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BIO130 > 2.3: Intracellular Compartments and Protein Sorting > Flashcards

2.3: Intracellular Compartments and Protein Sorting Flashcards

1
Q

what are the purposes of the following intracellular compartments:
- mitochondrion
- golgi apparatus
- endosome
- sysosome
- cytosol
- peroxisome
- free ribosomes
- nucleus

A
  • mitochondrion: atp synthesis
  • golgi apparatus: modifies proteins and lipids
  • endosome: endocytosis
  • lysosome: digestive enzymes
  • peroxisome: oxidative reactions
  • free ribosomes: protein synthesis
  • nucleus: rna, dna synthesis
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2
Q

the cytosol contributes to how much of the cell volume

A

1/2

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3
Q

what is the role of the cytosol

A

protein synthesis and degradation, many metabolic pathways, cytoskeleton

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4
Q

what are the roles of the rough er and smooth er

A

rough: membrane-bound ribosomes, synthesis of soluble proteins and transmembrane proteins for the endomembrane (until they are secreted for digestion)
smooth: phospholipid synthesis, detoxification

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5
Q

define an organelles

A

a discrete structure or subcompartment of a eukaryotic cell that is specialized to carry out a particular

differs from membrane bound and non membrane bound organelles

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6
Q

how are proteins sorted

A
  • proteins are nuclear encoded
  • mRNA arrives in cytoplasm and translation starts on ribosomes in cytosol
  • cytosolic protein: no sorting signals and default location is cytosol
  • some are sorted, have a sorting signal called the signal sequence (eg the er signal sequence)
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7
Q

what is a signal sequence

A

stretch of amino acid sequence in a protein which directs proteins to correct compartment

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8
Q

what are signal sequences recognized by

A

sorting receptors that also take proteins to their destination

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9
Q

WE DONT NEED TO KNOW THIS

where will proteins will the following signal sequences end up?
- long with 3 leus in a row
- lys asp glu leu COO
- long with arg spread out
- pro pro lys lys lys arg lys cval
- pretty mid length, ends with phe
- ser lys leu

A
  • long with 3 leus in a row: import into er
  • lys asp glu leu COO: retention in lumen of er
  • long with arg spread out: import into mitochondria
  • pro pro lys lys lys arg lys val: import into nucleus
  • pretty mid length, ends with phe: export from nucleus
  • ser lys leu: import into peroxisome
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10
Q

differ between post translational sorting and co translational sorting

A

for both: proteins are nuclear encoded
for post: the proteins are fully synthesized in cytosol before sorting, if folded it’ll go into nucleus and peroxisomes, if unfolded they go to mitochondria and plastids (degraded there (nonsense pathway) bc they aren’t supposed to be unfolded)
for co: proteins have an er signal sequence (hydrophobic) and is associated with er during protein synthesis in the cytosol - Ribosomes are translating a protein w an ER signal seq and the whole ribosome complex is brought to ER to continue translations such that the proteins will end up at the ER in the end

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11
Q

what is the signal sequence called for proteins destined for the nucleus

A

nuclear localization signal (NLS)

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12
Q

_________ ________ are required in the nucleus for eukaryotic transcription

A

transcription activators

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13
Q

describe the role of peroxisomes and how they can achieve it

A
  • contains enzymes for oxidative reactions: detoxify toxins, break down fatty acid molecules
  • enzymes imported into the peroxisome through a transmembrane protein complex
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14
Q

unfolded proteins for import are associated with what type of proteins

A

hsp70 chapersone proteins

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15
Q

most proteins for the mitochondria and chloroplasts are ___________- encoded

A

nuclear

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16
Q

why do proteins sort into the er

A

it is the entry point to the endomembrane system and can go into the er/golgi/endosomes/lysosomes dependent on purpose

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17
Q

is the er signal sequence in co-translational protein sorting hydrophobic or hydrophilic

A

hydrophobic

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18
Q

differ between the purposes of the rough er and smooth er

A

rough (w membrane bound ribosomes): synthesis of soluble and transmembrane proteins for the endomembrane
smooth: phospholipid synthesis, detoxification

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19
Q

proteins that are soluble and for transmembrane are entering which organelle

A

er

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20
Q

define co translational translocation

A

insertion of protein into er starts as translational continues

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21
Q

in both the free and membrane bound ribosome cycle, where will all ribosomal subunits return to

A

the common pool in the cytosol

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22
Q

(difficult q) what are the steps of co-translational translocation of soluble proteins

A
  1. translation starts, N terminal ER signal sequence emerges
  2. recognized by signal recognition particle (SRP), elongation arrest by SRP
  3. SRP-ribosome complex –> SRP receptor –> translocon
  4. translocon opens (due to er signal seq)
  5. protein synthesis resumes with protein transfer into er lumen
  6. signal peptidase cleaves er signal sequence (hydrophobic - in lipid bilayer)
  7. protein released into er lumen
  8. translocon closes
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23
Q

what is the destination of soluble protein (in co-translational translocation)

A

lumen of an endomembrane organelle or secretion at PM

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24
Q

t/f the signal seq gets degraded at the end of co-translational translocation of soluble proteins

A

true

25
Q

t/f the protein is able to fold once it’s inside the er lumen during co-translational translocation of soluble proteins

A

true

26
Q

(difficult q) describe the process of co-translational translocation of transmembrane proteins (same 1-5 steps)

A
  1. translation starts, N terminal ER signal sequence emerges
  2. recognized by signal recognition particle (SRP), elongation arrest by SRP
  3. SRP-ribosome complex –> SRP receptor –> translocon
  4. translocon opens (due to er signal seq)
  5. protein synthesis resumes with protein transfer into er lumen
  6. stop transfer sequence enters translocon (internal hydrophobic segment = membrane spanning a helix, 20-30 hydrophobic aa)
  7. protein transfer stops and transmembrane domain released into lipid bilayer
  8. signal peptidase cleaves er signal sequence – the start and stop are released into the lipid bilayer (internal hydropobic segments = membrane spanning a helix)
  9. translocon closes
  10. protein synthesis completed
27
Q

what is the destination of transmembrane proteins

A

membrane of an endomembrane organelle or in the plasma membrae

28
Q

compare and contrast between n terminal and internal er signal sequences

A

both: stretch of hydrophobic amino acids
n: at the n terminus of protein, removed by signal peptidase
internal: not removed, remains part of the protein = membrane spanning a helix

29
Q

what is the sequence called that is able to stop the process of the er signal sequence/hydrophobic start transfer sequence

A

hydrophobic STOP transfer sequence

30
Q

give an example of vesicle trafficking

A

Transfer of lipids when something like vesicles bind to the Golgi

31
Q

list the 3 pathways of the endomembrane system

A
  1. secretory pathway
  2. endocytic pathway
  3. retrieval pathway
32
Q

what is the point of the endocytic pathway

A

contents move into cell (endocytosis)

33
Q

what is the point of the retrieval pathway

A

retrieval of lipids, selected proteins for reuse

34
Q

what is the point of the secretory pathway

A

proteins and lipids made in er, which are then delivered to other compartments
- er to outside (exocytosis)
- er to lysosomes (via endosomes)

35
Q

compare and contrast between exocytosis and endocytosis

A

exo: vesicle contents delivered to extracellular space, the vesicle membrane becomes part of the PM (merges w pm to expel)
endo: vesicle luminal contents come from extracellular space, pm forms vesicle membrane (makes a bud from the pm)

36
Q

describe vesicular transport

A
  • small, membrane enclosed organelle in cytoplasm of a eukaryotic cell
  • shuttles components back and forth in the endomembrane system: eg from er to golgi, cargo receptors
37
Q

how can cargo get into vesicles

A

Cargo can get in through cellular diffusion, or can have cargo receptors (green protein that selects for the brown cargo) = how we get stuff inside the vesicle

38
Q

what are the two types of secretory pathway

A
  • constitutive exocytosis pathway
  • regulated exocytosis pathway
39
Q

is the constitutive exocytosis pathway in all eukaryotic cells

A

yes

40
Q

describe the constitutive exocytosis pathway

A

continual delivery of proteins (transmembrane, soluble) and lipids to pm
- includes constitutive secretion of soluble proteins eg collagen for ecm

41
Q

describe the regulated exocytosis pathway

A
  • regulated secretion in specialized cells
  • stored in specialized secretory vesicles
  • extracellular signal –> vesicle fusion with PM and contents released
    eg pancreatic b-cells – insulin release with increased blood glucose (Signal comes through that says its time to release the insulin)
42
Q

in which organelle does translation start

A

cytosolic ribosomes

43
Q

what directs a protein to the ER

A

ER signal sequence at N terminus

44
Q

through what organelles does the secreted protein (from co translational translocation) go through

A

er –> golgi –> PM

vesicle membrane fuses with plasma membrane during exocytosis and transmembrane protein transferred to plasma membrane

45
Q

describe the maintenance of membrane protein asymmetry

A

each membrane protein has a specific orientation. this is a result of membrane insertion in the ER. and protein asymmetry is maintained through vesicular transport (the vesicle ensures that the protein is maintained with the correct parts in the cytosolic and noncytosolic face)

46
Q

name the role of the golgi apparatus

A

receives proteins and lipids from the ER, modifies them, and then dispatches them to other destinations in the cell

47
Q

describe the look of the golgi apparatus

A

looks like a stack of membrane enclosed sacs with multiple cisternae

48
Q

where does protein glycosylation start and where does processing occur (there are diff types of processing)

A

starts in er, occurs in golgi

49
Q

what is protein glycosylation

A

a single type of oligosaccharide is attached to many proteins (turns in from cis to trans)
glycosylation modifications for proteins and lipids

50
Q

does all glycosylation have to appear on the same side, if so, which side

A

yes (i think), it won’t be glycosylated on the non cytosolic side

51
Q

what do endosomes (membrane bound organelles) contain

A

contain material ingested by endocytosis

52
Q

differentiate between early and late endosomes

A

endocytic vesicles fuse to early endosomes (ingested material sorted in late endosomes or golgi). early endosomes mature into late endosomes

late endosomes are lysosomal proteins (hydrolases, H pump (make the compartment more acidic)) continue to be delivered from trnas golgi network. late endosomes mature into lysosomes

53
Q

what are lysosomes

A

membrane bound organelles that contain hydrolytic enzymes to digest worn-out proteins, organelles and other waste

54
Q

how does the lysosomes carry out their function

A

they contain ~40 types of hydrolytic enzymes (acid hydrolases - proteases, nucleases, lipases etc) and are acidified by h+ pump (v type atpase) bc the low pH is needed for hydrolytic enzymes.

the membrane bounds are to protect the rest of the cell from digestion. lysosomal membrane (noncytosolic face) are glycosylated for protection from proteases

transport proteins in lysosomal membrane transfer digested products to cytosol

55
Q

lysosomes are the main site of __________ _________

A

intracellular digestion

56
Q

what gives vesicles directionality

A

directed movement of transport vesicles, pulled by motor proteins associated with cytoskeleton

57
Q

_________ sorts proteins to correct location

A

signal sequences

58
Q

how do proteins stay in the cytosol

A

they don’t have signal sequences

BIO130 (12 decks)

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