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Cell Biology Midterm 1 > Cell Biology final EXAM > Flashcards

Cell Biology final EXAM Flashcards

1
Q

How does membrane-less organelles form?

A

B/c of scaffold molecules!
-they have multiple, weak and fluctuating interactions among themselves.

They are called BIMOLECULAR CONDENSATES

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2
Q

What non-covalents interactions does “scaffold proteins” have?

A

Electrostatic

Pi-pi

Cation-pi

others

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3
Q

What causes organelles specialization?

A

Unique integral membrane proteins

Unique proteins in the organelle lumen

Unique peripheral proteins on the organelle surface

UNIQUE LIPIDS

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4
Q

What are three important facts about organelle function?

A

Each organelle has a specific set of functions

Each specialized function requires a specific set of proteins and lipids

Organelles are not isolated: They exchange content

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5
Q

How to target and transport proteins? (4)

A

Single peptide sequences target proteins to specific compartment

  1. delivery across a GATE
  2. Delivery through a translocator (or channel)
  3. Delivery by transport membrane vesicles
  4. Delivery by protein binding
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6
Q

How do proteins enter membrane bound organelles?

A

By soluble proteins and transmembrane and secreted proteins

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7
Q

What are three mechanisms of protein sorting between membrane-bound organelles?

A
  1. Gated transport
    BETWEEN CYTOSOL AND NUCLEUS
    controled by the nuclear pore
  2. Transmembrane transport
    between cytosol and ER
    INSERTION of proteins into membrane and lumen during translation by ribosome
    CONTROLLED BY the translocator
  3. Vesicular transport
    between ER, golgi, PM, endosomes and lysosomes
    transport membrane enclosed vesicles
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8
Q

What is the transport of nuclear-cytosol transport?

A

From the nucleus into the cytosol
-processed mRNA
-tRNAs
-assembled ribosomes
-transcriptional regulators

From the cytosol to the nucleus:
-Ribosomal proteins for assembling the ribosome
-DNA polymerase
-DNA repair proteins
-RNA polymerase
etccc

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9
Q

What does the nuclear envelope have

A

double, continuous bilayer
outer membrane continuous with ER

Lamina- nuclear skeleton underlying inner bilayer- GIVES SHAPE

Nuclear pore- Hole that crosses both inner and outer bilayers

CONTROLS BIDIRECTIONAL TRANSPORT between nucleus and cytosol

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10
Q

What is a nuclear pore complex (NPC)

A

Disordered region of the channel
- made up of proteins (nucleoporins) that are DISORDERED
FORMS BARRIER
so large molecules cannot pass without assistance

Large molecules require active transport

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11
Q

How does the nuclear pore complex form a gate that controls transport?

A

Central nucleoporins have UNSTRUCTURED DOMAINS that line the pore.

creates a meshwork that slows diffusion

HAVE A SELECTIVE GATE: some proteins need to be in the nucleus and OTHERS OUT

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12
Q

What targets a protein to the nucleus

A

NUCLEAR LOCALIZATION SIGNAL

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13
Q

What are nuclear import receptors?

A

Bind to cargo and bridge these to the NPC

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14
Q

What is a nuclear export signal and receptors?

A

Nuclear export occurs through signal peptide sequences: NUCLEAR EXPORT SIGNAL

Nuclear export signal is RECOGNIZED by NUCLEAR EXPORT RECEPTORS (karyopherins)

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15
Q

What happens in nuclear import cycle?

A

-IN THE CYTOPLASM, Ran-GDP does NOT bind to nuclear import receptor

  • Once past the Nuclear pore complex, the NIR bind to Ran-GTP (IN NUCLEUS)

-Ran-GTP forces the nuclear import receptors to release their protein cargo

NIC import receptors bound to Ran-GTP return to cytosol “empty”

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16
Q

What happens in nuclear export?

A

-IN THE NUCLEUS, Ran-GTP binds to nuclear export receptors, which allows binding to proteins

  • Once past the nuclear pore complex, the NER bind to Ran-GDP
  • Ran-GDP forces the nuclear export receptors to release their protein cargo

NUCLEAR EXPORT RECEPTORS BOUND TO RAN-GDP RETURN TO NUCLEUS EMPTY

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17
Q

What does the SRP need to do?

A

It recognizes and binds to ER signal peptide.

It DIRECTS this all to the ER translocation pore.

IT BINDS TO THE NASCENT SIGNAL SEQUENCE AND THE RIBOSOME

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18
Q

What is in the translocator Sec 61 complex

A

Three polypeptide chains Sec 61 alpha, Sec 61 beta, and Sec 61y, conserved in prokaryotes and eukaryotes

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19
Q

What are the three categories of proteins inserted into the Sec 61 pore:

A

Category 1: Translocation of proteins with a terminal signal sequence

Category 2: Translocation of proteins with an internal signal sequence

Category 3: Translocation of proteins with a multiple signal sequence (AND STOP TRANSFER SEQUENCES)

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20
Q

What is category 1: Translocation of proteins with a terminal signal sequence?

A

The N-terminal signal sequence binds and opens the pore of the translocator; SIGNAL SEQUENCE - START-TRANSFER SIGNAL.

the signal sequence remains embedded in the membrane

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21
Q

What is Category 2: Translocation of proteins with an internal signal sequence?

A

Proteins with an internal signal sequence are inserted into the sec61 pore to allow the rest of the protein to translocate through the pore.

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22
Q

What is Category 2: Translocation of proteins with an internal signal sequence?

A

They are inserted into the sec61 pore to allow the rest of the protein to translocate through the pore

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23
Q

What happens to proteins after insertion into the ER membrane or lumen?

A

The protein receptor VSVG is fused to GFP.

Proteins start off in ER
By 50min the protein is mostly in Golgi
By 1h and 30min, the protein begins to accumulate at the plasma membrane.

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24
Q

What organelle is affected due to a defect in protein import?

A

Mitochondrial import proteins can cause human diseases such as Human deafness Dystonia Syndrome, Dilated cardiomyopathy, spastic paraplegia 13

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25
Q

What is topology?

A

Continuity and ability to exchange without ‘‘crossing the membrane’’

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26
Q

What are the vesicle transport pathways? (3)

A
  1. biosynthetic pathway
  2. exocytosis pathway
  3. Endocytosis pathway
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27
Q

What is the biosynthetic pathway?

A

delivery of NEWLY synthesized proteins and membrane from ER to most other organelles: Golgi, plasma membrane, endosomes, lysosomes

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28
Q

What is the exocytosis pathway?

A

Delivery of NEWLY synthesized or STORED PROTEINS into the extracellular space
neurotransmitters
proteolytic enzymes to kill bacteria
released of signalling peptides like growth factors and insulin

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29
Q

What is the endocytosis pathway?

A

UPTAKE OF EXTERNAL AND PLASMA MEMBRANE-BOUND PROTEINS AND LIGANDS

-vitamins and nutrients
- cholesterol (LDL)
-growth factors and receptors
-changing of the properties of the cell surface
DESTINATION TO LYSOSOME FOR DEGRADATION OR ELSEWHERE IN THE CELL

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30
Q

wHAT are the four well-characterized protein coats?

A

Clathrin
COPI
COPII
retromer

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31
Q

What are the functions needed for protein coats to generate vesicles? (2)

A
  1. PROVIDE THE MACHINERY AND ENERGY for membrane budding and scission from the donor membrane
  2. SELECT FOR THE APPROPRIATE CARGO to be included in the vesicle product
32
Q

What scaffolds the shape of the budding vesicle?

A

CLATHRIN that forms structures called triskelions

33
Q

What controls where and when coat proteins assemble to form a vesicle?

A

Phosphoinositides and specific GTPases

34
Q

What is a phosphoinositides?

A

Controls clathrin coat assembly

35
Q

What is phosphatidylinositol?

A

It is located on cytosolic leaflet bilayer

INOSITOL headgroup has 6 hydroxyl groups

36
Q

How is the inositol headgroup of phosphatidylinositol phosphorylated or dephosphorylated?

A

The phosphorylation is carried out by specific lipid kinases

The dephosphorylation occurs due to specific lipid phosphates

37
Q

What does phosphatidylinositol-(4-5)-bisphosphate regulate?

A

CLATHRIN COAT PITS (controls clathrin coat assembly and disassembly)

38
Q

What does phosphatidylinositol-(4-5)-bisphosphate control?

A

It controls the openning of AP2

39
Q

What does Sar1 GTPase regulate?

A

ASSEMBLY OF COPII coat on the ER membrane

40
Q

What is a specific GTPase?

A

Controls COP coat assembly

GTPases
-Sar1=controls COPII on the ER membrane
-Arf=controls COPI

41
Q

What are the steps of Sar1 COPII coat assembly? (8 small steps)

A

San1-GEF displaces GDP from inactive cytosolic Sar1-GDP

GTP loads onto Sar1

Sar1-GTP exposed amphipathic helix

Sar1-GTP binds strongly to ER membrane

ER bounded Sar1-GTP recuits COPII coat subunits Sec23/24

Sec23/24 forms an inner coat that enriches specfic cargo molecules for export out of the ER

Sec13-31 COPII subunits are recuited to form an outer coat

Membrane is deformed and buds off from ER

42
Q

What are the two steps for membrane fusion?

A

Tethering and docking/fusion

43
Q

What is Rab GTPase?

A

it is mediated tethering to target organelles of transport vesicles

44
Q

What is Rab 5?

A

Early endosomes (endocytosis-degradation and recycling)

45
Q

What is Rab 7 and Rab 9?

A

Late endosomes (Endocytosis- degradation)

46
Q

What is Rab 2

A

Golgi > ER (Retrieval)

47
Q

What is Rab 1?

A

ER > Golgi (synthesis)

48
Q

What targets and fuse vesicles to the right organelle?

A

Rab GTPases
SNARE proteins
-SNAP(soluble NSF attachment protein)receptor
-Vesicular SNARE
-Target SNARE

49
Q

What is a v-SNARE?

A

transmembrane, single chain (synatobrevin)

50
Q

What is a t-SNARE?

A

2 or 3 chains, at least 1 transmembrane, others may be peripheral membrane proteins (syntaxin)

51
Q

What toxins attack SNARES?

A

Botulism and tetanus

52
Q

What is the steps of SNARE-mediated membrane fusion? (5)

A
  1. Trans-SNARE complex formation causes water exclusion: ENERGETICALLY UNFAVORABLE
  2. Membranes juxtaposed within 1.5nm-sufficient to causes lipids to cross layers
  3. Stalk formation: one layer of the membrane undergoes fusion
  4. Hemifusion: 2nd inner layer is juxtaposed, permitting lipid molecules to move across the inner layer of the membrane
  5. Full fusion occurs, two membrane compartments become one
53
Q

What does ER to Golgi deliver?

A

newly synthesized proteins and lipids: biosynthetic pathway

54
Q

How does ER to Golgi traffic occur?

A

occurs by COPII-mediated vesiculation of ER membrane

55
Q

What pathway must ER resident proteins be recycled back to the ER?

A

RETROGRADE PATHWAY

56
Q

What vesiculation is golgi to ER retrograde mediated by?

A

COPI-mediated vesiculation

57
Q

What organelle digest macromolecules and lipids?

A

Lysosomes, they are enriched in hydrolytic enzymes

58
Q

How are hydrolytic enzymes activated by?

A
  1. proteolytic cleavage of inactivating sequence amino acid sequence- Zymogens
  2. Acidic environment
59
Q

How are hydrolytic enzymes inactive?

A

if they leak into the cytosol

60
Q

What are the four vesicle traffic routes?

A
  1. biosynthetic: Golgi to late endosomes. Delivers new hydrolytic and lysosomal proteins
  2. Endocytosis: delivers solute and membrane-bound extracellular and PM cargo for degradation
  3. Phagocytosis: Delivers extracellular particles for degradation, like bacteria.
  4. Autophagocytosis: Delivers cell parts like DAMAGED ORGANELLES for degradation
61
Q

What is Mannose 6-phosphate?

A

Marks lysosomal proteins.

Unique sugar that is COVALENTLY attached to the end of a polysaccharide that is COVALENTLY attached to lysosome hydrolases

62
Q

What does Mannose 6-phosphate receptors deliver?

A

lysosomal proteins from the Golgi to late endosomes/lysosomes

63
Q

What is an example of extracellular components?

A

Proteoglycans

64
Q

What are delivery signalling molecules to the extracellular medium? (4)

A

Proteases: remodel extracellular medium or fight interactions

Hormones and growth factors: Signaling between cells

Neurotransmitters: neuronal communication

Immune and inflammatory factors: Histamine and interleukins

65
Q

What are pancreatic beta cells?

A

have pre-made vesicles loaded with INSULINE (in lumen)

Sence an increase in blood glucose

Trigger EXOCYTOSIS of vesicles that contain insulin when they sense an increase in glucose

INSULIN TRIGGERS A LOWERING OF BLOOD GLUCOSE

66
Q

What is histamine?

A

A small molecule responsible for itching and sneezing during ALLERGENIC REACTION

67
Q

What is endocytosis?

A

Transport from the plasma membrane into endosomes

68
Q

What is pinocytosis?

A

Internalized via small endocytic vesicles

Ingest bits of the plasma membrane in small pinocytic (or endocytic) vesicles

69
Q

What is phagocytosis?

A

Internalization of large particles, including whole cells]

A receptor-driven process by which particulate matter is engulfed by a cell

70
Q

What are endocytic organelles targeted to?

A

Endosomes for sorting, recycling, and/or degradation

71
Q

WHy must pinocytosis be balanced by exocytosis?

A

Bc the cell WILL SHRINK in surface area

therefore, endocytic-exocytic cycle

72
Q

How are clathrin coated pits drive pinocytosis?

A

Those bound to a cell surface receptor (HIGH EFFICIENT)

Those not bound to a receptor (fluid phase-much less efficient)

73
Q

What does receptor mediated endocytosus permit?

A

a Selection and enrichment of specific cargo molecules

74
Q

What does phagocytosis lead to?

A

Membrane traffic to the lysosome for DESTRUCTION, AND HYDROLYSIS OF MACROMOLECULES INTO SUBUNITS

75
Q

What are enriched in membrane area that vesiculates to form an ER transport vesicle?

A

Sar1-GTP, COPII, and cargo molecules

76
Q

What occurs between COP1 and COPII fission in ER-Golgi transport? (4)

A

COPII-vesicles shed COPII coat

Vesicles fuse together to form a vesicular tubular cluster (VTC)

VTPs fuse with cis face of the golgi

Recycling of ER proteins by COPI coat occurs at VTCs and Golgi

Cell Biology Midterm 1 (3 decks)

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