Small PTMs

Question 1

ATP

Answer 1

• always in excess
• recycled 1000-1500 times/day

Question 2

phosphorylation targets

Answer 2

• polar (OH side chains)
• basic
• acidic
• Cys

Question 3

A. kinome

Answer 3

918

Question 4

Protein Kinase A

Answer 4

• aka cAMP-dependent protein kinase
• promotes glycogen -> glucose during flight/fight (but multifunctional)
• 290aa kinase domain
• regulated by Regulatory Subunit

Question 5

Protein kinase A cascade

Answer 5

1) phosphorylates phosphorylase kinase
2) phosphorylates glycogen phosphorylase
3) glycogen -> glucose-1-phosphate

Question 6

PKA activation

Answer 6

1) adrenaline activates GPCR
2) GPalpha released, binds to adenylate cyclase
3) Regulatory subunit dissociates from cAMP
4) phosphorylated by PDK1 in activation loop; folds to orient catalytic residues

Question 7

PKA inactivation

Answer 7

• cAMP hydrolysis
• Regulatory subunit binds

Question 8

Dephosphorylation

Answer 8

• 189 in humans (mostly for cysteine)
• 0.89% proteome
• 10 different folds

Question 9

Methylation

Answer 9

• can occur on acidic and basic N and C termini
• N and O methylation
• S-adenosyl-methionine derived using MT

Question 10

MTs

Answer 10

• humans: 51
• A. thaliana: 49
• SET domains

Question 11

His methylation

Answer 11

• SETD8 methylates beta-actin His73
• decreases ATP-hydrolysis
• setd3 knockout: reduced progeny due to birth defects

Question 12

Lys methylation

Answer 12

• FliB methylates Salmonella
• promotes hydrophobic cell adhesion and invasion via hydrophobic epithelial interaction

Question 13

H3K4me

Answer 13

active

Question 14

H3K9me

Answer 14

constitutive heterochromatin

Question 15

H3K27me

Answer 15

facultative heterochromatin

Question 16

Demethylation

Answer 16

• O-methylation requires hydrolysis, releasing methanol
• N-methylation requires FAD-cofactor reduction and hydrolysis
• lysine specific HDMs

Question 17

acetylation

Answer 17

• general at N-terminus
• regulatory at Lys

Question 18

N-terminal acetylation

Answer 18

• 85% human proteins
• NATs with GNAT domains

Question 19

NATs

Answer 19

• 8 in eukaryotes
• 3 in bacteria
• 1 in archaea

Question 20

Lysine acetylation

Answer 20

KATs, HATs and GNATs

Question 21

KATs

Answer 21

• 17 in humans
• 12 in arabidopsis

Question 22

Deacetylation

Answer 22

• KDACs, HDACs (share the same KDAC fold)
• 18 in humans and arabidopsis

Question 23

H3K27ac

Answer 23

activates transcription