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Biochemistry Exam 3 > Intracelluar Compartents and Protein Sorting > Flashcards

Intracelluar Compartents and Protein Sorting Flashcards

0
Q

N terminal ER signal sequence at beginning of a cytosolic protein would lead to what result?

A

Redirectrion from cytosol to the ER for secretion from cell

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1
Q

How are proteins sorted generally?

A

Signal sequences

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2
Q

Where are signal sequences most often found?

A

N-terminal

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3
Q

What are signal peptidases?

A

Removes signal sequence from the finished protein core once the sorting process is complete

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4
Q

What is a signal patch?

A

Sorting signal composed of multiple internal amino acid sequences that form a three-dimensional arrangement of atoms on protein surface

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5
Q

Describe the specificity of sorting receptors for protein signal sequences

A

Usually on a protein class level

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6
Q

T or F: Orientation of proteins is maintained in budding and fusing of vacuoles

A

T, always maintain same domains facing the cytosol

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7
Q

Gated transport controls what exchange?

A

Between nucleus and cytosol

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8
Q

Transmembrane transport occurs between what?

A

Cytosol and Mitochondria/peroxisomes/plastids/ER

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9
Q

Vesicular transport occurs between what?

A

ER, Golgi, Endosomes, Lysosome, Secretory vesicles, Cell exterior

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10
Q

Proteins without a sorting signal end up where?

A

Cytosol

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11
Q

Where does protein synthesis begin?

A

Ribosomes in cytosol (except for mitochondrial ribosomes)

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12
Q

T or F: Translocation to the ER is co-translational

A

T

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13
Q

Resident ER, Golgi resident, plasma membrane proteins, secreted proteins, and lysosomal proteins are initially synthesized where?

A

RER

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14
Q

Where does glycosylation take place?

A

ER and Golgi

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15
Q

T or F: Proteins in cytosol, mitochondria, peroxisome, and nucleus are glycosylated

A

F

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16
Q

Proteins synthesized on free ribosomes are directed where when they lack ER translocation signal peptides?

A

Mitochondria, peroxisomes, or nuclei if have signal

Cytosol otherwise

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17
Q

Describe the structure of the nuclear envelope

A

Double membrane penetrated by pores in which nuclear pore complexes are positioned. It is contiguous with the ER.

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18
Q

Describe the inner nuclear membrane

A

Specific proteins that act as anchoring sites for chromatin and for the nuclear lamina.

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19
Q

Describe the outer nuclear membrane

A

Continuous with the membrane of the ER and is studded with ribosomes engaged in protein synthesis

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20
Q

Where are histones/DNA/RNA polymerases/gene regulatory proteins. and RNA processing processes all made?

A

Cytosol. imported into the nucleus

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21
Q

Where are tRNA and mRNA made?

A

Nucleus and exported to the cytosol

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22
Q

Describe the makeup of the nuclear porin complex

A

30 or so different NPC proteins or nucleoporins. Multiple copies i a octagonal symmetry

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23
Q

T or F: Small water soluble molecules can diffuse passively through the NPC

A

T

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24
What is the cut off for passive diffusion through the NPC?
60,000 daltons or so
25
What is responsible for the selectivity of active nuclear import processes?
Nuclear localization signals
26
Describe the typical makeup of a nuclear localization signal
1-2 short sequences rich in positively charged lysine and arginine
27
T or F: Unfolding is required to move a protein into/out of the nucleus
FALSE, can be moved fully assembled/folded
28
What recognizes nuclear localization signals?
Nuclear import receptors
29
Describe the function and specificity of nuclear import receptors
Recognize specific signals. Receptors bind to both the signal sequence and the protein to transport. Fibrils on the NPC are rich in phenylalanine and glycine, called FG repeats. These bind to the import receptors and move to next FG repeat and transfer the protein. continues all the way to the interior nuclear cytosol. Receptors are recycled
30
What is responsible for nuclear export similar to nuclear import proteins?
Nuclear export signals and nuclear export receptors
31
What is the function of Ran?
Required for nuclear import and export
32
Describe the function of Ran
GTPase found in cytosol and nucleus. Ran-GTP/Ran-GDP act as molecular switches. Ran-GTP is dense in the nucleus and Ran-GDP is dense in the cytosol. Gradient helps with nuclear import/export
33
Where is Ran-GDP located? What makes it?
Cytosol; Ran-GAP dephosphorylates Ran-GTP
34
Where is Ran-GTP located? What makes it?
Nucleus; Ran-GEF on chromatin exchanges Ran-GDP for Ran-GTP
35
Describe how Ran helps with nuclear transport
Export: Ran-GTP hops on to cargo and causes release in cytosol to Ran-GDP via Ran-GAP Import: Ran GDP hops on to cargo and causes release in nucleus to Ran-GTP via Ran-NEF
36
Describe where mitochondrial proteins are translated
First in the cytosol as mitochondrial precursor proteins and then translocated to the mitochondria by post-translational mechanism
37
Describe mitochondrial signal sequences
Amino terminal leader sequence up to 70 AA in length (not highly conserved) with many positively charged AA (lysine/arginine)
38
Describe the translocation of proteins to the mitochondria
Translocation is not co-translational. Proteins are in unfolded state. Requires ATP and chaperone proteins. Uses TOM and TIM because of two layers of membrane.
39
T or F: Mitochondrial translocation is co-translational
F, no translation is taking place. Were fully synthesized as mitochondrial precursor proteins
40
Where are peroxisomal proteins synthesized?
Cytosol
41
What is characteristic of a peroxisomal signaling sequence?
Three AA on the C-terminal.
42
T or F: Peroxisomal proteins are imported without unfolding
T; imported as fully folded proteins
43
What is the function of ER?
Lipid and protein biosynthesis
44
T or F: Import of proteins into ER is co-translational
T
45
T or F: Import into the nucleus, mitochondria, and peroxisome is post-translational
T
46
Why is the rough ER rough?
Studded with ribosomes that allow for co-translational translocation
47
What are microsomes?
Small closed vesicles that are formed when the ER is disrupted by homogenization. RER microsomes are more dense than SER microsomes
48
Describe the Blobel and Dobberstein experiment
Added microsomes to mRNA systems in-vitro. Found that proteins were smaller with RER than they were without. Cleavage of the signal sequence.
49
What is the signal hypothesis?
Leading signal sequence directs secreted protein to ER membrane and is cleaved off by signal peptidase in ER membrane before the polypeptide chain is completed
50
What is a SRP?
Signal recognition protein. Cycles between ER and cytosol binding to the signal sequence and the SRP receptor in the ER membrane. SRP are complex and made up of 6 different polypeptides bound to single small RNA molecule
51
Describe the ER signal sequence
Variable, but has 8 or more nonpolar AA at center.
52
Describe the recognition pocket of SRP
Large hydrophobic pocket lined with methionines and can accommodate hydrophobic signals or all sizes shapes and compositions
53
Besides localization, what other function does SRP perform?
Pauses translation until the ribosome binds to the ER membrane. Continues translation then. Ensures that protein isn't released to the cytosol
54
Describe the overall process of ER localization of proteins
SRP binds to protein sequence, SRP binds to SRP receptor on ER, ribosome binds to ER and continues translation into the ER lumen releasing SRP and SRP receptor complex
55
What are the two populations of ribosomes?
Membrane bound - attached to the cytosolic side of ER and engaged in ER translocated proteins Free - unattached to any membranes, synthesize all other proteins not destined for ER. ONLY differ in the type of proteins being made
56
What is Sec61?
A gated protein that imports into the ER when signal peptide is present
57
Signal sequences are recognized twice for ER translocation. Describe.
SRP in the cytosol. | Binding site in the pore of protein translocator to serve as a start-transfer signal to open the pore
58
Describe how a single pass membrane protein is synthesized
A secondary hydrophobic segment in the protein stops the transfer process of the protein before total translocation. This stop-transfer signal anchors the protein in the membrane. N terminal is on the lumenal side and C terminus is on cytosolic side
59
ER signal sequences are located on what terminal
N terminal
60
Peroxisome recognition sequences are on what terminal?
C terminal
61
Mitochondrial recognition sequences are on what terminal
N terminal
62
How are internal signal sequence proteins inserted into the ER membrane?
Same mechanism as if on N-terminal end. Brought by SRP to ER. Can make the N or C terminal on the ER lumen side depending on the nearby charged amino acids.
63
T or F: N or C terminals can be on the lumen side of an ER integrated protein
T, if via an internal signal sequence. Only N if the sequence is on N terminal
64
Directionality of protein synthesis?
N to C
65
How are multi-pass proteins integrated?
Internal signal sequences serve to start-transfer until a stop-transfer is encountered. Multiple start- and stop-transfer sequences
66
What is ERAD?
ER-associated degradation pathway. Quality control system that identifies misfolded proteins and transports them to cytosol and targets them for proteasome degradation.
67
Describe the link between Parkinson's disease and ERAD
Parkin, E3 ubiquitin ligase is mutated. An unfolded protein leads to ER stress.
68
Describe the link between ERAD and CF
Mutant misfolded protein in the ER is not recognized by mutation in CFTR (phenylalanine deletion at position 508). Loss of chloride regulation in CFTR expressing cells
69
Function of Golgi
Stacked disks of membranes with lots of vesicles. Each stack has a cis and trans face. Cisternae in each disk make up the cis and trans Golgi networks. Glycosylation occurs here.
70
Three major classes of glycoproteins
O-linked - hydroxyl chains of serine or threonine and a sugar N-linked - those with N-glycosidic linkage involving asparagine GPI-anchored - carboxyl terminal AA of a protein via a phosphorylethanolamine joined to oligosaccharide. Linked via glucosamine to phosphatidylinositol (PI)
71
N-linked glycoproteins have what common core?
Man3GlcNAc2 = 3 mannose in a branch attached to two n-acetylated glucosamines in series attached to a asparagine
72
What sequence after the signal peptide signals for glycosylation?
Asn-X-Thr/Ser where X can be anything except proline
73
What is the first step of N-linked glycosylation?
Dolichol-P-P-oligosaccharide transfers the oligosaccharide to Asn (membrane bound enzyme)
74
What does tunicamycin do?
Drug that inhibits the synthesis of the dolichol-oligosaccharide donor so no N-linked glycosylation occurs.
75
Where are high-mannose or complex oligosaccharides formed?
In the golgi, post-processing after the ER glycosylation
76
What is GPI-linked glycoprotein? Where is it located? Synthesis?
Glycosylphosphatidylinositol linked glycoproteins on the outer leaflet of the plasma membrane anchored to PI (i.e. on the lumen side of the ER). Synthesis begins in ER and GPI anchor is assembled separately and attached to the carboxyl terminal end of the protein after cleavage of the preexisting C terminal end

Biochemistry Exam 3 (11 decks)

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