Exam 1 Flashcards
membranes made of:
head:
tail:
phospholipid bilayer
hydrophilic
hydrophobic
hydrophobic + hydrophilic =
amphipathic
components of nuclear envelope (NE) structure:
outer membrane, intermembrane space, inner membrane, nuclear pore complexes (NPC), nuclear lamina
NE outer membrane:
continuous with ER, membrane proteins bind to cytoskeleton
NE inner membrane:
integral proteins that bind nuclear lamina
NE nuclear pore complex (NPC):
connect inner and outer membrane, traffic molecules that can’t diffuse, made of nucleoporin proteins (NUPs)
NE nuclear lamina:
connected to inner membrane, cytoskeleton, and chromatin; made up of lamins
lamin assembly:
1) two monomers dimerize
2) then tetramerize
3) then join end to end
proteins that connect nuclear lamina to inner membrane
LBR and emerin
proteins that connect nuclear lamina to cytoskeleton
LINC complex
diseases arising from heritable mutations in lamins or other envelope proteins
laminopathies
laminopathy hypotheses:
mechanical stress hypothesis and gene expression hypothesis
laminopathy mechanical stress hypothesis:
weakened cytoskeletal interactions
laminopathy gene expression hypothesis:
cell-type specific chromatin localization
nuclear pore complex (NPC):
passive diffusion and selective transport; eightfold symmetric complex
components of nuclear pore complex (NPC):
cytoplasmic filament, cytoplasmic ring, central channel/inner ring, FG-NUPs, nuclear ring, nuclear basket
FG-NUPs:
phenylalanine-glycine (FG) repeats in NPC inner ring that are unfolded to facilitate active cargo transport
selective transport of mRNAs direction and energy used:
unidirectional;
ATP
selective transport of mRNAs direction:
unidirectional
selective transport of proteins direction and energy used:
bidirectional;
GTP
selective transport of proteins: nuclear transport receptor (NTR) = ___;
recognize ___
karyopherin (importin/exportin);
amino acid signal sequences (NLS/NES)
protein import through NPC:
protein export through NPC:
mRNA export through NPC:
mRNP (messenger ribonuceloprotein) =
mRNA + proteins (including exporter complex)
NF-kB
transcription regulator, activates genes regulating cell survival when imported into nucleus
IkB
inhibitor of kB
regulation of nuclear import of transcription factors (NF-kB):
chromosome territories:
non-random distribution, spaced out, anchored at centromeres and telomeres to NE
fluorescence in situ hybridization (FISH):
helps visualize chromosomes, DNA probes with fluorescent molecule hybridize to sequences
chromosome conformation capture (3C):
elucidates chromosome architecture; freeze interactions between protein-linked sequences, ligate interacting sequences together end-to-end, NextGen DNA sequencing
euchromatin
active chromatin, associates with nuclear interior or NPC
heterochromatin
inactive chromatin, associates with nuclear envelope lamin associated domains (LADs) and nucleolus associated domains (NADs)
types of nuclear factories:
replication factories and transcription factories
nuclear bodies:
discrete (no membrane) organelles in nucleus; include nucleolus, polycomb bodies, and cajal bodies/nuclear speckles
nucleolus
site of rRNA (4 types) production and ribosome assembly
ribosome assembly:
polycomb bodies
sites of coordinately repressed genes, methylation to repress genes
cajal bodies
site of snRNP processing
nuclear speckles
site of snRNP storage
secretory system includes:
ER, golgi, plasma membrane, lysosomes, and transport vesicles
endoplasmic reticulum (ER)
extends from nuclear outer membrane, produces proteins (rough) and lipids (smooth), stores Ca2+ ions
polysome
multiple ribosomes on single mRNA
targeting proteins to the ER (two ways)
co-translational import (ER) or post-translational import (cytosolic, mitochondria, chloroplast, nuclear proteins)
co-translational targeting of secretory proteins to the ER:
signal recognition particle (SRP)
binds signal sequence, pause synthesis, binds SRP receptor on ER membrane, releases signal sequence
translocon
binding side recognizes signal sequence, ribosome binds, plug (for Ca2+ ions) is removed
signal peptidase
cleaves signal sequence after translation is complete
protein folding and QC
folding, assembly, and chemical modifications
chaperone
fold proteins into correct 3D structure based on AA sequence, has misfolded protein sensors
ER-associated degradation (ERAD)
chaperone finds sad protein, transmembrane ubiquitin ligase complex, cytosol proteasome, dead protein
unfolded protein response (UPR)
lumen domains of IRE1 (XBP1), ATF6, and PERK activated by excess unfolded proteins; together they stop translation and degrade sad proteins then increase chaperone, ERAD, and lipid production OR cell death
lipid synthesis
smooth ER’s job
which side are phospholipids, cholesterol, and ceramide synthesized on:
the cytoplasmic side of the smooth ER
flippases
translocate new lipids to lumen side of ER
lipid droplets
produced by all cells, source of nutrients and stress buffer
topological orientation of ER and golgi…
is maintained as it is moved through the secretory pathway
golgi structure
made of membrane enclosed sacs (cisternae) and transport vesicles
golgi cis side
the entry side facing the nucleus
golgi trans side
the exit side facing the plama membrane, trans golgi network (TGN)
golgi function
protein sorting and transport, glycoprotein processing, lipid metabolism
cis-golgi anterograde transport direction:
from ER to ERGIC to cis-golgi
cis-golgi anterograde transport types:
selective transport or bulk transport
cis-golgi anterograde transport ERES:
cargo clusters near ER exit sites (ERES) in smooth ER
cis-golgi anterograde transport ERGIC:
ER-golgi intermediate compartment (ERGIC) is the mid point between the ER and golgi
cis-golgi retrograde transport direction:
from cis-golgi to ERGIC to ER
cis-golgi retrograde transport sequences:
sequences mark polypeptides for retrieval, BiP on cargo proteins has a KDEL sequence that marks them for retrieval by the KDEL protein
trans-golgi anterograde transport direction:
from trans-golgi to TGN to plasma membrane/endosome
trans-golgi anterograde transport TGN:
trans-golgi network (TGN) is depot for newly synthesized cargo sorting to vesicles, specific sequences (or lack of) = destination
trans-golgi anterograde transport endosome:
intracellular sorting organelles of the endocytic pathway
trans-golgi retrograde transport direction:
from plasma membrane/endosome to TGN to trans-golgi
trans-golgi retrograde transport pathogens:
bacteria and viruses can exploit transport from plasma membrane to TGN to golgi to ER to nucleus and cause UPR
vesicles
move cargo though excretory system and from extra-cellular environment, membrane-enclosed, specific cargo = specific destination
vesicle coat protein assembly and budding
cargo selection and budding form donor membrane; form/maintain lipid bilayer shape, help select cargo, help budding
GTPase-dependent formation
manage assembly of coat proteins; Arf and Sar, GDP bound, GEF, associates with donor membrane, GAP, cytosolic inactive
COPII (coat protein 2 complex)
ER to ERGIC to golgi (anterograde), Sar-dependent
COPI (coat protein 1 complex)
golgi to ERGIC to ER (retrograde), Arf-dependent
clathrin
TGN to endocytic to plasma membrane OR in reverse (anterograde or retrograde), Arf-dependent and Dynamin-dependent
motor proteins
move transport vesicles along cytoskeleton from donor to target membrane
vesicle fusion = ___ and involves ___
cargo delivery;
tethering (Rab and tethering factor) and bilayer fusion (SNAREs)
receives and sorts molecules for recycling or degradation
endocytic system
synthesizes, processes, and delivers cargo to plasma membrane, extracellular environment, and collection of organelles
secretory system
movement through the endocytic pathway
1) vesicles form at cell surface
2) vesicles fuse with early (sorting) endosomes
3) vesicles sent to recycling endosomes OR
4) vesicles sent to late endosomes
endocytic pathway:
1) vesicles form at cell surface
coated or non-coated, selective to particular cargo
endocytic pathway:
2) vesicles fuse with early (sorting) endosomes
slightly acidic leads to ligand disassociation, sends cargo to late or recycling endosomes
endocytic pathway:
3) recycling endosomes
sorting station for cargo returning to plasma membrane (like receptor without a ligand)
endocytic pathway:
4) late endosomes
more acidic (pH 6) from ATP-dependent H+ pump, ubiquinated proteins, sends cargo to TGN or lysosomes
lysosomes
digestive secretory pathway organelles, most acidic (pH 4.5) from ATP-dependent H+ pump, acid hydrolases
lysosome formation
TGN sends vesicles with lysosomal proteins to late endosomes
acid hydrolases
break down polypeptides, nucleic acids, carbs, lipids; require acidic environment to perform
