Cours 2: Types de cinétiques à l'état stationnaire Flashcards
Que sont les interactions crucial for protein and ligand binding?
- liaisons covalentes
- interactions ioniques de type électrostatique, ion-dipôle ou dipôle-dipôle, les ponts
hydrogène et les complexes de transfert de charge - interactions de type van der Waals
- interactions hydrophobes
These interactions collectively stabilize the binding of substrates or inhibitors to enzymes.
What parameters are measured in a standard experimental condition with [E] = 1 nM?
Initial velocity and substrate concentration
These parameters help in determining the enzymatic activity under controlled conditions.
What are hydrogen bonds?
A type of dipole-dipole interaction that involves donors and acceptors, typically N and O, with F being a weak acceptor
Stabilization energy is approximately 3–10 kcal/mol.
What is the stabilization energy range of covalent bonds?
40 to 110 kcal/mol
Represents the energy required to form a covalent bond.
What are ionic interactions?
Electrostatic interactions that include:
* Electrostatic interactions: ~5 kcal/mol
* Ion-dipole and dipole-dipole interactions: ~1 kcal/mol
These interactions involve partial charges.
What do δ+ and δ- indicate?
They indicate dipoles
Used to represent partial charges in molecules.
What are charge transfer complexes?
Dipole-dipole interactions involving π electrons, often from aromatic groups like Phe, Tyr, Trp, His
Stabilization energy is less than 3 kcal/mol.
What are hydrophobic interactions primarily due to?
Desolvation leading to increased entropy
Stabilization energy is approximately 0.5 kcal/mol.
What are van der Waals interactions?
Result from the formation of temporary dipoles due to electron movement in atomic electron clouds
Stabilization energy is approximately 0.5 kcal/mol.
What is the Lennard-Jones curve?
A graph showing how energy varies between two atoms based on their distance
It indicates potential energy and the balance of attractive and repulsive forces.
What does the term r0 refer to?
The interatomic distance at minimum energy
It represents the most favorable distance between two atoms.
What does the transition state theory state?
Catalysis does not influence K_eq (ΔG0)
The transition state is the most unstable state in the reaction pathway.
How does an enzyme accelerate a reaction?
By stabilizing the transition state, increasing [X‡] and decreasing ΔG‡
This facilitates the reaction process.
What influences the catalytic properties of an enzyme?
Its three-dimensional structure
The active site interacts with the substrate to form the product.
What is the role of the active site in an enzyme?
It is the part of the enzyme that interacts with the substrate to form the product
Catalysis requires the substrate to bind to the active site.
What types of enzymatic catalysis exist?
Types include:
* Proximity and orientation
* General acid-base reaction
* Covalent modification
* Distortion
* Stabilization of the transition state
Each type contributes to the efficiency of enzyme-catalyzed reactions.
What is the significance of hydrogen bonds in acid-base catalysis?
They are important in mechanisms of general acid-base catalysis
They facilitate proton transfer during the reaction.
Fill in the blank: Catalytic covalent means that a _______ bond will form between the enzyme and a reactant during the reaction.
[covalent]
What does the term ‘effective concentration’ refer to in enzyme catalysis?
The increased proximity of reactants within the active site
This enhances the likelihood of a reaction occurring.
What happens during covalent catalysis?
A covalent bond forms between the enzyme and a substrate during the reaction
This bond must be broken for the enzyme to return to its free state.
True or False: Electrophilic attacks are more common in covalent enzyme catalysis.
False
What does the reduction of activation energy lead to in enzyme-catalyzed reactions?
It accelerates the reaction rate.
What happens to the substrate when the enzyme lysozyme binds to an oligosaccharide?
The bound substrate is distorted to resemble the transition state.
Fill in the blank: The principle of _______ states that the active site stabilizes the transition state, reducing activation energy.
transition state stabilization
What is the relationship between the concentration of the transition state and the reaction rate?
Increased concentration of the transition state increases the reaction rate.
For a 10^6 acceleration factor at 25°C, what ΔΔG is needed?
34.2 kJ·mol⁻¹
What happens to the substrate during the catalysis by distortion?
It causes a distortion that makes the E·S complex less stable.
How does pH affect enzymatic reactions?
1) It can directly affect catalysis by altering the ionization state of the substrate or enzyme residues.
2) inactivation du mécanisme catalytique de l’enzyme
3) modification de l’équilibre d’une réaction
What is the effect of incorrect ionization on enzyme catalytic mechanisms?
It prevents the formation of hydrogen bonds and proton transfer.
What is a competitive inhibitor?
A stable molecule that mimics the transition state structure and binds to the active site.
What type of profile do many enzymes exhibit regarding their maximum reaction velocity (Vmax) as a function of pH?
A bell-shaped profile.
How can the pKa values of amino acids be altered within the active site?
Through interactions with other residues and the local environment.
What stabilizes the negative charge of Asp when forming a salt bridge with Lys?
The positive charge of Lys.
In a nonpolar region, how does the pKa of ammonium change?
It becomes less basic and easier to deprotonate.
Fill in the blank: Two neighboring groups with the same charge can _______ one of the charges, making it neutral.
destabilize
What is the significance of understanding the molecular mechanism of enzyme reactions in drug design?
It aids in creating competitive inhibitors that effectively bind to enzyme active sites.
What can destabilize one of the two charges, making it neutral?
Charge (distance ~3-4 Å, equivalent to a hydrogen bond)
This destabilization can affect the pKa of amino acids involved.
What happens to the pKa of one of the two Lys residues when destabilized?
It becomes lower; easier to deprotonate.
Is it always possible to experimentally observe the complete pH-activity profile?
No, it is not always possible.
What may influence the solubility of an enzyme?
The ionization state of amino acids at the protein surface.
What does the pH affect regarding enzyme activity?
The catalytic rate, Vmax, and/or KM may be disrupted.
What are the two major types of reactions involving two substrates?
- Reactions involving ternary complexes (E + A + B)
- Reactions involving binary complexes (E・A or E・B)
In a reaction involving a ternary complex, what is the order of substrate binding?
The substrate A must be bound before substrate B.
What is the significance of pKa values in enzyme catalysis?
They provide important clues about the identity of amino acids at the active site and their role in the catalytic reaction.
True or False: The pKa linked to a variation in KM can indicate the identity of an amino acid involved in enzyme-substrate interaction.
True.
What does a pKa value around 4 suggest about an amino acid residue’s role?
It suggests that an Asp or Glu residue is essential for the process.
What characterizes the ‘ping pong’ mechanism in enzymatic reactions?
Modification of the enzyme by one substrate before the second substrate binds.
In the analysis of reactions forming a ternary complex, what condition simplifies the treatment of experimental data?
[B]0»_space; [A]0 (at least 10 times greater).
What does Vmax represent in enzymatic reactions?
The maximum rate at saturating levels of substrates A and B.
What are KA and KB approximations of in Michaelis-Menten kinetics?
They are approximations of the Michaelis-Menten constants for substrates A and B, respectively.
What is the relationship between pKa and substrate identity in enzyme reactions?
Changes in pKa can indicate specific amino acids involved in substrate interactions.
What is the mechanism analyzed in the binary complex ‘ping pong’?
A constant speed is determined by measuring several speed constants at multiple fixed concentrations of B
This requires that [B]0»_space; [A]0 throughout the reaction.
What characteristic is observed when repeating the analysis with several fixed B concentrations?
The lines are parallel
This characteristic is specific to the ping pong mechanism.
What does the analysis of binary and ternary complex formation help to determine?
The mechanism of an enzyme
This is important for developing inhibitors that exploit the enzyme’s mechanism.
What additional confirmation can be sought in enzyme analysis?
Presence of partial reactions
Specifically, whether the transformation of A into P occurs in the absence of B.
What indicates a ping-pong type mechanism in enzyme reactions?
Observation of E + A ➞ E’ + P
If this transformation occurs without B, it suggests a ping-pong mechanism.
What is an example of a modified form of an enzyme identified in the content?
E’
Example includes nucleotide diphosphate kinase.
Fill in the blank: The lines obtained from repeated analysis with fixed concentrations of B are _______.
parallel
True or False: The analysis allows differentiation between binary and ternary complex formation.
True
What can be observed to understand the mechanism of an enzyme?
Direct reaction or reverse reaction
This can provide insights into the enzyme’s behavior.
