Lecture 9 Flashcards
When is protein kinase c active
When it’s bound to the membrane and has calcium and DAG bound
what is the C2 region of protein kinase c made of an how does it help
It’s has a poly basic cluster of lysine residues that are postively charged
These lysine residues help it bind to the membranes negative charged phosphotidyl serine lipid heads
C1 and C2 domains of PKC binds what
C1A and C1B binds DAG
C2 binds the Phosphatidylserine and Phosphotidyl inositol lipid head groups (so the PIP2 groups) and calcium
To activate protein kinase C what domains have to be bound
The C1A or C1B (only need one bound to dAG to activate it)
The c2 to the membrane (Phosserine and PIP2)
What motif is in the c1 domains of PKC
The zinc finger motif
So it has two zinc ion (one in a and one in B)
Surrounded by 3 cysteine and 1 his each
What are the steps of PKC getting activated
DAG and ca are required
When ca, PKC goes to membrane, C2 domain binds pip2 and phosserine head groups
C1A or B bind DAG and the autoinhibitory site on PKC comes out (off)
The PKC is now active
What are the steps of PKC getting activated
DAG and ca are required
When ca, PKC goes to membrane, C2 domain binds pip2 and phosserine head groups
C1A or B bind DAG and the autoinhibitory site on PKC comes out (off)
The PKC is now active to activate other proteins involved in growth (because the kinase what activated by a growth factor)
What does PLC do
Once a GPCR is activated by a growth factor or other signal, the PLC is activated and cleaves PIP2 into DAG and IP3
This DAG binds to C1A of PKC to activate it
Why is magnesium in high concentrations in the cell (mM)
Because it is always bound to atp so it can stabilize the negative phosphate charge in atp
The amount of ato in the cell is also high, to mg would also have to be high
Is there free atp in cells
No since mg is always bound, mg-ATP is mostly what there is
To what phosphates is the mg in atp bound to
The beta (2nd) and gamma (3rd) phosphates
What is the coordination of mg when bound to the phosphates of atp
What does the mg bind to
Mg2+ so hard metal surrounded by oxygens, typically from water
octahedral geometry
Where else if magnesium found
In chrlorophyll
If magnesium isn’t bound to chlorophyll what happens
The absorbance of light from the sun changes, so red and blue light isn’t absorbed
It needs to absorb red and blue light for photosynthesis to happen and to make oxygen
Chlorophylls are a type of
Porphoryn (like hemoglobin)
Know how to draw general structure of chlorophyll
Slide 6
What is the exception of mg in chlorophyll and why
Mg2+ is a hard metal so it should bind to oxygen, but in chlorophyll it binds to nitrogen
This is because of the delocalized structure and electrons of chlorophyll surrounding it
What are the types of PTM in proteins
Phosphorylation
Ubiquitinations
Glycosylation
Methylation
Acetylation
Sumoylation
Sulfurylation
Fatty acylation (lipidation)
What do PTMS do
What is the evidence
they add groups to proteins to alter their function
When purified, proteins have modified amino acids (phosposerine, dimethylargenine)
What do PTMS do
What is the evidence
they add groups to proteins to alter their function
When purified, proteins have modified amino acids (phosposerine, dimethylargenine)
When can PTM happen
Cotranslationally (during translation)
Posttranslationally (after translation)
Are PTM specific or not
Yes specific, needs dedicated enzymes to doing the modification
Where to PTMS usually happen
How do they happen somewhere else
Usually on the surface of proteins
But if the modification is done cotranslationally and the protein folds, it can become internal
Are PTMS reversible
Yes
What are most PTMS triggered to happen by
Receptors on the cell surface (like GPCR receptors)
Like a singal for the cell to grow or kill itself makes the according PTM happen to do this
What is an example of a cotranslational modification
What does it help with
Disulphide bond formation (in extracellular proteins)
They form spontaneously and restrict the motion of previously flexible part of the protein
This limits proteolytic digestion
What an example of a protein with disulphide bonds
What type of protein is it
Bovine pancreatic trypsin inhibitor (BPTI)
It’s a toxic protein, toxic proteins usually have three disulphide bonds
If dipulphide binds aren’t present what happens to the structure of the protein
Structure Changes drastically
This is why disulphide bonds are really important to structure
What is hydroxyproline
What can it do
A modified proline (has extra OH on corner of ring)
Forms extra h bonds compared to just proline
What is hydroxyproline found in and what can it help with
It’s found in collagen, and thought the extra h binds it can make it stabilizes the strands of collagen
Required enzymes to do and vitamin c
What is gamma glutamayl carboxylase
An enzyme that adds an extra carboxyl group on the gama carbon of glutamate
This to makes gamma carboxy glutamic acid (Gla)
What is Gla used for
The extra negative charge from the extra gamma carboxy is used to coordinate calcium.
The now two coo- coordinate ca to create a membrane binding motif for the protein that Gla is in (to make the protein bind to the membrane)
Also heavily involved in the process of blood clotting (so enzymatic reactions
What is amino acid is a common target for sulfurylation
What enzyme does this
Where does it happen
Tyrosine
Sulfotransferase
In the golgi (so only happens to proteins that are secreted from the cell)
How does tyrosine sulphurylation happen
The precursor PAPS act like a sulfate donor (for many things)
Needs an OH group to transfer the sulfur (which is why tyrosine)
After transfer PAPS turns to PAP
What is the purpose of tyrosine sulfurylation
To increase interactions between two proteins
Ex. The GPCR and its hormone ligand bind closer together because of surphurylation
How is PAPS made in humans
Via PAPS synthase which is a bifunctional enzyme that takes both atp and sulfate in the cell and make PAPS
How is PAPS made in plants /bacteria
Needs two enzymes because it doesn’t have a bifunctianal enzyme
First atp turns to APS via ATP sulfurylase (adds sulphate)
Then APS turns to PAPS through APS kinase (adds phosphate)
What is polyubiquitin
What is ubiquitin
More than two ubiquitin proteins
A small 76AA protein
What happens if poly ubiquitin is added to a protein
What if one ubiquitin
The protein gets targeted for degredation by the proteasome (death star)
Cant target for death, the ubiquitin is used for signalling
What is the motif for polyubiquiting protien getting added to proteins
D-K-X-E
The lysine in the proteins motif is what’s targeted to get ubiquitinated
What is the Death Star structure
Has 2 19S caps and a 20S core
Total protein is 26S
How does the Death Star work
The 19s caps cleave the polyubiquitin and use atpases to unfold the protein
They then get the unfolded protein into the 20s core which chops up the polypeptide
The broken peptides are shot out the second 19s cap
Where is the protease activity of the Death Star
What does the Death Star depend on
In the 20s core
Atp dependent (to unfold protein)
What is normoxia and hypoxia
Normal levels of oxygen
Low oxygen
How do PTMS help cells sense and adapt to oxygen availability under normoxia
In normoxia (oxygen rich):
the 2 prolines of HIF 1aplha get hydroxylated
VHL gets recruited to HIF1a
Then the HIF1a gets targeted for degredation (meaning ubiquitination hapoens on a lysine residue)
How do PTMS help cells sense and adapt to oxygen availability under hypoxia
The hydroxylation of proline on HIF1a doesn’t happen
HIF1a goes into the nucleus and binds to ARNT to act as a transcriptional activator
Help to transcribe the HRE (hypoxia response element) genes that get more oxygen to us
What types of things does HIF1-a help make in hypoxia conditions
Genes for Blood vessels (angiogenesis)
Higher metabolism (glycolysis)
Body also makes more red blood cells (erthyropoesis)
What is sumoylation
What does it do
Also covalently binds to lysine (like ubiquitin, protien bind to protein)
Attachment of it to proteins changes the proteins subcellular localization, transcriptional activity, stability, protects it from degredation
What is the motif for sumoylation
yKXE
y= hydrophobic amino acid (diff from ubiquitination because that one is D (hydrophilic)
X= any amino acid
How does the sumoylation of something protect is from degredation
Once the protein is produced, One side of the protein is hydrophobic so it’s sticky.
Stick end Doesn’t want to be exposed , so the sumo gets added there to protect the protien from misfolding
How does the sumoylation of something increase its stability (acceptable answer)
Protects the exposed area of the protein from degredation
Give an example of What protein phosphorylation does to a protein
Induces conformational changes in glycogen phosphorylase
Glycogen phosphorylase releases glucose from glycogen
What thing phosphorylated proteins
Proteins kinase
How does phosphorylation help in smooth muscle contraction
Requires calcium Cam (so caM with calcium bound)
Needs myosin like chain kinase
Contraction happens when ca-cAM activate the MLCK
Myosin phosphorylated and contraction happens
A phosphotase would take off the P so get relaxation of smooth muscle
What are the kinase activators in the cell and what kinase do they activate
Cyclic - amp (PKA)
Ca-cam (cam dependent kinase)
Cyclic gmp (PKG)
DAG (PKC)
What are the kinase activators in the cell and what kinase do they activate
Cyclic - amp (PKA)
Ca-cam (cam dependent kinase)
Cyclic gmp (PKG)
DAG (PKC)
What motif does PKA recognize
arg-arg-xxx-ser-Val-xxx
R-R-X-S-V-X
The serine can also be a threonine (thr)
What motif does MAPK (proline directed kinase) recognize
Ser-Pro-Lys- Lys
S-P-K-K
Serine can also be threonine
What motif does casein kinase 2 recognize
Ser-xxx-xxx-glu/asp
S-X-X-E/D
Serine can be threonine
Need - charge at end
What is RYR
A calcium channel
