Regulation - Keeping The System In Balance Flashcards
Why does the cellular factory need to be regulated?
Because we need to regulate how much carbon goes towards each metabolic process. Regulate catabolism Vs anabolism
What are the two mechanisms by which regulation is achieved?
Mass action
Feedback loops
What are the mechanisms by which enzyme activity is regulated?
Allosteric regulation
Spatial clustering
Post translational covalent modification
Specific example of allosteric regulation of enzyme activity
Inhibition of ATCase action by the CTP product
Specific example of spatial clustering regulation
Biosynthesis of inosine monophosphate (IMP)
In deficiency of purines, enzymes respond by forming puranosomes which is associated with 50% increase in flux of purine formation pathway
Specific example of post translational covalent modification regulation
Phosphorylation of PDC enzyme (catalyses pyruvate to acetyl CoA) by kinase produced less active form of enzyme so decreases rate of its catalysis and acetyl CoA production
Dephosphorylation of PDC enzyme by phosphatase produced more active form of enzyme so increases rate of its catalysis and acetyl CoA production
Explain how CTP inhibits ATCase
CTP binds to an allosteric site on ATCase
How are the catalytic units in ATCase arranged?
6 catalytic sub units arranged as a pair of trimers which sit on top of each other
How are the regulatory units in ATCase arranged?
6 regulatory subunits arranged as three dimers that sit between each junction of the catalytic subunits
Where does CTP bind on ATCase?
CTP binds to an allosteric site on each regulatory subunit
On the trimer of catalytic subunits, where are the active sites located?
What does each active site contain?
At the junctions between the three catalytic subunits (three active sites)
Each active site contains key AA residues from each of the two catalytic subunits that it is in between
What state is the enzyme ATCase in when CTP is bound?
Activity?
T (tight) state
Less active
What state is the enzyme ATCase in when CTP is NOT bound?
R (relaxed) state
More active
When CTP is NOT bound and ATCase is in a relaxed state … rotation thing
Catalytic subunits are rotated 10 degrees about their common axis of symmetry
This brings the key AAs at the junctions of the subunits closer together which improves the rate of catalysis
When CTP IS bound and ATCase is in a tight state … distance thing
Catalytic trimers are moved 1.2 nm apart which provides better substrate access to active sites
What type of kinetic curve does ATCase have
Sigmoid all
Explain why ATCase has a sigmoidal curve
It is the combination of the two states (relaxed and tight) of the enzyme
Which enzyme regulates the feedback loop involved in regulating anabolic and catabolic reactions of glycolysis
Phosphofructokinase
What does phosphofructokinase catalyse
Fructose-6-phosphate
To
Fructose-1,6-biphosphate
What happens if ADP concentation is too high
ADP too high so activates PFK enzyme and rest of glycolysis
Overrides feedback loop so pfk noblonger inhibited, continues to makes more carbon skeleton to put into TCA cycle to increase ATP synthesis
What happens if too much PEP
Negative feedback loop = PEP binds allosterically to PFK and inhibits it
Typically, metabolic pathways contain…
Multiple feedback and feedforward loops
Important in metabolic engineering - trying to break this loops to make it do something it doesn’t normally do
Kinetic regulation by mass action
Mathematical model predicts changes in substrate concentration
More substrate = enzyme goes faster
As concentration of glucose increase, point where there’s no longer an increase in flux because we have reached Vmax of enzymes in system.
In mass action at which point is the kinetic response of the system limited?
When we reach the Vmax of the enzyme sin the system and the active sites of all the enzymes are saturated
What happens when you saturate available enzyme capacity
xx don’t get
Mass action
XX???
Kinetic propagation in response to variable glucose levels
Realistic organisation of metabolic pathway in the cell
Diffusing all the time
Moving around
Many copies of each enzyme
What’s a purinosome
Bodies of enzymes normally dispersed through the cell
Why is there an increase is rate of catalysis and bio synthetic pathway for purine formation when purinosomes form?
Because when the enzymes are all clustered it means there’s a LOCAL increase in concentration. So within the complex there’s a higher substrate concentration so Vmax is higher, so reaction goes faster as each substrate moves into enzyme etc)
Advantage of regulation through spatial organisation of enzymes
Enables control over branch points in pathways
Example of spatial organisation of enzymes helping control branch points in pathways
Branching point = one direction goes on to synthesise purines, other direction goes on to synthesise thiamine
If starved of purine we want to go the direction that synthesises purine
So all enzymes involved in purine synthesis put into cluster. This means it’s naturally more likely for the substrate that leaves one enzyme in this pathway to go to the next enzyme involved in this pathway rather than to leave the cluster and go to another enzyme which would take it to the thiamine pathway.
Explain feedback loop if TCA cycle is producing too much NADH
Too much NADH
Need to slow flow of pyruvate into cycle so need to slow catalyses of pyruvate to acetyl coA
NADH activates kinase
Kinase phosphorylates enzyme making it less active so less catalysis of pyruvate to acetyl CoA
Explain feedback loop if pyruvate is building up
Tells us enzyme (PDC) is going too slow
Pyruvate inhibits kinase
Kinase no longer phosphorylase’s enzyme making it inactive
What is phosphorylation controlled by
Kinases
What is dephosphorylation controlled by
Phosphorylase’s
How does phosphorylation produce amplified effects
One kinase can phosphorylase lots of target proteins Ina. Short amount of time
How is phosphorylation linked to cells energy status
It uses ATP to get the phosphate so if cell is depleted in ATP phosphorylation won’t go ahead if it doesn’t need to
What does adding a phosphoryl group do?
Adds two negative charges and can form 3 or more H bonds.
These changes alter structural conformation of the enzyme and affect substrate binding and catalytic activity
Why can’t binding of CTP to ATCase be competitive inhibition
because CTP canot fit into active site of ATCase due to diff shape, size and charge
