Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

BGM2002 CS > L4 - PTMs > Flashcards

L4 - PTMs Flashcards

1
Q

what is a PTM?

A

the addition of a chemical group or molecule to specific amino acids of a protein

can generally be added or removed

add to the complexity of the proteome

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

what do PTM give you?

A
  • information transfer
  • signal amplification
  • cross-talk between pathways
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

what can PTMs do to a protein?

A
  • create/block a binding site
  • change the conformation of a protein
  • affect stability of protein
  • affect location of protein in cell
  • lead to rapid amplification
  • allow cross-talk between pathways
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

what is phosphorylation?

A

addition of a phosphate to either a tyrosine, threonine or serine

adds a negative charge

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

how does phosphorylation occur?

A

gamma phosphate group of ATP donates the phosphate to the base by nucleophilic attack

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

what bases can phosphorylation occur at?

A
  • tyrosine
  • threonine
  • serine
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

how many human protein kinases are there?

A

518

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

why is phosphorylation/dephosphorylation an important control mechanism?

A
  • it is rapid
  • doesn’t require new proteins to be made/degraded
  • easily reversible
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

why does lysine get modified in lots of different ways?

A

has a very reactive positive epsilon-amino group

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

what is lysine acetylation?

A

the addition of an acetyl group by acetyl-CoA by acetylases

neutralises positively charged epsilon-amino group and creates a binding site for specific proteins that recognise acetylated lysine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

how do acetylases transfer the acetyl group to the epsilon-amino group?

A

a conserved glutamate residue in the acetylase activates a water molecule for removal of a proton from the amine group on lysine
activates it for nucleophilic attack on the carbonyl carbon of enzyme bound acetyl-CoA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

what are HATs?

A

histone acetyltransferases

co-activators that activate gene transcription

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

what are HDACs?

A

histone deacetylases

co-repressors that cause gene silencing

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

lysine methylation

A

doesn’t necessarily neutralise the positive charged epsilon-amino group

comes in 3 different types - mono, di and tri
• recognised by different proteins
• increases diversity of modification

S-Adenosyl methionine (SAM) serves as a co-factor & methyl donor group for lysine (and arginine) methylation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

arginine methylation

A

has a positively charged side chain with an amino group

comes in the de-methylated form

involved in chromatin structure

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

what histone modifications control chromatin structure?

A

lysine acetylation
lysine methylation
arginine methylation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

what are writers?

A
  • proteins that deposit the modification
  • write the modification code
  • kinases, acetylases, methylases
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

what are readers?

A
  • proteins that recognise modifications

* read and translate the code

19
Q

what are erasers?

A

proteins that remove modifications

20
Q

what do the different protein domains do?

A

can recognise phosphorylated motifs in target proteins

21
Q

what does the SH2 domain recognise?

A

recognises phospho-tyrosine in cell surface receptors

• allows the docking of proteins that promote growth and survival

22
Q

what does the WW domain recognise?

A

recognises phospho-serine/proline

• helps cell cycle control

23
Q

what does the FHA domain recognise?

A

recognises phospho-threonine domains

• is a DNA damage checkpoint

24
Q

what does the family of 14-3-3 proteins recognise?

A

recognises distinct phospho-serine/threonine motifs

• important in cytosolic retention and regulation

25
Q

what is BD?

A

bromodomain

26
Q

what is CD?

A

chromodomain

27
Q

combinational PTMs

A

modifications such as methylation, phosphorylation or acetylation are commonly recognised by proteins with PTM-recognition sites

modifications such as lysine methylation can occur up to 3 times on a single residue resulting in PTMs with distinct activity

neighbouring PTMs have different affects on the ability of proteins to recognise a phosphorylation site

they determine which protein-protein interactions lead to distinct biological outcomes

28
Q

what are histones?

A

proteins that condense and structure the DNA of eukaryotic cell nuclei into units called nucleosomes

they impact gene regulation - positively and negatively

29
Q

what are the core histones?

A

H2A
H2B
H3
H4

30
Q

what is the nucleosome core formed of?

A

2 H2A-H2B dimers

1 H3-H4 tetramer

31
Q

what are the histone H3 variants and modifications?

A

histone 3K4
histone 3K9
histone 3K27

(4,9,27)

32
Q

what are the histone H4 variants and modifications?

A 
histone 4K5 
histone 4K8
histone 4K12 
histone 4K16
histone 4K20

(5,8,12,16,20)

33
Q

histone 3K4

A

activation

can be methylated and acetylated

34
Q

histone 3K9

A

turns genes on when acetylated

silences genes when methylated

35
Q

histone 3K27

A

shuts down transcription

trimethylation is associated with inactive gene promoters

acts in opposition to H3K4me3

36
Q

histone 4K5

A

closest lysine residue to N-terminal tail of H4

can be acetylated and methylated

activator

37
Q

histone 4K8

A

lysine on tail of H4

only acetylated

activator

38
Q

histone 4K12

A

lysine on tail of H4

only acetylated

activator

part of a ‘backbone’ of histone modifications that are associated with active promoters

39
Q

histone 4K16

A

lysine on tail of H4

only acetylated

linked with both transcriptional activation and repression

40
Q

histone 4K20

A

lysine on tail of H4

only methylated - mono, di or tri

mono and di methylation associated with activation

tri methylation associated with repression

41
Q

how is H4 different to H3?

A

it has less sequence variation

structurally restrained by evolution

42
Q

how can we detect some PTMs?

A

some modifications can be visualised since they change the mobility of a protein on SDS-PAGE

the negative charge introduced by phosphorylation displaces negatively charged SDS from the protein, causing it to migrate more slowly in the gel

however, this gives no information about the locations of the modifications

43
Q

how can we find the locations of modifications?

A

by creating modification specific antibodies

mass spectroscopy can also be used

44
Q

how do we create modification specific antibodies?

A
  1. immunise animal with peptide and take blood and serum from the animal
  2. take the mixture of antibodies present in the serum and put them down a fractionation column composed of phosphopeptide
  3. when column is eluted, antibodies that specifically recognise the phosphopeptide are left in the column
  4. this will still be an antibody mix as contains antibodies that recognise the non-phosphorylated peptide
  5. a column made of non-phosphorylated peptide and antibody mixture poured in
  6. antibodies specific for phosphorylation flow through

left with antibodies that only recognise the phosphorylated form of the protein

BGM2002 CS (14 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions