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ANAT 212 pre midterm > Professor Uglade Lecture 9 (membrane proteins 3) > Flashcards

Professor Uglade Lecture 9 (membrane proteins 3) Flashcards

1
Q

Where are proteins encoded and translated?

A

all proteins are encoded by nuclear genes and translated in the cytosol (all proteins encoded by nucleus of the cell)

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2
Q

How can cellular membranes be made?

A

they can only be made by expanding pre-exisiting membranes

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3
Q

How are proteins sorted to their correct compartment?

A

proteins must be sorted during or after translation to their correct compartment or membrane
-sorting info is carried inside the proteins

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4
Q

Where are secretory pathway proteins inserted?
And what parts of the membranes are continious?

A

they are inserted into or across the ER membrane
-outer and inner membrane are continuous with ER

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5
Q

Where are secretory pathway proteins transported?

A

-transported to further compartments-Golgi, PM, endosomes, lysosomes

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6
Q

Difference between Rough ER and Smooth ER?

A

-Rough ER- many attached ribosomes, secretory protein synthesis
-smooth ER:no ribsomes, sites of lipid synthesis

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7
Q

What do targeting signals specify?

A

-they are sequences within a protein that specify its organelle localization (zip code) or signal peptide

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8
Q

How are targeting signals removed, and how are they related to the protein structure?

A

-they may be removed by proteolysis after the targeting is complete, or form part of the native structure
-they are often independent from the structure or biochemical function of the protein

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9
Q

How are targeting signals recognized?

A

-they are recognized by their pattern but usually not the exact sequence

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10
Q

What are the 3 targeting steps (in targeting signals)

A
  1. recognize a signal on a protein
  2. connect protein to the membrane (of the ER in this case)
  3. translocate protein into or across the membrane (if it is a lumenal protein)
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11
Q

When do secretory proteins enter the ER?

A

During the translation of their mRNAs

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12
Q

What is the signal hypothesis?

A

-extra sequence is a targeting signal peptide whose main function is to direct insertion into ER

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13
Q

How do signal peptides start the signal mechanism, and when is the signal peptide cleaved?

A

signal peptide must start mechanism to connect ribosomes to translocation pore
-signal peptide is cleaved off after targetin is finished

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14
Q

How do nascent polypeptides exit the ribosomes?

A

-through a tunnel in the large 60s subunit

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15
Q

what are the properties of the ribosomes exit tunnel?

A

-tunnel is neutral, polar, too small for tetiary folding (just a line of polypeptides)

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16
Q

what does the surface of the exit site in ribosome exit tunnel provide, and how many amino acids are between the transferase site and the exit?

A

surface around the exit site provides binding sites for ER targeting mechanisms
-30-40 amino acids of nascent polypeptide between peptidyl-transferase site and the exit

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17
Q

What do secretory signal peptides direct/do?

A

-they direct proteins to the ER for translocation into or across the membrane through cotranslational mechanism (mostly)

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18
Q

How are secretory pathway proteins directed into organelles

A

-they have additional targeting signals such as a polypeptide motif (sequence pattern)
-sometimes a post translational modification

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19
Q

What do organelles with no secretory pathway do, and what are examples?

A

-they have their own tareting signals
-ex: mitochondria, nuclei

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20
Q

What is the signal polypeptide pattern composed of?

A

-hydrophobic central region 8 or more residues long, with short polar regions on each side

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21
Q

what do polar regions of signal polypeptide pattern determine?

A

-they determine the direction of which end the protein is inserted

22
Q

Where are signal peptides normally found, and when are they cleaved?

A

-signal polypeptides are at the N-terminus
-shorter hydrophobic regions (8-16 residues)
-often cleaved off after translocation (cleaved off by peptidases)

23
Q

What are signal anchors and how do they differ from signal peptides?

A

-they are signal peptides that also become TM helices
-unlike signal peptides, signal anchors are not cleaved off, and they have a longer hydrophobic region (18-24 residues, since they have to be across the whole membrane
-they can also be in diff places in the protein

24
Q

How is a signal recognized on a newly translated protein, and what does SRP do?

A

ribosome begins translating polypeptide with a signal, signal recognition protein (SRP) which is a soluble protein that binds signal and ribosome during translation

25
Q

How is a protein connected to a membrane?

A

SRP-receptor (SRP-R) is a membrane protein that vinds the ribosome-SRP complex (has receptor in membrane of ER)

26
Q

What does the SRP-R link?

A

SRP-R links ribosomes to translocon pore in ER (where ribosomes attach, the ribosome pushes nascent peptide into ER)

27
Q

How are proteins translocated across the membrane?

A

The energy of translation on ribosome drives polypeptide through the translocon

28
Q

What is a signal receptor particle (SRP) composed of?

A

6 protein subunits and 1 RNA (macromolecule of RNA and proteins)

29
Q

What activity does SRP do?

A

it is a signal sequence recogition subunit with GTPase activity

30
Q

where is the translation regulatory domain on the SRP, and what does the RNA strand form?

A

-translation regulatory domain at the opposite end
-RNA strand form a flexible linker

31
Q

What does SRP sample?

A

SRP samples all nascent polypeptides that emerge from ribosomes

32
Q

Whena signal is recognized what does SRP do?

A

it attaches tightly to both the signal and the ribosome, it pauses translation at the ribosome and binds GTP

33
Q

what causes the ribosome do stop translation?

A

-when the hydrophobic region is recognized by the SRP there is a conformational change, so that translation stops and it can get to the ER membrane

34
Q

After ribosome translation is stopped, what does the ribosome SRP complex do?

A

it binds to the SRP-R on ER

35
Q

After ribosome-SRP is bound to SRP-R on the ER what occurs?

A

ribosome moves to the translocon and becomes tightly bound

36
Q

after translocon is tightly bound, what happens to SRP and SRP-R, and what 2 steps occur after this?

A

SRP and SRP-R dissociate from ribosome, and translation resumes and polypeptide translocates into lumen
-lumenal polypeptide does not contact the cytosol

36
Q

after translocon is tightly bound, what happens to SRP and SRP-R, and what 2 steps occur after this?

A

SRP and SRP-R dissociate from ribosome, and translation resumes and polypeptide translocates into lumen
-lumenal polypeptide does not contact the cytosol

37
Q

How is SRP attached to ribosomes ,and how is SRP-R bound to SRP-ribosomes?

A

SRP is attached in the GTP bound state
-SRP-R is also in GTPase, and is in GTP-bound state when it recognizes SRP-ribosomes

38
Q

What dissociates SRP and SRP-R from GTP- bound state?
What is GTP like in this context?

A

GTP hydrolysis by both SRP and SRP-R dissociate and recycle them
-GTP is used like a switch

39
Q

What does the Sec61 (ER translocon) form?

A

-it has 2 parts that form both sides of aqueous pore (open as a door in the membrane)

40
Q

What is the inactive Sec61 pore plugged by, and what are the properties of the active pore?

A

-inactive pore is plugged by part of a protein
-active pore is open but tightly sealed onto ribosome (pore only allows passing of nascent peptide)
-inside pore is neutral, polar

41
Q

how do the 2 parts of the Sec61 (ER translocon complex) open

A

the 2 parts of the pore open laterally to integrate TM helices into membrane

42
Q

How does translocation of lumenal protein occur?

A

-the signal peptide triggers opening of the translocon

43
Q

in what state are polypeptides translocated, and how is the movement driven?

A

translocated in an extended, unfolded state
-movement of polypeptide is driven by energy of translation pushing it out of the ribosome

44
Q

What removes signal peptides during translocation of lumenal proteins?

A

signal peptidase often removed signal peptide during translocation (not sequence specific but has a preferred site)

45
Q

How is a protein integrated into TM helix?

A

-protein starts with N-terminal sequence and TM helix

46
Q

What does the signal peptide do and how is the TM helix integrated in the integration of TM helix?
Where is the cytosolic part translated?

A

-signal peptide start stranslocation of lumenal part
-TM helix is recognized by translocon and integrated laterally into membrane during translation
-cytosolic part is translated in cytosol

47
Q

what is a type 1 TM protein?

A

Type 1 TM protein has N-terminus in lumen, C-terminus in cytosol

48
Q

What is a signal anchor in composition, and what does it become?

A

it is a signal pepide with long hydrophobic regions that is not cleaved off
-it becomes the TM domain-length of hydrophobic region is 18-24 amino acids

49
Q

What are the steps for signal anchor integration?
1. What does it open?

A
  1. signal anchor opens translocon like a signal peptide
50
Q

what is step 2 for signal anchor integration?
2.what does translocon recognize? Where are the charges

A

2.translocon recognzies charges next to the signal anchor to determine orientation in membrane
-positice charges in cytosol, negative charges in lumen

51
Q

Compare and contrast SRP (signal sequence, signal anchor) and HSP70
1. WHat do they recognize in a polypeptide
2. will they compete for binding to the same sites
3. how is binding regulated

A
  1. They both recognize hydrophobic residues
    2.they dont compete for biniding sites since SRP recognizes a stretch of amino acids that is in the n-terminus and HSP70 will recignize hydrophobic patches
  2. HSP70–> regulated by HSP40 bringing in the substrate and binding it tightly to ADP
    whereas SRP–> regulated by GTP

ANAT 212 pre midterm (9 decks)

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