Regulatory modifications can be removed
What is added in Palmitoylation?
The substrate in palmitoylation is added through a thio-ester bond
Where is the substrate in palmitoylation added?
The central cystine
The two flanking leucines
Describe Model 1 of regulatory modification
The modification changes the functional state (Active --> Inactive or vice versa)
The modification changes the affinity of the protein for its binding partner
In Model 2, what does the addition do?
Activates/deactivates the protein
Creates a new binding site that only exists with the modification
Marks the protein for destruction
Phosphorylation is the least used modification in eukaryotic cells
What is the donor for phosphorylation?
Gamma phosphate of ATP
Alpha phosphate of ATP
Beta phosphate of ATP
Name the two enzymes that add/remove the phosphate
Phosphates are added to amino acids with OH groups on the R chain
Phosphorylation can be used for both Model 1 & 2
Give an example of a Model 1 phosphorylation
Phosphorylation of Erk Kinase
Phosphorylation of tyrosine kinase
Phosporylation of Ras
Describe a Model 2 pathway for phosphorylation
Platelet derived growth factor self phosphorylates on Tyr
Allows binding of other proteins SH2 domains
Phosphorylation of Raf
Phosphorylation of MEK
Acetylation is used almost exclusively for model 1
To which residue is the substrate for Acetylation added?
Acetylysine is neutral
Acetyl-lysines are recognised by what?
The donor for Acetylation is?
Name the proteins that add/remove the substrate in acetylation
How is acetylation used for DNA density regulation?
The histone monomers (H3 & H4 especially) have tails rich in lysine for acetylation
T/A residues are acetylated, which signals to move them to the histone and be silenced
GTG repeats are acetylated to activate them, moving them away from the histone
Acetylation causes the DNA to relax
What is the role of bromodomains?
To interact with histones
To interact with nucleosoems
Bring in other proteins for the chromatin remodelling complex
What is the donor substrate for methylation?
Name the two protein sets that add/remove methyl groups
There are separate enzymes for lysine and arginine methylation
Methyl can be added to the same lysine how many times?
MeK, Me2K and Me3K are all created and recognised by the same enzyme
Some enzymes can mono/bi/ and tri methylate, some can only do one
Name the forms of dimethylated arginine
What's the difference between s & aMe2R
One is in Cis, the other is in trans formation
aMe2R has both methylations on the same arginine
aMe2R has both methylations on different arginines
Arginine has 5 nitrogens to be replaced
Tudor domains recognise methylation
Why is S-adenosyl methionine used as the donor
It has a 5-bonded carbon, which makes the methyl easy to remove
It has a 4-bonded phosphate, which makes the methyl easy to remove
It has a 3-bonded sulphur, which makes the methyl easy to remove
Tandem tudor cannot bind to Me3K as there is no longer a H for it to bind with
A type of tudor domain will recognise asymmetical Me2R
ADP ribosylation is mostly Model 2
What is the donor for ADP ribosylation?
How is the ADP gained from the substrate?
Cut off the nicotinamide and you're left with the ADP
Cut off the flavin and you're left with the ADP
Name the proteins that add/removed ADP
Poly-ADP Ribose Polymerase
Poly-ADP Ribose Glycohydrolases
Which amino acids are the ADP(s) added to?
Which amino acid has the ADP(s) added?
ADP ribose can be addded to ADP ribose in straight or branched chains
What is the role of glutamic acid ADP ribosylation?
Happens to linker histones
Happens to open stretches of DNA
Recognised by DNA damage response proteins
Recognised by silencing proteins
Name the 3 enzymes used in the addition of Ubiquitin
E1- Ubiquitin Conjugating Enzyme
E1- Ubiquitin Activating Enzyme
E2- Ubiquitin Conjugating Enzyme
U2- Ubiquitin Ligase
U3- Ubiquitin Activating Enzyme
U3- Ubiquitin Ligase
De-Ubiquitinating Enzyme removes Ubiquitin
What type of bond forms between Ubiquitin and the target residue?
Thio-ester, between the COOH of the ubiquitin and the lysine on the target protein
Isopeptide, between the COOH of the ubiquitin and the lysine on the target protein
Disulphide, between the COOH of the ubiquitin and the lysine on the target protein
Ubiquitinated lysine 63 are open and flexible and acts a signalling site for complex formation
Ubiquitinated lysine 48 are compact and mark the protein for destruction
What is the first step of ubiquitination?
Ubiquitin is activated by ATP hydrolysis
Ubiquitin is activated by GTP hydrolysis
Ubiquitin is activated by UTP hydrolysis
Once Ub has been activated, what enzyme does it bind to, and what bond forms?
The Ub is then passed on to..
What is the role of E3?
Binding of an E2-Ub complex
Binding on an E1-Ub complex
Binds to substrate protein & transfers ubiquitin to amino group of lysine
Protein specificity for Ubiquitination lives in E2
How many versions of E1 are there?
There are 35 versions of E2
How many E3's are there?