L10: How Enzymes Catalyse Flashcards
This is a specific site on the enzyme that has specific amino side chains projecting into it .
Active site
What determines the specificity of reactions? Why?
The active site determines the specificity of a reaction. This is because the side chains are a key part of the active site, and the side chains determine the function of a protein
What kind of interactions enable the substrate to bind into the active site?
Weak interactions
Remember: multiple weak interactions form strong bonds between molecules
Why do we want the substrate to not bind so tightly to the active sight of the enzyme? use LOGIC it is not that hard of a question so think about it
Because we don’t want the substrate to not be able to reach the activation energy.
The substrate staying in substrate minima means it will require even more energy to get it to overcome the AE.
Weak interactions ensure what two advantages?
Specificity and reversibility
Why are weak bonds advantageous in terms of reversability?
Because it is easier to break weak bonds, which means once the reaction is done, the substrate can unbind from the enzyme and the enzyme can be reused again.
This refers to the complementary set of weak bonds that can accomodate specific substrates.
Molecular complementarity
What are the 4 types of enzyme-substrate bonds?
Ionic bonds/salt bridges
Hydrogen bonds
Van der Waals interactions
Covalent bonds (opposites attract kind of bonds)
These bonds make use of charged side chains (either acidic: Aspartate, Glutamate, or basic: Arginine, Lysine)
Ionic bonds
These bonds are often classified as when the side chain of backbone O and N atoms can often act as hydrogen donors and acceptors.
Hydrogen bonds.
These are bonds that involve interactions between any protein and substrate atoms in close proximity. It is the weakest bonds of the 4 enzyme-substrate bonds.
Van der Waals Interactions/Bonds
These are the strongest of the bonds, and relatively rare when it comes to enzyme-substrate bonding.
Covalent bonds
True or false. The active site is symmetric, which allows the enzyme to distinguish between identical groups on the substrate.
False. The active site is asymmetric - its asymmetry allows it to be specific to a specific enzyme
What are the 2 models for enzyme-substrate binding?
Lock and key model and induced fit model
What does the lock and key model for enzyme-substrate binding state?
The shape of the substrate ad the conformation of the active site are complementary to each other.
- the substrate perfectly fits into the enzyme.
What is the problem with the lock and key model? What does it suggest?
That a) substrates perfectly fit into an enzyme for it specifically and b) that enzymes are static (unchanging) - which is a problem because one enzyme can be used for multiple different purposes (due to the nature of the amino side chains that are projecting into it)
What does the induced fit model stat?
The enzyme undergoes a conformational shape change upon binding to the substrate.
So the shape of the active site becomes complementary to the shape of substrate only after the binding has occurred.
- it states that enzyme is not perfectly shaped to fit the substrate.
What does the induced fit model suggest about the nature of enzymes?
That enzymes are dynamic and its active site can change depending on the substrate binding
What are the 3 ways to reduce the activation energy? (In this case, activation energy is energy needed to reach the transition state)
1) Ground state destabilisation (lift energy of reactants)
2) Ground state stabilisation (stabilising transition state) (reducing activation energy)
3) Alternate reaction pathway with a different transition state (with a lower energy)
How can 1 and 2 be achieved in the same way?
By having an active site that has shape/charge complementary to the substrate.
Remember: Ground state is referring ultimately to the nature of the active site; not the substrate
What are the 5 catalytic mechanisms?
1) Preferential binding of the transition state
2) Proximity and orientation effects
3) Acid-base catalysis
4) Metal ion catalysis
5) Covalent catalysis
What does the preferential binding of the transition state predict?
This predicts that an enzyme should bind the transition state more tightly than it binds the substrate.
- aka enzyme is shaped PREFERENTIALLY to transition state so that it will be more effective
What is the problem with preferential binding of the transition state? How do we solve this issue?
Transition states are transient; meaning they only last for a short period of time - so they are more difficult to isolate
So we design and make analogues
What are analogues?
Analogues are enzyme inhibitors -
they mimic the transition state of drugs/substrates to make enzyme-substrate complex viable and more effective.
This is an example of a transition state analogue. It is a powerful cholesterol-lowering drug, as it inhibits HMG CoA reductase (biosynthetic pathway for cholesterol)
Lipitor
These make ideal enzyme inhibitors.
Transition sate analogues
If someone is taking Enalapril and Aliskiren what kind of condition would that be modulating or helping with?
Lower blood pressure (meaning they have high blood pressure)
These lower serum cholesterol
Statins
Why are enzymes often targeted for drugs and other beneficial agents?
Because enzymes can inhibit the function of normal metabolic pathways. (interfere with that, and you can create health impacts that improve health conditions)
What are the 2 guidelines for molecules to successfully react with each other?
- they must be close to each other
- and react with the correct orientation
This is a catalytic mechanisms that involves proton transfers ad side chains that can accept/donate protons.
Acid-base catalysis
Why is Histidine particularly ideal to acid-base catalysis?
Because Histidine has a pKa of 6.5 => which is very close to physiological pH meaning it can move between different protonation states (depending on the environment of the active site)
pH > pKa = deprotonated (because it will be in base form)
pH < pKa = protonated (because it will be in acid form)
Helpful tip: to remember which is which, always think, is the pH greater or lower than the pKa? Lower than is always protonated (so acid form), and greater than is always deprotonated (so base form)
This involves the use of metal ions for catalytic activity. Metals provide correct substrate orientation, act as Lewis acids, and provide sites for electron transfers (redox reaction)
Metal ion catalysts
This involves the formation of a reactive, short-lived intermediate, which is covalently attached to the enzyme.
Covalent catalysis
