lec7 Flashcards
What are enzymes and what do they do?
Enzymes are proteins that catalyze biological reactions. They increase the rate of reactions (by a factor of 10⁶ or more) by lowering the activation energy. They are highly specific for their substrate and the reaction they catalyze. Enzymes do not drive reactions but help reactions reach equilibrium faster. They are not consumed in the reaction and function as catalysts
The same equilibrium point is reached in the absence or presence of an enzyme, it is just reached more quickly with enzyme.
What are the three key aspects of enzyme function?
- Enzymes bind substrates with high affinity and specificity.
- Substrate binding to the active site induces structural changes in the enzyme.
- Enzyme activity is highly regulated within the cell.
How do enzymes or catalysts affect activation energy?How do enzymes affect activation energy and Gibbs free energy?
Enzymes lower the activation energy (ΔG‡) by stabilizing the transition state. However, the overall Gibbs free energy (ΔG) of the reaction remains the same because enzymes do not affect the energy of the reactants or products. They only change the energy required to reach the transition state, making the reaction proceed faster without altering the final energy difference between reactants and products.
What are the lock-and-key and induced fit models of enzyme-substrate recognition?
Lock-and-key model (Emil Fischer): The substrate is a perfect fit for the enzyme’s active site, like a key fitting into a lock.
Induced fit model (Daniel Koshland): Both the substrate and active site undergo conformational changes to fit together, closely resembling the transition state. The enzyme’s binding site is most complementary to the transition state of the substrate, and weak non-covalent (and sometimes covalent) interactions occur. These interactions release energy, called binding energy (ΔGB), which helps stabilize the substrate and lower the activation energy.
How is water excluded from the enzyme’s active site?
When a substrate binds to an enzyme, the enzyme undergoes a conformational change, tightening around the substrate. This change blocks water molecules from entering the active site, preventing them from interfering with the catalytic process. Excluding water helps maintain optimal enzyme activity by preventing unwanted hydrogen bonding and ensuring that the enzyme functions efficiently.
Why are substrate analogs used in enzyme studies?
Substrate analogs are molecules that closely resemble the substrate but do not undergo the reaction or get released. They are used in enzyme studies (e.g., X-ray crystallography) to study enzyme-substrate binding. Since the analog binds to the enzyme but doesn’t get converted to the product, it remains bound, allowing researchers to observe the enzyme’s structural changes and understand how the enzyme catalyzes reactions.
What are cofactors and how do they assist enzymes?
Cofactors are non-protein compounds required for enzyme activity. They can be:
Inorganic metal ions (e.g., Fe²⁺, Cu²⁺)
Complex organic or metal-organic molecules called coenzymes
Cofactors may be tightly bound to the enzyme’s active site or associate transiently. About 30% of enzymes require cofactors to aid in catalysis.
What are coenzymes and how do they aid enzymes?
Coenzymes are small organic molecules that help enzymes catalyze reactions but cannot catalyze reactions by themselves. They bind to apoenzymes (inactive enzyme) to form the active enzyme (holoenzyme). Coenzymes cannot be synthesized by the cell and must be obtained from the diet. They often come from vitamins and provide a functional group involved in the catalytic reaction.
What are the key differences between coenzymes and inorganic cofactors?
Coenzymes:
Organic molecules (often derived from vitamins).
Cannot catalyze reactions by themselves; they help enzymes catalyze reactions.
Bind to apoenzymes (inactive enzymes) to form holoenzymes (active enzymes).
Diet-dependent; must be obtained from food sources.
Provide a functional group that participates in the catalytic reaction.
Inorganic Cofactors:
Inorganic (usually metal ions like Fe²⁺, Cu²⁺, Zn²⁺).
Can be tightly bound to the enzyme or transiently associate with it.
Do not need to be obtained through the diet in the same way (many are naturally occurring in cells).
Usually assist with stabilizing enzyme structure, electron transfer, or substrate binding but do not provide functional groups for catalysis.
How is NAD⁺ an example of a coenzyme?
is a redox coenzyme derived from vitamin B3 (niacin). It participates in redox reactions by accepting electrons and a proton, becoming reduced to NADH. This process allows enzymes to catalyze energy-transfer reactions, such as those involved in cellular respiration. NAD⁺ is essential for enzymes to transfer energy between molecules, aiding in the generation of ATP.
General Strategies for Enzyme Catalysis
Proximity and Orientation: The enzyme binds two substrates and positions them precisely for the reaction to occur, increasing the chance of effective collisions.
Electrostatic Stabilization: Binding of substrates to the enzyme rearranges electrons, creating partial charges that stabilize the transition state, favoring the reaction.
Strain and Distortion: The enzyme strains the bound substrates, forcing them into a transition state, lowering activation energy and making the reaction more favorable.
