Cellbio1 at Universität Wien | Flashcards & Summaries

Lernmaterialien für Cellbio1 an der Universität Wien

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Welche Eigenschaften haben Lipide, dass sie eine flexible, undurchlässige Doppellipidschicht bilden können?

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Lipids are amphiphilic, they have a hydrophilic/polar head group and a hydrophobic/apolar tail. If their shape resembles a cylinder (they have two acyl chains, one usually saturated the other unsaturated), they can form a lipid bilayer by turning their hydrophobic tails towards each other while their polar, hydrophilic parts face the aqueous solution.The lipids (mainly phospholipids in the membrane) pack against each other. This structure is not permeable for bigger water-soluble molecules. Lipid bilayers are flexible, it is a two dimensional fluid: individual lipids can rotate and diffuse in the plane of the membrane, their fluidity can be changed, and they are easy to bend.

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Wie wird selektierter Transport der Nucleare Pore gewährleistet? Ein Prinzip beschreiben wie dies funktioniert.

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Sorting signals called nuclear localization signals (NLS) are responsible for the selectivity of the active nuclear import process. In many nuclear proteins, the signals consist of one or two short sequences that are rich in the positively charged amino acids lysine and arginine. Nuclear localization signals can be located almost anywhere in the amino acid sequence and are thought to form loops or patches on the protein surface. If one protein subunit of a multicomponent complex displays a nuclear localization signal, the entire complex will be imported into the nucleus.

Import: To initiate nuclear import, most NLS must be recognized by nuclear import receptors, called importins, most of which are encoded by a family of related genes. Import receptors are soluble cytosolic proteins that bind both to the nuclear localization signal on the cargo protein and to the phenylalanine-glycine (FG) repeats in the unstructured domains of the channel nucleoporins that line the central pore. FG-repeats interact weakly, which gives the protein tangle gel-like properties that impose a permeability barrier to large macromolecules, and they serve as docking sites for nuclear import receptors. As import receptors bind to FG-repeats during this journey, they would disrupt interaction between the repeats and locally dissolve the gel phase of the protein tangle that fills the pore, allowing the passage of the receptor–cargo complex. Within the nucleus Ran-GTP displaces the cargo from the receptor.

Export: Cargo that is labelled with a nuclear export signal binds to export receptors (exportins) but only in the presence of Ran-GTP. These receptors bind to both the export signal and the FG repeats on the NPC to guide their cargo through the NPC to the cytosol. 

The Ran-GTP/GDP gradient imposes directionality on transport.

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SRP: Definition, Function, Properties. What is the Role of SRP in the synthesis of proteins targeted to the ER, and how does it work?

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The signal-recognition particle (SRP) is a ribonucleoparticle and is composed of 6 protein subunits and a RNA called 7S. The SRP cycles between the ER membrane and the cytosol and binds to the signal sequence. ER signal sequences vary greatly in amino acid sequence, but each has eight or more nonpolar amino acids at its center. 

The SRP can bind specifically to many different sequences because its signal sequence-binding site is a large hydrophobic pocket lined by methionine. Because methionines have unbranched, flexible side chains, the pocket is sufficiently plastic to accommodate hydrophobic signal sequences of different sequences, sizes, and shapes. The SRP recognizes the N-terminal signal sequence, binds to it and halts its translation. The SRP is a rod-like structure, which wraps around the large ribosomal subunit, with one end binding to the ER signal sequence as it emerges from the ribosome as part of the newly made polypeptide chain; the other end blocks the elongation factor binding site at the interface between the large and small ribosomal subunits. This block halts protein synthesis as soon as the signal peptide has emerged from the ribosome. This allows the SRP to guide the ribosome to the ER, where it binds to the SRP receptor in the ER membrane. The translocator (Sec61) transfers the growing polypeptide chain across the membrane, SRP receptor and SRP are released and will be recycled. 

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How and why do cis-double bonds in the acyl-chains of membrane lipids influence the transition temperature of the membrane?

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Transition temperature is the temperature where the lipid membrane changes from a liquid state to a crystalline or gel state. 

The double bond will not allow the acyl-chain to rotate, the kink formed by the double bond is fixed, and this means that the chain will occupy a larger volume within the monolayer, meaning that the membrane is more difficult to pack, allowing the membrane to stay fluid at much lower temperatures. A cis-double bond therefore greatly decreases the transition temperature of the membrane. 


This can be seen when imaged by light microscopy, two different lipids compared at 22°C, whereby one forms a para-crystalline structure (no cis-double bond, e.g. Palmitate/Stearate (16:0, 18:0 PC) – tt 49 °C) and the other is liquid (contains cis-double bond, e.g. Palmitate/Oleate (16:0, 18:1 PC) – tt -2 °C).


Also good example: Margarine is made from vegetable oil by chemically saturating the unsaturated fatty acid chains.

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Welches Enzym hilf bei der Faltung von falsch gefalteten Proteinen?

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The ER-membrane-bound chaperone protein calnexin binds to incompletely folded proteins containing one terminal glucose on N-linked oligosaccharides, trapping the protein in the ER. Removal of the terminal glucose by a glucosidase releases the protein from calnexin. A glucosyl transferase is the crucial enzyme that determines whether the protein is folded properly or not. Glycosyl transferase binds to hydrophobic patches on the surface of misfolded proteins. If the protein is still incompletely folded, the enzyme transfers a new glucose from UDP-glucose to the Nlinked oligosaccharide, renewing the protein’s affinity for calnexin and retaining it in the ER. The cycle repeats until the protein has folded completely.

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Wie unterscheiden sich ER- und Plasmamembran?

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The membrane of the ER compared to the membrane of Golgi or the PM is quite different. The ER membrane is the thinnest, then comes Golgi and the PM is the thickest. This is because cholesterol and Sphingolipids are added in the Golgi. The PM is supposed to be sturdy to protect the cell from everything on the outside. Since the PM is thicker than the ER and Golgi membranes, proteins with longer transmembrane domains tend to be localized in the PM. Each lipid has a negative charge, but phosphocholine and phosphatidylethanolamine have a positive charge, which results in a more positive net charge. Therefore, the ER has very little negative charge, the Golgi a bit more and the most charged membrane is the PM. The ER is symmetrical, which means the lipid composition in the luminal side and the cytosolic side is identical. The PM is asymmetrical, negative charged lipids are in the cytosol and glycosylated lipids are facing the cell surface. This asymmetry is mediated by the Golgi.

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Wie kann man experimentell feststellen, dass eine Signalsequenz auf einem Protein sowohl notwendig als auch ausreichend für dessen Lokalisation ist?

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TESTE DEIN WISSEN

The protein of interest will be tagged with Green Fluorescent Protein and transported into a cell, so the localization of the protein inside the cell can be followed. To prove that the signal sequence is necessary for the localization first a protein with GFP and with the signal sequence will be observed, and it will go to its destination. Then a GFP labelled protein without the signal sequence will be observed. This protein stays in the cytosol, and it proves that the signal sequence is necessary for the correct localization. In another set of experiments we’d put the signal sequence on a cytosolic GFP labelled protein, which will go to the respective organelle associated with the signal sequence. This proves that the signal sequence is also sufficient for localization.

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Protein import into Peroxisomes?

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Peroxisomes consist of a single membrane and mediate beta-oxidation and detoxification. The signal for import into peroxisomes is a C-terminal SKL motif. During de novo formation of peroxisomes, two different classes of ER- and mitochondrial derived vesicles fuse. Only after fusion an active translocon is assembled that mediates the transport of proteins into newly made peroxisomes. Later on, peroxisomes can multiply by division. 

The signal for import into peroxisomes is a C-Terminal SKL motif, which will be recognized by cytosolic receptor proteins. Numerous proteins called peroxins participate in the import process which is driven by ATP hydrolysis. A complex of peroxins forms a translocator which transports the protein into the nucleus. These translocator pores are huge and dynamic, the cargo protein doesn’t have to unfold to go through.

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Almost all proteins are synthesized in the cytoplasm yet many end up in other parts of the cell. What is the general principle that directs proteins to their correct destination? Illustrate said principle using an example.

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Although Mitochondria and chloroplasts contain their own DNA, ribosomes, and other components required for protein synthesis, most of their proteins are encoded in the cell nucleus and imported from the cytosol. Each imported protein must reach the particular organelle subcompartment in which it functions. Proteins imported into mitochondria are usually taken up from the cytosol within seconds or minutes of their release from ribosomes. Mitochondrial proteins are fist fully synthesized as mitochondrial precursor proteins in the cytosol and then translocated into mitochondria by a posttranslational mechanism. One or more signal sequences direct all mitochondrial precursor proteins to their appropriate mitochondrial subcompartment. The signal for import into the mitochondrial matrix is N-terminal amphipathic helix that contains positively charged amino acids on one face and negatively charged amino acids on the other face. The signal sequence is rapidly removed after import by a signal peptidase. The signal sequences are both necessary and sufficient for the import and correct localization of the proteins. Multisubunit protein complexes that function as protein translocators mediate protein movement across mitochondrial membranes. The TOM complex transfers proteins across the outer membrane, and two TIM complexes (TIM23 and TIM22) transfer proteins across the inner membrane. The TOM complex is required for the import of all nucleus-encoded mitochondrial proteins. It initially transports their signal sequences into the intermembrane space and helps to insert transmembrane proteins into the outer membrane. β-barrel proteins, which are particularly abundant in the outer membrane, are then passed on to an additional translocator, the SAM complex, which helps them to fold properly in the outer membrane. The TIM23 complex transports some soluble proteins into the matrix space and helps to insert transmembrane proteins into the inner membrane. The TIM22 complex mediates the insertion of a subclass of inner membrane proteins, including the transporter 5 that moves ADP, ATP, and phosphate in and out of mitochondria. Yet another protein translocator in the inner mitochondrial membrane, the OXA complex, mediates the insertion of those inner membrane proteins that are synthesized within mitochondria. It also helps to insert some imported inner membrane proteins that are initially transported into the matrix space by the other complexes.

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Oligosaccharide die im ER an Proteine angehängt werden, wie wirken sie sich auf die Faltung aus?

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The glycosylation is done by an enzyme called oligosaccharyl-transferase and it attaches a preformed precursor oligosaccharide to the NH2 group of an asparagine that’s why it’s called N-linked protein glycosylation.

Oligosaccharides are used as tags to mark the state of protein folding. Some proteins require N-linked glycosylation for proper folding in the ER, yet the precise location of the oligosaccharides attached to the proteins surface does not seem to matter. The ER-membrane bound chaperone protein Calnexin binds to incompletely folded proteins containing one terminal glucose on the N-linked oligosaccharides, trapping the protein in the ER. Removal of the terminal glucose by a glucosidase releases the protein from calnexin. A glucosyl transferase is the crucial enzyme that determines whether the protein has folded properly or not: if the protein is still incompletely folded, the enzyme transfers a new glucose on it, renewing the proteins affinity to calnexin. The cycle repeats until the protein has folded completely. Glucosyl transferase binds to hydrophobic patches on the surface of misfolded proteins.

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Wie können Proteine Membrane beugen?

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TESTE DEIN WISSEN

Proteins can change the composition of the acyl chain and head group. The membrane gets curved if the composition of one layer of the bilayer is changed. • Membrane proteins are able to oligomerize, which has an effect on the curvaton of the membrane. • Cytoskeleton: Actin as a molecular motor can induce the tube formation. • Scaffolding: There are direct and indirect scaffolds, which are linked to the membrane and are able to bend the membrane. • Through dimerization (banana-shaped), BAR-Domains are able to change the structure of a membrane by electrostatic interaction. • Insertion of an amphipathic helix into the membrane has an effect on membrane curvaton.

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TESTE DEIN WISSEN

What are the steps in the formation, targeting and fusion of vesicle mediated transport? Describe briefly in words or use a schematic.

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TESTE DEIN WISSEN

The general steps of vesicle mediated transport:

  1. Cargo needs to be enriched in a patch of the membrane
  2. This patch of membrane undergoes budding
  3. The vesicle is separated from the donor compartment by a scission reaction
  4. The coat disassembles
  5. The transport vesicle is targeted and tethered to its target compartment
  6. The vesicle is brought into close proximity to the target membrane (docking)
  7. The vesicle fuses with its target compartment

Molecular machinery for vesicular transport:

  • Cargo concentration and budding: coat proteins and adaptor proteins
  • Scission: GTPases
  • Targeting and tethering: rab proteins and tethering factors
  • Fusion: SNARE proteins
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Beispielhafte Karteikarten für deinen Cellbio1 Kurs an der Universität Wien - von Kommilitonen auf StudySmarter erstellt!

Q:

Welche Eigenschaften haben Lipide, dass sie eine flexible, undurchlässige Doppellipidschicht bilden können?

A:

Lipids are amphiphilic, they have a hydrophilic/polar head group and a hydrophobic/apolar tail. If their shape resembles a cylinder (they have two acyl chains, one usually saturated the other unsaturated), they can form a lipid bilayer by turning their hydrophobic tails towards each other while their polar, hydrophilic parts face the aqueous solution.The lipids (mainly phospholipids in the membrane) pack against each other. This structure is not permeable for bigger water-soluble molecules. Lipid bilayers are flexible, it is a two dimensional fluid: individual lipids can rotate and diffuse in the plane of the membrane, their fluidity can be changed, and they are easy to bend.

Q:

Wie wird selektierter Transport der Nucleare Pore gewährleistet? Ein Prinzip beschreiben wie dies funktioniert.

A:

Sorting signals called nuclear localization signals (NLS) are responsible for the selectivity of the active nuclear import process. In many nuclear proteins, the signals consist of one or two short sequences that are rich in the positively charged amino acids lysine and arginine. Nuclear localization signals can be located almost anywhere in the amino acid sequence and are thought to form loops or patches on the protein surface. If one protein subunit of a multicomponent complex displays a nuclear localization signal, the entire complex will be imported into the nucleus.

Import: To initiate nuclear import, most NLS must be recognized by nuclear import receptors, called importins, most of which are encoded by a family of related genes. Import receptors are soluble cytosolic proteins that bind both to the nuclear localization signal on the cargo protein and to the phenylalanine-glycine (FG) repeats in the unstructured domains of the channel nucleoporins that line the central pore. FG-repeats interact weakly, which gives the protein tangle gel-like properties that impose a permeability barrier to large macromolecules, and they serve as docking sites for nuclear import receptors. As import receptors bind to FG-repeats during this journey, they would disrupt interaction between the repeats and locally dissolve the gel phase of the protein tangle that fills the pore, allowing the passage of the receptor–cargo complex. Within the nucleus Ran-GTP displaces the cargo from the receptor.

Export: Cargo that is labelled with a nuclear export signal binds to export receptors (exportins) but only in the presence of Ran-GTP. These receptors bind to both the export signal and the FG repeats on the NPC to guide their cargo through the NPC to the cytosol. 

The Ran-GTP/GDP gradient imposes directionality on transport.

Q:

SRP: Definition, Function, Properties. What is the Role of SRP in the synthesis of proteins targeted to the ER, and how does it work?

A:

The signal-recognition particle (SRP) is a ribonucleoparticle and is composed of 6 protein subunits and a RNA called 7S. The SRP cycles between the ER membrane and the cytosol and binds to the signal sequence. ER signal sequences vary greatly in amino acid sequence, but each has eight or more nonpolar amino acids at its center. 

The SRP can bind specifically to many different sequences because its signal sequence-binding site is a large hydrophobic pocket lined by methionine. Because methionines have unbranched, flexible side chains, the pocket is sufficiently plastic to accommodate hydrophobic signal sequences of different sequences, sizes, and shapes. The SRP recognizes the N-terminal signal sequence, binds to it and halts its translation. The SRP is a rod-like structure, which wraps around the large ribosomal subunit, with one end binding to the ER signal sequence as it emerges from the ribosome as part of the newly made polypeptide chain; the other end blocks the elongation factor binding site at the interface between the large and small ribosomal subunits. This block halts protein synthesis as soon as the signal peptide has emerged from the ribosome. This allows the SRP to guide the ribosome to the ER, where it binds to the SRP receptor in the ER membrane. The translocator (Sec61) transfers the growing polypeptide chain across the membrane, SRP receptor and SRP are released and will be recycled. 

Q:

How and why do cis-double bonds in the acyl-chains of membrane lipids influence the transition temperature of the membrane?

A:

Transition temperature is the temperature where the lipid membrane changes from a liquid state to a crystalline or gel state. 

The double bond will not allow the acyl-chain to rotate, the kink formed by the double bond is fixed, and this means that the chain will occupy a larger volume within the monolayer, meaning that the membrane is more difficult to pack, allowing the membrane to stay fluid at much lower temperatures. A cis-double bond therefore greatly decreases the transition temperature of the membrane. 


This can be seen when imaged by light microscopy, two different lipids compared at 22°C, whereby one forms a para-crystalline structure (no cis-double bond, e.g. Palmitate/Stearate (16:0, 18:0 PC) – tt 49 °C) and the other is liquid (contains cis-double bond, e.g. Palmitate/Oleate (16:0, 18:1 PC) – tt -2 °C).


Also good example: Margarine is made from vegetable oil by chemically saturating the unsaturated fatty acid chains.

Q:

Welches Enzym hilf bei der Faltung von falsch gefalteten Proteinen?

A:

The ER-membrane-bound chaperone protein calnexin binds to incompletely folded proteins containing one terminal glucose on N-linked oligosaccharides, trapping the protein in the ER. Removal of the terminal glucose by a glucosidase releases the protein from calnexin. A glucosyl transferase is the crucial enzyme that determines whether the protein is folded properly or not. Glycosyl transferase binds to hydrophobic patches on the surface of misfolded proteins. If the protein is still incompletely folded, the enzyme transfers a new glucose from UDP-glucose to the Nlinked oligosaccharide, renewing the protein’s affinity for calnexin and retaining it in the ER. The cycle repeats until the protein has folded completely.

Mehr Karteikarten anzeigen
Q:

Wie unterscheiden sich ER- und Plasmamembran?

A:

The membrane of the ER compared to the membrane of Golgi or the PM is quite different. The ER membrane is the thinnest, then comes Golgi and the PM is the thickest. This is because cholesterol and Sphingolipids are added in the Golgi. The PM is supposed to be sturdy to protect the cell from everything on the outside. Since the PM is thicker than the ER and Golgi membranes, proteins with longer transmembrane domains tend to be localized in the PM. Each lipid has a negative charge, but phosphocholine and phosphatidylethanolamine have a positive charge, which results in a more positive net charge. Therefore, the ER has very little negative charge, the Golgi a bit more and the most charged membrane is the PM. The ER is symmetrical, which means the lipid composition in the luminal side and the cytosolic side is identical. The PM is asymmetrical, negative charged lipids are in the cytosol and glycosylated lipids are facing the cell surface. This asymmetry is mediated by the Golgi.

Q:

Wie kann man experimentell feststellen, dass eine Signalsequenz auf einem Protein sowohl notwendig als auch ausreichend für dessen Lokalisation ist?

A:

The protein of interest will be tagged with Green Fluorescent Protein and transported into a cell, so the localization of the protein inside the cell can be followed. To prove that the signal sequence is necessary for the localization first a protein with GFP and with the signal sequence will be observed, and it will go to its destination. Then a GFP labelled protein without the signal sequence will be observed. This protein stays in the cytosol, and it proves that the signal sequence is necessary for the correct localization. In another set of experiments we’d put the signal sequence on a cytosolic GFP labelled protein, which will go to the respective organelle associated with the signal sequence. This proves that the signal sequence is also sufficient for localization.

Q:

Protein import into Peroxisomes?

A:

Peroxisomes consist of a single membrane and mediate beta-oxidation and detoxification. The signal for import into peroxisomes is a C-terminal SKL motif. During de novo formation of peroxisomes, two different classes of ER- and mitochondrial derived vesicles fuse. Only after fusion an active translocon is assembled that mediates the transport of proteins into newly made peroxisomes. Later on, peroxisomes can multiply by division. 

The signal for import into peroxisomes is a C-Terminal SKL motif, which will be recognized by cytosolic receptor proteins. Numerous proteins called peroxins participate in the import process which is driven by ATP hydrolysis. A complex of peroxins forms a translocator which transports the protein into the nucleus. These translocator pores are huge and dynamic, the cargo protein doesn’t have to unfold to go through.

Q:

Almost all proteins are synthesized in the cytoplasm yet many end up in other parts of the cell. What is the general principle that directs proteins to their correct destination? Illustrate said principle using an example.

A:

Although Mitochondria and chloroplasts contain their own DNA, ribosomes, and other components required for protein synthesis, most of their proteins are encoded in the cell nucleus and imported from the cytosol. Each imported protein must reach the particular organelle subcompartment in which it functions. Proteins imported into mitochondria are usually taken up from the cytosol within seconds or minutes of their release from ribosomes. Mitochondrial proteins are fist fully synthesized as mitochondrial precursor proteins in the cytosol and then translocated into mitochondria by a posttranslational mechanism. One or more signal sequences direct all mitochondrial precursor proteins to their appropriate mitochondrial subcompartment. The signal for import into the mitochondrial matrix is N-terminal amphipathic helix that contains positively charged amino acids on one face and negatively charged amino acids on the other face. The signal sequence is rapidly removed after import by a signal peptidase. The signal sequences are both necessary and sufficient for the import and correct localization of the proteins. Multisubunit protein complexes that function as protein translocators mediate protein movement across mitochondrial membranes. The TOM complex transfers proteins across the outer membrane, and two TIM complexes (TIM23 and TIM22) transfer proteins across the inner membrane. The TOM complex is required for the import of all nucleus-encoded mitochondrial proteins. It initially transports their signal sequences into the intermembrane space and helps to insert transmembrane proteins into the outer membrane. β-barrel proteins, which are particularly abundant in the outer membrane, are then passed on to an additional translocator, the SAM complex, which helps them to fold properly in the outer membrane. The TIM23 complex transports some soluble proteins into the matrix space and helps to insert transmembrane proteins into the inner membrane. The TIM22 complex mediates the insertion of a subclass of inner membrane proteins, including the transporter 5 that moves ADP, ATP, and phosphate in and out of mitochondria. Yet another protein translocator in the inner mitochondrial membrane, the OXA complex, mediates the insertion of those inner membrane proteins that are synthesized within mitochondria. It also helps to insert some imported inner membrane proteins that are initially transported into the matrix space by the other complexes.

Q:

Oligosaccharide die im ER an Proteine angehängt werden, wie wirken sie sich auf die Faltung aus?

A:

The glycosylation is done by an enzyme called oligosaccharyl-transferase and it attaches a preformed precursor oligosaccharide to the NH2 group of an asparagine that’s why it’s called N-linked protein glycosylation.

Oligosaccharides are used as tags to mark the state of protein folding. Some proteins require N-linked glycosylation for proper folding in the ER, yet the precise location of the oligosaccharides attached to the proteins surface does not seem to matter. The ER-membrane bound chaperone protein Calnexin binds to incompletely folded proteins containing one terminal glucose on the N-linked oligosaccharides, trapping the protein in the ER. Removal of the terminal glucose by a glucosidase releases the protein from calnexin. A glucosyl transferase is the crucial enzyme that determines whether the protein has folded properly or not: if the protein is still incompletely folded, the enzyme transfers a new glucose on it, renewing the proteins affinity to calnexin. The cycle repeats until the protein has folded completely. Glucosyl transferase binds to hydrophobic patches on the surface of misfolded proteins.

Q:

Wie können Proteine Membrane beugen?

A:

Proteins can change the composition of the acyl chain and head group. The membrane gets curved if the composition of one layer of the bilayer is changed. • Membrane proteins are able to oligomerize, which has an effect on the curvaton of the membrane. • Cytoskeleton: Actin as a molecular motor can induce the tube formation. • Scaffolding: There are direct and indirect scaffolds, which are linked to the membrane and are able to bend the membrane. • Through dimerization (banana-shaped), BAR-Domains are able to change the structure of a membrane by electrostatic interaction. • Insertion of an amphipathic helix into the membrane has an effect on membrane curvaton.

Q:

What are the steps in the formation, targeting and fusion of vesicle mediated transport? Describe briefly in words or use a schematic.

A:

The general steps of vesicle mediated transport:

  1. Cargo needs to be enriched in a patch of the membrane
  2. This patch of membrane undergoes budding
  3. The vesicle is separated from the donor compartment by a scission reaction
  4. The coat disassembles
  5. The transport vesicle is targeted and tethered to its target compartment
  6. The vesicle is brought into close proximity to the target membrane (docking)
  7. The vesicle fuses with its target compartment

Molecular machinery for vesicular transport:

  • Cargo concentration and budding: coat proteins and adaptor proteins
  • Scission: GTPases
  • Targeting and tethering: rab proteins and tethering factors
  • Fusion: SNARE proteins
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