MVU6 MEMBRANES - 1

Question 1

is it possible that a polypeptide sequence is not degraded by the proteasome?

Answer 1

yes, if it doesnt have lysines

Question 2

how many proteins in total do the cutting in a proteasome?

Answer 2

6

Question 3

what do AAA family ATPases do?

Answer 3

unfold proteins till primary structure

Question 4

why do proteins need to be in primary structure before entering proteasome?

Answer 4

because the ring is very narrow

Question 5

what is the function of the Ub receptor?

Answer 5

increases efficiency of targeting
on the outside of the cap
recognises the polyUb tail
selects only the K48 chains
protects against premature DUB activity

Question 6

what are the two types of Ub receptors and what do they do?

Answer 6

1. Intrinsic receptors: the cap subunit Rpn10 and Rpn13 bind polyUb
2. extrinsic (shuttling) Ub receptors
   separate from the proteasome
   bind polyUb through Ub-associated domain (UBA)
   have a Ub like domain (UBL) that is recognised by the cap
   recognise poly UB proteins and bring them to the proteasome

Question 7

what is the unfoldase protein called?

Answer 7

Rpt 1-6

Question 8

what is the DUB protein called?

Answer 8

Rpn8/11

Question 9

what happens when the Ub receptors recognise the tail?

Answer 9

conformational change and the tail is removed

Question 10

what happens in the proteasome core?

Answer 10

cavity inside is small and narrow
proteins have to stay unfolded
3 active subunits in each beta ring, 6 in total
one cuts basic AAs, one cuts at acidic AAs, and one cuts at hydrophobic AAs

Question 11

what happens after the proteins are cut?

Answer 11

peptides diffuse out and are digested into amino acids by peptidases

Question 12

what defines the cell?

Answer 12

the membrane

Question 13

what is the secretory pathway?

Answer 13

a transport system between several types of organelles in the cell surface
synthesis of proteins and proteins at the ER
traffic through the GA, to the plasma membrane
internalisation through endosomes, to degradation in lysosomes
some organelles (mitochondria) are not connected in the secretory pathway

Question 14

what are characteristics of the lumen of secretory organelles?

Answer 14

the interior of the lumens is continuous with each other and the extracellular space
the lumental environments are similar to the extracellular space (blood plasma) and different from the cytosol

Question 15

what do vesicles do?

Answer 15

bud from one organellar membrane and fuse with another without releasing contents to the cytosol
closed till they reach the target

Question 16

what type of environment is the cytosol?

Answer 16

reducing

Question 17

what type of environment is the lumenal/extracellular fluid?

Answer 17

oxidising

Question 18

what functions do biological membranes fulfill?

Answer 18

provide enclosure to cells and to organelles within cells
allow regulated transport of materials between compartments
provide sites within cells for biochemical reactions (accumulate certain types of molecules)
photosynthesis, oxidative phosphorylation, metabolism of biological molecules
support contacts with the environment outside cells (cell motion, cell recognise other cells, cell fusion)
transmission of signals from exterior to interior of cells

Question 19

what are properties of membranes?

Answer 19

form hydrophobic barriers between aqueous compartments within cells
flexible and can be folded into different shapes
selectively permeable to small hydrophobic molecules, but not to larger or charged/polar molecules
specialised protein complexes control the movement of impermeable molecules across membranes
can store energy as concentration gradients
- voltage (nerve cells)
- pH, potassium, sodium, calcium gradients

Question 20

what are membranes made of?

Answer 20

lipid molecules and membrane proteins

Question 21

how are lipids organised?

Answer 21

into a bilayer, polar on each side and hydrophobic in the middle

Question 22

what can membrane proteins do in the fluid bilayer?

Answer 22

membrane proteins can rotate and diffuse laterally in the bilayer
they cannot flip

Question 23

what are the major lipids in membranes?

Answer 23

phospholipids - in all membranes
glycolipids - only at plasma membranes (not in ER or GA)
cholesterol
other types with special functions
all have polar and hydrophobic sections

Question 24

what does lipid composition determine?

Answer 24

physical properties of the membrane
mobility (diffusion rotation) and curvature, thickness

Question 25

how can lipids move in the membrane?

Answer 25

lateral diffusion
flexion
rotation
can flip (rarely occurs)

Question 26

what are characteristics of phospholipids?

Answer 26

most abundant lipid
polar head groups:
has choline or other charged group
phosphate and glycerol (attaches tail to phosphate)
classification by head groups
2 fatty acid tails:
different lengths
saturated or unsaturated (makes a bend)
found in many different combinations with head groups

Question 27

through what linkage is glycerol linked to the tail?

Answer 27

ester linkage

Question 28

what are the most common phospholipid head groups?

Answer 28

phosphatidyl choline (PC)
-ethanolamine (PE)
-serine (PS)

Question 29

what is special about phosphoserine?

Answer 29

the only one that has a negative charge

Question 30

what is another related head group that is related but is not a glycerolipid?

Answer 30

sphingomyelin (SM)
has an amide linkage with the fatty acid tail

Question 31

what are characteristics of phosphatidyl-inositol (PI)

Answer 31

not abundant but can be phosphorylated and act as a signaling molecule
has a sugar as a head (has hydroxyls, can be phosphorylated)

Question 32

what does head group affect?

Answer 32

size and charge affect lipid mobility

Question 33

what are characteristics of fatty acid tails?

Answer 33

14 to 24 carbons
varying number of double bonds
saturated tails are straighter and more flexible (increase length)
double bonds introduce bends in the tail, reduce flexibility and overall length

Question 34

what do the types of tails in membranes determine?

Answer 34

thickness and fluidity of the membrane

Question 35

what are characteristics of glycolipids?

Answer 35

only found on the outside surface of the plasma membrane
head groups contain different sugar groups in many combinations
important for cell contacts with environment and other cells
the sugar is a glucose, galactose or NANA sugar

Question 36

what are the characteristics of cholesterol?

Answer 36

structurally different from other lipids
steroid ring structure makes it very rigid
lateral mobility, rotation is much lower
reduces mobility of surrounding phospholipids, makes fatty acids more rigid
amphipathic
integrated in the membrane
makes the PM thicker
interacts with tails through hydrophobic interactions

Question 37

why is the asymmetry of the plasma membrane important for function?

Answer 37

exterior has glycolipids
interior has stronger negative charge (transmit signals) (high PS levels)
asymmetry is not absolute but is actively maintained

Question 38

what is mostly present on the outside and inside of the membrane?

Answer 38

outer leaflet: PC, SM, glycolipids
inner: PE, PS, PC (low amounts of PI)

Question 39

what are the different lipid compositions between the organelles?

Answer 39

PM has highest level of cholesterol, SM
ER and mitochondria have higher levels of PC and PE
other specialised lipids are found in different membranes

Question 40

what are microdomains?

Answer 40

regions of a membrane that are organised laterally (sideways) in patches
PM and trans golgi have special mitochondria called lipid rafts
thicker than surrounding membrane, enriched in cholesterol
lipids with longer tails cluster together in rafts
cholesterol binding straightens lipid tails, causing thicker membrane
different protein content and biological function