Week 9 Textbook

Question 1

what are membrane enclosed organelles

Answer 1

parts of such organelles which contain a unique set of molecules and carries out a specialized function

Question 2

list the structure and function of some basic membrane enclosed organelles

Answer 2

1. cytosol - enclosed by the membrane
2. nucleus - prominent organelle
3. nuclear envelope - communicates with the cytsol via nuclear pores
4. endoplasmic reticulum - a system of interconnected sacs/tubes (synthesis of new membranes - Large ER has ribsomes attached to the surface = rough ER, the Small ER = smooth ER because it lacks ribsomes and is the site of steroid hormone synthesis and etc
   - the smooth ER also sequesters Ca2+ from the cytosol and is involved in muscle contraction and other responses to extracellular signals
5. golgi appartus - recieves proteins and lipids from the ER and modifes them and then dispatches them to other destinations in the cell
6. lysosomes - small sac of digestive enzymes which degrade organelles that are worn out or damaged
7. peroxisomes - small organelles that contain enzymes that break don lipids and destroy toxic molecules by producing hydrogen peroxide
8. mitochondria/chloroplast and surrounded by a double membrane and are the sites of oxidative phosphorylation and photosynthesis - have internal membranes which are for the production of ATP
9. cytoskeleton - microtubules which provides tracks for moving the organelles around and for directing the traffic of vesicles between one organelle and another - driven by motor proteins

Question 3

t/f the membrane enclosed organelles occupy very little of the cells volume

Answer 3

false
they occupy nearly half of the volume
the mitochondra = 22%

Question 4

what is the purpose of a sorting signal

Answer 4

the fate of where the protein is supposed to be or is required is dependent on the sorting signal which is encoded in the mRNA

Question 5

if a protein has a sequencing signal that requires it to be inside a membrane enclosed organelle, how do they get the hydrophilic protein across the hydrophobic part of the membranr?

Answer 5

proteins moving from the cytosol into the nucleus are transported through the nuclear pores which penetrate both the inner and outer nuclear membranes
- act as gates for macromolecules

proteins moving from the cytosol into the ER, mito or chloroplast are transported across the organelle by protein translocators

proteins moving from the ER to another compartment of the endomembrane system to another are transported by transport vesicles which are pinched off from the membrane of one compartment and fused to the next

Question 6

what is a signal sequence

Answer 6

amion acid sequence that directs a protein to a specific location in the cell such as the nucleus or mitochondria
deleting a signal sequence from an ER protein converts it into a cytosolic protein
but placing an ER signal sequence in the code of a cytosolic protein redirects it to move to the ER

Question 7

t/f even if two proteins have the same signal sequence to be required at the same destination, they will be identicL

Answer 7

FALSE
they will be very different
in the function - physical properties such as hydrophonic or placement of R groups in AA

Question 8

protein signal sequences are usually removed after getting to destination but some proteins that are destined for the nucleus keep their signals, why?

Answer 8

because the nucleus breaks down during cell division and is then reformed so the proteins “save their ticket” to return to the nucleus again in the daughter cells

Question 9

explain the structure of the nucleus including the inner and outer membrane, pores, lamina

Answer 9

inner nuclear membrane - contains some proteins that act as binding sites for chromosomes
theres also an outer membrane - which is similar to the ER membrane bc i tis continuous
the nuclear lamina is a finely woven meshwork of protein filaments that line the inner face of the membrane - structural support
the nuclear pores form gates that molecules can enter or leave - they have cytsolic fibres hanging outside of the pores and disorted soft proteins filling up the hole to prevent large molecules from coming inside

Question 10

how does a protein that needs to go to the nucleus get recognized?

Answer 10

has nuclear localization signals which are several positively charges lysines or arginines
- these get recognized by cytsolic proteins called nuclear import receptors - they bind to the receptor and move it to a nuclear pore - the receptor shoulders it way thru the gel like meshwork of the pore (disrupting it) and then once released, it returns to the cytsol for resure

Question 11

what precents nuclear import receptors from entering the nucleus empty-handed

Answer 11

the process is steered into one direction where the movement is guided by the hydrolysis of a nucleoside triphosophate (ATP, GTP, CTP, TTP)
needs to be mediated by the monomeric GTPase named ran or ATPase named __
the Ran exists in 2 forms, the one holding the GTP and the other one holding the GDP
the nuclear receptor is binded to RAN, the GTP is hydrolyzed and the Ran-GDP dissociates from the receptor turning it into Ran-GDP
the receptor is now ready to bind to the protein with the signal sequence. they move thru the pores and into the nucleus together and then RanGTP binds to the receptor which releases the protein into the nucleus, the complex moves into the cytoplasm whom is ready to be hydrolyzed again to turn into GDP causing its release and activation to bind to a protein with a NLS (nuclear localization signal)

Question 12

t/f proteins with a signal sequence are usually found in the C terminus

Answer 12

false
N terminus

Question 13

explain how the process of proteins entering the mitochondria or chloroplast

Answer 13

the double membrane at specialized sites are found closer to each other
the mitochondrial precursor protein is recognized by a receptor in the outer mitochondrial membrane (TOM = translocator of the outer membrane) once binded they move laterally into the protein until the signal sequence is recognized, then the intermembrane protein (TIM translocator of the intermembrane) then recognizes and goes thru into the matrix of the mitochondria
the sequence is then cleaved off by a signal peptidase
chaprone proteins that help pull proteins across the membrane are used again to refold it
-energy is needed for this translocation - it comes from the hydrolysis of a nucleosde triphosphate such as ATP, GTP, CTP, TTP

Question 14

explain the role of chaperone proteins in the movement of proteins in the mitochondria

Answer 14

chaperone proteins inside the organelle help to pull the protein across the two membranes and refold it to a particular site within the organelle

Question 15

explain the process of proteins entering the peroxisomes

Answer 15

like the nuclear import sequence, the sequence is recognized by receptor proteins in the cytosol
- one of the receptors acts like a cargo protein to the peroxisome membrane
- the other protein aids in protein transport thru the membrane
- it is still unknown but some peroxisomal proteins come from the cytosol - a few of the proteins are embedded in the membrane and come from vesicles that come from the ER
- either they fuse with per existing peroxisomes or become their own

Question 16

what would happen if you block the peroxisomal protein import process

Answer 16

mutations that occur = severe illness
abnormalities in the brain, liver, kidneys
serves as proper cell function and the health of the organism

Question 17

explain WHY proteins would want to enter the endoplasmic reticulum

Answer 17

serves as an entry point for proteins that are destined for other organelles + the ones that are meant to be in the ER themselves
- proteins that are destined for the golgi, endosomes, cell membrane or lysosomes will first enter the ER from the cytosol and then once in the lumen they will only reenter the cytosol if ferried by transport vesicles

Question 18

what are the two kinds of proteins that get transferred from the cytosol to the ER

Answer 18

1. water soluble proteins are translocated across the ER membrane and are released into the ER lumen
   - usually used for secretion or for the lumen of an organelle in the endomembrane system
2. prospective transmembrane proteins are only partly translocated across the ER membrane and then become embedded in it

regardless of the final destination all of these proteins end up in the ER by an ER signal sequence
- proteins that enter the ER are usually translated by the membrane, the ribosomes attach to the ER membrane (this is why the rough ER is coated in ribosomes)
- since ribsomes can stimultanelous translate parts of a long mRNA, if a mRNA molecule encodes a ER signal sequence they become connected to each other on the ER membrane

no energy is required, the elongation of each polypeptide coming out of the ribosome is enough to push the growing chain through the ER membrane

Question 19

what are the 2 proteins that help guide ER signal sequences to the ER membrane

Answer 19

1. signal recognition PARTICLE (SRP) which is in the cytosol and binds to both the ribosome and the ER signal sequence as it emerges from the ribosome
2. an SRP RECEPTOR which is embedded in the ER membrane and recognizes the SRP
   once the ribosome is detected by an SRP it then passes the ribosome along to the protein translocator and the SRP receptor in the membrane of the ER to start synthesizing
   - since the sequence is on the N terminus the end going into the protein translocator first and remains inside the translocator while the rest of the polypeptide is threaded through in a large loop
   - after the sequence is removed by a transmembrane signal peptidase which has an active site facing the lumenal side of the ER membrane
   the cleaved signal sequence is then release and the protein translocation closes and degrades and may require help from chaperone proteins to fold

Question 20

how does the process differ if a protein is entering the ER but is destined to another organelle?

Answer 20

SINGLE PASS TRANSMEMBRANE PROTEIN
the N terminus binds to the protein translocator which keeps it open, it remains inside while the polypeptide synthesizing passes through and forms a loop in the lumen side, it then hits a stop-transfer sequence - which is hydrophobic (the N terminus is inside and the C terminus is on the outside and didnt pass through yet) it is then discharged into the lipid bilayer, the N terminus is removed from the translocator and the

Question 21

explain the process of a double pass transmembrane protein

Answer 21

some proteins have a start-transfer sequence and a stop-transfer sequence and once the stop signal is reached the 2 hydrophobic sequences are then released into the bilayer where they remain in the bilayer as membrane spanning alpha helices
within a long mRNA they can be multiple start and stop sequences which allow the double pass proteins to be anchored side by side with each other and span a large area of the membrane

Question 22

what is an example of an organelle that cannot recieve proteins directly from the cytosol

Answer 22

golgi apparatus
these proteins need to be transported from the ER first and do not go back out to the cytosol to enter the golgi membrane
they are transported by vesicles by the endomembrane system

Question 23

what is transport vesicles

Answer 23

membrane vesicles that carry proteins from one intracellular compartment to another
like Er to golgi
= VESICULAR TRANSPORT

Question 24

explain exocytosis vs endocytosis

Answer 24

exo = a vesicle fuses with the plasma membrane and releases it contents inside the cell

endo = extracellular materials and budded off inward from the plasma membrane and releasing its contents outside of the cell

keeps the orientation so that the cytosolic and noncytosolice sides faces the corresponding areas

Question 25

how does the transport system of vesicles function optimally

Answer 25

a transport vesicle that buds off from a compartment must take only the proteins appropriate to its destination and must fuse only with the appropriate target membrane each organelle must maintain its own distinct identity with its own protein and lipid compositions so that vesicle transports can recognize

Question 26

what is the significance of a Rab protein

Answer 26

it is apart of the family of small GTP-binding proteins on the surface of transport vesicles and organelles that serves as a molecular marker to help ensure that transport vesicles fuse only with the correct membrane to help them recognize their tethering protein

Question 27

what is a tethering protein

Answer 27

transmembrane protein involved in the docking of transport vesicles to target membranes each organelle and transport vesicle carriers a unique combination of rab proteins = molecular markers

Question 28

what is SNAREs

Answer 28

additional recognition is provided by a family of transmembrane proteins once the tethering protein has captured a vesicle by holding onto its rab protein, the SNAREs (v-SNARE) on the vesicle interact with the complementary SNAREs on the target membrane (t-SNARE) the same SNARE involved in docking also play a role in catalyzing the membrane fusion required for a transport vesicle to deliver its cargo - it also adds the besicle membrane to the membrane of the organelle - sometimes requires a special stimulatory signal - to prevent membranes from fusing rapidly a highly unfavourable process which includes the vesicle and the membrane coming very close to each other which displaces water makes the process not likely to happen randomly - this is why they must all be catalyzed by specialized proteins that assemble to form a fusion complex that means to cross the energy barrier

Question 29

how does SNARE proteins catalyze the vesicle fusion process

Answer 29

they catalyze the process the v-SNAREs and t-SNAREs wrap around each other tightly and pulls the 2 lipid bilayers into close proximity

Question 30

why are many proteins that enter the ER lumen or membrane converted into glycoproteins

Answer 30

converted in the ER by the covalent attachment of short branched oligosccharide side chains composed of multiple sugar = glusoylation carried out by glycosylating enzymes present in the ER but not in the cytosol oligosaccharides serve as protection from degradtion and help guide it to the appropriate organelle by serving as a transport signal

Question 31

why are disulfide bonds formed

Answer 31

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

Question 32

explain the structure of the golgi apparatus

Answer 32

located near the cell nucleus collection of flattended membrane enclosed sacs = cisternae which are piled each golgi stack has 2 faces, an entry (cis) and an exit (trans) cis = face is side by side to the ER trans = points towards the plasma membrane soluble proteins and pieces of membrane enter the cis golgi network via transport vesicles derived from the ER - they then travel to thru the cisternae by transport vesicles that bud from one cisternae to the next OR by a maturation process in which the golgi cisternae themselves migrate thru the golgi stack proteins exit thru the trans exit

Question 33

what is the importance of the cis and trans areas of the golgi body

Answer 33

cis = can move either onward thru the golgi stack or if they have a ER signal they will be returned to the ER trans = sorted according to where they are destined to be (lysosome or cell surface) - oligosaccharide chains are added to proteins in the ER and modified

Question 34

explain the constitutive exocytosis pathway in the golgi network

Answer 34

a steady stream of vesicles buds from the trans golgi network and fuses with the plasma membrane in the process of exocytosis = constitutive exocytosis pathway supplies and the plasma membrane with newly made lipids and proteins - allows the plasma membrane to expand prior to cell division and refresh old lipds nad proteins it also carried soluble proteins to the cell surface to be released to the outside = secretion

Question 35

explain regulated exocytosis pathway

Answer 35

operates only in cells that are specialized for secretion

Question 36

what is stored in secretory vesicles

Answer 36

Each specialized secretory cell produces large quantities of a particular product—such as a hormone, mucus, or digestive enzymes—which is stored in secretory vesicles for later release they bud off from the trans golgi network and accumulate near the plasma membrane - they wait for a extracellular signal that will stimulate the fuse and releases the contents to the cell exterior by exocytosis

Question 37

what are the 2 kinds of endocytosis

Answer 37

1. pinocytosis which involves the ingestion of fluid and molecules via small pinocytic vesicles 2. phagocytosis involves the ingestion of large particles such as microorganisms and cell debris via large vesicles called phagosomes - phagocytic cells defend against infection by ingesting invading organisms - to be taken up by macrophages or neutrophils particles must first bind to the phagocytic cell surface and activate one of a variety of surface receptors. bacteria that has anti-body coating and when binding to the receptors it induces the phagocytic cell to rearrange its cytoskeleton to extend pseudopods which engulf the bacterium

Question 38

explain how pseudopods work

Answer 38

they fuse together their 2 tips and form a phagosome which fuses with a lysosome and the microbe is destroyed

Question 39

how has mycobacterium tuberculosis evolved tricks for subverting the pseudopods system

Answer 39

when engulfed the organism survives and multiplies within the macrophage

Question 40

t/f the interior of the endosome compartment is kept acidic

Answer 40

true by an ATP driven H+ pump in the endosomal membrane that pumps H+ into the endosome lumen from the cytosol - plays a crucial role in the sorting process by causing many receptors to release their bound cargo

Question 41

what are 3 routes taken by receptors once they have entered an endosome

Answer 41

they differ according to the receptor 1. most are returned to the same plasma membrane domain from which they came from 2. some travel to lysosomes where they are degrades 3. some proceed to a different domain of the plasma membrane and transfer their bound cargo across one extracellular space to another = transcytosis

Question 42

explain the lysosome membrane

Answer 42

contains transporters that allow the final products of the digestion of macromolecules such as amino acids, sugars, and nucleotides to be transferred to the cytosol - where then they are used by the cell their membrane also contains a ATP driven H+ pump which keeps its contents acidic The specialized digestive enzymes and membrane proteins of the lysosome are synthesized in the ER and transported through the Golgi apparatus to the trans Golgi network. While in the ER and the cis Golgi network, the enzymes are tagged with a specific phosphorylated sugar group (mannose 6-phosphate), so that when they arrive in the trans Golgi network they can be recognized by an appropriate receptor, the mannose 6-phosphate receptor. This tagging permits the lysosomal enzymes to be sorted and packaged into transport vesicles, which bud off and deliver their contents to lysosomes via endosomes

Question 43

what is autophagy

Answer 43

mechanism by which a cell eats itself - digesting molecules and organelles that are damaged or obsolete it is an additional pathway that supplies materials to the lysosome

Question 44

explain the process of autophagosome

Answer 44

the process involved in the enclosure of an organelle by a double membrane it then fuses with a lysosome authophagy of organelles increase when eukaryotic cells are starved or when they remodel themselves extensively during development

Question 45

t/f cytosol is half of the cells volume

Answer 45

true many metabolic pathways cytoskeleton protein synthesis and degradation

Question 46

differentiate between the rough and smooth ER

Answer 46

rough = membrane bound ribosomes - synthesis of soluble proteins and transmembrane proteins for the endomembrane smooth = PL synthesis and detoxification

Question 47

what are some of the organelles that are not membrane bound

Answer 47

centrosomes nucleolus

Question 48

what determines where a protein ends up

Answer 48

the mRNA that the ribosomes translate has a signal sequence encoded if there is a protein in the cytosol that means it doesn't have a sorting signal

Question 49

signal sequences as recognized by ____

Answer 49

sorting receptors

Question 50

what are the 2 types of sorting

Answer 50

1. post translational sorting - proteins are nuclear encoded and fully synthesized in cytosol before sorting need to be folded if transported to the nucleus or peroxisomes dont need to be folded if going to the mito or plastids 2. co-translational sorting proteins are nuclear encoded - have an ER signal sequence to take it to the ER during protein synthesis (translation) and then taken to its destination

Question 51

explain post translational sorting in thru the nuclear pores

Answer 51

post translational sorting: (protein is fully translated before) the nuclear protein (folded) has a localizing signal that is recognized by the sorting receptor and moved into the nucleus after binding together thru a pore the pore = gated and allows passing thru because of the signal sequence present

Question 52

explain how sorting proteins get into the peroxisomes

Answer 52

post translational sorting: need to be folded fully synthesized in cytosol before sorting - the peroxisomes contain enzymes for oxidative reactions like breaking down toxins, fatty acid molecules the cargo (protein) with the signal sequence binds to its sorting receptor which goes thru a transmembrane complex into the lumen and the receptor and signal/cargo disassemble

Question 53

how do you sort proteins into the mitochondria and chloroplast

Answer 53

post translational sorting: doesnt need to be folded most proteins are nuclear encoded even tho these organelles usually have their own genomes protein for transport has a signal sequence which is associated with hps70 chaperone proteins to keep it unfolded. it is then brought to the transmembrane complex and thru the secondary complex (mito has multiple PMs) - the signal sequence goes into the cell first and then the hps70 proteins helps to fold it in the matrix - depending on the signal sequence if it should be cut off or not

Question 54

why do proteins sort to the ER

Answer 54

co translational sorting where proteins are nuclear encoded and have an ER signal sequence that is hydrophobic - they enter the endomembrane system thru the ER (system = ER, golgi, endosomes, lysosomes)

Question 55

explain the process of co translational sorting into the ER

Answer 55

the mRNA arrives in the cytoplasm after the transcription in the nucleus - translation starts on ribosomes - they translate into proteins until the ER signal sequence is reached - the signal recognition particle (SRP) brings it to the SRP receptor in the PM beside the translocon - when the SRP particle and receptor bind the translocon opens and feeds the N terminus of the signal sequence inside (stays inside bc its hydrophobic) the rest of the translated protein (co translating bc ribosome is still attached) fishes the rest of the protein inside and loops the signal peptidase cuts the protin at the signal sequence leaving the signal peptide in the PM (the beginning of protein in the lumens sequence is not MET bc it was cut) - once the stop-transfer sequence enters the translocon (it has a internal hydrophobic segement of the alpha-helix) which sits inside the translocon to stop. the signal peptidase cuts the signal sequence and the translocon closes and protein synthesis is complete leaving the protein attached to the stop sequence (the N terminus is inside and the C terminus is on the outside)

Question 56

whats the difference between the N-terminus ER signal sequence and the internal ER signal sequence

Answer 56

N terminus - is cleaved off my signal peptidase bc it is a stretch of hydrophobic AAs the interna; = start-transfer sequence found later on in the protein not cleaved off becomes a membrane spanning protein

Question 57

what are the 3 outcomes of co translational protein

Answer 57

can be a soluble protein fully into the lumen TRANSMEMBRANE (2) 1. 1 transmembrane protein with the stop transfer sequence 2. 2 transmembrane protein with the internal start-transfer and the stop-transfer sequence adjacent

Question 58

how do you make the 2 transmembrane protein for co translational sorting

Answer 58

the mRNA arrives in the cytoplasm after the transcription in the nucleus - translation starts on ribosomes - they translate into proteins until the ER signal sequence is reached - the signal recognition particle (SRP) brings it to the SRP receptor in the PM beside the translocon - when the SRP particle and receptor bind the translocon opens and feeds protein inside until reaching the start-transfer sequence (stays inside bc its hydrophobic) and then the rest of the protein loops thru until it reaches the stop-transfer sequence which is also hydrophobic and stays inside the translocon closes and your left with both N terminus and C terminus on the outside * the start-transfer sequence is the one that opens the translocon so that some of the protein goes inside the lumen - when scanning and its not found that area gets sent back outside

Question 59

what are the organelles in the endomembrane system

Answer 59

ER, golgi, endosomes, lysosomes they carry lipids, proteins, soluble molecules

Question 60

explain the secretory pathway

Answer 60

proteins made in the ER delivered to other compartments via exocytosis

Question 61

explain the endocytic pathway

Answer 61

contents move into the cell

Question 62

explain the retrieval pathway

Answer 62

retrieval of lipids, selectec proteins can be reused

Question 63

contrast exo and endocytosis

Answer 63

exo: vesicle fuses with PM to become part of PM and release contents endo: the lumen contents of the vesicle come from the EXC space and cuts off part of the PM to form a vesicle

Question 64

what are the 2 types of exocytosis (secretory pathways)

Answer 64

1. constitutive exocytosis pathway - in all eukaryotes - continuous delivery of proteins to PM - unregulated (no signal required) to carry soluble proteins like collagen for the EXC matrix 2. regulated exocytosis pathway - needs signal - only in specialized cells - extracellular signal, the vesicle fuses with the PM and contents are released EX: insulin levels get high, signal, releases insulin out of the cell via vesicles

Question 65

how does the secreted protein move from translation to fusing to the PM

Answer 65

translation on ribosomes, ER signal sequence, N terminus inside translocon, (co translational), ER signal sequence is cleaved behind and the protein is folded inside the lumen - moves in transport vesicles thru secretory pathway (ER --> vesicles --> golgi --> vesicles --> PM --> EXCM

Question 66

explain the path of a transmembrane protein from translation to plasma membrane

Answer 66

translation on ribosomes, ER signal sequence (N-terminus or the internal one - to create 1/2 transmembranes) directs the protein to the ER, co translational translocation, protein can be inserted into the translocon in different ways depending on if it was the N terminus or internal - the transmembrane protein remains in the same orientation as it moves thru secretory pathways like ER --> vesicles --> golgi --> vesicles --> PM --> EXCM

Question 67

what is the role of the golgi

Answer 67

recieves proteins and lipids from the ER and modifies them and then sends them to other compartments via vesicles - structure: golgi stack, animals usually have 1 and plants have 2+

Question 68

explain oligosaccharide processing in the golgi for the protein glycosylatoin

Answer 68

the protein starts in the ER, it is a single type of oligosaccharide attached to many proteins - complex processing occurs in the golgi - there are different enzymes in each cisterna (stack of golgi) - glycosylation modifications needed for proteins and lipids in golgi

Question 69

explain the pathway between endosomes and lysosomes

Answer 69

early endosomes mature into late endosomes the late endosomes have lyposomal proteins which continue to be delivered from the golgi (H+ pump, hydrolyase, makes pH drop) - late endosomes mature into lysosomes the early can also fuse with the late endosomes

Question 70

explain lysosomes

Answer 70

acid hydrolyases (proteases, nucleases, lipases) designed to work t a specific pH - these are all enzymes that break down proteins, nucleotides, lipids) they get acidic by having H+ (V-type ATPase) protects rest of the cell from digestion the transport proteins in lysosomal membrane transfer digested products to cytosol (AA, sugars, nucleotides)

Question 71

what gives the vesicles of the endomembrane system direction

Answer 71

they are either directed by the movement of the vesicles and the compartments they are sent to (ER, golgi) or they are pulled by motor proteins associated with the cytoskeleton of the cell