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ANAT 212 pre midterm > Professor Ugalde lecture 6-7 > Flashcards

Professor Ugalde lecture 6-7 Flashcards

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1
Q

What is the key part of protein folding quality control?

A

Ubiquitination bc it has an important regulatory/homestatic mechanism

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2
Q

What is the major route of ubiquitination, what is it done by?

A

ubiqutin mediated degradation is done by proteasoms in the cytosol

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3
Q

Where can ubiquitin be covalently linked?

A

it can be covalently linked to lysine side chains of other proteins and to itself since it is a small 8kDa protein

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4
Q

what does the poly-Ub chain mark?

A

it marks a protein for degradation

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5
Q

What enzymes add length to the Ub tail?
What receptor detects the chain?

A

E2/E3 get together and add UB to Lys on the previous UB the tail
-receptors on proteasomes recognize the chain

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6
Q

What enzyme determines specificity in the ubiquitin proteasome system?

A

E3 Ub ligases select the substrates to determine what protein to degrade

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7
Q

What does the proteasome do in the UPS?

A

-it degrades/unfolds the substrates, and cuts the UB tail to recycle the amino acids (like a garbage recycling truck)

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8
Q

What is the first enzyme to bind UB in the UPS, and where does UB end up after that in E2/E3?

A

E1 binds ubiquitin to itself,then transfers it to E2 enzyme, which transfers it to E3 or the protein that is going to be degraded

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9
Q

What is the role of DUB (deubiquinated)?

A

can remove the UB if the protein is found to be useful and it does not want to get rid of it

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10
Q

Where does the E1 enzyme bind the UB

A

it binds on a cys side chain forming a thioester bond, and attaches a Ub to itself

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11
Q

Where does the E2 enzyme bind the UB?

A

it binds Ub to its own Cys, after being transfered from E1

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12
Q

What type of transfer does E3 trigger?

A

E3 triggers UB transfer from E2 to Lys side chain on substate

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13
Q

what bond does the UB c-terminus covalent link form?
How many Ub sites can a substrate have?

A

it forms an isopeptide bond and it binds to side chain amine of lysine
-it can have many sites

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14
Q

what lysines can the UB c-terminus be linked to?

A

Lys 63, 48 or 11 of another Ub

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15
Q

What lysine form can be recognized for degradation and which ones cannot?

A

Lys 48 poly-Ub chains target protein for degradation by proteasomes
-mono Ub or lys 63 Ploy Ub are not recognized but signal other things

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16
Q

How many E3 enzyme genes are there and what does this diversity signify? can the same proteasome be used?

A

more than 600 E3 enzymes
-bc of diversity cells express diff E3 enzyme for various degradation situations (which all use the same proteasome since genes have only have 1)

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17
Q

What enzyme controls the substrate rate of degradation?

A

E3 ligase selectivity controls the degradation

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18
Q

What are 3 examples of E3 ligase selectivity degradation control?

A
  1. quality control degradation of a misfolded protein
  2. constitutive degradation of a native protein to control its level
  3. degradation of a native protein in response to a signal
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19
Q

What co-chaperone regulates mislfolded protein degradation, and what do the TPR domain and E3 ligase domain bind?

A

CHIP co chaperone
-TPR domain binds HSC70 and HSP90
-E3 ligase domain binds E2

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20
Q

What forms a complete E3 ligase complex?
What is selectively Ubiquintinated?

A

Chaperone, CHIP, and E2 from the E3 ligase complex
Chaperone-bound substrate is selectively UB

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21
Q

Why are interactions with the chaperones transient (fast binding and release)

A

this is bc if the substrates ar bound by chaperones for a long time they will form a complex with chip and be UB, so the short time allows them to escape being UB.

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22
Q

what are all proteins translated with?

A

with N-terminal Methionine (AUG start codon)

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23
Q

Why does a different residue become the N-terminus in proteins?

A

many proteins are processed by clevage within their sequences, so a diff residue is present at N-terminus

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24
Q

What does the N-End rule do and what happens when N-terminal residues are bound by N-end rule E3 ligases?

A

-N -end rule degrades the proteins rapidly, whether or not they are folded
-N-terminal residue bound by N-end rule E3 ligases Ub the protein

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25
What amino acids side chains are recognized by E3 ligases?
Arg, Lys, His, Phe, Trp, Tyr, Leu, Ile (basic or large hydrophobic amino acids)
26
How are n-end modifications done on acidic amino acids vs amindes?
Acidic- for aspartic acid and glutamic acid-->Arginine is added to N-terminus Amides-for asparagine (Asn) and glutamine (Gln)---> side chains converted to Aspartic acid (Asp), and Glutamic acid by removal of amine, then Arginine is added to N-terminus
27
What is the N-end rule pathway for Asparagine (N) vs Glutamine (Q)?
if n-terminal N, convert to aspartic acid (D) if n terminal Q, convert to glutamic acid (E)
28
what is N-end rule if N-terminal is D (aspartic acid) or glutamic acid (E)
-add N-terminal arginine (R) by arginine transferase
29
What is N-end rule for Arginine (R), lysine (k), histidine (H), phenylalanine (F), tryptophan (W), tyrosine (Y), Leucine (L), isoleucine (Ile)?
ubiquintinate the protein
30
what is the E3 UB ligase complex composed of in the degradation of the native state protein (SCF complex)?
1. its composed of Skp1, cullin (scaffold protein), f-box
31
What does the scaffold protein bind to
it binds E2 and substrate binding (f-box) protein
32
what does F-box protein bind to?
binds to the phosphorlyated substrate
33
Where is the fully binded substrate presented in the degradation of native protein?
presented to E2 for UB
34
what is used as a signal for degradation, what signal prevents degradation?
phosphorlyation by kinase is used as a signal for degradation dephosphorlyation prevents degradation
35
What does the SCF ligase complex degrade
it degrades the native state protein to stop their function
36
What composes the core and the caps of the proteasome?
central-20s core particle 2 caps on either end- 19s regulatory particles all together they form a 26s proteasome
37
where does the proteasome degrade proteins?
cytosol, nucleus and ER
38
What type of receptors does the 19S regualtory cap of the proteasome have?
it has ATPase and non ATPase subunits: ATPase- 6 AAA family (protein unfoldase) non ATPase- poly-UB receptor and deubiquintase (DUB)
39
what are the 3 functions of the UB receptor?
1. increase efficiency of targeting 2. select only K48 chains 3. protect against premature DUB activity
40
what are the 2 types of UB receptors?
1, intrinsic receptors- The Cap subunits Rpn10, 13 bind poly Ub 2. extrinsic (shubtting) Ub receptors
41
What does the Extrinsic (shuttling) Ub receptors do? What do they bind, what recognizes the cap?
-separate from proteasome -bind poly Ub through Ub associated domain (UBA) -have Ub-like domain (UBL) that is recognied by Cap
42
what are the 3 active subunits in each Beta ring of the proteasome core and what do they cut?
one cuts at basic AAs one cuts at acidic AAs One cuts at hydrophobic AAs
43
in what form do proteins have to stay in the proteasome core?
proteins have to stay unfolded since the cavity in the core is small and narrow
44
Is it possible to have a polypeptide sequence that is not degraded by the proteasome?
Yes, if we have a protein without a lysine it doesnt get degraded by the proteasome
45
What is the inner 20S core of the proteasome composed of?
it has 2 outer rings of 7 alpha subunits and 2 inner rings with 7 beta subunits
46
Where are proteins mainly found in the cell?
proteins are mainly found in the cytosol which is the soluble part of the cytoplasm
47
(START OF LEC 7) What is the secretory pathway and where does the system operate? Where are proteins/lipids synthesized?
-its a transport system between several types of organelles and the cell surface (plasma membrane) -synthesis of proteins/lipids both occur at the endoplasmic reticulum (ER)
48
where do the protein/lipids traffic through? where do they get internalized and degraded?
trafficked through the golgi, to the plasma membrane -internalized through the endosomes, to degradation in the lysosomes
49
what organelle is not connected to secretory pathway?
mitchondria
50
how do lumenal environment compare to extracellular vs cytosol?
lumenal environment is similar to the extracellular space but diff from the cytosol.
51
where do vesicles bud from and how do they fuse?
they bud from one organellear membrane and fuse without releasing contents into the cytosol
52
main difference between lumenal/extracellular compartment and cytosol
cytosol is reducing lumenal/extracellular is oxidizing (losing electrons)
53
what do biological membranes provide to cells, and regulate?
They provide an enclosure to cells and to organelles in the cells -they allow regulated transport of materials between compartments (like doors opening/closing)
54
What biochemical reactions do membranes provide sites for?
-photosynthesis, oxidative phosphorylation and for metabolism of biological molecules like lipids, glycans,etc
55
how do membranes support contact with the outside cell environment?
-they have cell motion, recognition of other cells, cell fusion -and transmission of signals from exterior to interior of cells
56
how do membranes support contact with the outside cell environment?
-they have cell motion, recognition of other cells, cell fusion -and transmission of signals from exterior to interior of cells
57
Where does the membrane form hydrophobic barriers, and is it flexible?
it forms hydrophobic barriers between aqeuous compartments within the cell (cytosol and organellar lumens) -it is flexible and can be formed into diff shapes
58
What is the peremability of the membrane?
selectively permeable to small hydrophobic molecules, but not to larger or charged/polar molecules
59
What controls the movement of impermeable molecule across the memebrane?
specialized protein complexes
60
How is energy stored in the cell membrane, what are the types of gradients?
it stores energy as concentration gradients -voltage in nerve cells -ph, potassium, sodium, calcium gradients
61
What are membranes made out of?
lipid molecules and membrane proteins
62
What is the bilayer composed of?
a sheet that is polar on each side, and hydrophobic in the middle
63
What does hydrophobicity act as? How do membrane proteins move?
hydrophobicity acts as a barrier to water-soluble molecules -membrane proteins can rotate and diffuse laterally in the fluid bilayer
64
what are the major lipids in membranes?
phospholipids-in all membranes glycolipids- only at plasma membrane cholesterol-in all membranes but very enriched in plasms membrane
65
What physical properties do the lipids determine?
it determines mobility (diffusion/rotation) and the curvature/thickness of the membrane
66
What is the phospholipid polar head group composed of?
choline/other charged groups -phosphate and glycerol (glycerol acts as a linkage between non polar and polar parts) -they are hydrophillic
67
What are the 2 fatty acid tails composed of?
-they are different lengths -they can be saturated (no double bonds) or unsaturated (with double bond) -they are hydrophobic
68
what are the different types of phospholipid head groups?
phosphophatidyl-choline (PC) phosphophatidyl-ethanolamine (PE) -phosphophatidyl-serine (PS) -phosphophatidyl sphingomyelin (SM)
69
what phospholipid can act as a signaling molecule?
phosphophatidyl-inositol (PI) is not abundant but can be phoshphorylated and act as a signaling molecule
70
How does the head group affect mobility?
the different charges/size
71
How many carbons is the hydrocarbon chain composed of?
usually 14-24 carbons
72
What are saturated tails?
they have no double bonds and are straighter and more flexible
73
What do unsaturated/double bonds introduce?
they introduce bends in the tail, and reduce flexibility and overall length
74
What does the type of tail in the membrane determine?
-determines the thickness and fluidity of the membrane
75
Where are glycolipids found?
only found on the outside surface of the plasma membrane
76
why is it important that the head groups contian different sugar groups in many combinations?
it is important for cell contacts with the environment and other cells
77
what can the different sugar groups be on the glycolipids?
Glucose, galactose and NANA
78
What structure makes cholesterol rigid, and how does this affect its mobility?
steroid ring structure makes cholesterol very rigid -the lateral mobility and roation is much lower -and it reduces mobility of surrounding phospholipids by making fatty acid tails more rigid
79
how does cholesterol affect the length of fatty acid tail?
it makes the tail longer which makes the membrane thicker causing the channel sizes to change
80
what is membrane asymmetry?
asymmetry of the plasma membrane means lipid composition on each side is diff
81
What does the exterioe of asymmetrical membranes have, and how does the charge change?
extereior has glycolipids -the interior has a stronger negative charge due to a high phosphophatidyl-serine levels(PS)
82
How is the assymtry maintained?
it is actively maintained
83
What has the highest level of cholesterol?
plasma membrane has highest cholesterol level
84
what has the highest level of phosphophatidyl-choline (PC) and phosphophatidyl-ethanolamine (PE)
ER and mitchondria
85
what are microdomains?
they are regions of the membrane that are organized laterally in patches
86
What specialized microdomains does the plasma membrane and trans-golgi have, and what does the microdomain do?
lipids rafts: which are thicker than the surrounding membrane, enriched and cholesterol (helps straighten fatty acid tails) -and lipdis with longer tails cluster together in rafts

ANAT 212 pre midterm (9 decks)

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