through pinhole then viewed

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45
Q

focal place (z-stack)

A

single layer of light through sample, assembled into z-stack

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46
Q

photobleaching

A

no longer fluorescent

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47
Q

phototoxcity

A

react with oxygen to produce free radicals that damage membranes

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48
Q

super-resolution CLSM

A

10x better resolution than CLSM, visualize smaller structures

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49
Q

vesicle coat proteins

A

-select cargo proteins
-regulate vesicle formation and budding

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50
Q

biosynthetic pathway

A

ER-> golgi-> endosomes -> lysosomes

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51
Q

secretory pathways

A
  1. constitutive (secretory vesicle)
  2. regulated (secretory granules)
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52
Q

exocytosis

A

trafficking and fusion/release to PM

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53
Q

endocytosis

A

PM->endosomes->lysosomes

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54
Q

autoradiography

A

-secretory pathway
-radiolabelled amino acids

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55
Q

live-cell imaging

A

-autofluorescent proteins

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56
Q

subcellular fractionation

A

-separate and purify organelles using size/density

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57
Q

microsomes

A

fragments of ER membrane reform into spherical vesicles

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58
Q

equilibrium density gradient centrifugation

A

separate intact organelles on basis of density
-sucrose gradient

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59
Q

liposomes

A

spherical vesicles with phospholipid bilayer and aqueous centre

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60
Q

mutant phenotype analysis

A

observe vesicle trafficking by screening for mutant phenotypes

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61
Q

yeast sec mutants

A

secrete proteins at permissive temperature only
-proteins accumulate depending on altered step

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62
Q

endoplasmic reticulum components

A

tubules, cisternae, lumen

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63
Q

reticulons

A

regulate tubule/cisternae shape

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64
Q

er subdomains

A

rough ER, smooth ER, nuclear envelope, mitochondria & PM associated membranes, ER exit sites

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65
Q

signal recognition particle

A

binds ribosome during cotranslational translocation, halts translation

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66
Q

RER targeting signal sequence

A

8-15 hydrophobic amino acids

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67
Q

srp receptor

A

ER integral membrane protein, docks SRP, binds GTP

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68
Q

sec61 translocon aqueous channel components (2)

A

pore ring: 6 hydrophobic aa’s
alpha-helix plug: swings open/shut

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69
Q

signal peptidase

A

cleave RER signal sequence

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70
Q

reticuloplasmins / ER molecular chaperones

A

properly fold protein transported to RER

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71
Q

transmembrane domain

A

alpha-helix 16-25 hydrophobic amino acids

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72
Q

type 1 TMD proteins

A

signal sequence, STA, Nin-Cout

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73
Q

type IV TMD proteins

A

multiple TMDs, STA&SA, Nin-Cout

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74
Q

stop-transfer anchor sequence

A

stop translocation through translocon

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75
Q

type 2 TMD proteins

A

no signal sequence, SA, Nout-Cin

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76
Q

type 3 TMD proteins

A

no signal sequence, SA, Nin-Cout

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77
Q

signal-anchor sequence

A

-halt translocation and serve as membrane anchor

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78
Q

positive-outside rule

A

positive amino acid residues always face cytosol (type 2- flipped)

79
Q

glycosylation

A

addition of carbohydrate side chains

80
Q

n-linked glycosylation

A

adding sugar monomers to terminal Asparagine (N) group

81
Q

glycosyltransferases

A

synthesize core oligosaccharide

82
Q

dolichol phosphate

A

first sugar is added to dolichol phosphate during glycosylation
-membrane anchor and carrier

83
Q

tunicamycin

A

blocks first step of n-linked glycosylation, prevent proper folding

84
Q

n-linked glycosylation sequence motif

A

-N-X-S/T-

85
Q

glucosidases

A

cleave 2/3 terminal glucose units

86
Q

protein disulfide isomerase

A

forms disulfide bonds between Cys
-promote proper folding

87
Q

er protein quality control

A

reticuloplasmins mediate proper folding (BiP, calnexin)

88
Q

mannosidase

A

removes one mannose unit from folded protein

89
Q

uggt monitoring enzyme

A

glycosyltransferase - conformation sensing protein
-recognize hydrophobic residues
-add back single glucose unit to misfolded protein

90
Q

p97 AAA ATPase

A

ERAD pathway - ATP hydrolysis to pull misfolded protein into cytosol

91
Q

ubiquitin (mono vs poly)

A

mono: target proteins -> endosomes
poly: target for degradation by proteasome

92
Q

PERK mediated unfolded protein response pathway

A

-active: dimerized
-phosphorylate and inactive eIF2 alpha
-decrease protein synthesis

93
Q

ATF6 mediated unfolded protein response pathway

A

-TF domain cleave by golgi protease, move to nucleus
-upregulate reticuloplasmins

94
Q

cop1/copII/clathrin coat proteins

A

cop1: golgi->ER
copII: ER->golgi
clathrin: golgi->endosomes / PM->endosomes

95
Q

anterograde transport

A

forward ER->golgi

96
Q

retrograde transport

A

backward golgi->ER

97
Q

sar1

A

-COPII assembly
-GTPase

98
Q

sec12

A

ER integral membrane protein, bind Sar1 during COPII assembly
-GEF (GDP->GTP)

99
Q

sec23/sec24

A

strucural scaffolding & membrane curvature during COPII assembly

100
Q

er-export sorting signal

A

di-acidic ER export signal
-asp-x-glu-

101
Q

sec13/sec31

A

recruited by Sec23/24 during COPII assembly, mediate bending and scission

102
Q

rab proteins vs rab effector

A

rab: lipid anchored, GTP-binding
effector: bind active rab, on target membrane

103
Q

v-snares vs t-snares

A

v- transport vesicle membrane
t- target membrane

104
Q

NSF & SNAP

A

ATP hydrolysis to unwind SNARE complex

105
Q

er retrieval sorting signal (soluble vs membrane)

A

soluble: C-terminal -KDEL sequence
membrane: C-terminal di-lysine

106
Q

KDEL receptor

A

binds -KDEL of escaped ER proteins, assemble to COPI coat

107
Q

cis/medial/trans cisternae

A

golgi metabolism, polysaccharide synthesis

108
Q

trans-golgi network

A

sorting station - clathrin coat assembly to endosomes

109
Q

grasps

A

tethering proteins linking golgi subcompartments

110
Q

alpha-mannosidase I

A

cis cisternae, remove 3 mannose sugars from core oligosaccharide

111
Q

mannose-6-phosphate

A

sorting signal for lysosome, phosphorylated in cis cisternae

112
Q

signal patch

A

M6P groups -> soluble lysosome protein targeting

113
Q

n-acetylglucosamine phosphotransferase

A

recognize lysosome-destined proteins

114
Q

cisternal maturation model

A

cis->medial->trans

115
Q

COP1 function

A

move resident golgi proteins back to proper cisternae

116
Q

lysosome

A

digestive organelle, degrade larger cell components

117
Q

autophagy

A

degradation of large cell components by lysosome

118
Q

acid hydrolyase

A

inside lysosome, active only at low pH

119
Q

lysosome signal patch

A

M6P signal patch

120
Q

m6p receptor

A

recognize and bind soluble M6P-bearing lysosomal destined proteins

121
Q

clathrin-coated vesicle assembly

A
  1. M6P receptor bind AP1 and GGA
  2. GTP binding->bind Arf1
  3. clathrin binds AP1/GGA, curve membrane and bud off
122
Q

ap1/gga (ap complex)

A

-mediate cargo selection, clathrin linker

123
Q

arf1

A

-GTPase, recruit AP1/GGA from cytoplasm during clathrin-coated assembly
-lipid anchored when GTP bound

124
Q

clathrin assembly

A

triskelions (hexogon->pentagon = curvature)

125
Q

dynamin

A

scission of clathrin coated vesicle, GTP-binding protein, form dynamin ring

126
Q

gamma-gtp

A

non-hydrolyzable analog of GTP, continued dynamin ring polymerization = stalk

127
Q

retromer transport vesicle

A

transport empty M6P receptors back to TGN, can also traffic to PM

128
Q

receptor-mediated endocytosis

A
  1. PM receptor binds ligand
  2. AP2 coat binds, accumulate in clathrin coated pit enriched in phosphatidylinositol
  3. vesicle budding and scission
129
Q

constitutive secretion pathway

A

secretory vesicles , TGN->PM

130
Q

phagocytosis

A
  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
Q

fc receptor

A

on leukocyte to bind ab on opsonized bacteria

132
Q

fc domain

A

on opsonized bacteria/ab

133
Q

pseudopod/phagosome

A

changes in shape of leukocyte uptaking bacteria to degrade

134
Q

bulk phase endocytosis

A

non specific uptake of materials into small vesicles

135
Q

ap2 binding domains

A

-PI(4,5)P2
-PM receptors
-clathrin

136
Q

clathrin-coated pit

A

formed during receptor mediated endocytosis by binding AP2

137
Q

phosphatidylinositol (4,5) P2

A

lipid microdomain - recruit AP2 with bound ligand receptors to clathrin coated pit

138
Q

multivesicular body

A

inward budding of vesicles into late endosome interior

139
Q

ESCRT machinery

A

mediate cargo selection to MVB and inward vesicle budding

140
Q

Hrs

A

ESCRT machinery, mono-ubiquinated, mediate inward budding and scission into MVB lumen

141
Q

Vps4 ATPase

A

disassembles ESCRT complex in MVB

142
Q

HIV gag protein

A

similar to ESCRT Hrs, mono-ubiquinated, mediate vesicle formation for virus particles

143
Q

endosymbiont theory

A

first eukaryotic ancestor was engulfed prokaryote

144
Q

organelle biogenesis

A

protein targeting, membrane assembly, morphology, motility, replication, degradation, inheritance

145
Q

semi-autonomous

A

replication controlled by nuclear and organelle genome

146
Q

mitochondria components

A

outer/inner membrane, intermembrane, matrix

147
Q

mitochondrial network

A

long, interconnected set of tubules

148
Q

mitochondrial fusion

A
  1. ER subdomain MAM constrict site
  2. Drp1 form Drp ring with cardiolipin
  3. GTP hydrolysis constricts ring and cell splits
149
Q

mitochondrial fusion

A
  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
Q

organelle homeostasis

A

rates of fission vs fusion, control number, size and connections in network

151
Q

drp1

A

uses GTP hydrolysis to constrict mitochondrial for fission

152
Q

cardiolipin

A

microdomain in mitochondrial OM, helps fission and is converted to phosphatidic acid in fusion

153
Q

mitofusions (mfn1, mfn2)

A

-GTPase cytoplasmic domain, protein interaction domain
-form tethering complex in mitochondrial fusion

154
Q

bak and bax

A

mitochondrial OM proteins - help OM fusion

155
Q

phospholipase d

A

converts cardiolipin -> phosphatidic acid to allow mitochondrial fusion

156
Q

phosphatidic acid

A

mitochondrial OM curvature inward

157
Q

opa1

A

use GTP to promote inner mitochondrial membrane fusion

158
Q

prohibition

A

ensures OPA1 only fuses other membranes - prevent self-fusion

159
Q

matrix targeting sequence

A

-20-50 aa long
-N terminus, + aa’s one side, (S/T) hydroxylated other side

160
Q

cytosolic molecular chaperones

A

recognize mitochondrial matrix destined proteins

161
Q

cytosolic hsp70

A

cytoplasmic molecular chaperone, recognize mitochondrial matrix destined proteins

162
Q

mitochondrial rna cloud

A

mRNAs encoding mitochondrial proteins enriched in cytoplasm surrounding mitochondria

163
Q

import receptor complex

A

recognize & bind matrix targeting signal on mitochondrial OM

164
Q

tom20 / tom22

A

form import receptor complex on mitochondrial OM

165
Q

tom40

A

forms general import pore and transmembrane channel in mitochondrial membrane

166
Q

tim23 / tim17

A

form mitochondrial inner membrane channel

167
Q

membrane contact sites

A

between general import pore and inner membrane channel in mitochondrial membrane

168
Q

matrix processing protease

A

cleave matrix targeting signal in mitochondrial matrix

169
Q

matrix hsp70

A

bind protein entering mitochondrial matrix, bound to Tim44

170
Q

tim44 (molecular motor)

A

uses ATP to pull protein into mitochondrial matrix

171
Q

h+ electrochemical gradient

A

[H+]intermembrane>[H+]matrix, drives mitochondrial protein transport

172
Q

matrix molecular chaperones

A

uses ATP hydrolysis to fully fold protein in mitochondrial matrix

173
Q

chloroplasts

A

plant cell organelle, site of photosynthesis

174
Q

photosynthesis

A

CO2+H2O+sunlight->sugars+ATP

175
Q

chloroplast components

A

inner/outer membranes, intermembrane, envelope, thylakoids, stroma

176
Q

stromules

A

connect chloroplasts

177
Q

chloroplast fission

A
  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
Q

FtsZ1 / FtsZ2

A

form FtsZ ring at chloroplast division site

179
Q

ARC3, MinD & MinE

A

position FtsZ proteins during chloroplast division

180
Q

ARC6

A

links FtsZ ring to inner chloroplast membrane during division

181
Q

plastid dividing machinery

A

interact with ARC5/6, form PD-ring and uses GTP hydrolysis to divide chloroplast

182
Q

PD-ring

A

formed by ARC5

183
Q

stromal import sequence

A

-N-terminus
-hydroxylated (S/T) and hydrophobic aa’s

184
Q

TOC/TIC chloroplast complex

A

recognize and bind chloroplast stromal import sequence with GTP

185
Q

stromal processing enzyme

A

cleave stromal import sequence in chloroplast stroma

186
Q

hsp93

A

stromal chaperone protein, recognize and bind incoming protein, uses ATP to pull protein into stroma

187
Q

thylakoid targeting sequence

A

revealed when stromal import sequence is cleaved

188
Q

SRP-dependent chloroplast targeting pathway

A
  1. chloroplast signal recognition particle binds thylakoid sequence and SRP receptor
  2. translocate through membrane via thylakoid Sec61-like translocon
189
Q

pH-dependent chloroplast targeting pathway

A
  1. protein fully folded in stroma
  2. di-Arg sequence binds unique receptor
  3. pH gradient pulls protein stroma->thylakoid
190
Q

chloroplast signal recognition particle

A

recognize and bind thylakoid-targeting signal

191
Q

chloroplast SRP receptor

A

bind SRP and GTP to translocate protein stroma->thylakoid

192
Q

thylakoid Sec61-like translocon

A

translocate protein stroma->thylakoid

193
Q

thylakoid lumenal protease and molecular chaperones

A

remove thylakoid-targeting sequence and fully fold protein

194
Q

di-arginine-containing thylakoid targeting sequence

A

pH dependent thylakoid translocation pathway, fully folded protein

mcb2050 (7 decks)

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