Topic 1, Lecture 3

Question 1

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

Answer 1

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

Question 2

describe the 19S cap, what it must have,

Answer 2

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

Question 3

what is the unfoldase ring (hexameric ring)

Answer 3

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

Question 4

what is ubiquitin receptor?

Answer 4

ensures that protein is recognized by their ubiquitin tag

Question 5

what is ubiquitin hydrolase?

Answer 5

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

Question 6

what is a degron

Answer 6

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

Question 7

what does the degron do?

Answer 7

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

Question 8

what 2 things must happen in the degron process?

Answer 8

activated degron signal, activate E3

Question 9

what could the degron be?

Answer 9

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

Question 10

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

Answer 10

80%

Question 11

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

Answer 11

over 600

Question 12

how many distinct E2 molecules

Answer 12

30

Question 13

Ubiquitin ligase can also signal the degron via E3 by

Answer 13

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

Question 14

what is allosteric regulation and what does it do?

Answer 14

shape change, it adopts multiple (slightly different) conformations

Question 15

what is kinase? what does it need?

Answer 15

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

Question 16

what is the function of phosphatase?

Answer 16

it takes the phosphate off

Question 17

what is the purpose of kinase families?

Answer 17

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

Question 18

how can we alter affinity?

Answer 18

by conformation change

Question 19

Describe cyclic AMP

Answer 19

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.

Question 20

what is GTP

Answer 20

the active hydrolysis

Question 21

what is GDI

Answer 21

guanine dissociation inhibitor, binds to GDP bound form

Question 22

what is GDP

Answer 22

inactive dissociation

Question 23

what is GEF

Answer 23

guanine exchange factor GDP to GTP increasing activation

Question 24

what is GAP

Answer 24

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

Question 25

have to add what to make active again?

Answer 25

GTP

Question 26

What is GDI's purpose to GDP ?

Answer 26

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

Question 27

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

Answer 27

GTP is in postion and GDP is out of position

Question 28

what controls how active/ inactive a protein is?

Answer 28

a spectrum of covalent modifications that produces a regulatory protein code

Question 29

what are the covalent modifications?

Answer 29

activity location interaction with other proteins