Week 2 - Cell Structure - Holy Flashcards
To help us all rock this next exam.
Holy emphasized that the inner part of the organelle was most similar to what?
The extracellular space
List a few functions of cell membranes:
There are more... Transport Protection Modifications Signaling ion gradients etc. etc....
What are the 3 important functions of cholesterol?
-Stiffens membrane
-Reduces permeability
-They inhibit phase transitions.
This means that they can behave more uniformly despite changes in temperature or other similar disturbances.
(i had never heard this before, so i thought it might be important to explain)
Estimated number of differnt eukaryotic membrane proteins:
500-1000
What is the structure of a glycolipid
It is a lipid with a sugar group added.
Holy emphasized that these are relatively small oligosacharides that are added compared to the ones we will see on proteins
What are the 4 major phopsholipids?
Where are they synthesized and how do they travel?
Phosphoglyerides:
Phosphatidyl-Ethanolamines, -serines, and -cholines
(Made in the ER, transported by membrane flow)
Sphingolipids:
Sphingomyelin
(Made in the golgi and transported by membrane flow)
Functions of glycolipids:
Protection - Glycocalyx!
Create surface properties of membranes
Cell identification
Cell adhesion
(Can also be an entry point for toxins, like cholera)
How are phosphatidylinositol phospolipids involved in cell signaling?
(2 ways)
Well they stick out of the membrane surface and they can be bound to and activate various enzymes
ALSO
PI phospholipds can serve as a substrate for membrane associated phospholipids.
An example is the G-prot-coupled receptor/DAG/IP3 pathway
Flippases do what?
Flip phospolipids between opposite leaflets
How are phospholipds assymetrically ditrsibuted in different cellular membranes?
Initially distribution is even but what happens is that phosphocholine and sphingomyelines are flipped to the non-cytosol side.
The cytosolic leaflet, as a result, is enrisched with phosphatidylethanolamine and phosphatidylserine
To signal macrophages to destroy the cell, how do you change the phospholipid distribution?
Move a bunch of the phosphatidl serines to the non-cytosolic side!!!
Bam!
Most transmembrane proteins have what structure?
alpha-helix
but some are crazy beta barrels
Where are the sugar groups on the cell membrane and why?
The non-cytosolic side, because thats how they re made. Also its important to function.
What is the function of the glycocalyx?
Protection
Identification
Adhesion
Most mem. proteins are glycosylated!
4 methods to organize proteins in a membrane:
-self assembly into aggregates
-tether to extracellular molecules
-tether to intracellular molecules (cytoskeleton)
Bind to adjacent proteins for cell-cell junctions
What is the main protein that forms the critical architecture for red blood cells?
Spectrin!
actin has shrunk down to be way less important
Important integral protein for cell-cell adhesions
Cadherins!
need Ca to function
Where are integral proteins made?
Rough ER
Where are cytosolic proteins made?
The cytosol, on free ribosomes not attached to the ER at all!
How can smooth ER adjust to personal needs?
Can actually expand or shrink depending on detox needs. Like alcoholics have big expanded smooth ER’s
Interesting that sometimes the most toxic compunds are produced while trying to detox other compunds.
Like dogs and antifreeze!
3 functions of smooth ER
lipid synthesis
Ca regulation
detoxification
What actually determines whether a polyribosome becomes attached to an ER membrane or remains free-floating in the cytoplasm?
The information is actually coded within the emrging polypeptide itself. Crazy right?
(Its called an ER signal sequence, in the absence of the signal it will remain free-floating)
List the steps of a ribosome attaching to the ER membrane to feed the peptide through:
1 - polypeptide signal sequence (attached to the ribosome and mRNA) bind to signal recognition particle (SRP)
2 - the SRP receptor on the ER membrane binds and anchors in the mRNA-ribosome-SRP complex
3- The complex displaces the SRP and attaches to a translocator
4- The translocator has a pore where the peptide can be fed through the membrane
The number of times a protein dips through the membrane depends on the number of ___________
stop transfer sequences
Proteins made in the ER undergo what kind of glycosylation?
N-linked glycosylation
How does N-linkage work?
14-sugar oligosacchardide is added to a lipid called a dolichol, then this is added to the polypeptide later as it is being spooled into the ER lumen
What are proteoglycans
A special calss of HEAVILY-glycosylated proteins
The protein itself is made in the ER, but the o-linked glycolation occurs in the Golgi
Also remember this is O-linked glycosylation!!!!!!!
What is the purpose of proteogylcan sugars being sulfated and negatively charged?
They can attract cations and water, which creates a sort of gel-like extracellular area. I don’t exactly know what is so great about that…
What should happen to misfolded proteins?
ubiquitinated and destroyed by proteosomes!
Reactions to misfolded proteins n the cytoplasm and the ER: Describe what happens in each!
Cytoplasm:
-Increased expression of chaperones to facilitate refolding
ER
-increased expression of chaperones for refolding
-Increased expression of genes for proteosomal degradation and retrotranslocation
-Selective suppression of further protein synthesis
Exit face of golgi =
Entrance face of golgi =
exit = trans entrance = cis
List some functions of the golgi
- receives products from ER
- returns escaped proteins back to ER
- modifies glycoproteins (trim or add)
- postranslational modificaitions
- Produces sphingomyelin and glycolipids
- Adds O-linked oligosaccharides to proteoglycans
The golgi has 3 primary routes to send material on:
Lysosomes
Regulated Secretion - secretory vesicles
Constitutive Secretion - straight out
What are the main proteins helping transport between the golgi and ER?
COP-II : ER to golgi
COP-I : Golgi to ER
What is GEF?
Guanine nucleotide exchange factor
They switch GTP in for GDP in order to activate stuff
How is Sar-1 important for COP-II function?
It is activated by GEF then binds the membrane and associated with other proteins into a cage structure. As these proteins build up a vesicle begins to form and pinch off. Ta-da! Vesicle formation!
What receptor is responsible for returns all those escaped proteins from the golgi back to the ER???
The KDEL receptor can be recognized as belonging in the ER
How do Rabs, rab effectors, and snares work together for vesicle fusion?
Rab recognizes and binds to the rab effector, which tethers it above the target membrane
Next the v-snare and t-snare meet and twist around each other brining the vesicle closer in and fusing it to the membrane
How do phosphatidylinositols play a role in vesicle fusion?
Various phosphatidyl inositol variations can be expressed more in certain membranes, which is very useful for determining the right place for vesicles to form
What suagr is a uniqye identifier of a vesice as beign fileld with lysosomal hydrolytic enzymes?
Mannose -6-phosphate!
Are endosomes or vesicles containing hydrolytic enzymes more acidic before the two meet to form a lysosome??? why?
The endosome is more acidic because it is using proton pumps to fill the inside with H+ and acidify it. This allows the enzymes to activate quickly after they fuse.
Other vesicles and stuff can fuse together with stuff to chew up too (phagosomes, autophagosomes etc.)
Transcytosis is?
Stuff is just sent in vesicles straight thru a cell and back out the other end of it.
Coated vesicles use what kind of protein to function?
Clathrin
Have a crazy geometric shape to them in epectromicrographs
Uncoated vesicles use what kind of protein?
Caveolae! A permanent integral membrane protein
mitochondria tend to localize where?
-Along microtubules
close connections with the ER
-They also seem to localize in areas of high ATP utilization (like around contractile myofibers of heart muscle and sperm flagellum)
What are the dynamics of mitochondria like?
Highly plastic and constatnly undergoing fusion and fission.
MAny times more appropriate to call them a mitochondrial netwok
Proteins of mitochondria originate where?
A few originate in the mitochondria through mitoDNA.
Others are made in the ER and transported to the mitochodnria. Not through membrane flow, inserted into mitochondria through specific transporters. Have signal in the polypeptide to send them to mitochondria
What are TOM’s and TIM’s and OXA’s ????
TOM - transporter of outer mitochondrial membrane
TIM - transporter of inner mitochondrial membrane
Basically they work together to route a protein all the way into the matrix of the mito.
OXA -transports proteins made in the mito outward. Most are part of elec transport chain in the mito itself
What are peroxisomes? What are they for?
Spherical structures that contain high concentrations of enzymes Used for: Detox reactions Beta oxidation of fatty aids Formation of myelin phospholipids
How do chromosomes organize in the nucleus?
Turns out they actually tend to occupy certain territories in the nucleus.
Within that territory they interact with the nuclear matrix
What is a MAR? Whats its function?
Regions of chromosome that actually scaffold well witht the proteins forming the nuclear matrix.
- The loops that form on the unattached parts are usually HIGHLY expressed
- These loops can be insulated from other surrounding DNA.
- The loops also are hypothesized to help relieve tension stress along with the toposimerases
Gene neighborhoods? What is that all about?
Some areas of the nucleus are more expressed than others. By changing the lcoation of certain genes, you can get high expresssion or gene silencing
Main function of nucleolus?
Ribosome producing factory
Key points about microfilaments?
Support/organize plasma membrane Cell shape Cell division Cell motility (LOTS, located just under plasma membrane)
Key points about microtubules
Organize cytoplasm Intracellular transport Cell division Cilia/flagellae motility (RADIATE from centrosome, and extends outward like spider legs)
Key points about intermediate filaments?
Strengthen cytoplasm/tissues (cell-cell interactions)
Support nucleus
Epidermal appendages (nails, hair)
(Located spread throughout the cytoplasm, lots at junctions with other cells)
How are microfilaments, microtubules and intermediate filaments regulated in regard to polymerization??
Microfilaments: Is regulated by the binding and hydrolysis of ATP (remember actin-ATP) ADP creates some destabilization
Microtubules: Regulated by binding and hydrolysis of GTP. GDPs make the microtubule extemely unstable once the hydrolysis catches all the way up to the (+) end
Intermediate FIlaments: Phosphorylation causes depolymerization
Dephosphorylation causes polymerization
In reference to the cytoskeleton, what are ARP’s? What do they do?
Activated ARPs (actin-related protein) act like seeds in the sides of existing actin microfilaments. They then “sprout” outward
What does ADF/cofilin do to microfilaments?
It severs microfilaments to make free ends that can begin to grow
Name the 3 kinds of structures that actin can make and where they are found in the body
contractile bundles - in muscle fibers (alternating polarities)
Tight parallel bundles - in microvilli
Gel-like networks - everywhere else
Would the drug taxol be more likely to create irregular microvilli or inhibit spindle formation for mitosis in a cell?
Spindle formation. Taxol is a microtubule-specific drug
It binds and stabilizes microtubules
If you were murdered by a deathcap mushroom smoothie, what would be seen in your cells?
Irregular actin activity
Your actin would be incapable of being dynamic. Phalloidin binds and stabilizes actin filaments
The Rho proteins affect microfilament assembly.
What special formations are created by Rho, Rac, and Cdc42?
Rho - stress fibers (parallel bundles that associate with myosin)
Rac - lamellipodia (meshworks especially around the edges of the cell)
Cdc42 - filopodia (parallel bundles that reach out from the outside of the cell)
Differences between type 1 and type 2 myosin?
Type 1 - Tend to mediate interactions between membrane and microfilaments
Type 2 - have a long tail that allows them to form filaments, they are then found in muscle where they associate with actin in contractile fibers
What actually creates the powerstroke in myosin 2?
The powerstroke is created at the stage after ATP hydrolysis. The point at which the inorganic phosphate leaves the myosin head. This causes the head to revert back to its original conformation and pulls at the actin
What is the linker protein between actin adn the integral protein cadherin?
catenins
What is a MAP? What are the motor MAPs?
Microtubule Associated Protein
Motor MAPs are Dynein and Kinesin
Dynein moves toward ( - ) end of microtubules
Kinesin moves toward ( + ) end of microtubules
What types of cell junctions use intermediate filaments?
Desmosomes: Cell to cell interaction
(linker proteins are desmoplakin and integral proteins part of cadherin family)
Hemi-desmosome - cell to Extracellular matrix
(linker proteins are plectin and dystonin and integral proteins called integrins)
Where do we see intermediate filaments in the nucleus??????
The nuclear lamina, a structure that helps support the nuclear envelope
What is the size range for passive trasnport through a nuclear pore complex?
5,000-60,000 daltons
How does the g-protein “Ran” affect the import or export directionality?
Proteins that are imported:
Bind import receptors in the presence of GDP
Dissociate in presence of GTP
Proteins that are exported:
Bind receptors in presence of GTP
Dissociate in presence of GDP
Now here comes the kicker. Ran-GEF is concentrated in the nucleus so it is phosphorylating the Rans to make Ran-GTP’s there. In the cytosol the Ran-GAP is dephosphoylating RAN to become Ran-GDP.
So it goes in a cycle. Check the picture in the powerpoint if this is confusing…
