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cell biology > week 5-Cell compartments and trafficking > Flashcards

week 5-Cell compartments and trafficking Flashcards

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AP® Biology flashcards Biology 101 flashcards
1
Q

all regions of the cytosol are what

A

topologically equivalent

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2
Q

how many proteins are being sorted at a given time within the cell

A

many (~10,000!) proteins at any given time.

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3
Q

how are the correct protein sorted to their respective places in a cell

A

cellular proteins contain signal sequences which are read by sorting receptors so the protein is directed to its correct ‘cell address’.

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4
Q

what are the 3 ways proteins can move around in the cell

A
  • Protein translocation (transmembrane transport
    * Gated transport
    * Vesicular transport
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5
Q

what are the 2 types of ER

A
  • rough ER (rER) is studded with ribosomes; and
    smooth ER (sER) lacks bound ribosomes.
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6
Q

what are the main functions of the ER

A
  • Lipid and protein biosynthesis
    Intracellular Ca2+ storage and cell signalling
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7
Q

what are the 2 places a protein can be synthesises

A

1) on free ribosomes into the cytosol and then they can be post translationally translocated into the ER lumen
2) the ribosomes likely are bound in the protein will undergo cotranslational translocation that is there simultaneously translated on ER bound ribosomes and translocated across the ER membrane into the ER lumen

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8
Q

What happens if the peptide has an ER signal sequence?

A

If the peptide has an ER signal sequence, it is recognized by an SRP (Signal Recognition Particle).

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9
Q

What role does the SRP play in translation?

A

The SRP binds to the ribosome to slow translation and targets it to an SRP receptor in the ER membrane.

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10
Q

What occurs when the ribosome is targeted to the ER membrane?

A

Translation continues, and the peptide is co-translationally translocated across the ER membrane into the ER lumen

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11
Q

What is the function of the signal peptidase?

A

The signal peptidase clips off the signal sequence during translation, allowing the mature protein to be released into the ER lumen.

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11
Q
A
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12
Q

How is the permeability barrier of the ER membrane maintained?

A

The translocator is closed until the ribosome has bound to maintain the ER membrane’s permeability barrier.

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13
Q

What happens after protein synthesis is completed?

A

After synthesis is completed, the SRP and the SRP receptor dissociate and can be recycled for reuse.

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14
Q

what are the two signals that are used for proteins to get retained or returned to the ER and what terminus

A

1) ER Entry:A hydrophobic stretch of amino acids at the N-terminus or internally (start-transfer sequence/ER signal sequence) signals entry into the ER.
2) ER Retention: A KDEL or HDEL retention peptide at the C-terminus retains proteins in the ER.

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15
Q

what are Stop-Transfer Sequences:

A

These sequences facilitate the translocation of multi-pass transmembrane proteins.

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16
Q

what is the chaperpon interaction between the protein and the ER

A

Translocated proteins typically interact with chaperones like the Binding Protein (BiP) in the ER lumen.

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17
Q

what are the modification that the ER does to proteins

A

Assisted Folding: Proteins achieve their secondary and tertiary structures with the help of chaperones.

Recognition of Faulty Proteins: Misfolded or faulty proteins are identified, removed from the pathway, and degraded in the cytosol.

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17
Q
A
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18
Q

what are some structural changes that the ER does to proteins

A

Disulphide bond formation
Enzymatic cleavage
Formation of quaternary structure

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19
Q

what is Glycosylation

A

the addition of carbohydrate groupsn

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20
Q

What type of glycosylation occurs for most proteins synthesized in the rER?

A

N-linked glycosylation.

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21
Q

Where are oligosaccharides added in N-linked glycosylation?

A

To the NH2 group of asparagine (Asn) residues.

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22
Q

What is the role of N-linked oligosaccharides in the ER?

A

They act as a quality control ‘stamp’ to aid in the identification of correctly folded proteins.

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23
Q

Which enzyme transfers the oligosaccharide to the protein in the ER?

A

Oligosaccharyl transferase.

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24
Q

What happens to terminal glucoses during the quality control process in the ER?

A

Terminal glucoses are trimmed by the enzyme glucosidase.

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25
Q

What role do chaperones (calnexin or calreticulin) play in glycosylation?

A

They recognize proteins with one terminal glucose and trap them at the ER membrane for folding.

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26
Q

What is the function of glucosyltransferase in the ER?

A

It checks if the protein is correctly folded and ready for export from the ER.

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27
Q

What happens if a protein is not correctly folded after multiple rounds of glycosylation quality control?

A

The protein is degraded in the proteasome.

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28
Q

: What is the structure that encloses the nucleus and contains nuclear pore complexes?

A

The nuclear envelope, which is a double membrane.

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29
Q

What are the proteins called that form a ring around the central nuclear pore?

A

Scaffold nucleoporins and channel nucleoporins

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30
Q

What do cytosolic fibrils and nuclear baskets do in the context of nuclear pore complexes?

A

Cytosolic fibrils extend from the NPCs on the outer nuclear membrane, and nuclear baskets form on the inner membrane side, aiding in transport

31
Q

What role do GTPases play in cellular processes?

A

They act as molecular switches, toggling between inactive GDP-bound and active GTP-bound states.

32
Q

What do GTPase-activating proteins (GAPs) do?

A

They hydrolyze GTP to GDP, inactivating GTPases.

33
Q

What are guanine nucleotide exchange factors (GEFs) responsible for?

A

They stimulate the exchange of GDP for GTP, activating GTPases.

34
Q

What is the function of Ran GTPases in nuclear transport?

A

They regulate nuclear import and export by switching between RanGDP in the cytosol and RanGTP in the nucleus.

35
Q

How does cargo with a nuclear localization signal (NLS) get imported into the nucleus?

A

It binds to nuclear import receptors (importins) in the cytosol, moves through NPCs, and is released in the nucleus where RanGTP binds to importins.

36
Q

Describe the process of nuclear export.

A

Cargo with a nuclear export signal (NES) binds to exportins and RanGTP in the nucleus, moves through NPCs, and is released in the cytosol where RanGAP hydrolyzes RanGTP to RanGDP.

37
Q

What ensures the directionality of nuclear transport?

A

The concentration gradients of RanGTP in the nucleus and RanGDP in the cytosol, along with the energy from GTP hydrolysis.

38
Q

How do proteins reach their final destination within the cell?

A

Proteins can be transported via various pathways, including vesicular transport, diffusion through the cytosol, or passage through organelle membranes.

39
Q

What is the fate of protein sorting signals after the protein reaches its destination?

A

Protein sorting signals are sometimes cleaved off after the protein reaches its final destination.

40
Q

What occurs after a protein is transported to its final destination?

A

The protein becomes functionally integrated into its new environment, contributing to cellular processes specific to that location.

41
Q

What term describes the process of removing protein sorting signals?

A

Signal removal refers to the cleavage of sorting signals from proteins after they reach their final destination

42
Q

Summarize the steps involved in protein sorting and localization.

A

Protein sorting signals are exposed ->

Recognized by cellular machinery ->

Protein is transported to its destination ->

Sorting signals may be removed ->

Protein integrates into its functional environment

43
Q

Why is it important for protein sorting signals to be exposed?

A

so cellular machinery can read them and recognise them

44
Q

what are COPII

A

COPII-coated vesicles from ER to golgi

45
Q

what are COPI

A

golgi to ER

46
Q

What occurs across the different Golgi cisternae?

A

Protein modification and sorting direct vesicles to various cellular destinations like lysosomes, the plasma membrane, and secretory vesicles.

47
Q

How are ER resident proteins returned to the ER?

A

ER resident proteins are captured by the KDEL receptor and transported in COPI-coated vesicles back to the ER. The KDEL receptor may change conformation upon ligand binding to facilitate its recruitment into budding COPI-coated vesicles.

48
Q

What is the role of the KDEL receptor in vesicular transport?

A

The KDEL receptor captures soluble ER resident proteins in vesicular tubular clusters and the Golgi apparatus, transporting them back to the ER in COPI-coated vesicles. Upon ligand binding, the receptor may change conformation, aiding its recruitment into budding COPI-coated vesicles.

49
Q

How does retrieval of ER proteins occur in the Golgi?

A

Retrieval of ER proteins begins in vesicular tubular clusters and continues in later parts of the Golgi. ER resident proteins dissociate from the KDEL receptor in the ER environment, allowing the receptor to return to the Golgi for reuse.

50
Q

What are the three pathways of protein sorting in the trans Golgi network?

A

M6P-marked proteins to lysosomes via endosomes.
Secretory proteins to secretory vesicles.
Constitutive secretory proteins to the cell surface.

51
Q

How are proteins sorted in the trans Golgi network?

A

Proteins in the trans Golgi network are sorted into different pathways based on specific signals, directing them to lysosomes, secretory vesicles, or the cell surfacev

52
Q

What is the endocytic pathway?

A

The endocytic pathway involves the uptake of molecules from the cell surface into the cell, directing them to endosomes and lysosomes.

53
Q

What do COPII-coated vesicles do?

A

COPII-coated vesicles facilitate forward transport from the ER to the Golgi.

54
Q

What do COPI-coated vesicles do?

A

COPI-coated vesicles facilitate reverse transport from the Golgi to the ER.

55
Q

What role does clathrin play in vesicular transport?

A

Clathrin mediates the formation of vesicles from the plasma membrane and Golgi, facilitating endocytosis and transport to endosomes and lysosomes.

56
Q

What is the role of the mannose 6-phosphate (M6P) marker?

A

The M6P marker directs lysosomal enzymes to lysosomes via clathrin-coated vesicles

57
Q

What happens to proteins with no special sorting signals in unpolarized cells?

A

Proteins with no special sorting signals are delivered to the cell surface via the constitutive secretory pathway.

58
Q

How are proteins sorted in polarized cells?

A

In polarized cells, proteins are selectively directed to either the apical or basolateral plasma membrane domain, requiring specific targeting signals.

59
Q

What initiates the formation of secretory vesicles at the Golgi?

A

Specific coat proteins, such as COPI, coat the cytoplasmic surface of the Golgi membrane, initiating vesicle budding.

60
Q

What happens to the KDEL receptor after delivering ER proteins?

A

The KDEL receptor returns to the Golgi for reuse after delivering ER resident proteins back to the ER.

61
Q

What are acid hydrolases in lysosomes?

A

Acid hydrolases are hydrolytic enzymes that are active under acidic conditions.

62
Q

How is the acidic pH in lysosomes maintained?

A

An H+ ATPase in the lysosomal membrane pumps H+ into the lysosome, maintaining its lumen at an acidic pH.

63
Q

What are the four pathways to degradation in lysosomes?

A
  1. Endocytosis

Phagocytosis
Autophagy
Macropinocytosis

64
Q

Q: What distinguishes the autophagosome in the degradation pathway?

A

A: The autophagosome has a double membrane.

65
Q

What occurs during lysosome maturation?

A

Late endosomes fuse with preexisting lysosomes or endolysosomes, which mature into lysosomes as hydrolases complete the digestion of their contents.

66
Q

How are mannose 6-phosphate (M6P) groups added to lysosomal enzymes?

A

ction of two enzymes in the cis and trans Golgi network adds M6P groups to the precursors of lysosomal enzymes.

67
Q

What role do M6P receptors play in lysosomal enzyme transport

A

M6P receptors bind M6P-tagged lysosomal hydrolases, segregating them from other proteins in the trans-Golgi network.

68
Q

What ensures that lysosomal hydrolases do not return to the Golgi with the receptor?

A

the phosphate is removed from the M6P attached to the hydrolases in endosomes, preventing their return to the Golgi with the receptor.

69
Q

What is Mucopolysaccharidosis I (MPS I)?

A

disorder resulting in cellular damage.

70
Q

What is Mucolipidosis II (ML II)?

A

inherrieted metabolic disorder affecting the addition of M6P tags to hydrolytic enzymes.

71
Q

What occurs during exocytosis?

A

a transport vesicle fuses with the plasma membrane, releasing its content into the extracellular space, and the vesicle membrane becomes continuous with the plasma membrane.

72
Q

What occurs during endocytosis?

A

A patch of the plasma membrane internalizes, forming a transport vesicle containing extracellular content

73
Q

What is phagocytosis?

A

Phagocytosis is the process of engulfing solid particles, like bacteria or cell debris, by specialized cells such as macrophages.

74
Q

What is pinocytosis?

A

Pinocytosis is the non-specific uptake of fluids and solutes by cells through small vesicles.

75
Q

What is receptor-mediated endocytosis?

A

Receptor-mediated endocytosis is the specific uptake of ligands bound to receptors on the cell surface into clathrin-coated vesicles for sorting.

76
Q
A

cell biology (8 decks)

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