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BIOL-3221 > Chapter 8 > Flashcards

Chapter 8 Flashcards

1
Q

What is the endomembrane system and what does it include

A
  • A network of membrane-bound organelles that function together to transport, process and sort things in the cell
  • ER, Golgi, endosomes, lysosomes and vacuoles
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2
Q

Why are chloroplasts and mitochondria not part of the endomembrane system?

A
  • They fxn independently, possess their own DNA and are not interconnected with the membrane trafficking system
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3
Q

How are materials packaged for transport in the endomembrane system

A
  • In small vesicles that bud off donor compartments, transported by motor proteins and fuse with the acceptor component
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4
Q

What is the role of motor proteins in vesicle transport

A
  • Kinesins and Dyneins move vesicles along microtubules for precise delivery to target locations
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5
Q

What is the difference between biosynthetic and secretory pathways

A
  • Biosynthetic pathway = involves protein and lipids synthesis in the ER, modification in the golgi and transport to various destinations
  • Secretory pathway = discharge of synthesized proteins to the cell surface
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6
Q

Describe the process of constitutive secretion

A
  • Involves the continuous transport of materials in secretory vesicles to the cell surface
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7
Q

What triggers regulated secretion and what it is the difference between constitutive (CS)?

A
  • Requires an external signal (hormones, digestive enzymes neurotransmitter) to trigger the release of stored materials and CS does not
  • Occurs in endocrine cells, pancreatic acinar cells and nerve cells
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8
Q

The function of sorting signals in the biosynthetic pathway

A
  • they are amino acid sequences that ensure proteins and lipids are delivered to the correct place with destination-specific information
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9
Q

How does the release of neurotransmitters (regulated secretion) relate to [Ca2+]?

A
  • This is triggered by an increase in [Ca2+] stimulating vesicle fusion with the plasma membrane
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10
Q

Why are secretory granules importing in endocrine and nerve cells?

A
  • They store hormones, enzymes or neurotransmitters so they release them with specific stimuli
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11
Q

What is autoradiography? how is it used to study the endomembrane system

A
  • It involves using radioactively labeled molecules to visualize and track biochemical processes
  • Labeled aa’s were sent into pancreatic enzymes to trace their synthesis and transport (P and J)
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12
Q

What is the purpose of the “pulse-chase” experiment

A
  • It identifies the pathway of secretory proteins by tracking their movement after being exposed to labeled aa’s (pulse) to see their site of synthesis and discharge
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13
Q

How does GFP-tagging help visualize protein movement in living cells?

A
  • GFP (green fluorescent protein) tagging involves attaching a fluorescent GTP to a protein to see its movement in living cells.
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14
Q

What is the role of vesicular stomatitis virus (VSV) in protein movement

A
  • The virus has a GTP-tagged viral gene to express GTP and hijack the host cell machinery for protein synthesis
  • GTP is useful bcos its non-toxic, it integrates well with viral proteins, and it can fluoresce without assistance
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15
Q

What is the purpose of cell homogenization in studying the endomembrane system

A
  • It breaks cells open to release their contents while preserving subcellular organelles.
  • You can isolate ER or golgi for analysis
  • Differential centrifugation separates cellular components based on their size/density.
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16
Q

How are microsomes formed

A
  • Small fragments from the ER when cytoplasmic membranes are disrupted during homogenization
  • Smooth microsomes from smooth ER and rough ones are from the rough ER
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17
Q

What is density gradient centrifugation

A
  • Separating organelles/vesicles based on their buoyant density by spinning in something of increasing density. This is for precise isolation
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18
Q

What is the structure and primary function of the endoplasmic reticulum (ER)

A
  • It is a network of interconnected membranes that are involves in protein synthesis, lipid metabolism, Ca2+ storage etc
  • Rough and smooth ER
  • Cisternae make up the rough ER by providing surface area for ribosomes to attach
  • Lumen specializes in protein folding, modification and storage
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19
Q

What is the difference between smooth and rough ER

A
  • RER: It has ribomses on its cytosolic end and flattened sacs (cisternae) and is responsible for synthesizing membrane-bound and secretory proteins. The starting point of the biosynthetic pathway
  • SER: no ribosomes and tubular membranes. Used for lipid and steroid hormone synthesis, detoxification (cyt P450) and Ca2+ storage.
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20
Q

Explain the synthesis of proteins in the RER

A
  • Secretory proteins have aa’s on the n-terminus of the polypeptide with a signal sequence directing it to the cisternae
  • This is co-translational translocation by the signal sequence and the translocon channel
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21
Q

Protein synthesis on free ribosomes

A
  • The ribosome has mRNA and tRNA
  • SRP binds to the ribosome to stop translation till it reached the ER membrane
  • SRP binds to its receptor which allows the ribosome to be associated with the translocon with the peptide binding to its interior
  • Translocon gets unplugged and the peptide gets translocated through the membrane cotranslationally to undergo folding with a chaperone (BiP)
  • GTP hydrolysis triggers peptide cleavage by the SRP
  • Lysosomes/vacuoles are synthesized by membrane-bound ribosomes of the RER.
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22
Q

What role does the signal recognition particle (SRP) play in protein targeting

A
  • Binds to the nascant peptide to halt translation temporarily.
  • Guides the ribosome-peptide complex to the translocon to resume translation and the protein enters the ER
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23
Q

Why is GTP hydrolysis important for protein trafficking in the RER

A
  • This is caused by SRP and its receptor and it provides energy to release the complex to the translocon
24
Q

What is glycosylation

A
  • Post-translational enzymatic addition of sugars to proteins, happens in the ER.
  • Glycosyltransferases are enzymes that catalyze the addition (specialized to transfer a specific monosaccharide)
  • N (Nitrogen + sugar glucosamine) and O-linked (Oxygen + sugar galacatosamine) glycosylations
25
Q

What is the quality control mechanism for glycoproteins in the RER

A
  • This ensures that only correctly folded glycoproteins go through the secretory pathway
  • Misfolded ones remain in the ER and are tagged for degradation (ERAD)
26
Q

Explain the glycosylation process in the RER

A
  • Sugars are attached to dPP in the cytosol and they’re flipped into the RER lumen
  • more sugars are attached one at a time to form an oligosaccharide with glc, mannose and N-acetylglucosamine (NAG)
  • The oligosaccharide is transferred to the Asn on the nascent polypeptide
27
Q

What is the unfolded protein response (UPR)

A
  • It is a cellular stress response that is activated by the accumulation of misfolded proteins in the ER. (two pathways)
    1
  • The sensors are associated with BiP and are inactive
  • When the # of misfolded proteins increase, BiP goes to help with folding and sensors are activated = PERK (kinase)
  • PERK phosphorylates a translation factor that is needed for protein synthesis which stops initiation
  • This gives more time for processing proteins
    2
  • The release of BiP allows an unbound sensor to go to the golgi where it cleaves the cytosolic domain of the sensor
  • This sensor diffuses thru cytosol to the nucleus where it allows the expression of genes = proteins that reduce ER stress
28
Q

What is the difference between the cis GN and the trans GN

A
  • CGN: faces the ER and sorts proteins for either recycling to the ER or forwarding to the golgi
  • TGN: faces the plasma membrane and is responsible for sorting proteins to their final destinations
29
Q

Describe vesicular transport model and the cisternal maturation model

A
  • Vesicular: Cargo moves between static golgi cisternae by vesicles
  • Cisternal: the golgi cisternae mature, moving from cis to trans while carrying cargo
30
Q

How do coated vesicles facilitate transport between compartments

A
  • (COPI, COPII or clathrin-coats)
  • Provide structural support for vesicle formation and recruit cargo molecules for transport
31
Q

What are the differences between the COPI, COPII and clathrin-coated vesicles?

A
  • COPI: Transport materials form the ER to the golgi (forward - anterograde transport)
  • COPII: Transport materials form the golgi to the ER from trans to cis golgi cisternae (backward - retrograde transport
  • Clathrin-coated: They move materials from the TGN to endosomes and lysosomes
32
Q

Explain the roles of COPII coat proteins

A
  • COPII proteins interact with ER export signals and cargo molecules to initiate vesicle formation
  • Inactive Sar1 (bound to GDP) is recruited by GEF (guanine exchange factor) on membrane by replacing GDP for GTP = active Sar1
  • This activated protein gets incorporated into the membrane = curving
  • It recruits other protein coats = more curving and vesicle formation.
33
Q

What is ERGIC

A
  • The Endoplasmic Reticulum-Golgi Intermediate Compartment
  • Facilitates the sorting and transport of vesicles between the ER and the golgi
34
Q

How are escaped proteins transported back to the ER

A
  • the escaped molecules are retrieved back to their normal compartments, retention of resident molecules are excluded from transport vesicles
  • Resident proteins have retrieval signals at their C-terminus, they’re captured and brought to the ER in COPI-coated vesicles
35
Q

What is the role of mannose-6-phosphate (M6P) in protein sorting

A
  • M6P is a molecule address tag that makes sure lysosomal enzymes are packaged and sent to lysosomes
  • Their receptors (MPRs) recognize them and direct the enzymes to clathrin-coated vesicles for their delivery to lysosomes
36
Q

Explain the process of vesicle fusion with target compartments

A
  • This involves tethering proteins bring the vesicles close to their target membranes (microtubules and motor proteins), then SNARE proteins of both membranes interact to facilitate the lipid bilayers merging = cargo delivery
37
Q

What is the function of SNARE proteins in vesicle formation

A
  • They mediate vesicle docking and fusion by forming tight complexes between the vesicle and targent membranes
  • v-SNARES are found in transport vesicles and t-SNARES are found in the target compartment
38
Q

What triggers the process of exocytosis in cells

A
  • This is triggered by and increase in intracellular [Ca2+]. The Ca2+ influx activates the proteins that mediate vesicle fusion with the membrane
  • Contacts btw the vesicle and plasma membranes = fusion pore (temp. opening at the plasma-vesicle interface allowing contents to be released to the ECM)
39
Q

t- and v-SNARES

A
  • The plasma membrane has two t-SNARES (syntaxin and SNAP-25)
  • The synaptic vesicle membrane hand one v-SNARE (synaptobrevin)
  • They interact to form Four-stranded bundles that are parallel, they zip to form a complex that pulls the two bilayers closer
40
Q

What types of enzymes are found in lysosomes

A
  • They have hydrolytic enzymes (proteases, lipases) that peak down proteins. Function well in acidic environment to degrade macromolecules
41
Q

Explain the process of autophagy

A
  • It involves encapsulating damaged organelles/proteins in a double membrane vesicle (autophagosome) which fuses with a lysosome for degradation (autolysosome)
  • It helps to protect an organism agains intracellular threats and prevents aging and prevention of some cancers
42
Q

What are the storage functions of plant cell vacuoles

A
  • They store water, solutes, macromolecules and toxic compounds creating turgor that keeps the cell rigid
  • They’re resorvoirs for enzymes involved in metabolism
43
Q

How does the tonoplast regulate ionic concentration within the vacuole

A
  • Has active transporters that pump ions into the vacuole, creating an electrochemical gradient that draws water into the vacuole by osmosis
44
Q

What is phagocytosis, what cells specialize in it

A
  • The process of engulfing large particles into vesicles called phagosomes which then fuses with a lysosomes = phagolysosome
  • Macrophages, neutrophils
45
Q

What is the difference between receptor-mediated endocytosis (RME) and bulk-phase endocytosis

A
  • RME: selectively internalizes specific macromolecules on the membrane = clathrin-coated proteins
  • Bulk-phase: (Pinocytosis), nonspecifically takes up ECF and solutes
46
Q

How do clathrin-coated pits facilitate endocytosis

A
  • They form specialized regions on the membrane where receptors bind to ligands, the pits invaginate = vesicles to deliver cargo to endosomes
  • Dynamin (G-protein) needed for the fission of the vesicle from the membrane, inhibit GTP hydrolysis and fission wont occur
47
Q

What is the role of adaptors (AP2) in selecting cargo for endocytosis

A
  • These adaptors link clathrin to the cytoplasmic tails of receptors, selecting specific astro for inclusion in clathrin-coated vesicles
  • 4 subunits
48
Q

What is a triskelion

A
  • It is a three-legged clathrin structure that assembles into a lattice to drive membrane curvature and vesicle formation
49
Q

LDLS

A
  • Low-density lipoproteins (LDLs) have cholesterol ad proteins
  • Their receptors are transporter to the membrane an bound to a coated pit
  • These are taken up by RME to the lysosomes to realize their cholesterol
50
Q

How does protein targeting differ between the ER and other organelles like mitochondria

A
  • Proteins for the ER are translocated co-translationally, with ribosomes attached to the membrane
  • Proteins targeted for mitochondria are synthesized in the cytosol and imported post-translationally, guided by specific signal sequences
51
Q

Explain how protein are imported into peroxisomes

A
  • Proteins for the peroxisomes have specific PTS that are recognized by cytosolic receptor proteins to guide the protein to the peroxisome& facilitate their translocation across the membrane
52
Q

Explain protein import into a mitochondrion

A
  • A protein that is targeted to the mitochondria bcos of N-terminus sequence gets unfolded by a chaperone which allows it to go through the TOM complex into the outer mitochondrial membrane
  • The protein is directed to the TIM complex into the matrix where it either gets bound to a chaperone to unfold it and cleave its pre sequence enzymatically or it assumes its native unfolded conformation by itself
53
Q

What is the difference between between a TOM and TOC complex

A
  • TOM: a complex responsible for recognizing and importing mitochondrial proteins across the outer membrane
  • TOC: a complex responsible for recognizing and importing proteins across the outer chloroplast membrane
54
Q

How is RNA interference used to study gene expression

A
  • RNAi uses small interfering RNAs to bind to mRNA, leading to their degradation, this allows to study specific genes by silencing others
55
Q

What is the role of siRNAs in identifying genes involved in secretion

A
  • siRNAs target and silent genes potentially involves in secretion pathways, the roles of the genes are then analyzed
56
Q

What is the structure of Clathrin

A
  • Outer lattice of clathrin
  • Inner shell of GGA adaptor proteins interacting with M6P, G-proteins and clathrin
  • G-protein Arf-1

BIOL-3221 (6 decks)

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