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Absolutely Need to Know Flashcards

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1
Q

What is the stop transfer anchor sequence? How does it work?

A

Used to create a transmembrane protein, the stop transfer anchor sequence is a hydrophobic amino acid sequence; it blocks the translocon when trying to enter the RER membrane, preventing further translation; a cleft passage allows the sequence to enter the membrane and translation continues once the stop transfer sequence leaves the translocon, but no more of the polypeptide goes inside the membrane

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2
Q

Why can the stop transfer sequence be taken out of the translocon?

A

The inside of the translocon is very hydrophilic, but the inside of the membrane is hydrophobic (where the tails are). It’s energetically favorable for the stop transfer sequence to remain in the membrane.

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3
Q

What is the result of the stop transfer sequence working?

A

A transmembrane protein is created with the N terminus inside the ER lumen, the C terminus inside the cytoplasm, and the stop transfer sequence embedded in the membrane.

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4
Q

What is the result of the signal-anchor (start-transfer) sequence working?

A

A transmembrane protein is created with the C terminus inside the ER lumen, the N terminus inside the cytoplasm, and the signal anchor sequence embedded in the membrane.

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5
Q

What are the 4 kinds of protein processing that occur in the RER?

A
  1. Proteolysis (signal peptidase cleaves signal)
  2. Disulfide Bond Formation
  3. Folding
  4. N-linked glycosolation
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6
Q

What amino acid facilitates the N-linked glycosolation?

A

Asparigine, Asn, N

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7
Q

What do oligosaccharide side chains do?

A
  1. Increase the stability of extracellular proteins.
  2. Confer specificity to protein-protein interactions.
  3. Promote proper protein folding in the ER.
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8
Q

What is BiP? How does it work?

A

a chaperone protein in the ER with a 4 amino acid sequence that allows it to stay in ER (instead of being secreted); when polypeptides are misfolded, they bind, preventing the polypeptide from leaving the ER and providing opportunity for refolding

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9
Q

What are calnexin and calrecticulin? How does it work?

A

calcium-dependent proteins (lectins) that work as chaperones in the ER; bind to a polypeptide and help fold after signal from glucose on oligosaccharide (placed on tree by glucosyltransferase).

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10
Q

What is glucosyltransferase? How does it work?

A

binds glucose to oligosaccharide trees in the ER; this binding signals for calnexin and calreticulin to act as chaperones to assist a misfolded protein

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11
Q

What does protein disulfide isomerase do?

A

enzyme in the RER that catalyzes the creation of disulfide bonds between cysteine residues on a polypeptide

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12
Q

What are the two responses to misfolded proteins in the ER?

A

Unfolded Protein Response
ER-Associated Degradation (ERAD)

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13
Q

Describe the unfolded protein response.

A

A misfolded protein in the RER binds to a transmembrane receptor, activating it. After activation, the receptor triggers the translation of transcriptional regulators. The transcriptional regulators enter the nucleus and activate the transcription of chaperone proteins. The chaperone polypeptides are co-translationally inserted into the ER; after folding, it assists the misfolded protein in correct folding.

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14
Q

Describe the ER-Associated Degradation (ERAD) response.

A
  1. The chaperone fails to properly fold the polypeptide in the ER lumen.
  2. Polypeptide moves through the ER-protein translocator into the cytosol.
  3. The N-glycanase cuts the oligosaccharide tree off.
  4. Poly-ubiquitination.
  5. Proteosome destroys misfolded protein
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15
Q

Is there a protein inside the ER that destroys proteins?

A

No

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16
Q

What does N-glycanase do?

A

cleaves the oligosaccharide tree in the cytosol during an ERAD response before a misfolded protein is poly-ubiquitinated and degraded by the proteosome

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17
Q

What is the ER-protein translocator (Sec61 complex)?

A

the pathway through which a misfolded protein undergoing ERAD can leave the ER to be destroyed in the cytosol

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18
Q

Describe the signal model of cotranslational import into the ER.

A
  1. An mRNA is translated into a polypeptide. The first amino acids are a signal sequence.
  2. The signal sequence triggers the signal recognition particle (SRP) to bind to it, stopping translation in the cytosol.
  3. The SRP, ribosome, and mRNA complex all bind to the SRP receptor embedded in the RER membrane.
  4. SRP receptor and SRP both hydrolyze GTP (2 different ones). The SRP is freed from the complex and recycled. Simultaneously, the nascent polypeptide is inserted into the translocon (which was previously closed).
  5. The transmembrane signal peptidase cleaves the signal sequence and translation continues.
  6. After translation is complete, the ribosome leaves and the translocon closes. The polypeptide folds inside the RER lumen.
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19
Q

What is the RER exit site?

A

spot on the RER where there are no ribosomes and where the bud forms that later becomes a secretory vesicle and moves towards the Golgi; associated with GEF protein, which activates the G protein (GDP bound -> GTP bound)

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20
Q

What is the SAR-1 (ARF) protein?

A

an ARF family protein that is activated at the bud formed on the RER exit site when the GEF activates the G protein; when activated it undergoes a conformational change and can interact with COP2; after the COP2 protein buds off, the SAR1 deactivates the G protein and can no longer interact with COP2, encouraging the coat to come off

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21
Q

What are COP2 proteins?

A

COP2 proteins coat the cytosolic surface of a bud on the RER in the secretion process to the Cis Golgi network, interacts with cytosolic domain of transmembrane membrane cargo-receptor proteins

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22
Q

What does the membrane cargo-receptor protein on the cytosolic leaflet of the RER membrane during secretion interact with?

A

COP2 proteins and the cargo

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23
Q

What happens after the COP2-coated protein arrives at the Cis-Golgi network?

A

The SAR1 hydrolyzes GTP and returns to a GDP-bound form. It can no longer interact with the COP2, so the COP2 loses its coat.

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24
Q

What do Rab GTPases do?

A

mediate docking of vesicles; if GTP-bound; binds to rab effector protein and brings the vesicle to the target membrane

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25
Q

What do SNARE proteins do?

A

after the Rab proteins bring the vesicle to the target membrane, the SNARE proteins bring it closer so the membranes can fuse together

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26
Q

What do NSF and SNAPs do?

A

dissociate the SNARE proteins when a vesicle fuses with the cis Golgi networkW

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27
Q

How does retrograde retrieval from the Golgi to the ER work?

A

KDEL binds to a KDEL receptor; the COP2 coated vesicle returns to the ER. An ARF G protein turns off and the now uncoated vesicle docks at the ER, then releases the cargo.

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28
Q

What allows the retrieval pathway to work?

A

changes in pH between compartments; generally, the ER lumen is neutral. In the anterograde direction, the pH drops

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29
Q

What are the Golgi’s functions?

A
  1. Completion of sphingolipid (glycolipids) synthesis.
  2. Processing of N-linked carbohydrates on glycoproteins.
  3. O-linked glycosylation of select Ser and Thr.
  4. Post-translational modification (sulfation, amidation, acylation, phosphorylation).
  5. Proteolytic processing.
  6. Packaging of secretory proteins
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30
Q

What is the diameter of a vesicle going between the Golgi cisterna?

A

50 nm

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31
Q

What is the vesicular transport model for the Golgi? Was it correct?

A

Idea that Golgi cisterna don’t change and proteins are trafficked between in distinct vesicles. Wrong

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32
Q

What is the cisterna maturation model? Was it correct?

A

Cisterna mature once they receive the molecules needed for the next cisterna. Correct

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33
Q

What is the difference between COP1 and 2?

A

COP2 is for anterograde trafficking. COP1 is for retrograde trafficking.

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34
Q

What is constitutive secretion?

A

Vesicles are loaded with soluble proteins at the trans-Golgi network, move to the plasma membrane and release the cargo.

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35
Q

What is regulated secretion?

A

The cell receives a signal, then the vesicle rushes to the plasma membrane to release the cargo.

36
Q

How does Total Internal Reflection Microscopy work?

A

The microscope objective lenses and slides are both very refractive. Light bends at sharp angles. The light from below is bent through the lens, forced to focus on the sample. The sharp refraction angle causes the light to re-enter the microscope lens, creating an evanescent field’s energy that penetrates the sample at 100 nm.

37
Q

What is the penetration range (not right phrase) for Total Internal Reflection Microscopy?

A

100 nm. Any fluorescent molecules within 100 nm of the slide (closest to the plasma membrane when viewing exocytosis) are activated and the fluorescent molecule is seen.

38
Q

What’s the diameter of a secretory vesicle going to the plasma membrane?

A

100 nm

39
Q

Describe the apical domain of the plasma membrane

A

finger like projections from the cell’s surface; composed of proteins that allow the uptake of nutrients

40
Q

Describe the basolateral domain of the plasma membrane.

A

location where nutrients move into the body

41
Q

Where does apical vs basolateral domain sorting occur?

A

the trans-Golgi network

42
Q

What determines if a protein will be sorted to the apical or the basolateral domain?

A

presence of dileucine (2 leucine residues next to each other) on the cytosolic domain directs a bud to the basolateral domain; lack of presence indicates will be sorted to apical

long transmembrane alpha helix sorts to the apical domain;

43
Q

What determines the domain sorting of transmembrane proteins?

A

the gradient of biomembrane thickness

44
Q

How thick is the plasma membrane?

A

8 nm

45
Q

How thick is the ER membrane?

A

5 nm

46
Q

What happens to proteins with short transmembrane domains?

A

They’re retained in the Golgi or go to the basolateral domain. They cannot move laterally through a hydrophobic region due to charged amino acids (thermodynamically unfavorable).

47
Q

Why does the length of the alpha helix on a transmembrane protein matter?

A

Longer alpha helices allow a protein to sort into area of thicker membrane (e.g., towards the plasma membrane). Shorter transmembrane domains remain in the Golgi (area of thinner membrane).

48
Q

What does BFA do?

A

blocks transport between the ER and the cis-Golgi network; was used to experimentally prove non vesicular secretion of lipids occurs

49
Q

What are membrane contact sites?

A

sites of non-vesicular trafficking; contact between the ER and other organelles that allows the bulk exchange of lipids between membranes without requiring membrane fusion

50
Q

How do membrane contact sites work?

A

They allow the bulk transfer of lipids between membranes without fusing membranes by using lipid transfer proteins like Vps13.

51
Q

Why is it important to phosphorylate mannose on N-linked oligosaccharides?

A

it’s necessary for the lysosome to function

52
Q

What is the pH of the lysosome?

A

5

53
Q

What is the diameter of the lysosome?

A

0.2 - 0.5 micrometers

54
Q

What maintains the lysosome’s low pH?

A

250 H ions free inside

55
Q

How thick is the inner leaflet of the lysosomal membrane?

A

12 nm thick (2-3x thicker than other membranes)

56
Q

How do protons get inside the lysosome?

A

They’re pumped with a proton pump (using ATP).

57
Q

How many acid hydrolases are in the lysosome?

A

40

58
Q

What are vacuoles?

A

large lysosomes in plant cells and fungi (with other functions)

59
Q

What do vacuoles do for plants and fungi?

A

regulate osmotic pressure in the cell

60
Q

Why do acid hydrolases go to lysosome instead of plasma membrane via secretion pathway?

A

Golgi has a recognition sequence of the sugar residues in glycosolated biomembrane and sorts it into the lysosome.

61
Q

Where does mannose 6 phosphate get added to the lysosomal hydrolase precursor?

A

cis Golgi network

62
Q

What kind of coat is used to transport between the trans Golgi network and the endosome?

A

clathrin coat

63
Q

What is the signal for the transport vesicle to bind to the manose 6 phosphate receptor when traveling to the late endosome?

A

phosphate covalently attached to the manose residue

64
Q

What happens to the late endosome?

A

No budding, matures and takes on characteristics of the lysosome (primary to secondary lysosome)

65
Q

What coat is used for the retrograde direction?

A

COP1

66
Q

What coat is used for the anterograde direction?

A

COP2

67
Q

What coat is used if heading towards the late endosome (or involved in endocytosis)?

A

clathrin

68
Q

What do adaptor protein complexes do?

A

under the clathrin coat, they interact with cytosolic domain of transmembrane proteins

69
Q

What initiates coat assembly for clathrin?

A

ARF GTPase

70
Q

What does the dynamin GTPase do?

A

pinches the budding vesicle at the trans-Golgi network when lysosome bound

71
Q

How many triskelions are needed to form a sphere for clathrin?

A

36

72
Q

What is endocytosis?

A

when small amounts of fluid and small molecules are taken up; facilitated by the formation of small vesicles that go to the lysosome

73
Q

What is autophagy?

A

when parts of the cytoplasm are digested when a cell is stressed or starved for energy - certain organelles are marked for destruction; regulated, never engulfs nucleus

74
Q

What is phagocytosis?

A

when a foreign object is engulfed and infuses into a phagosome

75
Q

What is the fate of the autophagosome?

A

matures into a lysosome or fuses into an existing lysosome

76
Q

How does phagocytosis work?

A

An object arrives at the plasma membrane and is completely surrounded by a pseudopod. A phagocytic vacuole forms, taking the object inside, then merging with the early endosome. There’s contact with the early and late endosomes during maturation; then the late endosome becomes a mature lysosome and the bacterium is broken down by lysosomal hydrolases.

77
Q

What does endocytosis do for a cell?

A
  1. Recycling of membrane and proteins
  2. “Ingestion” (feeding, defense)
  3. Regulation
  4. Trafficking
  5. Harm – route of entry for some pathogens
78
Q

How does clathrin independent endocytosis work?

A

The cell creates invaginations on the surface of a membrane. A bud is released and brings molecules into the cell.

79
Q

What determines if an excision event occurs during clathrin-independent endocytosis?

A

lipid composition of plasma membrane

80
Q

What is the start product to synthesize cholesterol?

A

Acetyl CoA

81
Q

What is the rate determining step of synthesizing cholesterol?

A

HMG-CoA reductase

82
Q

What inhibits HMG-CoA reductase?

A
  1. Presence of cholesterol in the environment
  2. Statin drug
83
Q

Why do statin drugs work?

A

If HMG-CoA reductase is inhibited, cholesterol synthesis stops and cells are required to take up more cholesterol from the blood, removing plaque from arteries.

84
Q

What are lipoproteins?

A

large molecular complexes that house cholesterol; have a core made of cholesterol ester that is surrounded by model layer of phospholipids and regular cholesterol molecules; around sphere, there’s an apolipoprotein (band around the equator of the sphere)

85
Q

What’s the difference between HDLs and LDLs?

A

Low vs. high density lipoproteins; difference is protein composition, amount, and density

Cellular Biology (23 decks)

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