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Lecture 6 Inracellular Compartments and protein tranport > Lecture 6 > Flashcards

Lecture 6 Flashcards

1
Q

What are the three mechanisms by which membrane-enclosed organelles import proteins?

A
  1. Transport through nuclear pore (only in the nucleus)
  2. Transport across membrane.
  3. Transport by Vesicles.
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2
Q

What is the function of signal sequences?

A

Singal squences direct proteins to the correct destination.
Proteins destined for the ER, for example, possess an N-terminal signal sequence that directs them to the organelle (where they go depends on the signal sequence, like an address.
Proteins lacking signal sequences remain in the cytosol.

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3
Q

What happens if a signal sequence is removed from an ER protein and attached to a cytosolic protein?

A

If the signal sequence is removed from an ER protein and attached to a cytosolic protein, both proteins are reassigned to the expected, inappropriate location.

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4
Q

Structure of the Nucleus

A

It consists of the envelope and Nuclear pore, the site at which nuclear proteins enter. The outer nuclear membrane is continuous with the ER membrane.
Double membrane.
Ribosomes bound to the cytosolic surface of the ER membrane and outer nuclear membrane.

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4
Q

Function of the Nuclear Pore Complex.

A

The nuclear pore complex forms a gate through which selected macromolecules and larger complexes can enter or exit the nucleus.
Figure 15-8 textbook.

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5
Q

How do prospective nuclear proteins enter the nucleus from the cytosol?

A

Prospective nuclear proteins contain Nuclear localization signals that are recognized by nuclear import receptors.

Nuclear import receptors interact with cytosolic fibrils.

The receptors carrying the cargo jostle their war through the unstructured regions of the nuclear pores until nuclear entry triggers cargo release.

After cargo delivery, the receptors return to the cytosol via nuclear pores for reuse.

Figure 15-9

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6
Q

What is the signal sequence that directs a protein from the cytosol into the nucleus?

A

NUCLEAR LOCALIZATION SIGNAL.

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7
Q

What recognizes the nuclear localization signal on proteins destined for the nuclear?

A

Nuclear import receptors.

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8
Q

Describe the two conformations of GTPase Ran and the location of their respective accessory proteins. Ran GAP AND Ran GEF.

A

The energy supplied by GTP hydrolysis drives nuclear transport.

GTPase Ran exists in two confirmations, one carrying GTP and the other carrying GDP.

Ran is converted from one confirmation to the other with the help of accessory proteins that are differently localized.

Ran-GAP: Triggers GTP hydrolysis, found exclusively in the cytosol, converts Ran-GTP to Ran-GDP. GTPase-activating protein.

Ran-GEF: Releases its GDP and takes up GTP. Ran-GEF (guanine nucleotide exchange factor), is found exclusively in the nucleus.

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9
Q

What does the localization of accessory proteins achieve?

A

The localization of
these accessory proteins guarantee that the concentration of Ran-GTP is higher in the nucleus, thus driving the
nuclear import cycle in the desired direction.

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10
Q

Describe the full process of protein delivery to the nucleus through the nuclear pore.

A

The protein binds to the Nuclear import receptor. With the help of nuclear localization signals. Enter the nuclear from the cytosol.

Ran-GTP binds to the import receptor, causing it to release the nuclear protein.

The receptor is now carrying the Ran-GTP and transports it back the to cytosol. Ran hydrolyzes GTP. Ran-GDP falls off the import receptor and now it is free to bind to another free protein destined for the nucleus.

Ran-GDP is carried into the nucleus by its own unique import receptor

Proteins binds to receptor
Ran-GTP binds to the receptor
Protein delivered to nucleus
GTP is hydrolyzed Ran-GDP dissociated from the receptor.
FIGURE 15-10.

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11
Q

Mitochondria Import: Mitochondrial precursor proteins are unfolded during import

A

In order for the mitochondrial precursor protein to enter the organelle they must cross the outer and inner membrane of the mitochondrion.

The signal sequence on the precursor protein is recognized by the receptor in the outer mito. membrane.

A protein translocator transports the signal squence across the outer mito. membrane.

The receptor,precursor protein, and translocator complex didduses in the outer membrane until the signal sequence is recognized by a secomd translocator in the inner membrane.

The two translocators transport the protein across both outer and inner layers unfolding the protein in the process.

The signal sequence is then cleaved off by a signal peptidase in the mito. mactrix.

Energy for this process comes from ATP hydrolysis.

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12
Q

What for Mitochondrial chaperone proteins do.

A

Help pull the protein across the membranes and help it to refold are not shown.

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13
Q

Peroxisomes

A

are packed with enzymes that digest toxins and synthesize certain phospholipids.

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14
Q

Peroxisomes transport What singlas transport to peroxisomes?

A

A sequence of 3 amino acids signals transport to peroxisomes

Receptor proteins in the cytosol
recognize transport sequence
Protein Translocator
No conformational change

Vesicular transport

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15
Q

Endoplasmic Reticulum

A

Most proteins destined for Golgi apparatus, lysosome and endosomes enter the ER first

ER signal sequence is 8 or more amino acids long

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16
Q

Two kinds of proteins are transferred from the cytosol to the ER.

A

1) -Water soluble proteins translocated across the ER membrane and are released into the ER lumen. destined either for secretion (by release at the cell surface) or for the lumen of an organelle of the endomembrane system.

2)-Transmembrane proteins partly translocated across the ER membrane and become embedded in it. Destined to reside in the membrane of one of these organelles or in the plasma membrane.

All of these proteins are initially directed to the ER by an ER signal sequence, a segment of eight or more hydrophobic amino acids

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17
Q

ER Proteins: How are Proteins targeted to the ER

A

Proteins are targeted to ER through
1) Signal recognition particle (SRP): Binds to signal and ribosome.
2) SRP receptor: On the ER membrane.

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18
Q

An ER signal sequence
and an SRP direct a ribosome to the ER membrane.

A

SRP binds to both the exposed ER signal sequence and the ribosome. slowing protein synthesis by the ribosome.

The SRP-ribosome complex binds to an SRP receptor in the ER membrane.

The SRP is released, and the ribosome passes from the SRP receptor to a protein translocator in the ER membrane.

protein synthesis resumes and the translocator starts to transfer the growing polypeptide across the lipid bilayer.

The polypeptide is threaded across the ER membrane through a channel in the translocator.

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19
Q

What are the two protein component that help guide the ER signal sequences to the ER membrane ?

A

1) signal recognition particle (SRP, present in the cytosol binds to the ribosome and the ER signal squence as it emerges from the ribosome.

2) SRP receptor embedded in the ER membrane recognizes the SRP. Binding of an SRP to a ribosome displays an ER signal sequence.

The SRP and SRP receptor function as molecular matchmakers. Bringing together ribosomes that are synthesizing proteins with an ER signal sequence and protein translocators within the ER membrane.

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20
Q

A soluble protein crosses the ER membrane and enters the lumen.

A

STEPS:
1. The protein translocator binds the signal sequence and threads the rest of the polypeptide across the lipid bilayer as a loop.

  1. during the translocation process, the signal peptide is cleaved
    from the growing protein by a signal peptidase.
  2. The cleaved signal sequence is ejected into the bilayer, where it is degraded. Once protein synthesis is complete, the translocated polypeptide is released as a soluble protein into the ER lumen, and the protein translocator closes
  3. Result is a MATURE SOLUBLE PROTEIN IN THE ER LUMEN

The signal sequence for soluble protein is always at the N-terminus. It remains bound to the translocator while the rest of the polypeptide chain is threaded through the membrane as a large loop.

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21
Q

Transmembrane Protein tranlcation.

A

More complicated than water soluble proteins.
- N-terminal signal sequence.
-Stop transfer sequence.

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22
Q

Single-Pass transmembrane protein. Figure 15-16.

A
  1. N-Terminal ER signal sequence initiates transfer.
  2. The protein contains a second hydrophobic sequence that acts as a stop-transfer sequence.
  3. When the hydrophobic stop-transfer sequence enters the protein translocator, the growing polypeptide chain is discharged into the lipid bilayer.
  4. Mature single-pass transmembrane protein in the ER membrane.

After this Protein synthesis on the cytosolic side continues to completion.

What happens to the N-terminal signal sequence ?

The n-terminal signal sequence is cleaved off, leaving the transmembrane protein anchored in the membrane.

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23
Q

What does the N-terminal in a single-pass do, and where does it end up?

A

The N-terminal signal sq. is cleaved off, leaving the transmembrane protein anchored in the membrane.

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24
Q

A double-pass transmembrane protein has an internal ER signal sequence.

A
  • A start transfer sequence is recognized by SRP. Similar to the N-terminal ER signal sequence.
  • Then, the SRP receptor will get the protein, then it will be passed to the translocator.
  • In the case of double-pass there are two hydrophobic regions, the stop and start transfer sequence.
  • every time we reach a hydrophobic region the direction of translation is changed.
  • The protein is translated in the cytosol, then when it reaches the HYDROPHOBIC start sequence, in goes to the ER lumen, THEN at the end of when it reaches the second hydrophobic region, the stop sequence, it WILL CHANGE THE DIRECTION TO TRANSLATION INTO THE CYTOSOL.
  • At the end of the double pass transmembrane, both the stop and start transfer sequences remain within the membrane.
25
Q

What is the main difference between single-pass and double-pass transmembrane proteins? NAME TWO.

A

Single pass proteins have an n-terminal signal sequence that is cleaved off, while the stop transfer sequence remains in the bilayer.

Double pass proteins have an internal signal sequence that is used to start the protein transfer (start-transfer sequence) that is never removed from the polypeptide.

For membrane proteins, single pass means that the polypeptide chain goes through the membrane once. Double pass means that the polypeptide chain goes through the membrane twice. Therefore, a single-pass membrane protein has its C terminus and its N terminus on opposite sides of the membrane. A double pass membrane protein has its N terminus and C terminus on the same side of the membrane (since the protein has to loop to go through the membrane a second time).

26
Q

RECALL, IN DOUBLE PASS TRANSLATION WHAT HAPPENS EVERY TIME YOU REACH A HYDDROPHOBIC SEQUENCE?

A

THE DIRECTION OF TRANSLATION IS CHANGED. For example, if it was in the cytosol, it would go to the ER LUMEN.

27
Q

Start-signal sequences (NOT THE SAME THING AS N-TERMINUS) are typically not removed from polypeptide polypeptides that are embedded into the membrane. What does this create?

A

A double pass (multi-pass) transmembrane protein.The polypeptide chain passes back and forth across the lipid bilayer. Hydrophobic signal sequences are thought to work in pairs; they have an internal start-transfer sequence that serves to initiate translocation until a stop-transfer sequence is reached. Both hydrophobic sequences are released into the bilayer, remaining as membrane-spanning alpha helices.

28
Q

What exactly is a start/stop transfer signal?

A

Hydrophobic stretches of amino acids which favorably interact with the hydrophobic interior of phospholipid membranes

29
Q

What is the difference between a start signal sequence and an n-terminus?

A

A start signal sequence is a specific point on the polypeptide that tells translocation where to begin. An N-terminus is the exact point where the signal first starts at.

30
Q

What is a single-pass transmembrane protein?

A

A protein inserted in the membrane with a defined orientation; these only have one hydrophobic region spanning the membrane (N-terminus on the lumen side of the bilayer and the C-terminus on the cytosolic side)

31
Q

What is the process for the opening of the channel of the protein translocator?

A

The signal sequence remains bound to the channel while the rest of the chain is threaded through the membrane as a large polypeptide chain. It is then removed by a transmembrane signal peptidase, which has an active site facing the lumen side of the ER membrane. They are, then, released from the channel into the lipid bilayer and degraded.

32
Q

Vesicle Transport

A

Transport from the ER to other organelles that are part of the endomembrane system are carried out through a process called transport vesicles.

  • Extends outwards from the ER to the plasma membrane.
  • Allows proteins and other molecules to be secreted by exocytosis.
33
Q

Transport Vesicles

A

Transport Vesicles bud and detach from ER or Golgi Apparatus
Major secretory pathway
starts with ER, going
through Golgi apparatus
to cell surface

Major endocytic pathway
starts from plasma
membrane, leading to endosomes and ending at the lysosome.

34
Q

Coated Vesicle

A

Proteins coat the cytosolic surface of vesicles.

35
Q

Vesicle Budding Is Driven by the Assembly of a Protein Coat

A

Vesicles that bid from membranes have a distinctive protein coat on their cytosolic surface this is called a coated vesicle.

Cells produce several kinds of coated vesicles, each with a distinctive protein coat.

The coat serves at least two functions: it helps shape the membrane into a bud, and it captures molecules for onward transport.

Transport vesicle dock to organelles to transfer cargo molecules
Process with high specificity
Rab proteins identify tethering proteins
v-SNAREs interact with t-SNAREs
the vesicle fuses to target the membrane

36
Q

Clathrin coated vesicles

A

Bud from both the Golgi apparatus on the outward secretory pathway and from the plasma membrane on the inward endocytic pathway.

37
Q

Adaptins

A

Help capture specific cargo molecules by trapping the cargo receptors that bind them.

38
Q

COP-coated vesicles

A

Involved in transporting molecules between the ER and the Golgi apparatus and from one part of the Golgi apparatus to another.

39
Q

Clathrin-coated vesicles transport selected cargo molecules

A
  1. Cargo receptors, with their bound cargo molecules, are captured by adaptins. Adaptins bind clathrin molecules to the cytosolic surface of the budding vesicle.
  2. Dynamin proteins assemble around the neck of budding vesicles.Once assembled, the dynamin molecules hydrolyze their bound GTP and, pinch off the vesicle.
  3. After budding is complete, the coat proteins are removed, and the naked vesicle can fuse with its target membrane.
40
Q

Rab proteins type of GTPases. and tethering proteins. How does the combination of Rab and tethering protein help ensure the transport vesicles fuse only with the correct membrane.

A

The coding system of matching Rab and tethering proteins helps to ensure that transport vesicles fuse only with the correct membrane.

identification process of the vesicles to make sure that the vesicles fuses with the correct membrane.

Rab proteins on the surface of each type of vesicle are recognized by corresponding tethering proteins on the cytosolic surface of the target membrane.

Each organelle and each type of transport vesicle carries a unique combination of Rab proteins, which serve as molecular markers for each membrane type

41
Q

SNAREs

A

Once the tethering protein has captured a vesicle by grabbing hold of its Rab protein, SNAREs on the vesicle (called v-SNAREs) interact with complementary SNAREs on the target membrane (called t-SNAREs), firmly docking the vesicle in place.

42
Q

Rab proteins, tethering proteins, and SNAREs help direct transport vesicles to their target membranes.

A

Rab and tethering proteins provide the initial recognition between a vesicle and its target membrane, complementary SNARE proteins ensure that transport vesicles dock at their appropriate target membranes

43
Q

Secretory pathway

A

Exocytosis: process of proteins, carbohydrates or lipids traveling from ER through Golgi apparatus to cell surface
Path by which proteins travel from ER through Golgi apparatus to plasma membrane.

SNARE proteins can catalyze the fusion of the vesicle and target membranes

44
Q

ER modification

A

Most proteins are chemically modified in ER
-Disulfide bonds
-Glycosylation

45
Q

Disulfide bonds

A

formed by the oxidation of pairs of cysteine side chains.
reaction catalyzed by an enzyme that resides in the ER lumen.
The disulfide bonds help to stabilize the structure of proteins that will encounter degradative enzymes and changes in pH outside the cell.
Disulfide bonds do not form in the cytosol because the environment there is reducing.

46
Q

Glycosylation

A

carried out by glycosylating enzymes present in the ER but not in the cytosol.

Very few proteins in the cytosol are glycosylated, and those that are have only a single sugar attached to them.

oligosaccharides, form part of the cell’s outer carbohydrate layer or glycocalyx. containing 14 sugars is added to proteins.

Oligosaccharyl transferase is a membrane protein complex that transfers a 14-sugar oligosaccharide from dolichol to nascent protein.

oligosaccharide processing begins in the ER and continues in the Golgi apparatus.

47
Q

ER exit

A

ER retention signal is attached to the C-terminus of proteins remaining in the ER

Misfolded proteins and partially assembled antibodies are retained in the ER

Cystic fibrosis is an example of misfolded protein retained in the ER

48
Q

Unfolded protein response

A

UPR is a complex program triggered in response to accumulation of misfolded proteins in the ER.

The misfolded proteins are recognized by several types of transmembrane sensor proteins in the ER membrane. Each activate transcription regulators and a different componenet of UPR.

misfolded proteins bound to sensors ——-««<
ACTIVATION OF CHAPERONE GENES PLUS OTHER GENES THAT INCREASE THE PROTEIN-FOLDING CAPACITY OF THE ER

49
Q

What do misfolded protein sensors do?

A

activated transcription regulators
ACTIVATION OF CHAPERONE GENES PLUS OTHER GENES THAT INCREASE THE PROTEIN-FOLDING CAPACITY OF THE ER.

50
Q

Golgi apparatus: Proteins Are Further Modified and Sorted in the Golgi Apparatus.

A

The Golgi apparatus consists of a collection of flattened, membrane-enclosed sacs called cisternae.

Each Golgi stack has two distinct faces: an entry, or cis, face and an exit, or trans, face.

The cis face is adjacent to the ER, while the trans face points toward the plasma membrane.

51
Q

Exocytosis

A

Constitutive exocytosis pathway: proteins and lipids are transported to plasma membrane. Does not require extracellular signals.

-Secretion is release of proteins to the extracellular space

-Regulated exocytosis pathway is specific to secretory cells which produce specific products, Requires an extracellular signal.

-Secretory vesicles store products like hormones or enzymes

52
Q

Endocytic pathway

A

Uptake of fluid and molecules refers to endocytosis
Endocytic vesicle

Endosome can recycle material and send back to plasma membrane or to lysosome for degradation

Pinocytosis

Phagocytosis

53
Q

Pinocytosis

A

Pinocytosis is a continuous process in eukaryotic cells
-Pinocytosis vesicles.

Clathrin-coated proteins carry out pinocytosis.

54
Q

Phagocytosis

A

In some unicellular cells its form of feeding

  • Involves phagosome

In animal cells it is involved in defense mechanism

-White blood cells

55
Q

Receptor mediated endocytosis

A

In this process, macromolecules are recognized by receptors on the cell surface and enter the cell by clathrin-coated proteins.

56
Q

LDL enters cells via receptor-mediated endocytosis. Example of Receptor mediated endocytosis

A

LDL binds to LDL receptors on the cell surface and is internalized in clathrin-coated vesicles.

The vesicles lose their coat and then fuse with endosomes. In the acidic environment of the endosome, LDL dissociates from its receptors.

The LDL ends up in lysosomes, where it is degraded to release free cholesterol .

while the LDL receptors are returned to the plasma membrane via transport vesicles to be used again.

57
Q

The fate of receptor proteins following their endocytosis depends on the type of receptor

A

Retrieved receptors are returned either to the same plasma membrane domain from which they came (recycling). or to a different domain of the plasma membrane (transcytosis).

Receptors that are not specifically retrieved from early endosomes follow the pathway from the endosomal compartment to lysosomes, where they are degraded.

  1. Recycling
  2. Transcytosis.
  3. Degraded.
58
Q

A lysosome contains a large variety of hydrolytic enzymes, which are only active under acidic conditions.

A

The lumen of the lysosome
is maintained at an acidic pH by an ATP- driven H+ pump in the membrane that hydrolyzes ATP to pump H+ into the lumen.

59
Q

Materials destined for degradation in lysosomes follow different pathways to the lysosome.

A

.

Lecture 6 Inracellular Compartments and protein tranport (3 decks)

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