1.8: Regulation of the Proteome

Question 1

are ubiquitination and ubiquitylation the same

Answer 1

yes

Question 2

where is the proteasome found

Answer 2

cytosol and nucleus (~1% of cellular protein)

Question 3

describe the 3d structure of a proteasom

Answer 3

a hollow cylinder w a cap at each end and an active site in the cope

Question 4

state the purpose of the caps on the proteasome

Answer 4

protects cellular proteins from degradation

Question 5

state the tag that the receptor on the proteasome looks for + can it be reused

Answer 5

ubiquitin, yes it can be reuused

Question 6

the longer the polyubiquitin chain = higher or lower chance of destroying prot

Answer 6

higher chance

Question 6

which system adds ubiquitin to proteins and what enzymes is it made up of + explain the enzyme

Answer 6

ubiquitin-conjugating system
E1. an atp dependent ubiquitin activating enzyme creates an activated e1 bound ubiquitin
E2. ubiquitin-conjugating enzyme accepts ubiquitin from e1 and exists as a complex w E3, a ubiquitin ligase that selects substrates (which prot gets ubiquitin)
E2-E3 complex work together w diff specificities
E3. binds to specific degradation sequences (sees hydrophobic aa exposed)

Question 7

how many of each enzyme in the ubiquitin-conjugating system are there in humans

Answer 7

a couple E1s, ~30 E2, 100s of E3

Question 8

which residue is ubiquitin added to

Answer 8

lysine reside - on the r group (repeat process to make the polyubiquitin chain)

Question 9

what is the ubiquitin-modification’s function dependent on

Answer 9

number of ubiquitin molecules and type of linkage

Question 10

describe the other function of ubiquitin modifications and how many ubiquitin they need

Answer 10

monoubiquitylation: histone regulation
multiubiquitylation: endocytosis
polyubiquitylation: if on lys48 then proteasomal degration, if on lys63 then dna repair

Question 11

how can ubiquitin ligase (e2-e3 complex but it’s incorrect to call it a ligase) be activated (3)

Answer 11

1. phosphorylation by a protein kinase req atp
2. allosteric transition caused by ligand binding
3. allosteric transition caused by protein subunit addition

Question 12

how can a degradation signal be activated (3)

Answer 12

1. phosphorylation by a protein kinase req atp
2. unmasking by protein dissociation
3. creation of destabilizing n-terminus

Question 13

covalent modification is an example of _________ regulation

Answer 13

post-translational regulation

Question 14

t/f can multiple modificatoins occur on the same protein

Answer 14

yes

Question 15

(something wrong with) protein p53 may related to what disease

Answer 15

cancer - in abt 1/2 of human cancer, there’s something wrong with this

Question 16

what are 7 ways to turn an inactive protein into its active form

Answer 16

protein synthesis, ligand binding, covalent mods, addition of 2nd subunit, unmasking, stimulation of nuclear entry, release from membrane

Question 17

describe the full example of gene expression regulation by pka (goodluck). terms to involve: cAMP, compare inactive to active form, where it’s invovled

Answer 17

numerous extracellular stimuli result in increased levels of cAMP which activates protein kinase a (pka). inactive pka (in cytosol) has 2 regulatory subunits and 2 catalytic subunits. binding of cAMP to the regulatory subunits causes a conformational change and release of the active catalytic subunits (in nucleus). pka substrates include the enzymes involved in glycogen metabolism in skeletal muscle and liver (ligand is adrenaline to promote glucose release). activated pka results in glycogen breakdown promotion and inhibition of glycogen synthesis. glycogen is broken down into glucose-1-phosphate (–> glucose-6-phosphate–>glycolytic pathway)

Question 18

activated pka catalytic subunits are translocated from where to where

Answer 18

from cytosol where it was inactive to nucleus where it is active

Question 19

pka catalytic subunits phosphorylate specific substrate proteins which activate target genes containing what

Answer 19

cAMP responsive elemenets (CRE)

Question 20

the activation of target genes w cre leads to

Answer 20

activated pka phosphorylates creb (cre binding protein) –> creb recruits cbp (Creb Binding Protein) coactivator –> target genes are transcribed (eg in the liver, transcription of the gene glucose-6-phosphatase (dephosphorylates glucose-6-p to glucose –> released into the blood)

Question 21

what is the interactome map

Answer 21

complete collection of protein-protein interactions of an organism

Question 22

on the human interactome - each dot is a _____ and each line is a ______

Answer 22

each dot is a protein node and each line is an interaction edge

Question 23

describe the guilt by association framework

Answer 23

protein interaction can provide insights into function thus guilt by association. assume that an unknown protein has related functions to proteins it interacts w (eg if one does damage then they both do) == guilt by association

Question 24

In humans, there are a couple of different E1 proteins, approximately thirty
different E2 proteins, and hundreds of different E3 proteins. Which of the
following likely has the greatest effect on a cell?
A. A miRNA targeted at an E1 RNA.
B. A miRNA targeted at an E2 RNA.
C. A miRNA targeted at an E3 RNA.
D. All of the above would have an equal effect.

Answer 24

a. bc only a few E1s so cascading effect

Question 25

The introduction of a miRNA targeting adenylyl cyclase will likely result in
which of the following?
A. Increased phosphorylation of glycogen phosphorylase kinase.
B. Increased phosphorylation of CREB.
C. Increased genomic CRE sequences.
D. Decreased cyclic AMP production.

Answer 25

d.
bc it’ll target adenylyl cyclcase rna - no camp, no activated pka, no phosphorylation