1 - Regulatory Strategies Flashcards
Why must metabolism be regulated?
To meet the requirements of energy, nitrogen, carbon and other vitamins, minerals or nutrients without creating an excess.
Why is substrate control important?
Because the concentration of any given substrate in the cell at any given time is very low.
What are conserved metabolites?
Metabolites used in many reactions to provide energy or electrons, often being reverted back to their original state by a different cellular process.
Name the most important conserved metabolites.
ATP GTP NADH NADPH FADH2
What is the ‘Energy Charge’ of a cell?
The proportion of adenosine phosphates capable of being utilised for energy, weighted for their comparative capability.
([ATP] + 0.5[ADP] ) / ([ATP] + [ADP] + [AMP])
In what four ways can cells respond to an increase or decrease in substrate availability?
1 - Alteration of membrane transport proteins (activity or population)
2 - Preferential use of alternative substrate (eg lac operon)
3 - Metabolic Pathway Control (increasing breakdown/use of abundant material and vice versa)
4 - Scarse Substrate Synthesis
In what ways can a cell changes its effective protein concentration to regulate its metabolism?
1 - Protein translation (via transcriptional, mRNA or translation regulation) 2 - Protein degradation 3 - Protein sequestration 4 - Covalent modification 5 - Allostery
On what sort of proteins is transcriptional control most effective on? Why is this?
Proteins with a short half-live/livespan (AKA high turnover) as if transcription is stopped the supply of the protein will quickly drop, and stopping degradation leads to sharp increase in concentration due to the fast production.
What is the primary method of increasing protein production?
Transcriptional control.
Why is transcriptional control unsuited to short term regulation?
The time delay between transcription and translation prevents it from being of much short term use, except for proteins with high turnover rates.
What are the two primary mechanisms of protein degradation?
(Poly)Ubiquitination followed by 26S proteasome degradation or marking for lysosome degradation.
Give two examples of protein sequestration as a regulatory technique.
Glucokinase nuclear sequestration and the removal of GLUT4 receptors from the membrane into vesicles that can be quickly re-inserted.
How do allosteric effectors work?
They preferentially bind either the tense or relaxed state and hence shift the equilibrium towards that conformation.
What is homotropic allostery?
When the allosteric effector is also the substrate or product of the enzyme.
What is heterotropic allostery?
When the allosteric effector is unrelated to its target.
What is feedback inhibition?
A form of allostery in which the product of the enzyme acts as an inhibitor for the enzyme that produces it (homotropic) or an enzyme near the beginning of the metabolic pathway (heterotropic).
What is feedforward activation?
A form of allostery in which the substrate of an enzyme or pathway increases the activity of one or more of the enzymes in that pathway.
How can allosteric inhibitors be classed?
As competitive, uncompetitive or non-competitive, just as with non-allosteric inhibitors.
How do competitive inhibitors act?
By increasing the Km of the enzyme.
How do non-competitive inhibitors act?
By decreasing the Vo of the enzyme by binding to either the enzyme or the enzyme-substrate complex and inactivating it - effectively reducing the concentration of active enzyme.
How do uncompetitive inhibitors act?
By decreasing the Vo of the enzyme by binding specifically to the enzyme-substrate complex and inactivating it - effectively reducing the concentration of active enzyme.
What properties do covalent modifications of proteins share?
They are stable and reversible.
What are some examples of covalent protein modifications used in regulation?
Phosphorylation Adenylation ADP Ribosylation Glycosylation Ubiquitination Acetlyation Hydroxylation Methylation
What residues can be phosphorylated?
Ser, Tyr, Thr
What residues can be glycosylated?
Ser
Thr (O-linked glycosylation)
Asn (N-linked glycosylation)
What residues can be hydroxylated?
Lys and Pro
What residues can be methylated?
Lys and Arg
What residues can be acetylated?
Lys only.
What residues can be ubiquitinated?
Lys only.
In what timescale does covalent modification act?
Seconds to minutes.
In what timescale does allosteric regulation act?
Milliseconds to seconds.
How are cascades used in cell signalling?
For signal amplification, for example in kinase pathways each kinase activated at one stage is able to phosphorylate many of the next stage of kinases causing up to 100x signal amplification with each step.
In a metabolic pathway, most enzymes are ……..
At equilibrium.
What are rate limiting enzymes?
Enzymes in a pathway that catalyse irreversible, often exothermic, and hence are very tightly controlled. They are often regulated by several allosteric effectors and possess multiple covalent modification sites and so are often used to control the rate of the entire pathway.
Where in a pathway are rate-limiting enzymes often found?
At ‘branch points’ in which two pathways diverge or substrates separated, thus being the first ‘committed’ step in the pathway.
What is the flux control coefficient of an enzyme?
The degree to which regulation of that enzyme affects the overall rate of the pathway. This may change in different circumstances.
How are flux control coefficients derived?
Experimentally.
What is the sum of the flux control coefficients for a pathway always equal to?
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