Topic 1, Lecture 3 Flashcards

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1
Q

What is the structure of proteasome? And what is the components…

A

keeps the entire substrate bound until all of it is converted into short polypeptides, 19S cap and 20S core

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2
Q

describe the 19S cap, what it must have,

A

clips off ubiquitin and sends it back to be used again
Ubiquitin hydrolase, cap must have ubiquitin receptor, hydrolase, and unfoldase ring

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3
Q

what is the unfoldase ring (hexameric ring)

A

it is 6 proteins with loop that sticks out in the middle loop catch. completely denatures the proteins to allow the protease to reach the amino acids

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4
Q

what is ubiquitin receptor?

A

ensures that protein is recognized by their ubiquitin tag

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5
Q

what is ubiquitin hydrolase?

A

clips off ubiquitin from target protein as it is pulled into proteasome

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6
Q

what is a degron

A

a minimal element within a protein that is sufficient for degradation by a proteolytic system

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7
Q

what does the degron do?

A

binds to E3, and ubiquitin binds on the side, polymerizes when enough ubiquitin is added

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8
Q

what 2 things must happen in the degron process?

A

activated degron signal, activate E3

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9
Q

what could the degron be?

A

phosphorylation by protein kinases, unmasking by protein dissociation, creation of destabilizing n-terminus

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10
Q

what percent of human proteins will have an exposed acetylated protein on the n-terminus

A

80%

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11
Q

How many E3 ligase genes to ensure that the wide variety of proteins to be polyubiquitinated, can be modified when necessary?

A

over 600

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12
Q

how many distinct E2 molecules

A

30

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13
Q

Ubiquitin ligase can also signal the degron via E3 by

A

phosphorylation by protein kinases, allosteric transition caused by ligand binding, allosteric transition caused by protein subunit addition

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14
Q

what is allosteric regulation and what does it do?

A

shape change, it adopts multiple (slightly different) conformations

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15
Q

what is kinase? what does it need?

A

enzyme that phosphorylates proteins can be inactive or active, it needs phosphate binding loop (catalytic loop)

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16
Q

what is the function of phosphatase?

A

it takes the phosphate off

17
Q

what is the purpose of kinase families?

A

changing the function of a protein, and translocation, activity, interactions with other proteins

18
Q

how can we alter affinity?

A

by conformation change

19
Q

Describe cyclic AMP

A

it is bound to the folded protein, multiple covalent bonds present, h-bond between amino and side chain of cyclic amp, cyclic amp has a high affinity for binding site.

20
Q

what is GTP

A

the active hydrolysis

21
Q

what is GDI

A

guanine dissociation inhibitor, binds to GDP bound form

22
Q

what is GDP

A

inactive dissociation

23
Q

what is GEF

A

guanine exchange factor GDP to GTP increasing activation

24
Q

what is GAP

A

GTPase activation (accelerating protein, inactivate protein by speeding up hydrolysis

25
Q

have to add what to make active again?

A

GTP

26
Q

What is GDI’s purpose to GDP ?

A

it locks GDP in site so it cannot be replaced (it keeps it inactive

27
Q

on the picture of the switch helix which is in position and which is out of position?

A

GTP is in postion and GDP is out of position

28
Q

what controls how active/ inactive a protein is?

A

a spectrum of covalent modifications that produces a regulatory protein code

29
Q

what are the covalent modifications?

A

activity
location
interaction with other proteins