Enzymes Flashcards
What are ribozymes?
Catalytic RNA molecules with no protein component
What is a cofactor?
A non-protein component needed for activity, usually metal ions
What is a co-enzyme?
A complex organic molecule, usually produced from a vitamin FAD NAD+
What is a prosthetic group?
A non-protein group forming part of or combined with a protein.
i.e - A cofactor covalently bound to an enzyme or very tightly associated with an enzyme
What is an apoenzyme?
An inactive enzyme, activation of the enzyme occurs upon binding of an organic or inorganic cofactor.
What is a holoenzyme?
WHole enzyme, the apoenzyme plus the cofactor
Why isn’t a spontaneous reaction instantaneous?
Because of the activation energy barrier
What is the activation energy used for?
Positioning chemical groups correctly
What is the transition state?
The moment that chemical bonds are formed and broken The reaction from this point could then go to products or reactants
What type of bonds occur between substrate and enzyme?
Non-covalent
What is the active site complementary to?
The transition state
How do enzymes reduce activation energy?
Entropy reduction Desolvation Induced fit
How does entropy reduction reduce activation energy?
Molecules react by bumping into each other, enzymes orientate the substrates improving the chance of a successful collision and a resulting reaction
How does desolvation decrease the activation energy?
H bonds with the substrate and the solution are replaced by the weak bonds between the substrate and the enzyme.
How does induced fit decrease activation energy?
Conformational changes occur in the protein structure when the substrate binds
Which part of an enzyme reaction occurs more slowly?
The second part of the equation, producing E and P from the enzyme substrate complex
Which stage of an enzyme reaction is reversible?
The formation of ES from E and S K1 denotes the forward reaction K-1 denotes the reverse reaction
What is Km?
It is the substrate concentration when the reaction velocity is exactly half of the max velocity
On a lineweaver burke plot what does the y intercept represent?
1/VMax
On a lineweaver burke plot what does the X intercept represent?
1/Km
What does Km measure?
The ration of rate constant for breakdown of ES to E+S compared to the rate constant for formation of ES from E+S It gives you a clue to the affinity of the enzyme with it’s substrate
What does a large Km value indicate?
Less stable ES complex
Which enzyme activity fluctuates directly with blood glucose intake?
Glucokinase Catalyses Glucose + ATP to glucose - 6 - phosphate
What is used to determine normal enzyme activity?
Arbitrary values such as 1U/ml or 100%
How are enzymes separated?
Gel electrophoresis
Where can you find creatine kinase?
In the heart Elevation of plasma CK2 is diagnostic for myocardial infarction
What are the possible reaction mechanisms for enzymes with two or more substrates
Random or ordered with a ternary complex No ternary complex formation
Describe the reaction involving a ternary complex
Random order
Can bind to either substrate first
Eventually complexes with both substrates
Forms two products
Describe the reaction involving a ternary complex
Ordered
Attaches to one substrate first, it is the fed the other substrate
Describe the reaction with no ternary complex formed
Reaction occurs with enzyme and substrate producing altered enzyme and a product
Second reaction occurs with the altered enzyme and the second substrate, producing a second product
What type of reactions have no ternary complex formation?
Transamination reactions
How does temperature affect the function of an enzyme?
Increase temperature will increase molecule collisions and it will increases the internal energy of molecules
Eventually denautres the enzyme
How does pH alter the function of an enzyme?
pH changes the charge of an amino acid, can stop the active site functioning if the amino acids in the active sites change charge.
Extreme pH will denature the enzyme
pH will affect the substrates
What effect does a competetive inhibitor have on the Vmax and Km?
Same Vmax
Km increases (since affinity active site has for the enzyme substrate complex decreases)
What is an example of a transition state anologue?
Oseltamavir
What does a catalytic antibody resemble?
It resembles the active site of the original enzyme, since it is specific to a transition state molecule
What effect do non-competitive inhibitors have on the Vmax and the Km values?
V max will decrease - inhibition remains the same regrdless of the change in substrate concentration
Km remains the same as the substrate is still able to bind to the active site
Which type of inhibitors bind in an rreversible manner?
Those that bind in a covalent manner
Which enzyme in a pathway holds the regulatory step for that pathway?
Often the first one in the pathway
What are the regulatory types of enzymes called?
Allosteric enzymes and covalently modified enzymes
What is feedback inhibition?
When there is a build up of an end product in a pathway or a key junction in a pathway that ultimately slows down the entire pathway
How is the change in the structure of an enzyme brought about in allosteric control?
An allosteric effector (usually a metabolite) binds non-covalently to a site on the enzyme that is not the active site, changing the enzymes structure
What are the two different types of allosteric effectors?
Activators and inhibitors
How does the concerted model show how a small amount of substrate increases an enzymes sensitivity to a substrate?
Concerted model suggests that enzyme sub-units are always flipping between two conformational formations
Binding of S to one substrate locks the other subunits in the same conformation
How do allosteric inhibitors and activators function in the concerted model?
Activators - stabilise the the open conformation, allowing S to bind more effectively
Inhibitors - stabilise the ‘closed’ conformation and make it difficult for S to bind effectively
How does the sequential model show how a small amount of substrate increases an enzymes sensitivity to a substrate?
Substrate binding causes a change in ONE sub unit, this causes a change in another sub-unit allowing it to bind to S more readily
What enzymes are responsible for covalent modification?
Protein kinases (add phosphoryl groups to proteins)
Protein phosphatases (remove phosphoryl groups)
What do multiple phosphorylation sites allow?
Very fine control of enzyme funciton
What is an inactive precursor of an enzyme called?
A proprotein or a proenzyme
What can be produced when a proprotein is cleaved?
Proteases
Give an example of a an enzyme that is regulated by proteolytic cleavage
Trypsin - activated in the small intestine
Its precursor trypsinogen is formed in the pancreas
Describe the bonding between a protein and :
- A prosthetic group
- A coenzyme
Prosthetic group - Tight bonding (sometimes even covalent bonds)
Coenzyme - Loose bonding
