Regulation of Protein Activity Flashcards
Why is important that we are able to control a proteins activities?
Proteins need to be functional at specific times for specific reasons
What are the short term methods of protein regulation?
NAME?
How can a change in protein conformation be induced?
- Allosteric inhibition
- Covalent regulation
- Proteolytic cleavage
What are the long term methods of protein regulation?
- Change in rate of protein synthesis
- Change in rate of protein degradation
How does substrate concentration affect the rate of enzyme activity?
Substrate availability affect the rate of enzyme activity
What are isoenzymes?
Different forms of the same enzyme- they catalyse the same reaction
How do isoenzymes differ from one another?
NAME?
What is the advantage of isoenzymes?
Allow for greater control
How can coenzymes regulate enzyme activity?
Some have limited availability
What is product inhibition?
When the accumulation of the products of a reaction inhibits the forward reaction
How does product inhibition work?
The product molecule acts as a competitive inhibitor
What relationship do allosteric enzymes show between rate and substrate concentration?
Sigmoid
How does the relationship between rate and substrate concentration for allosteric enzymes differ form normal?
Usually is a rectangular hyperbola for simple enzymes
What is allosteric inhibition a method of?
Controlling enzymes depending on their structure
How can multi subunit enzymes regulate?
They can vary the efficiency in which they bind to their substrate
How can multi subunit enzymes exist?
In 2 conformations, the T state (low state) and the R state (high affinity)
What does substrate binding to one subunit of a multi sub unit enzyme result in?
Subsequent binding to other sub units is easier
What can allosteric regulation add?
Small molecules
What effect does the addition of small molecules in allosteric regulation have?
Affects enzyme activity
What do allosteric activators do?
Increase the proportion of enzyme in the R state
Where do allosteric activators bind?
Somewhere over than the active site
How do allosteric activators work?
They tend to change the conformation of one sub-unit, stabilising the high affinity state
What do allosteric inhibitors do?
Increase the proportion of enzyme in the T state
Give an example of an enzyme that is allosterically regulated
Phosphofructokinase
What does phosphofructokinase set the pace of?
Glycolysis
When do allosteric activators tend to control things?
In low energy
What activates phosphofructokinase?
AMP, fructose-2,6-bisphosphate
What inhibits phosphofructokinase?
ATP, citrate, H +
When does modification of proteins occur?
Post translation
Are post translational modifications of proteins transient or permanent?
Can be either
How are proteins covalently modified?
Phosphorylation
What phosphorylates proteins?
Protein kinases
What do protein kinases do?
Transfer the terminal phosphate from ATP to the -OH group of Ser, Thr, Tyr
What reverse the effects of protein kinases?
Protein phosphatases
What do protein phosphatases do?
Catalyse hydrolytic removal of phosphoryl groups from proteins
How can signals be amplified?
By protein cascades
What is being amplified in protein cascades?
Signals by kinase cascades
What do protein cascades allow for?
Amplification of signals by several orders of magnitude in a few milliseconds
Give an example of where reciprocal control of pathways is used?
Glycogen breakdown and synthesis
Where is specific proteolytic cleavage common?
Activating enzymes in biological systems
What happens in specific proteolytic cleavage?
Specific proteases cut proteins in a specific place
What is the effect of specific proteolytic cleavage?
The enzyme goes from completely off to completely on instantly
What type of molecule is specific proteolytic cleavage needed for?
Digestive enzymes
What are digestive enzymes synthesised as?
Zymogens
What are zymogens?
Inactive precursors
Where are digestive enzyme zymogens synthesised?
Stomach and pancreas
Why do digestive enzymes need to be synthesised as zymogens?
Don’t want enzymes active in wrong location
Other than digestive enzymes, what else is synthesised as zymogens?
Some protein hormones, e.g. insulin
What is blood clotting mediated by?
Cascade of proteolytic activations
What does the mediation of blood clotting ensure?
A rapid and amplified response
What are many developmental processes controlled by?
Activation of zymogens
How do zymogens control developmental processes?
They contribute to tissue remodelling
What is apoptosis?
Programmed cell death
Is is apoptosis mediated by?
Caspases
What are caspases?
Proteolytic enzymes
How are caspases synthesised?
In their inactive form- procaspases
Give an example of a molecule that is proteolytically activated
Chymotrypsinogen
How is chymotrypsionogen activated?
Cleaved, some amino acids removed, and then rejoined by disulphide bonds
Where is a cascade effect often found?
In the digestive system
Give an example of the cascade effect in the digestive system
Pancreatic proteases- starts at enteropeptidase → trypsin → different molecules, all with different specificites
What regulates protease activity?
Endogenous inhibitors
Give an example of an endogenous inhibitor?
Pancreatic trypsin inhibitor, which stops the activity to trypsin
Give an example of a disease caused by failure of pancreatic trypsin inhibitors?
Emphysema
What causes emphysema?
α 1 -antitrypsin deficiency
What does theα 1 -antitrypsin deficiency cause?
Destruction of the alveolar walls by elastase
How can a change in rate of protein synthesis be induced?
Enzyme induction/repression
How can a change in rate of protein degradation be induced?
Ubiquitin-proteasome pathway
What is required for the blood clotting cascade?
A range of inactive zymogens
What does the intrinsic pathway for blood clotting do?
Damaged endothelial lining of blood cells promotes factor XII binding
What does the extrinsic pathway for blood clotting do?
Trauma releases tissue factor III
What is the common end point of blood clottings intrinsic and extrinsic pathway?
Factor X activation
What does Factor X activation lead to?
Thrombin activation
What does thrombin activation lead to?
Formation of a fibrin clot
What does the blood clotting cascade allow?
The formation of a clot from activation of a very small amount of initial factor
Why is important that a clot can be formed from a very small amount of factor?
Because there is a very low concentration of clotting factors in the blood
What are proenzymes?
Proteins of blood coagulation that don’t do anything until we need to clot
What kind of enzymes are used in blood coagulation?
Lots of peptidases
What do the peptidases in blood coagulation do?
Break peptide bonds in specific places in target proteins
What is activated in the extrinsic pathway?
Factor VII
What causes the activation of factor VII?
Membrane damage
How does membrane damage lead to the activation of factor VII?
It exposes the extracellular domain of tissue factor III, which leads to the autocatalytic activation of factor VII
What is the purpose of the intrinsic pathway?
It keeps blood clotting going
What plays a role in intrinsic pathway activation?
Membrane damage
What happens in the intrinsic pathway?
Factor XI and X are targeted to the membrane by Gla domains
What ion plays a role in the intrinsic pathway
Calcium
What is the intrinsic pathway needed for?
For sustained thrombin activation
What part of prothrombin has the protease function?
The thrombin part
Where is the thrombin part of prothrombin?
Contained in the C terminal domain
What helps keep the prothrombin in its inactive form?
2 kringle domains
What targets prothrombin to the appropriate sites for its activation?
Gla domains (carbyoxyglutamate domains)
How is thrombin activated?
- Proteolytic cleavage at Arg274 to release fragment containing first 3 domains
- Cleavage after Arg323 releases fully active thrombin
What does active thrombin consist of?
2 chains, linked by a disulphide bond
What is the role of Gla residues in blood clotting?
- Post translational modification of factors II, VII, IX and X in liver
- Addition of COOH groups to glutamate residues to form carboxyglutamate
- Allows interaction with sites of damage and brings together clotting factors
What odes capillary damage attract?
Calcium
What is the function of calcium in blood clotting?
NAME?
Describe the structure of fibrinogen
- 3 peptide chains wound around each other
- 2 sets of tripeptides, α, ß andγ, joined at N-termini by disulphide bonds
- 3 globular domains linked by rods
What is the charge of N terminal regions of α and ß chains?
Highly negative
What is the advantage of the negative charge on the N terminal regions of fibrinogen?
Prevents aggregation of fibrinogen
How is a fibrin clot formed?
- Thrombin cleaves fibrinopeptides at cleavage site from central globular domain of fibrinogen
- Globular domains at the C-terminal ends of ß and γ chains interact with exposed sequences at N-termini of the cleaved ß and α chains to form fibrin mesh/clot
- Newly formed clot stabilised by formation of amide bonds between the side chains of lysin and glutamine residues in different monomers
What is the cross linking reaction of fibrinopeptides catalysed by?
Transglutaminase
How is transglutaminase activated?
From protransglutaminase, by thrombin
What is haemophilia?
A defect in factor VIII
What does factor VIII do?
Stimulates activity of IXa
What is factor IXa?
A serum protease
What is the importance of factor VIII?
Activity of factor VIII markedly increased by limited proteolysis by thrombin and factor Xa- positive feedback amplifies the clotting signal, accelerating clot formation
What is the treatment for haemophilia?
With recombinant factor VIII
What mechanisms are involved in stopping the clotting process?
- Localisation of (pro)thrombin
- Digestion by proteases
- Specific inhibitors
How is (pro)thrombin localised?
Dilution of clotting factors by blood flow, and removal by the liver
Give an example of something that stops clotting by digestion?
Protein C
What does protein C do?
Degrades factors Va and VIIIa
How is protein C activated?
By thrombin binding to endothelial receptor, thrombomodulin
What can defects in protein C cause?
Thrombotic disase
Give an example of a specific inhibitor for the clotting process?
Antithrombin III (AT3)
What does AT3 do?
Binds extremely tightly to thrombin and factor V, whcih stops the activity
What is the advantage of AT3 stopping activity?
Means can be degraded more efficiently
What enhances AT3?
Heparin binding
Does AT3-heparin act on thrombomodulin-bound thrombin?
No
How does fibrinolysis occur?
NAME?
Why is plasminogen secreted in the inactive form?
Because we don’t want it to be activated at the wrong time
How can fibrinolysis be a point of control?
Can control rate of conversion of plasminogen into plasmin, and hence breakdown of fibrin
What increases the rate of conversion of plasminogen into plasmin?
- †-PA
- Streptokinase
