Lecture 2 - PTM of Proteins Flashcards
What are Central Dogma stages ?
DNA –> RNA –> Protein
DNA -> RNA = Transcription
RNA -> Protein = Translation
100,000 transcripts, but 1,000,000 proteins due to PTM
What do PTMs help to produce?
Primary, secondary and tertiary structure
What are PTMs and when are they important?
Covalent addition to or cleavage of a functional group off proteins
Important component of cell signalling, certain cells have to operate at specific time scales, proteins need to be activated and deactivated when required
Example of why we need PTMs…
Pluripotent Stem Cells
These have the ability to renew and differentiate, it is unclear how it is maintained, but it is thought to be due to PTMs
What are the 3 types of germ layers PSC can differentiate into?
Endoderm
Mesoderm
Ectoderm
Direction and destination of PSC seams to be controlled at a PTM level
Cleavage as a PTM
Cleaving of peptide bonds - removing unwanted parts
Give an example of cleavage as a PTM
Insulin
Insulin is produced as a polypeptide chain, but it has to be modified
Ribosomes produces polypeptide chain, which then passes through the sec61 translocon into the ER, where it forms it structure, but it is still bound to the membrane by the signal peptide
Once fully formed into its tertiary structure, it is cleaved by protease enzyme to remove the signal peptide
To modify it further it gets exported from the ER to the Golgi where is it packaged into a vesicle
The vesicle contains peptidases which remove one of the polypeptide chains, and then C-peptidase cleaves the last 3 amino acids to produce the final product
What are the examples functional groups being added to proteins?
Acetylation, Methylation, Phosphorylation, SUMOylation, Ubiquitination
Phosphorylation as a PTM:
1/3 all cellular proteins thought to be phosphorylated at one time
Can reversibly add/remove a phosphate group which causes a conformational change in the protein
Can either activate or deactivate the protein/enzyme
Phosphate has 2 negative charges so can cause significant conformational change, can also form a site which can be recognised by other proteins, or can mask a binding site preventing protein-protein interaction
What do Protein Kinases do?
Enzymes that catalyse the transfer of a phosphate group from a high energy donor molecule to a specific substrate – phosphorylation
Takes ATP, removes a phosphate group from it, and adds this phosphate to the protein, causing an alteration to the protein
How many protein kinases have been characterised?
513 characterised, 478 have a homologous catalytic domain, 35 are ‘atypical’
The catalytic site carries out the same function, the structure past the active site determines the function of the specific protein kinase
What do Phosphatases do?
Enzymes that catalyse the removal of a phosphate group from a substrate by hydrolysing phosphoric acid monsters into a phosphate ion and a molecule with a free hydroxyl group (dephosphorylation)
The opposite reaction of a kinase
What is Glycosylation?
A carbohydrate (either a monosaccharide or a complex) is covalently bound to a functional group (e.g. hydroxyl) on a protein, via a glycosidic bond
What are the functions of glycosylations?
Helps correct folding Increases protein stability Cell-cell/Cell-environemnt adhesion Immune response Hormone activity Embryonic development
How are N-glycans synthesised?
Through the common pathway
Core glycol structure is two N-acetyl glucosamine and tree mannose residues
The core glycol is then modified further resulting in the diversity of N-glycans
What are MHC class I and II?
Glycoproteins that can present peptides for recognition by circulation T cells
What are the 5 types of glycosylation?
N-linked O-linked Glyplation C-linked Phosphogly-cosylation
What is N-linked glycosylation?
Glycol binds to amino group of asparginine in the ER
What is O-linked glycosylation?
Monosaccharides bind to hydroxyl group of serine or threonine in ER, Golgi, Cytosol or Nucleus
What is Glyplation glycosylation?
Glycol core linkes a phospholipid and a protein
What is C-linked glycosylation?
Mannose binds to the indole ring of tryptophan
What is phosphogly-cosylation?
Glycol binds to serine via phosphodiester bonds
What is manning?
A sugar monomer of the aldohexose series of carbohydrates
A C2 epimer of glucose
What is Acetylation/Deacetylation? And when does it occur?
Addition of removal of an acetyl group
Can either occur co or post translationally
Where does the acetyl group come from for acetylation?
Acetyl-CoA
Is acetylation enzymatic?
Can be enzymatic or non-enzymatic
Enzymes are acetylase or deacetylase
What is the most common co-translational modification in eukaryotes?
N-terminal acetylation
Causes synthesis localisation stability
What enzymes are involved in acetylation?
N-terminal acetyltransferases - catalyse N-terminal acetylation
KATs = Lysine acetyl transferase (KDAC - Lysine deacetylases)
What do NATs do?
NATS - transfer acetyl to the alpha amino group on the first amino acid residue in the protein
Give an example of antagonistic acetylation/deacteylation?
Histones
Histone acetyltransferase/deacetylase (KAT and KDAC)
Located in the cytoplasm or nucleus
Acetylation removes the +ve charge from the histone, so DNA wraps less tightly
So, Acetylation encourages binding of effector proteins, relaxation of chromatin
What is Methylation?
Transfer of a methyl group onto either lysine or arginine
What can lysine methylation lead to?
Activation or suppression
Where is methyl donated from for methylation?
S-adenosylmethionine
Is methylation reversible?
Carbonyl methylation is generally reversible - used to modulate a reaction
Nitrogen methylation is generally irreversible, creating a new amino acid
Where does arginine methylation occur and what are the functions of it?
Mainly in the nucleus Regulation of RNA processing Gene transcription DNA damage repair Protein translation Signal transduction
What are the functions of lysine methylation?
Histone function regulation Epigenetic regulation of transcription Lysine methyltransfers (KMT)
What is p53 known for?
Its tumour suppressor activity
What does p53 regulate and how?
Apoptosis, DNA repair, Autophagy
Targeting expression of downstream target genes
p53 is rich in Lys and Arg - so is targeted by 5 KMT
