Intracellular Compartments, Membrane Trafficking and Protein Signaling

Question 1

What kind of processes occur in the Eukaryotic cell to transport materials in and out of cell? What do these processes require?

Answer 1

Endocytosis- move materials inside cell and Exocytosis- move materials outside of cell
Both processes require cargo sorting

Question 2

Explain the reason why eukaryotic cells cannot simply use molecular transporters alone for transporting substances across cell membrane, and mention what solutions can help this issue.

Answer 2

Eukaryotic cells have lower surface to volume ratio and using only molecular transport is not efficient to transport substances across membrane.
Hence eukaryotic cells have evolved to acquire extracellular material in large bulk quantities by trapping outside content in PM pits so that engulfed material is isolated in TRANSPORT VESICLES before being transported inside cell.
Material needs to be SORTED OUT before processed in cell.

Question 3

What membrane enclosed compartment functions in major sorting of endocytosed material or components in cell?

Answer 3

Endosomes.

Question 4

What are the functions of the membrane enclosed organelles: Cytosol, nucleus, endoplasmic reticulum, golgi appartus, lysosome, mitochondria, choloroplast, peroxisomes?

Answer 4

Cytosol- contains many metabolic pathways; site of protein synthesis; cytoskeleton
Nucleus- contains main genome; DNA and RNA synthesis
Endoplasmic Reticulum- synthesis of lipids, proteins for distribution to many organelles and to PM.
Golgi- modification, sorting, packaging of proteins and lipids for either secretion or delivery to another organelle.
Lysosome- intracellular degradation
Mitochondria- ATP synthesis by oxidative phosphorylation
Chloroplasts- ATP synthesis and carbon fixation by photosynthesis
Peroxisomes- oxidative breakdown of toxic molecules.

Question 5

How do cell organelles or compartments exchange material in the cell? How is it controlled,

Answer 5

Through vesicular transport.
Vesicular transport is controlled, as transport vesicles of a certain type are SORTED from the rest of the vesicles and are targeted to exact membrane they should fuse with.

Question 6

Where are all proteins synthesized in the cell?

Answer 6

Cytosol

Question 7

Who was Gunter Blobel and what did he discover? How was this important in using methods to study intracellular protein transport?

Answer 7

Blobel was a biologist who discovered signal hypothesis in 1999; discovered that proteins had intrinsic signals that would govern their transport and localization in the cell.
Methods used to study intracellular protein transport:
had radioactively labeled proteins with signal sequence and free proteins (no signal) and isolated organelle, transport occurs, and only protein with signal is imported into isolated organelle, centrifugation, when adding protease, free protein without signal degraded, protein with signal co-sediments with organelle.

Question 8

Describe the scientists and methods used to study secretory pathways.

Answer 8

Shekman, Sudhoff and Rothman discovered machinery of how cells transport major molecules in a cargo system and delivers them at the right place, at the right time. They also experimented through trials, to prove proteins did not accumulate in ER, Golgi or transport vesicles, but they were SECRETED and released through secretory vesicles.
Scientists found:
genes required for vesicle traffic, machinery that allows vesicles to fuse with their target to permit transfer of cargo, signal directs vesicles to release cargo with precision.
How cells organize system to transport molecules within cell and outside of cell. (ER to Golgi vesicles, to secretory vesicles to cell surface outside cell.

Question 9

Differentiate between the 2 processes endocytosis and exocytosis? which process does fusion of vesicles , while which does budding of vesicles?
Also, which 2 organelles do not have the same mechanism of vesicular transport and exchange of material between intracellular membrane compartments as most organelles.

Answer 9

Exocytosis- FUSION of vesicle with membrane to release contents out of cell
Endocytosis- BUDDING OF vesicle to allow cellular content into the cell.

MITOCHONDRIA AND CHLOROPLASTS do not have the same vesicular transport and material exchange mechanism as other organelles. This is because they evolved differently than any other organelles. (symbiosis, engulfing).

Question 10

What makes a vesicle different from an organelle.

Answer 10

Organelle are permanent, and vesicles are transient

Question 11

What is the most extensive network in the eukaryotic cell?

Answer 11

The Endoplasmic reticulum

Question 12

Differentiate between the Smooth and rough ER, in terms and structure and function.

Answer 12

Rough ER- has ribosomes, elongated sacs (LAMELLAS) are abundant in each cell (especially those use secretion like pancreatic cells) and easily distinguished from other cells. Function: protein synthesis
Smooth ER- without ribosomes; narrow appearance of tubules, makes it hard to distinguish morphologically from other microsomes and transport vesicles.
Function: LIPID BIOSYNTHESIS, including synthesis of CHOLESTEROL and PHOSPHOLIPIDS

Question 13

What are additional functions of Smooth ER and describe the kind of cells ER are well-developed in?

Answer 13

Additional functions of Smooth ER: synthesis and breakdown of GLYCOGEN. CALCIUM STORAGE, DETOXIFICATION of lipid-soluble drugs and toxins including alcohol.
Smooth ER is present in every cell but well-developed in specialized cells like:
1. cell that specialize in metabolism, like STEROID hormone synthesis (GONADAL Cells)
2. hepatocytes where glycogen is stored and then broken down
3. muscle cells- that have specialized smooth ER called SARCOPLASMIC RETICULUM, a major storage of calcium, which release triggers contraction of muscle fibers.

Question 14

Explain what directs Ribosomes to the ER and the entire process of how it is achieved.

Answer 14

ER signal and Signal-recognition particle (SRP) directs ribosomes to the ER.

process:
1. As soon as ER signal emerges, SRP (signal recognition particle) will bind both the signal sequence and ribosome, slowing down (halting) translation.
2. After SRP finds its receptor, the synthesized polypeptide is transferred to PROTEIN TRANSLOCATOR and translation resumed.
3. During synthesis, N-terminus remains attached to translocator.

Question 15

What allows for soluble ER protein to be released into ER lumen and how does this occur?

Answer 15

Signal peptidase releases soluble ER protein into ER lumen.
at some point, N-terminal ER signal will be cut off or by specialized SIGNAL PEPTIDASE that cleaves new polypeptide downstream the signal.
threading of synthesized polypeptide continues until protein falls off through the membrane of rough ER.

Question 16

What is Dolichol Phosphate and what is it used for?

Answer 16

Dolichol phosphate is a polyisoprenoid that’s a donor of glycosyl group in ER.
it is used to carry activated sugars in the membrane associated synthesis of glycoproteins, polysaccharides.

Question 17

What is the role of chaperones in the ER? What specific feature do they recognize and how does it differ from what’s normal?
Where are folding of both membrane and soluble proteins controlled?

Answer 17

Chaperons prevent misfolded or partly assembled proteins from leaving ER.
ER CHAPERONES recognize hydrophobic moieties of IMPROPERLY FOLDED proteins together with their characteristic oligosaccharides
In properly folded proteins- hydrophobic patterns should be BURIED inside HYDRROPHOBIC CORE.
The folding of both membrane-bound and soluble, secreted proteins are controlled in ER.

Question 18

where is the Golgi located and why are they important in transport of proteins? What kind of organelle is GOLGI, and what other structures does it have.

Answer 18

Golgi is located between ER and Cell periphery.
GOLGI APPARATUS- FINAL destination (through vesicles) of proteins prior to their excretion or delivery into organelles.
Golgi- polar organelle; Cis face, entry network, cisternae, trans face, exit, network

Question 19

What is the unfolded protein response?

Answer 19

Unfolded protein response activates a number of pathways to prevent further clogging of ER.
It will activate chaperone genes and other genes (sensors, transcription regulators) that increase protein-folding capacity of ER.

Question 20

What are the three mechanisms proteins are transported into organelles (specify which organelle uses particular transport) ?

Answer 20

1. Transport through NUCLEAR PORES-
   -fully synthesized and FOLDED proteins move through large pores in NUCLEUS.
2. Transport across membranes using TRANSLOCASES
   -fully synthesized UNFOLDED polypeptides transported through membranes and fold inside organelles How MITOCHONDRIA PEROXISOMES, and CHLOROPLASTS receive proteins.
   This is mechanism for how both soluble and membrane proteins for mitochondria and chloroplast are transported.
3. Transport by VESICLES
   -MEMBRANE BOUND (enclosed, secreted, or integrated) proteins are anchored at the membrane of ER at beginning of their synthesis and then special translocase system (TRANSLOCATOR) will move them into ER. (used by organelles part of endomembrane- Golgi, ER, endosome)
   all mitochondria-encoded proteins are membrane-integrated proteins.

Question 21

What mediates membrane fusion?

Answer 21

SNARE Proteins

Question 22

What is key component of phosphatidylinositol phosphates?

Answer 22

Omega-3

Question 23

What three steps are involved for membrane fusion?

Answer 23

Vesicle TETHERING, DOCKING, and FUSION

Question 24

What is used to synthesize all proteins encoded by nuclear genome?

Answer 24

common pool of ribosomes (made of both membrane bound ribosomes and free ribosomes)

Question 25

Distinguish between synthesis of cytosolic proteins vs membrane bound proteins. What kind of ribosomes do cancer cells have and how does the need for soluble and membrane proteins vary in cells. Explain what a Nissl body is.

Answer 25

Cytosolic proteins- synthesized by free, unattached polyribosomes (protein with no ER signal sequence)
Membrane bound proteins- polyribosome is bound to ER as (proteins has ER signal sequence, targeted to ER)
Cancer cells (poorly differentiated, fast dividing), that have limited surface contacts have lots of free, cystolic ribosomes.
need for soluble and membrane proteins vary in cells. Some cells normally require lots of the 2 proteins. EX: NEURONS need it. NISSLE STAINING for ribosomes color the entire neuronal cell body inside (used to be called NISSLE body, or NISSLE SUBSTANCE

Question 26

What determines the way polypeptides are delivered into the organelles? How are membrane proteins delivered?

Answer 26

The way polypeptides are delivered into organelles is based on their origin
Membrane proteins are synthesized next to the place they will be used and are intercalated into membrane while they are synthesized (at the same time)

Question 27

Describe the kind of genetic apparatus mitochondria have and how many proteins are mitochondrial-encoded. Also describe how the rest of mitochondrial proteins are encoded and how it relates to chloroplast proteins.

Answer 27

Mitochondria still retains their bacteria like genetic apparatus (circular genome, bacteria-type tRNAS, rRNAs, ribosomes).
Mitochondria only encode 13 polypeptides and all of the mitochondria-encoded proteins are membrane-integrated proteins.
Rest of mitochondrial proteins (1500) are encoded in Nuclear genome and delivered into organelles by bacteria-type translocation mechanism CHLOROPLAST proteins are synthesized in the same way
most chloroplast and mitochondrial proteins encoded by nuclear genes, synthesized on cytosolic ribosomes, and imported through translocases into organelles.

Question 28

What is the function of organelle-targeting signals in proteins?

Answer 28

Each signal sequence of a protein will dictate where the protein will be imported and what organelle it will be transported to. (ex: signal sequence to import proteins into ER will contain many Glutamine, and alanine amino acid, or hydrophobic aa). signal sequence differs for each destination organelle (nucleus, mitochondria, ER, peroxisomes).

Question 29

What can change the protein destination site? How can this be predicted? How is this confirmed?

Answer 29

by adding or deleting signal sequences, it can change protein destination site (can be internal, or termini, widely used in genetic engineering).
The signals can be predicted by computer sequence analysis and prediction rate which may vary depending on complexity of signal. Signals have to be EXPERIMENTALLY Confirmed.

Question 30

What kind of molecules does the nuclear pore complex allow to enter or exit nucleus?

Answer 30

Only allows selected macromolecules and large macromolecules to enter and exit the nucleus.

Question 31

Describe how imported proteins, signals and receptors are used to import proteins into nuclear pore.
What kind of receptors are used for Nuclear export and import receptors?

Answer 31

Nuclear import receptor proteins interact with cytosolic fibers and allow proteins with nuclear localization signals to enter nuclear pore. They enter pore through meshwork that prevents other proteins from entering nucleus.
Nuclear Export and Nuclear Import receptors are SOLUBLE RECEPTORS , that work by similar mechanism.
import proteins have signal that is recognized by nuclear import receptor.

Question 32

What process ensures unidirectional nuclear transport? How does this occur?

Answer 32

GTP hydrolysis ensures unidirectional nuclear transport.
small GTPASES like RAN can provide the energy of GTP hydrolysis to drive nuclear transport in the appropriate direction.
ACCESSORY PROTEINS that cannot cross the pore can make RAN PROTEIN exchange GDP to GTP or make RAN-GTP hydrolyze GTP, liberating the receptor and ensuring unidirectional transport.

Question 33

Differentiate between the 2 confirmation of Ran protein and describe the the things that help Ran covert between these 2 structures.

Answer 33

Ran has 2 confirmations: one carrying GTP (high [} in nucleus) , other carrying GDP.
accessory proteins help RAN convert between these two confirmations.
Accessory proteins:
- RAN-GAP(GTPASE activating Proteins) - triggers GTP hydrolysis (convert ran-gtp to ran-GDP), RAN GAP is in cytosol
-RAN-GEF (Guanine nucleotide exchange factor)- causes ran-GDP to release its GDP and uptake GTP is.
RAN GEF- found in nucleus.

Question 34

Differentiate between the signals for proteins to be imported in nucleus vs exported from nucleus.

Answer 34

import into nucleus- positively charged Lys and arginine residues (pro and val too)
Export from nucleus- hydrophobic aa, like Leu and Met, Phe, ser, gln)

Question 35

Describe the complex process of sorting mitochondrial proteins and also list the two major translocases of mitochondrial transport. What happens to import in mitochondrial signal after protein is imported and folded?

Answer 35

Majority of mitochondrial proteins are nuclear-encoded, synthesized in cytosol
5 known pathways of mitochondrial protein transport that each target either inner/outer membranes, between membrane space, or matrix.
The major translocases are Translocase of outer membrane (TOM) and translocase of inner membrane (TIM) protein complexes.
Import in mitochondrial signal (Mitochondria-targeting peptide
)- sequence is usually strong, positively charged/hydrophobic alpha helix that is REMOVED after protein is imported and folded.

Question 36

Explain how a single-pass membrane protein is retained in ER, and be sure to include how this process works. Also describe the components of single-pass protein and what will happen to polypeptide if certain signal is passed through translocator.

Answer 36

Single pass membrane protein is retained in ER by stop-transfer signal.
in addition to N-terminal ER signal(which is essentially Start transfer signal), new single pass protein has INTERNAL HYDROPHOBIC motifs that acts as a Stop-transfer signal.
passing of stop-transfer sequence through translocator will cause dissociation of protein translocator from polypeptide and anchor transmembrane domain into the membrane.
N-terminal signal is CLEAVED OFF by Signal PEPTIDASE

Question 37

what differentiates the double-pass membrane protein from single-pass membrane protein?

Answer 37

Double pass membrane proteins has INTERNAL ER SIGNAL (start-transfer signal).
Similar to N-terminal ER signal, translocator is capable of recognizing and binding the internal start-transfer signal.
Internal signal NEVER gets cleaved by signal peptidase since the enzyme can only cleave protein at N-terminus.
hence even after stop-transfer signal reach translocator and discharges polypeptide, the start-transfer and stop-transfer signal will be retained) polypeptide remain anchored to domain of ER membrane.

Question 38

What is the purpose of multi-pass membrane proteins and what kind of signals do they have?

Answer 38

Multi-pass proteins have pairs of sequential internal (repetitive pattern) start-transfer and stop-transfer signals that will keep being used over and over.
After the first pair is released, the translocator remains nearby and regain association with polypeptide as soon as next start-transfer shows up.

Question 39

What defines the position of N- and C- termini across the membrane? How does translocator pick up signal, and how does this affect the transmembrane proteins?

Answer 39

Orientation of the start and stop-transfer signals define where n and c termini are across membrane.
Translocator picks up signal in only upright orientation-
(+) faces cytosol and (-) faces lumen.
thus the orientation of loops between domains of multi-pass transmembrane proteins are directed by orientation of signal sequence (that can be flipped)
additional start-transfer, signal may also follow initial one.

Question 40

Where does protein glycosylation occur? what is role of the glycosylation in ER and what does it composed of?
Which are the only 2 cells who have N-linked glycosylation?

Answer 40

Protein glycosylation occurs in the ROUGH ER and GOLGI.
main role of glycosylation in ER is to have QUALITY CONTROL OF PROTEIN FOLDING.
In ER, glycosyl group is attached to NITROGEN at Asparagine (Asn) side chain amino group. Thus such glycosylation is is N-LINKED GYLCOSYLATION.
This is different from O-glycosylation (that attached sugar to OH of threonine or serine aa group and occurs in golgi).
Only Eukaryotes and Archaea have N-linked glycosylation.

Question 41

What are the major chaperone proteins involved in ER protein quality control cycle, and what occurs before the chaperone’s actions.

Answer 41

after N-linked oligosaccharide is trimmed to single glucose residue (1 and 6), chaperones CALNEXIN and CALRETICULIN recognizes the remaining glucose residue and help protein fold.

Question 42

Describe the two types of glycosylation in the cell in terms of their role where this process occurs.

Answer 42

N-linked glycosylation (N-glycosylation) occurs in ER. Role: assist in protein folding
O-linked glycosylation (o-gylcosylation)- occurs in GOLGI. role: TERMINAL FUNCTIONL GLYCOSYLATION.
in Golgi, N-linked oligosaccharides are modified, trimmed and new ones are added.
you can add sugars to transmem glycoprotein, adsorbed glycoprotein, glycolipid, transmem proteoglycan and mucin.

Question 43

proteins can enter peroxisomes from which two places?

Answer 43

from both the cytosol and endoplasmic reticulum.

Question 44

Where are soluble proteins made and released?

Answer 44

Soluble proteins made on ER and released into ER lumen

Question 45

what determines the arrangement of transmembrane protein in the lipid bilayer?

Answer 45

The start and stop signals.

Question 46

What controls the size of the ER? What occurs after proteins in ER are folded?

Answer 46

size of ER is controlled by demand for protein folding

after ER proteins are folded, they are further modified and sorted in the GOLGI.

Question 47

How are secretory proteins released from the cell

Answer 47

By exocytosis

Question 48

What happens to proteins in Golgi, before reaching final destination (into other organelles)?

Answer 48

Proteins will undergo additional O-glycosylation.

Question 49

what are the two types of exocytosis? Distinguish between the two, in terms of how the processes occur.

Answer 49

The two types of Exocytosis are Constitutive (unregulated) and Induced (regulated- or stimulation-dependent).
Constitutive Exocytosis- when worn out membrane components (lipids and housekeeping receptors) are replaced with freshly synthesized ones on a regular basis. Or, when membrane material is recycled back to PM from sorting compartment (early endosome) or returned from golgi to ER (after delivery of synthesized proteins) for further processing (glycosylation).
Regulated Exocytosis-secretory molecules are stably accumulated in secretory vesicles as storage sites (Responsive to external stimuli and specialized for secretion)

Question 50

Describe what occurs in stimulant dependent exocytosis in neurons?

Answer 50

In neurons, a stimulus or electrical signal will stimulate the functions of DOCKING and FUSION of synaptic vesicles. Synaptic vesicles will eventually fuse with membrane and release contents of vesicle (neurotransmitters) out of the cell into synaptic cleft.

Question 51

What are two major examples of regulated exocytosis?

How do exocytotic vesicles differentiate from other compartments on EM?

Answer 51

Secretion of insulin and adrenaline are 2 examples of regulated exocytosis.
On EM, the exocytotic vesicles (Secretory vesicles containing insulin) can be differentiated from other compartments by their proximity to cell surface (PM) and presence of cargo

ex: increase in blood glucose signals insulin producing cells in pancreas to secrete hormone. Also insulin that i destined for secretion, form aggregates that will be later be packaged in vesicles, for fusion, release.

Question 52

Describe how Exocytosis ensures proper transport of vesicles. What is a Rab protein and what is its specific role in vesicular transport? what other instruction is involved with Rab?

Answer 52

Exocytosis- highly regulated, multistep process that ensures that transport vesicles fuse with CORRECT membrane only.
Rab protein is a small GTPase that is recruited for TETHERING process of vesicular transport. They aid in tethering vesicles to target membrane
The tethering process involves synthesis of specific PHOSPHATIDYLINOSITOL PHOSPHATES on vesicular membrane that only recognized by certain Rabs.

Question 53

What are all of the specificity factors that make sure only the right membranes fuse with each other?

Answer 53

phosphatidylinositol phosphates and associated proteins, Rabs, tethering proteins and SNARES all mediate the direction of fusion between compartments and prevent their mistargeting.

Question 54

What is the important role of phosphatidylionositol phosphate (PIPS)? What is another way of ensuring specificity of membrane targeting.

Answer 54

They are signaling phospholipids that facilitate the recruitment of necessary Rab proteins.
Various PIPS serves as membrane RECOGNITION SITES for specialized RAB proteins.
Having a specific PHOSPHOINOSITIDE head (using PIP kinases and phosphatases) in a signaling will ensure specificity of membrane targeting and ID cellular membrane compartments (similar process in endocytosis).

Question 55

What kind of process if Membrane fusion? what specific proteins are involved and what must occur right before.

Answer 55

Membrane fusion is energy dependent. It is a tightly controlled process that does not occur spontaneously.
Following docking, SNARE PROTEINS directly drive the fusion of vesicle and target membranes

Question 56

how do SNARE proteins complete vesicle fusion? What structures are involved and what is the force needed?

Answer 56

Following vesicle docking, SNARE proteins catalyze the fusion of vesicle and target membrane.
V and T SNARE tangles rotate around each other, creating a force that brings the membranes together and ensures fusion.
This mechanical force created by SNARES pulls two lipid bilayers into close proximity, squeezing out nay water molecules that remain trapped between two membranes, and bypassing repulsion of lipid polar heads.

Question 57

What are the two major factors that Stimulation-dependent (regulated) exocytosis in chemical synapses depend on?

Answer 57

depend on Ca^2+ signaling and SNARE proteins.
once, depolarization (of AP) opens voltage gated calcium channels and calcium enters cell, it will trigger exocytosis of synaptic vesicle content (neurotransmitter diffuse across cleft)

Question 58

What controls the membrane fusion in synaptic vesicle fusion? Name the auxiliary SNARE proteins involved. also, which proteins are involved in core synaptic vesicle snare complex? What is the other special SNARE Protein called and what is it’s function?

Answer 58

Auxiliary SNARES and calcium control membrane fusion in synaptic vesicles
Auxiliary proteins:
Synaptobrevin- V SNARE
Syntax- T-SNARE
SNAP25- auxiliary SNARE (for support)
the synaptobrevin, syntax and snap 25 all combine to form CORE SYNAPTIC Vesicle SNARE COMPLEX
SYNAPTOTAGMIN- auxiliary v-SNARE that triggers Ca+ dependent membrane fusion.

Question 59

Explain how the timing of fusion is controlled by auxillary SNAREs, including Calcium. What protein senses calcium and how many binding domain does it have?

Answer 59

inside the terminal, calcium interacts with synaptotagmin , a calcium sensing v-Snare that has 4 calcium binding domains
In presence of calcium, synaptotoagmin stabilizes V and t snares together, allowing fusion between neurotransmitter storage vesicle and presynaptic membrane to occur.

Question 60

How do SNARES accumulate energy (after fusion) to separate from each other? What event also occurs during the separation?

Answer 60

A special protein called NSF uses ATP hydrolysis to untangle V and T snares and separate them from each other.
During separation, NSF twists SNARES in way that they acquire charged confirmation that will remain stable until v and t snares meet each again and unwind.

Question 61

What kind of mechanism do viruses use to invade host cell? which kind of viruses that infect mammalian cells use this mechanism? What happens after virus leaves infected cells?

Answer 61

Viruses use SNARE-LIKE mechanism (virus binds to receptor, and fuse with membrane) to invade host cell
viruses like INFLUENZA, HIV, ENCEPHALITIS, that infect mammalian cells use similar SNARE mechanism to invade host cells.
After leaving infected host cells, the viruses are coated with leftover of host cell PM called LIPID or MEMBRANE ENVELOPE infused with viral membrane proteins.

Question 62

What are fusases and how do they differ from SNARES? Describe how fusases are used in viruses and where domains are positioned. What is the issue with one of fusase domains?

Answer 62

Fusases- special proteins that Membrane envelope viruses have that work like SNARE proteins, but have different parts.
Unlike SNARE proteins that have one membrane-anchoring domain, Fusases have 2 domains.
One domain anchors fusase to viral membrane and the second is exposed at the opposite end of helical domain.
The exposed domain is very hydrophobic and used for anchoring virus to host PM
issue- hydrophobic moieties tend to aggregate in polar environment, so how will it be protected?

Question 63

What is a nucleocapsid

Answer 63

The capsid (shell of virus enclosing genetic material) of virus with nucleic acid

Question 64

How is the external membrane domain of fusase protected? What structures doe anti-viral therapies target?

Answer 64

A hydrophobic membrane intercalating patch of HIV fusase is covered by viral protein GP120.
Gp120 will first interact with CD4, a T-cell specific receptor. Then formed complex will gain high affinity to chemokine receptor that will liberate hydrophobic helixes of membrane domain and permit insertion (conformational change, fusion and entry of viral capsid follow)
Fusases and their protecting proteins are targets of anti-viral target therapies?

Question 65

Explain the role of proteases in Clostridium Botulinum (bacteria) and what specific structures they target? Be sure to include what botulism, tetanus and Botox is. How can tetanus be prevented?

Answer 65

In Botulism (illness ) due to toxin from Clostridium Botulinum, that is a specific protease that CLEAVES SNARE proteins.
This botulinum toxin affects MOTOR NEURONS.
Tetanus- is caused by toxin from Clostridium TETANI that is preferentially INHIBITORY INTERNERUONS (RENSHAW cells). This causes spinal motor neurons to become disinhibited, causing muscle overexcitation, spasm and paralysis.
Immunization works as great preventative measure
Botox- one of Clostridium Botulinum toxins (TOXIN A) that is used in cosmetics as a pain management/muscle relaxant.

Question 66

What proteases cleave SNARE proteins and are used in various therapies?

Answer 66

Botulinum toxins.

Question 67

What structures drive endocytosis and endocytic vesicles?

Answer 67

The plasma membrane receptors drive endocytosis and endocytic vesicles.

Question 68

what specialized organelles are used for cargo sorting?

Answer 68

Early endosomes used for CARGO SORTING.

Question 69

What are the two major types of endocytosis?

What 2 factors distinguish them?

Answer 69

phagocytosis and pinocytosis

the size of endocytic vesicles and size of cargo distinguish the two forms.

Question 70

Describe the process of phagocytosis. What specialized cells in humans are capable of phagocytosis?

Answer 70

Phagocytosis (“cellular eating”) involves the ingestion of large particles, such as whole microorganisms or dead cells via LARGE vesicles called Phagosomes (> 250 nm in diameter), it is mediated by formation of PSEUDOPODS (engulfing action) and restructuring of ACTIN filaments.
In humans and higher vertebrates, only specialized cells like MACROPHAGES and NEUTROPHILS can do phagocytosis.

Question 71

What structures create a unique membrane identity, serve as markers for specific compartments?

Answer 71

Membrane-associated PIP-specific KINASES and PHOSPHATASES that synthesize specific phosphatidylinositol phosphates (PIPS). create a unique membrane identity.

Question 72

what process serves as an entry port for various micro and macromolecules, including viruses?

Answer 72

Receptor mediated endocytosis (intense process)

Question 73

Describe the process of pinocytosis, another name for it and explain what form of endocytosis it is.

Answer 73

Pinocytosis- (cellular drinking) or ingestion of extracellular compounds.
Pinocytosis is also known as FLUID-PHASE endocytosis
Pinocytosis is a form of receptor-mediated endocytosis (pino driven by clathrin protein)

Question 74

describe the intense and continuous process of pinocytosis (receptor-mediated endocytosis) and how it is used in cancer cells.

Answer 74

Pinocytosis is a continuous process. The intensity varies from cell type. Macrophages ingest 3% of their membrane surfaces per minute. while fibroblasts ingest 1% of their membrane surfaces.
In energy-deprived cancer cells, pinocytosis is intensified to deliver additional nutrients (ex: serum albumin from lymph nodes)

Question 75

What is pinocytosis driven by? Explain this process

Answer 75

Pinocytosis is solely driven or mediated by MEMBRANE SURFACE RECEPTORS.
process:
1. the membrane surface receptors recognize and bind to their own cargo from extracellular fluid (hence why pino called receptor-mediated)
2. the receptor-cargo complex accumulate on membrane
3. before being endocytosed.
The extracellular parts of receptors appear inside the vesicle lumen together with cargo, while cytosolic parts face cytosol

Question 76

what stabilizes the formation of endocytic vesicles in pinocytosis? How does this compare to structures in phagocytosis?

Answer 76

specialized coating proteins called CLATHRIN stabilizes formation of small endocytic vesicles in pinocytosis.
while, formation of phagosomes during phagocytosis are stabilized by plasma extensions (pseudopods) with ACTIN filaments.

Question 77

Explain how clathrin is assembled, including other proteins and structures involved. Also explain how the clathrin cloating helps the efficiency of endocytosis

Answer 77

Clathrin is assembled by being bound to membrane through ADAPTOR proteins.
The adaptor proteins each recognize and bind to cytosolic part of specific cargo receptor.
The clathrin coating contributes to high concentration of receptors on limited membrane surface, which increases the efficiency of endocytosis.

Question 78

How many receptor molecules can each clathrin-coated pit accommodate?

Answer 78

each clathrin-coated pit can accommodate 1000 receptor molecules.

Question 79

what are the two mechanisms that contribute to increasing efficiency of endocytosis (clathrin cloating)

Answer 79

This can be achieved by two mechanisms:
1. each adaptin molecule can bind more than one receptor.
2. clathrin TRISKELIONs bind adaptins, through connecting to each other, they hold many receptors together in one pit.
(clathrin coating leads to high [ ] of receptors on surface).

Question 80

How are membrane receptors recycled? what happens if they are not?

Answer 80

through EARLY ENDOSOMES (major SORTING organelle)
receptor-mediated endocytosis would be very inefficient if receptors or membranes did not go back to the plasma membrane.
Normally, the membrane receptors are recycled.
In early endosomes, receptors and their cargo are sorted out.

Question 81

What kind of organelles (compartment) are early endosomes and how do they differ from endocytic vesicles?

Answer 81

Early endosomes are highly DYNAMIC and PERMANENT organelles. 
unlike endocytic vesicles that are transient (form and disappear upon fusion with early endosomes)
Early endosomes (EE) are permanent organelles that each cell has. Due to constant fusion and detachment of vesicles, they are highly dynamic and have extended tubular appearances.

Question 82

Describe a typical example of receptor-mediated endocytosis, including structures involved and its functions in human living cells. What is apolipoprotein?

Answer 82

LDL- Low density lipoprotein receptor is the most studied receptors of all 25 well studied receptors.
LDL receptor is in LIVER cells.
Apolipoproteins are synthesized in the intestine and excreted into bloodstream. They are also synthesized in liver and released into bloodstream to capture cholesterol molecules by similar mechanism. It is responsible for 100-fold enrichment of cholesterol inside cell.

LDL receptor allows for endocytosis of LDL (contain apolipoproteins) that is cholesterol rich and brought inside bloodstream

Question 83

Describe the Transferrin receptor pathway and include the role of transferrin. Why does Iron need to be trapped?

Answer 83

Transferrin- soluble protein that liver cells excrete into blood to trap iron.
Iron is essential component of HEME, a cofactor for Hemoglobin and respiratory chain proteins.
Since iron is scarce, stationary receptors alone won’t be efficient in trapping iron.
Hence, transferrin is more efficient way of capturing iron and delivering it to the tissues.

Question 84

How do early endosomes serve as reserved pools? what do they reserve? Provide 2 examples.

Answer 84

Early endosomes reserve PM receptors and transporters in their membranes.
ability of MYOCYTES to increase glucose uptake is due to large number of GLUCOSE TRANSPORTERS (GLUT4) in readily available pool of molecules stored in early endosomes.
AMPA GLUTAMATE receptors in hippocampus (brain) during LONG-TERM POTENTIATION (LTP); adding more receptors (stored in endosomes) after signal is received underlies ability of brain to memorize after signal is repeated.