Unit 1: Biochemistry - Chemical Reactions and Enzymes

Fundamentals of Chemical Reactions

• Definition of Chemical Reaction: A chemical reaction is a biological or chemical process that transforms one set of chemical substances into another set of chemical substances.

• Example - Combustion of a Match:

  • When a match is struck and lit, a rapid chemical reaction occurs involving key elements:

  • Potassium

  • Chlorine

  • Phosphorus

  • Sulfur

  • Reaction Output: The reaction causes combustion, releasing energy in the form of light and heat.

• Core Components of Chemical Reactions:

  • Reactants: The starting elements or chemical compounds that undergo change and cause the reaction to occur.

  • Products: The resulting elements or compounds produced at the end of the chemical reaction.

  • Mathematical Analogy: A chemical reaction functions like a mathematical equation, where the yields arrow ($\rightarrow$) serves as an equal sign that separates reactants on the left from products on the right.

• Example - Methane Combustion Equation:

  • Chemical Equation:     $\text{CH}_4 + 2\text{O}_2 \rightarrow \text{CO}_2 + 2\text{H}_2\text{O}$

  • Reactant Composition:

  • One methane molecule ($\text{CH}_4$), consisting of $1$ carbon atom and $4$ hydrogen atoms.

  • Two diatomic oxygen molecules ($2\text{O}_2$), consisting of $4$ oxygen atoms.

  • Product Composition:

  • One carbon dioxide molecule ($\text{CO}_2$), consisting of $1$ carbon atom and $2$ oxygen atoms.

  • Two water molecules ($2\text{H}_2\text{O}$), consisting of $4$ hydrogen atoms and $2$ oxygen atoms.

Energy Dynamics in Reactions

• Energy Exchange: Every chemical reaction involves either the release or absorption of energy.

• Thermal Classification of Reactions:

  • Exothermic Reactions:

  • Definition: Chemical reactions in which energy is net-released into the surroundings.

  • Temperature Effect: Radiates heat and feels warm or hot to the touch.

  • Energy Level: Product molecules possess lower potential energy than the initial reactant molecules.

  • Endothermic Reactions:

  • Definition: Chemical reactions in which energy is net-absorbed from the surroundings.

  • Temperature Effect: Absorbs heat and feels cold to the touch.

  • Energy Level: Product molecules possess higher potential energy than the initial reactant molecules.

• Activation Energy:

  • Definition: The initial minimum quantity of energy required to kickstart a chemical reaction.

  • Role: Functions as an energy barrier that reactant molecules must reach to enter a transition state before transforming into products.

  • Energy Progress Profiles:

  • Endothermic Energy Profile: Begins at a low reactant energy level, absorbs energy up to the activation peak, and settles at a higher product energy level.

  • Exothermic Energy Profile: Begins at a baseline reactant energy level, ascends to the activation peak, and drops significantly to a lower product energy level.

Enzymes as Biological Catalysts

• Biological Necessity:

  • Essential metabolic chemical reactions that make life possible naturally proceed far too slowly or possess activation energies that are too high for cellular survival.

• Definition of Enzyme:

  • An enzyme is a organic biocatalyst that speeds up the rate of a chemical reaction without being permanently consumed.

• Lowering Activation Energy:

  • Enzymes accelerate biological reactions specifically by lowering the required activation energy.

  • Enzymes do not alter the starting potential energy of reactants or the final potential energy of products; they reduce only the peak energy required to initiate the reaction.

The Enzymatic Mechanism

• Key Enzymatic Terminology:

  • Substrate: The specific reactant molecule that binds to an enzyme and undergoes a chemical transformation.

  • Active Site (Activation Site): The specialized three-dimensional region on an enzyme where substrate molecules physically bind and react.

• Lock-and-Key Model:

  • The lock-and-key model describes the structural complementary fit between an enzyme and its substrate:

  • Substrate = Key

  • Enzyme = Lock

  • The substrate fits precisely into the active site to form the temporary Enzyme-Substrate Complex.

• Sequential Reaction Steps:

  • 1. Substrate Binding: Substrate molecules collide with and bind specifically to the active site of the target enzyme.

  • 2. Bond Weakening: Binding to the active site strains and weakens the chemical bonds within the substrate structure, lowering the activation energy barrier.

  • 3. Product Conversion and Release: Chemical bonds are broken or formed, converting the substrate into products, which are then released from the active site.

  • 4. Enzyme Recycling: The enzyme remains structurally unchanged by the reaction and is reused again and again for subsequent catalytic cycles.

Regulation and Factors Affecting Enzyme Function

• Representative Human Enzymes:

  • Amylase: Catalyzes the breakdown of complex carbohydrates (starches) into simpler sugars.

  • Lactase: Catalyzes the breakdown of lactose into digestible simple sugars.

• Structure-Function Relationship:

  • The precise three-dimensional molecular shape of an enzyme directly dictates its functional catalytic ability.

• Factors Influencing Enzymatic Activity:

  • pH Values: Operating outside an enzyme's optimal pH range alters internal ionic bonding, leading to structural alteration and reduced function.

  • Temperature Changes: Temperature fluctuations impact kinetic energy; high heat disrupts molecular stability and structurally deforms the active site.

  • Denaturation: Extreme shifts in pH or high temperatures cause an enzyme to lose its specific functional shape (denature), preventing substrate binding.

  • Substrate Availability: Insufficient substrate levels limit reaction velocity and can halt enzymatic processes altogether when active sites are empty.

  • Competitive Inhibitors: Molecules that resemble the substrate bind to the active site, physically blocking genuine substrates and preventing enzyme activation.