EXAM II - Lecture 3 (Enzymes and Substrates + Velocity)

Definition of Terms:
- Ligands: Small molecules that bind to a target, such as drugs or specific biochemical molecules (carbohydrates, fats, proteins).
- Target: The molecule that a ligand binds to, which can be a protein (most common), DNA, or RNA.

Common Ligands:
- Drugs, biochemical molecules (carbs, fats, proteins).
Common Targets:
- Primarily proteins, but can also include DNA and RNA (important for newer therapeutics targeting RNA).

Classification of Proteins:
- Enzymes: Catalysts that facilitate biochemical reactions.
- Receptors: Proteins that interact with ligands to elicit a biological response.

Role of Enzymes:
- Enzymes like salivary amylase act on substrates (e.g., carbohydrates) to catalyze reactions.
- Example: Salivary amylase acts on glucose, breaking down carbohydrates when mixed with saliva.

Definitions:
- Substrate: The molecule upon which an enzyme acts.
- Agonist: A ligand that binds to a receptor to invoke a biological response; typically refers to native ligands.

Types of Ligands:
- Native Substrate: Normal ligand interacting with the enzyme.
- Inhibitor: A ligand that binds to the enzyme and reduces its activity, often referred to as a Non-native substrate.

Binding and Activity:
- Ligands can either activate enzymatic activity (through agonism) or inhibit it (through antagonism).
- Dose-Response Relationship:
- Agonists and Antagonists:
  - Agonists produce a biological effect.
  - Antagonist produces no effect or inhibits the effect of the agonist.
  - Inverse Agonist: Produces the opposite effect of an agonist.

Active Site:
- Location on an enzyme where the substrate binds, crucial for the enzyme's activity.
Non-covalent Interactions:
- Binding involves various non-covalent interactions facilitating substrate attachment, like:
- Ion-ion
- Ion-dipole
- Dipole-dipole
- Hydrogen bonds
- Van der Waals forces
- Pi stacking
Additive Energy:
- Energy from these interactions is additive, affecting the overall stability and reactivity of the enzyme-substrate complex.

Dissociation Constant (B1):
- $K<em>d$ is the measure of the binding strength between substrate and enzyme. Lower $K</em>d$ indicates higher affinity.
Michaelis-Menten Constant ( $K_m$ ):
- A specific value that describes the affinity of the enzyme for the substrate.
- It reflects the rate at which the substrate binds to and dissociates from the enzyme. Lower values mean higher affinity.

Enzyme Properties:
- Enzymes catalyze reactions efficiently and specifically for their substrates.
- They operate under optimal conditions for pH and temperature.
- Enzymes are effective in low concentrations and work to convert substrate to product rapidly.

Velocity of Reaction:
- The rate at which substrates are converted to products.
- $V_{max}$ represents the maximum rate of reaction.
Half-Maximal Velocity:
- $V<em>{0}$ represents the reaction rate at a specific time, often studied with respect to $K</em>m$ .

Energy of Activation ( $E_a$ ):
- The minimum energy required for a reaction to occur. Enzymes lower the activation energy, facilitating faster reactions.
Transition State:
- The state at which substrate bonds are strained enough to form products; highest reactive energy point in the enzyme-catalyzed reaction.
Enzyme-Substrate Complex:
- An intermediate formed when an enzyme binds to its substrate, stabilizing them during the conversion to product.

Specific to substrates (example: salivary amylase only acts on carbohydrates).
Operate in catalytic amounts relative to the substrate.
Maintain optimal conditions required for activity.
Perform very specific reactions and are highly efficient, limiting waste.
Example of catalytic efficiency:
- With enzyme: $10^6$ substrates can convert to the product in one minute.
- Without enzyme: only $10$ substrates convert to product in the same time frame.

Kinetics Graphing:
- The relationship between substrate concentration and reaction rate produces a hyperbolic curve, indicating velocity increase until a plateau is reached at $V_{max}$ .
Dose-Efficacy Relationship:
- The concept used in pharmacology for receptor-ligand interactions, where effective concentration induces a specific biological effect.

Enzymatic reactions involve complex processes governed by the interactions between substrates and enzymes, influenced by many factors including substrate concentration, temperature, and enzyme structure. By comprehensively studying these dynamics, we gain insights into drug design and therapeutic applications in biochemistry and pharmacology.