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Biochem 385 Unit 3 > Lecture 36: Protein Targeting > Flashcards

Lecture 36: Protein Targeting Flashcards

1
Q

protein targeting (just in eukaryotic cells)

A

gest proteins where they need to go

glycosylation

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2
Q

protein synth signal sequences

A

signal sequences at N terminus

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3
Q

signal sequences at N terminus

A

of nascent polypeps

direct protein transport

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4
Q

How do signal sequences at N terminus direct protein transport?

A

by interacting with receptors and processing enzymes

signal sequences are 10-30 aas long
highly conserved

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5
Q

Signal Recognition Particle (SRP)

A

directs ribosome w/ nascent polypets destinred for:
secretion
insertiion into plasma membrane
or inclusion into lysosomes

to ER to complete protein synth

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6
Q

what do the 3 vesicle transport systems do?

A

sort ER localized proteins (many are glycosylated) to various destinations by packing into vesciles

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7
Q

what are the 3 vesicle transport systems

A

COPI, COPII, clathrin

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8
Q

ubiquitinated proteins…

A

are recycled by proteasomes in order to regulate protein turn over

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9
Q

Function of N-terminal sequence in protein transport

A

direct protien to right subcellular compartment

how? bind receptor protein

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10
Q

most signal sequences…

A

15-35 amino acids
10-15 aas are hydrophobic
have either lisine or argenine at beginning (POSTIVELY CHARGED)

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11
Q

what can hydrophobic aas do?

A

transverse the ER membrane

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12
Q

where is the N terminus

A

FIRST

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13
Q

Why lisine or argenine?

A

they are positively charged!

so pos charged residue followed by hydrophobic stuff

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14
Q

What marks the C terminal end of sequence

A

protease cleaveage site

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15
Q

why are signal sequences cleaved and what by

A

cleaved by specific proteases

in order to generate a new N-terminus in mature polypeptide

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16
Q

signal sequence

A

positive charge (lys or arg) followed by hydrophobic amino acids

targets protein with this sequence to the ER

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17
Q

if no signal sequence

A

protein is retained in cytoplasm

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18
Q

So proteins destined for ____1_____ are insterted into ___2__ by ___3___

A

1: secretion, integration into plasma membrane, inclusion into lysosomes
2: lumen of ER
3: SRP (signal recognition complex)

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19
Q

signal sequence directs protein transport

A

signal peptide of end terminus synthed first (N terminus)

hydrophobic sequence recognized, tells ribsome to bind to ER membrane

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20
Q

where is rest of growing protein inserted?

A

through membrane protein

so that growing polypep chain can keep growing in ER

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21
Q

if you take a cytosolic protein and manipulate it to encode an end terminal signal peptide on the protein…

A

protein will go into the ER!!!

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22
Q

if you take a protein that usually has ER signal sequence (should be in ER) and remove the signal sequence…

A

it stays in the cytosol

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23
Q

Based on these experimental data, are signal sequences necessary BUT NOT sufficient (to direct localization) or necessary AND sufficient?

A

necessary AND sufficient
if it has tag it goes into ER, if it doesn’t it doesn’t, stays in cytoplasm

this tag is enough, doesn’t need other properties

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24
Q

SPR cycle does what

A

inserts proteins into ER lumen

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25
Q

if a signal sequence is present on growing polypep chain at n terminus…

A

SRP recognizes it and it interacts with the SRP receptor on ER membrane

as polypep grows, it goes through pore and ends up in ER

this is driven by GTP

26
Q

how long is protein synth halted

A

till ribosome, mRNA, and SRP-polypep complex is bound to peptide translocation complex

27
Q

What biochemical property of signal sequences facilitattes binding to the translocon protein?

A

hydrophobic property!!!!

28
Q

SRP cycle slide 6

A

slide 6

29
Q

what is synthed frist

A

signal sequence

recognized by SRP

30
Q

interaction with translocation complex in ER membrane

A

docking of ribosome happens

newly synthed chain ends up in lumen

31
Q

do mature proteins retain the signal peptide

A

No, they are processed

32
Q

how are proteins processed?

A 
by protease (cleaves proteins)
mature end terminus and mature protein left in ER
33
Q

glycosylation

A

adding of sugar units to proteins

happens in ER

34
Q

what do we do with glycolyated proteins

A

transport them into plasma membrane

they are used in membrane for cell recognition function

35
Q

why glycosylate proteins?

A

for cell cell recognition
happens AS synthesized

NOT in RNA code!

36
Q

things that happen in ER

A

glycosylation

formation of disulfide bonds between SH and cystine residues

37
Q

how to glycosylated

A

link sugar unit to aspariagine residue of protein
sugar first binds in cytosol
process completed in ER

38
Q

core glycan

A

the first sugars that are added

39
Q

How are proteins degredaded

A

proteosomes

lysosomes (not talked about much, low pH, have proteases in them, degrade more than just proteins)

40
Q

proteosomes

A

just degrade proteins
recognize proteins for degredation because tagged with ubiquitin
allow cell to regulate proten levels

41
Q

cellular protein life times

A

finite
degraded at end
tagged

42
Q

ubiqutin

A

small (76 amino acids)
covalently linked to lysine residues in proteins marked for destruction
very well conserved across species

43
Q

important features of ubiquitin

A

lysine residues

cc-terminus

44
Q

importance of lysine residues

A

sites where ubiqutin can be conjucated to other ubiquitin molecs so chains of ubiquitin molecs can form

45
Q

What enzymes ubiquinate

A

E1
E2
E3
target proteins for ubiquitination for degredation

46
Q

E1

A

attached ubiquitin to itself

forms covalent bond

47
Q

E2

A

ubiquitin transferred here

another covalent bond formed so that Ub is bound to E2 enzymes

48
Q

E3

A

E3 binds to E2 and substrate

Substrate is protein tagged for degradation here

49
Q

making a chain of ubiquitin

A

after E3 step…

ubiquitin transferred from E2 to substrate FOUR times (at least) to make chain of ubiqutin molecs attached to substrate

50
Q

what is the substrate

A

the protein tagged for degredation!

need at least 4 Ubs attached for the protein to be marked for degredation

51
Q

what happens after substrate is marked by at least 4 Ubs

A

signal for degredation sent
proteosme protyolizes proteins, degrades it (using ATP)
Ubs recycled so it can happen again

52
Q

Proteosome structure

A

20S core

two 19 S caps (one per end)

53
Q

what to the caps on the proteosome do?

A

can cause conformation change and open to let the protein to be degraded in

they have binding sites for ubiquitinated proteins
encode ATP hydrolyzing enzymes

54
Q

proteasome core

A

protease sites are here

proteolyze protein down to peptides (which are released when cap opens up again)

55
Q

The inner chamber contains the protease enzymes, what doe the outer chamber to do “prepare” proteins for degredation?

A

1) cap recognizes targeted ubiquitinated proteins

2) unfolds the protein so sites are accessible for proteases in the core

56
Q

how many kinds of proteases?

A

Just one!
uses ATP for unfolding
general because all it has to recognize is the ubiqutinated part

57
Q

Ubiquitinatation requires 3 classes of enzymes

A

1) E1 enzymes ACTIVATE ubiquitin (C-terminus)
transfer to
2) E2 enzymes CONJUGATE ubiquitin to target proteins at lysine residues
interact with
3) E3 enzymes RECOGNIZE TARGET PROTEINS and facilitate ubiquitination by forming complexes with E2 enzymes

58
Q

remember… why do we need lysine and C terminus

A

to form the ubiquitin chain

59
Q

so how do we ID how long the half life of a protein is?

A

based on what the amino acid after Met is (b/c Met is often taken off)

60
Q

really brief overview of ubiquitination

A

Ub is added to E1, transferred to E2, interaction between E2 and E3 happens, Ub transferred to target protein

61
Q

N-end rule

A

identifies proteins with N-terminal amino acid after Met is removed

tells us how long the protein will be around in cells

62
Q

Explain why humans have 2 E1 genes, 40 E2 genes, but 400 E3 genes.

A

E1 works independently of the target protein, just works with Ub
E2 enzymes have to interact with LOTS of E3 genes
E3: lots of genes so that you can degrade a lot.

Biochem 385 Unit 3 (11 decks)

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