Post Translational Modification: Lecture 2

Question 1

What cellular events is PTM involved in? (6)

Answer 1

gene expression
signal transduction
cell-cell interaction
protein-protein interaction
communication between intra and extracellular environment

Question 2

What is trasncriptome?

Answer 2

whole mass of mrna transcripts in the body

Question 3

what is PTM?

Answer 3

Covalent addition to or cleavage of proteins
After/ during biosynthesis
important in cell signalling
occurs on amino acid chains or at a terminal

Question 4

What is proteome?

Answer 4

total mass of proteins in body- roughly 1 million

Question 5

How are there more proteins than genes?

Answer 5

splicing process and PTM

Question 6

what are the 3 types of germ layers that cells can differentiate into?

Answer 6

Endoderm- internal layer e.g. lung, thyroid, pancreatic cell
Mesoderm- middle layer e.g. cardiac, rbc, smooth muscle gut, skeletal muscle
Ectoderm- outer layer e.g. skin cells, neurone brain, pigment cells.

Question 7

how does PTM relate to proteome?

Answer 7

PTM increase diversity of proteome whilst extending function and stability- because it affects the longevity as well as activity of protein.

Question 8

Types of PTM to a protein? (5)

Answer 8

Glycosylation
Phosphorylation
Disulfide bond
Methylation
Acetylation

Question 9

summary of glycosylation?

Answer 9

attach sugar- usually to N or O in amino acid side chain

Question 10

summary of methylation?

Answer 10

add methyl group- usually at lysine or arginine residues

Question 11

summary of acetylation?

Answer 11

add acetyl group to N-terminus of protein or at lysine residues

Question 12

summary of disulfide bond?

Answer 12

covalent bond of S at two cysteine residues

Question 13

summary of phosphorylation?

Answer 13

Add phosphate to serine, threonine or tyrosine

Question 14

genres of PTM? (4)

Answer 14

cleavage- proteolysis
complex molecules- glycosylation
chemical- acetylation, methylation, phosphorylation
proteins/peptides- ubiquitylation, sumoylation

Question 15

example of cleavage PTM in cell?

Answer 15

Insulin production. Unwanted parts of the peptide removed after translation and translocation and folding. It gets PMT with disulfide bonds (signal peptide) and then gets exported to Golgi where it’s cleaved

Question 16

Whats the point of adding functional groups as PMT?

Answer 16

enable cell signalling and cell can react specifically and rapidly to events like environmental conditions. Fast bc can just activate/inactivate protein for rapid response e.g. insulin

Question 17

key points of effects of phosphorylation? (4)

Answer 17

1. Reversible addition/removal
2. Phosphate from hydrolysis of ATP to ADP
3. Cause conformational change bc phosphate -2 charge. Cause charge disparity in amino acids and change structure
4. Can activate (open up/reveal active site) or deactivate (mask binding site)

Question 18

2 ways phosphate can be added/taken away?

Answer 18

protein kinase and phosphatase

Question 19

What does protein kinase do?

Answer 19

catalyse transfer of phosphate from high energy donor to specific substrate phosphorylation

Question 20

what is kinome?

Answer 20

whole family of 513 kinases- 35 atypical catalytical domain, 478 homologous domain

Question 21

what does phosphatase do and key points about it? (4)

Answer 21

catalyses dephosphorylation- removal of phosphate from substrate by hydrolysing monoesters into phosphate ion and molecule with free hydroxyl group
Broad range or specific
broad range controlled by regulatory proteins
often in chain-cell signalling

Question 22

Steps of phosphorylation in regulating glycogen breakdown?

Answer 22

1. epinephrine bind receptor
2. activates adenylyl cyclase
3. adenylyl cyclase convert atp to cAMP
4. cAMP activate cAMP-dependant protein kinase
5. this activates phosphorylase kinase by phosphorylation
6. this activates glycogen phosphorylase by phosphorylation
7. converts glycogen to glucose-1-phosphate

Question 23

What is definition of glycosylation?

Answer 23

carbohydrate (monomer to complex) covalently bound to functional group e.g. hydroxyl on protein by glycosidic bond

Question 24

Functions of glycosylation? (6)

Answer 24

1. correct folding
2. increase protein stability- secreted proteins
3. cell/cell or cell/environment adhesion
4. immune response
5. hormone activity
6. embryonic development

Question 25

what is the molecule which anchors carbohydrate to the membrane?

Answer 25

Dolichol

Question 26

Whats the process of dolichol, glycosylation and golgi?

Answer 26

membrane of ER have dolichol with phosphate on the side of cytosol. Then carbs added. Then flipase flips it so its on the lumen side. Simultaneously, ribosome translating mrna and folding Glycosyl transferase attach the carb structure to the polypeptide Gets transferred to golgi where gets modified- n-linked or o-linked glycosylation

Question 27

what are all the types of places glycosylation can get linked?

Answer 27

N-linked O-linked C-linked Glypiation Phosphoglycosylation

Question 28

Bond, location example of N-linked?

Answer 28

Glycan bind to amino group on asparagine endoplasmic reticulum insulin receptor, ecm, regulation

Question 29

bond, location, example O -linked?

Answer 29

monosaccharides bind to hydroxyl group serine/threonine ER, golgi, cytosol collagen, pathogenic bacteria e.g. clostridium toxins

Question 30

Bond, loaction example Glypiation?

Answer 30

glycan core links a phospholipid and protein plasma membrane? anchors cell surface proteins

Question 31

bond of C-linked?

Answer 31

Mannose binds to indole ring of tryptophan

Question 32

Main points of acetylation? (4)

Answer 32

addition/removal of acetyl group (CO-CH3) donated by Ac-CoA co or post translational 80-90% co translational at N-terminal of polypeptide

Question 33

what are the 2 types of acetylation?

Answer 33

N- terminal: *co-translational modification eukaryotes *synthesis localisation stability *80-90% proteins Lysine acetylation: *acetylation /deacetylation linked to transcription factors *activation of gene expression

Question 34

what is NAT and what it do?

Answer 34

N-terminal acetyltransferases- catalyses n terminal acetylation transfer acetyl group from coA to the alpha amino group on the first amino acid residue of polypeptide chain

Question 35

how does histone modification work and what controls it?

Answer 35

histone acetylation- controlled by HAT/ KAT (histone/lysine acetyltransferase). Relaxes chromatin structure. histone deacetylation- controlled by HDAC/KDAC (histone/lysine deacetylase) remove acetyl group and DNA get more tighter, reduce gene expression

Question 36

How does acetylation of histone increase transcription?

Answer 36

removes positive charge from the histone, encourage binding of effector proteins and relaxation of chromatin

Question 37

Therapeutic applications of acetylation? (3)

Answer 37

1. targeting HDAC in malignant cells- because these are in charge of reducing gene expression 2. HDI- small molecule inhibitors 3. T cell lymphoma targeted by issuberoylinine hydroxamic acids

Question 38

Methylation and key points? (3)

Answer 38

addition of methyl group CH2- changes activity of protein lysine- 3 times methyl can be transferred arginine- 2 times methyl transferred

Question 39

key points of lysine methylation? (4)

Answer 39

activation/suppression reversed with demethylase histone function regulation epigenetic regulation of transcription

Question 40

What is KMT?

Answer 40

lysine methyltransferase. Donates the methyl group from S-adenosylmethionine

Question 41

difference between carbonyl and nitrogen methylation?

Answer 41

carbonyl- reversible and used to modulate reaction nitrogen- irreversible and used to create new amino

Question 42

Key points of arginine methylation? (5)

Answer 42

regulating RNA processing gene transcription DNA damage repair protein translocation signal transduction

Question 43

what's p53 got to do with PMT? (4)

Answer 43

1. p53 activity controlled by acetylation, phosphorylation, methylation 2. concentrated in N and C terminals 3. acetylation increase p53 stability- increase dna interaction 4. under stress, upregulation of kinase activity- reduce p53 activity and increase cofactor activity