Cours 2: Types de cinétiques à l'état stationnaire

Question 1

Que sont les interactions crucial for protein and ligand binding?

Answer 1

• 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.

Question 2

What parameters are measured in a standard experimental condition with [E] = 1 nM?

Answer 2

Initial velocity and substrate concentration

These parameters help in determining the enzymatic activity under controlled conditions.

Question 3

What are hydrogen bonds?

Answer 3

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.

Question 4

What is the stabilization energy range of covalent bonds?

Answer 4

40 to 110 kcal/mol

Represents the energy required to form a covalent bond.

Question 5

What are ionic interactions?

Answer 5

Electrostatic interactions that include:
* Electrostatic interactions: ~5 kcal/mol
* Ion-dipole and dipole-dipole interactions: ~1 kcal/mol

These interactions involve partial charges.

Question 6

What do δ+ and δ- indicate?

Answer 6

They indicate dipoles

Used to represent partial charges in molecules.

Question 7

What are charge transfer complexes?

Answer 7

Dipole-dipole interactions involving π electrons, often from aromatic groups like Phe, Tyr, Trp, His

Stabilization energy is less than 3 kcal/mol.

Question 8

What are hydrophobic interactions primarily due to?

Answer 8

Desolvation leading to increased entropy

Stabilization energy is approximately 0.5 kcal/mol.

Question 9

What are van der Waals interactions?

Answer 9

Result from the formation of temporary dipoles due to electron movement in atomic electron clouds

Stabilization energy is approximately 0.5 kcal/mol.

Question 10

What is the Lennard-Jones curve?

Answer 10

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.

Question 11

What does the term r0 refer to?

Answer 11

The interatomic distance at minimum energy

It represents the most favorable distance between two atoms.

Question 12

What does the transition state theory state?

Answer 12

Catalysis does not influence K_eq (ΔG0)

The transition state is the most unstable state in the reaction pathway.

Question 13

How does an enzyme accelerate a reaction?

Answer 13

By stabilizing the transition state, increasing [X‡] and decreasing ΔG‡

This facilitates the reaction process.

Question 14

What influences the catalytic properties of an enzyme?

Answer 14

Its three-dimensional structure

The active site interacts with the substrate to form the product.

Question 15

What is the role of the active site in an enzyme?

Answer 15

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.

Question 16

What types of enzymatic catalysis exist?

Answer 16

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.

Question 17

What is the significance of hydrogen bonds in acid-base catalysis?

Answer 17

They are important in mechanisms of general acid-base catalysis

They facilitate proton transfer during the reaction.

Question 18

Fill in the blank: Catalytic covalent means that a _______ bond will form between the enzyme and a reactant during the reaction.

Answer 18

[covalent]

Question 19

What does the term ‘effective concentration’ refer to in enzyme catalysis?

Answer 19

The increased proximity of reactants within the active site

This enhances the likelihood of a reaction occurring.

Question 20

What happens during covalent catalysis?

Answer 20

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.

Question 21

True or False: Electrophilic attacks are more common in covalent enzyme catalysis.

Answer 21

False

Question 22

What does the reduction of activation energy lead to in enzyme-catalyzed reactions?

Answer 22

It accelerates the reaction rate.

Question 23

What happens to the substrate when the enzyme lysozyme binds to an oligosaccharide?

Answer 23

The bound substrate is distorted to resemble the transition state.

Question 24

Fill in the blank: The principle of _______ states that the active site stabilizes the transition state, reducing activation energy.

Answer 24

transition state stabilization

Question 25

What is the relationship between the concentration of the transition state and the reaction rate?

Answer 25

Increased concentration of the transition state increases the reaction rate.

Question 26

For a 10^6 acceleration factor at 25°C, what ΔΔG is needed?

Answer 26

34.2 kJ·mol⁻¹

Question 27

What happens to the substrate during the catalysis by distortion?

Answer 27

It causes a distortion that makes the E·S complex less stable.

Question 28

How does pH affect enzymatic reactions?

Answer 28

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

Question 29

What is the effect of incorrect ionization on enzyme catalytic mechanisms?

Answer 29

It prevents the formation of hydrogen bonds and proton transfer.

Question 30

What is a competitive inhibitor?

Answer 30

A stable molecule that mimics the transition state structure and binds to the active site.

Question 31

What type of profile do many enzymes exhibit regarding their maximum reaction velocity (Vmax) as a function of pH?

Answer 31

A bell-shaped profile.

Question 32

How can the pKa values of amino acids be altered within the active site?

Answer 32

Through interactions with other residues and the local environment.

Question 33

What stabilizes the negative charge of Asp when forming a salt bridge with Lys?

Answer 33

The positive charge of Lys.

Question 34

In a nonpolar region, how does the pKa of ammonium change?

Answer 34

It becomes less basic and easier to deprotonate.

Question 35

Fill in the blank: Two neighboring groups with the same charge can _______ one of the charges, making it neutral.

Answer 35

destabilize

Question 36

What is the significance of understanding the molecular mechanism of enzyme reactions in drug design?

Answer 36

It aids in creating competitive inhibitors that effectively bind to enzyme active sites.

Question 37

What can destabilize one of the two charges, making it neutral?

Answer 37

Charge (distance ~3-4 Å, equivalent to a hydrogen bond) ## Footnote This destabilization can affect the pKa of amino acids involved.

Question 38

What happens to the pKa of one of the two Lys residues when destabilized?

Answer 38

It becomes lower; easier to deprotonate.

Question 39

Is it always possible to experimentally observe the complete pH-activity profile?

Answer 39

No, it is not always possible.

Question 40

What may influence the solubility of an enzyme?

Answer 40

The ionization state of amino acids at the protein surface.

Question 41

What does the pH affect regarding enzyme activity?

Answer 41

The catalytic rate, Vmax, and/or KM may be disrupted.

Question 42

What are the two major types of reactions involving two substrates?

Answer 42

* Reactions involving ternary complexes (E + A + B) * Reactions involving binary complexes (E・A or E・B)

Question 43

In a reaction involving a ternary complex, what is the order of substrate binding?

Answer 43

The substrate A must be bound before substrate B.

Question 44

What is the significance of pKa values in enzyme catalysis?

Answer 44

They provide important clues about the identity of amino acids at the active site and their role in the catalytic reaction.

Question 45

True or False: The pKa linked to a variation in KM can indicate the identity of an amino acid involved in enzyme-substrate interaction.

Answer 45

True.

Question 46

What does a pKa value around 4 suggest about an amino acid residue's role?

Answer 46

It suggests that an Asp or Glu residue is essential for the process.

Question 47

What characterizes the 'ping pong' mechanism in enzymatic reactions?

Answer 47

Modification of the enzyme by one substrate before the second substrate binds.

Question 48

In the analysis of reactions forming a ternary complex, what condition simplifies the treatment of experimental data?

Answer 48

[B]0 >> [A]0 (at least 10 times greater).

Question 49

What does Vmax represent in enzymatic reactions?

Answer 49

The maximum rate at saturating levels of substrates A and B.

Question 50

What are KA and KB approximations of in Michaelis-Menten kinetics?

Answer 50

They are approximations of the Michaelis-Menten constants for substrates A and B, respectively.

Question 51

What is the relationship between pKa and substrate identity in enzyme reactions?

Answer 51

Changes in pKa can indicate specific amino acids involved in substrate interactions.

Question 52

What is the mechanism analyzed in the binary complex 'ping pong'?

Answer 52

A constant speed is determined by measuring several speed constants at multiple fixed concentrations of B ## Footnote This requires that [B]0 >> [A]0 throughout the reaction.

Question 53

What characteristic is observed when repeating the analysis with several fixed B concentrations?

Answer 53

The lines are parallel ## Footnote This characteristic is specific to the ping pong mechanism.

Question 54

What does the analysis of binary and ternary complex formation help to determine?

Answer 54

The mechanism of an enzyme ## Footnote This is important for developing inhibitors that exploit the enzyme's mechanism.

Question 55

What additional confirmation can be sought in enzyme analysis?

Answer 55

Presence of partial reactions ## Footnote Specifically, whether the transformation of A into P occurs in the absence of B.

Question 56

What indicates a ping-pong type mechanism in enzyme reactions?

Answer 56

Observation of E + A ➞ E' + P ## Footnote If this transformation occurs without B, it suggests a ping-pong mechanism.

Question 57

What is an example of a modified form of an enzyme identified in the content?

Answer 57

E' ## Footnote Example includes nucleotide diphosphate kinase.

Question 58

Fill in the blank: The lines obtained from repeated analysis with fixed concentrations of B are _______.

Answer 58

parallel

Question 59

True or False: The analysis allows differentiation between binary and ternary complex formation.

Answer 59

True

Question 60

What can be observed to understand the mechanism of an enzyme?

Answer 60

Direct reaction or reverse reaction ## Footnote This can provide insights into the enzyme's behavior.