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Biochemistry I > Membranes, IC trafficking, protein sorting > Flashcards

Membranes, IC trafficking, protein sorting Flashcards

1
Q

What are functions of cellular membranes?

A
  • cell recognition + signaling
  • compartmentation
  • keep components of some metabolic pathways in place
  • transport of materials
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2
Q

What are lipid rafts?

Function?

There is a special type of lipid rafts that are small invaginations. How do you call them?

A

areas in outer leaflet of lipid bilayer enriched in cholesterol, sphingomyelin + glycosphingolipids, stabilized through interactions w/ cytoskeleton

→ signal transduction

invaginations = caveolae

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3
Q

Which structures/organelles belong to the endomembrane system?

A
  • nucleus
  • endoplasmic reticulum (ER), endoplasmic reticulum - Golgi intermediate compartment (ERGIC), Golgi apparatus
  • lysosome (phagosome, autophagosome), endosome, peroxisome, autophagic vacuole
  • transport vesicles
  • lipid droplets

​

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4
Q

What is a lysosome?

Function.

A

cell organelle responsible for breakdown of polymers

  • contains acid hydrolases that break down almost everything
  • V-ATPase generates a low pH of 5 inside the organelle (powered by ATP hydrolysis)
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5
Q

What are lipofuscin granules?

A

yellow-brown pigment granules composed of lipid-containing residues of lysosomal digestion

  • one of the aging or “wear-and-tear” pigments
  • especifically arranged around the nucleus
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6
Q

What happens with the lysosome?

A

fuses w/ primary endosome to form secondary endosome

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7
Q

What are the main functions of Golgi?

A
  • processing of oligosaccharide chains
  • sorting of proteins + delivery to intrac. destinations
  • synthesis of sphingomyelin, glycolipids, proteogylcans, glucosaminoglycans
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8
Q

What are the functions of the ER?

A
  • protein, lipid synthesis
  • glucose production
  • Ca2+ storage
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9
Q

What is the function of chaperones and chaperonins?

A

chaperones:

  • folding of proteins, ATPase activity
    → ADP, ATP binding until protein is folded
  • resp. for correct targeting of proteins to intracell. destinations

chaperonins:

barrel-like structures that enclose proteins until completed folding

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10
Q

Explain the cytosolic (non-secretory) pathway of protein sorting + related transport mechanism.

A

starts in cytosol when lacking ER signal sequence

either:

  • mature cytosolic protein
  • organelle specific
    • mitochondria - transmembr. transp.
    • peroxisome - transmembr. transp.
    • nucleus - gated transp.
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11
Q

Explain the rER (secretory) pathway of protein sorting + related transport mechanism.

A

starts in cytosol if ER signal sequence

  1. guided to ER
  2. Golgi
    • cell surface (excreted)
      - lysosome
      - plasma membrane

​all transported by vesicles

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12
Q

How do the 2 sorting pathways differ w/r/t to translation?

A
  • cytoplasmic pathway = posttranslational
  • ER pathway = cotranslational
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13
Q

Explain the mitochondrial protein sorting for matrix proteins.

A
  1. protein synthesized on cytosolic polyribosomes
    →    containpresequence (sim. to sign. sequ.) targeting matrix
  2. translocation through outer and inner mitochondrial membranes
    • interaction with chaperones bc must be in unfolded state to pass through complexes
  3. presquence split off by maxtrix-processing protease (MPP)
  4. proteins refolded inside organelle
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14
Q

Explain the process of import of large molecules into the nucleus
since small molecules can easily diffuse through nuclear pore complexes (NPCs).

A
  1. cargo containing nuclear localization signal NLS binds to importin
  2. binds to NPC
  3. inactive Ran (GDP) translocates cargo + NLS through nuclear envelope
  4. Ran activated by GEFs → GTP, cargo released inside
  5. importins+ Ran recirculate to cytoplasm
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15
Q

How does nuclear export happen?

Differentiate btw 2 classes of molecules.

A

for not-mRNA molecules:

exportins​ guide cargo with nuclear export signals NES together w/ Ran through pores

for mRNA:

transported to cytoplasm as part of ribonucleoprotein mRNP w/o usage of Ran, but ATP needed

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16
Q

What is a preprotein?

A

protein w/ signal sequence

→ signal sequence removed

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17
Q

How are proteins directed to their destinations?

A

by signal sequences, either:

  • signal peptide = sequence at end of protein
  • signal patch = pocket formed by diff. polypeptide chains

→ bind to distinct signal recognition particle SRP consisting of RNA + 6 proteins

note function of individual proteins + Met amino terminal

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18
Q

Explain the process of ribosome coupling to the ER.

What is the fate of the proteins?

A
  1. SRP binds to signal sequence on nascent polypeptide chain on ribosome → elongation arrest
  2. SRP bound ribosome binds to SRP receptor protein on rER
  3. SRP released, GTP → GDP + P
    translation continues
  4. translocation of protein through translocon into ER lumen
  5. signal peptidase detaches signal sequence + released back into cytosol, protein released into ER lumen

→ sorted

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19
Q

Which proteins are N-glycosylated in the ER?

Explain.

A

secretory proteins + soluble proteins destined for organelles distal to ER

  • N-glycan chains added by oligosaccharide-protein transferase
  • involves Asn side chains
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20
Q

How are ER membrane proteins incorporated?

A

steps 1-4 (cf. ribosome coupling to ER), then lateral transfer into membrane instead of release into ER lumen due to retention signals

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21
Q

What is a halt-/stop-transfer signal?

A

highly hydrophobic segment in transmembrane proteins → unfinished translocation → retention as transmembrane protein in the membrane

22
Q

Differentiate btw transmembrane proteins.

Examples.

A

4 types

  • type I: cross membrane once, N-terminal in ER lumen/cell exterior (ex: LDL receptor)
  • type II: cross membrane once, C-terminal in ER lumen/cell exterior (ex: transferrin receptors)
  • type III: sim. to type I, but no cleavable signal peptide (ex: cytochrome P450)
  • type IV: cross membrane multiple times (ex: G proteins, glucose transporters)
23
Q

How is the correct folding status of proteins in the ER monitored?

A
  • by chaperones
  • by calnexin: Ca2+ needed, in ER membrane
  • by calreticulin: Ca2+ needed, not memb.-bound
  • by protein disulfide isomerase (PDI): reshuffling of disulfide bonds
  • by peptidyl prolyl isomerase (PPI): folding of prolin-cont. proteins
24
Q

What happens with misfolded or incompletely folded proteins?

A

remain in ER, disposed by ER associated degradation (ERAD) if homeostasis perturbed = ER stress

25
Q

What is the exact pathway of ERAD?

A
  1. ER stress (cf. ERAD) sensed + induces unfolded protein response (UPR)
    → transient inhibition of translation
    → incr. synthesis of degradation enzymes + ER chaperones
  2. ubiquination of misfolded proteins
  3. retrotranslocation of proteins through ER membrane
  4. escorted to proteasomes by polyubiquitin-binding proteins
26
Q

Explain the structure of mitochondria.

A

2 compartments: matrix + intermembraneous space (btw inner/outer membrane)

  • outer membrane: porous, permeable
  • inner membrane: impermeable, proteins for respiratory chain
27
Q

What are the functions of mitochondria?

A
  • oxidative phosphorylation in respiratory chain → produces most ATP for cell’s demands
  • Ca2+ buffering + storage
  • heat production
  • catabolism of fatty acids
28
Q

Describe the structure and function of the mitochondrial genome.

A

double stranded circular → heavy + light strand

⇒ 37 genes code for 13 proteins translated by mitochondrial ribosomes (no introns due to prokaryotic origin!)

29
Q

Can mitochondrial diseases be inherited?

A

ONLY inherited maternally (oocyte provides all organelles, spermium only provides nucleus)

→ mostly associated w/ protein deficiency/production

30
Q

Describe the different types of transport.

A

active: via ATP-driven pumps against gradient

passive: along gradient

  • simple diffusion: higher to lower conc.
  • faciliated diffusion: higher to lower conc., but cannot pass through membrane normally due to size/hydrophilic character etc.
    • via ​pumps
    • via ion channels
31
Q

Differentiate btw types of endocytosis.

Explain briefly.

A
  • phagocytosis: macrophages/granulocytes ingest viruses, bacteria, cell debris
  • pinocytosis: cellular uptake of fluid + fluid contents
  • potocytosis: receptor-dependent in caveolae
  • clathrin-mediated endocytosis: receptor-dependent
32
Q

What are the requirements of endocytosis?

A
  • E (usually hydrolysis of ATP)
  • Ca2+
  • microfilament system
33
Q

Explain the process of exocytosis.

Fate of the “exocytozed” molecule?

A
  1. components snythesized in ER/Golgi put in vesicles
  2. hormone guides vesicle to cell-surface receptor
  3. local, transient change of [Ca2+]
  4. fuses w/ plasma membrane →
    • remains associated as membrane proteins
    • become part of extracellular matrix
    • signal other cells
34
Q

Explain the formation of vesicles.

A
  1. initiation: coatomer proteins assemble
  2. invagination: membrane is budding
  3. constriction: coat proteins shape membrane into a sphere
  4. fission: vesicle is detached
  5. uncoating: coat dissasembles
35
Q

Differentiate btw coatomers and for which vesicles they are apparent.

A

clathrin

  • endocytosis
  • regulated exocytosis: Golgi → plasma membrane
  • Golgi → late endosome

COPI

  • retrograde: Golgi → ER
  • constitutive exocytosis: Golgi → plasma membrane

COPII

  • anterograde: ER → Golgi
36
Q

Explain the structure of clathrin.

A

3-limbed structure = triskelion

each limb: light + heavy chain

37
Q

Explain the process of receptor-mediated endocytosis.

A
  1. assembly of clathrin to cargo receptors on plasma membrane directed by adaptins → coated pit
  2. bud formation
  3. dynamin (GTPase) binds → fission
  4. vesicle formation
  5. uncoating by hsc70 (ATPase)
38
Q

What is the difference btw COPI/clathrin and COPII coated vesicles w/r/t their intracellular transport?

A

for COPII:

  1. Sar1 binds to plasma membrane
  2. GTP binds → activates Sar1 → budding initiated

⇒ later: Sar1 inactivated when GTP hydrolyzed → coat disassembly

for COPI/clathrin-coated vesicles:

  • Arf instead of Sar1
39
Q

What is the function of Rab GTPases?

A

vesicle targeting

  1. GEF: Rab·GDP in cytosol → Rab·GTP
  2. Rab·GTP binds to Rab effector proteins on vesicle→ tether to membrane
  3. fusion w/ membrane → GTP hydrolyzed, Rab·GDP released
40
Q

What is the function of SNAREs?

A

initiate fusion

  1. v-SNARE on transport vesicle binds to complementary t-SNARE on target membrane
  2. 4-helix boundle
  3. ATPase (NSF) + αSNAP dissociate 4-helix boundle
41
Q

What is the difference btw antero- and retrograde transport?

What is the importance of KDEL receptors?

A
  • anterograde = ER → Golgi (COPII)
  • retrograde = Golgi → ER (COPI)

BUT: KDEL receptors guide vesicles from ER to Golgi → there retained

42
Q

What are G-proteins?

A

GTPases (activated when GTP bound) that transmit signals from outside stimuli to interior of a cell

43
Q

What does colchicine do?

A

can be gained from autumn crocus

“mitotic poison” or spindle poison binds to tubulin and inhibits microtubule polymerization

44
Q

What are the functions of the cytoskeleton?

Differentiate btw filaments.

A
  • cellular protein scaffolding → structure and shape
  • vesicular transport and cell division

3 filaments:

  • microfilaments (actin)
  • intermediate filaments
  • microtubules
45
Q

Differentiate btw types of actin.

Function?

A
  • 3 types: α, β, γ
  • β-actin: globular (G) subunit and filamentous (F) polymer (pointed and barbed ends polymerize)

function = actomyosin complex

  • moving organelles, cellular motion during cell division
  • cell adhesion structures
  • maintenance of cell volume
46
Q

Explain the reassembly of actin filaments

A
  1. at pointed end of actin filament: “old” actin·ADP bearing actin depolymerizing factor ADF cofilin disassembles to actin monomers
  2. actin·ADP → actin·ATP
  3. profilin directs actin monomers to barbed end
47
Q

Which molecules are responsible for actin branching?

A

Arp2/3 complex

48
Q

Which structures crosslink actin filaments?

A
49
Q

Explain the structure of a microtubule.

Function?

A

polymer of tubulin subunits (α + β) → protofilmanets, 13 form→ microtubule

  • polarized polymerization (- and + ends)

function:

  • organelle movements
  • mitotic spindle
  • cilia and flagella
50
Q

Explain the term dynamic instability w/r/t microtubules.

Why is this behavior important?

A

at + end

  • A: intermediate cc of tubulin → frayed end in slow growing filaments
  • B: high free GTP-tubulin dimer cc, hydrolysis outpaced → rigid end GTP-cap, rapid assembly
  • C: GTP hydrolysis weakens the tubulin dimer interaction → protofilaments rapidly disassemble

​⇒ growth from centrioles, ability to direct intrac. movement

51
Q

Differentiate btw dyneins.

In which direction do dynein and kinesin walk on the microtubule?

A

cytosolic dynein → + end (axonemal dynein in flagella)

kinesin → - end

52
Q

What are the properties of intermediate filaments?

Classes?

A
  • no polarity
  • no motor proteins associated
  • high tensile strength, resistant to compression, twisting and bending forces
  • heterogeneous

Biochemistry I (13 decks)

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