Week 5 - Sept 29

Energy and Enzymes

Introduction to Enzymes

Enzymes are biological catalysts that accelerate chemical reactions in living organisms by lowering the activation energy required. They are essential for sustaining life by enabling metabolic processes to occur rapidly and efficiently under physiological conditions.

• Enzyme: A protein (or RNA molecule) that increases the rate of a chemical reaction without being consumed.

• Substrate: The reactant molecule(s) upon which an enzyme acts.

• Active Site: The region of the enzyme where substrate binding and catalysis occur.

Example: Glucokinase catalyzes the phosphorylation of glucose using ATP as a substrate.

How Enzymes Work

Mechanism of Enzyme Action

Enzymes function through a series of steps that involve substrate binding, transition state facilitation, and product release. The specificity and efficiency of enzymes depend on their three-dimensional structure, particularly the shape of the active site.

1. Initiation: Substrates bind to the enzyme's active site, forming an enzyme-substrate complex.

2. Transition State Facilitation: The enzyme stabilizes the transition state, lowering the activation energy required for the reaction.

3. Termination: The product is released, and the enzyme returns to its original conformation.

Key Point: Shape matters—the enzyme's active site is complementary to the substrate's shape, ensuring specificity.

Factors Affecting Enzyme Activity

Cofactors

Some enzymes require additional non-protein molecules called cofactors to function properly.

• Inorganic ions: Examples include copper (Cu2+), zinc (Zn2+), and iron (Fe2+/3+).

• Non-protein organic molecules: Often called coenzymes (e.g., NAD+, FAD).

Substrate Concentration

The rate of an enzyme-catalyzed reaction increases with substrate concentration but eventually reaches a maximum velocity (Vmax) when the enzyme is saturated.

• At low substrate concentrations, the reaction rate increases sharply with increasing substrate.

• At high substrate concentrations, the rate plateaus as all enzyme active sites are occupied.

Equation:

$V = \frac{V_{max}[S]}{K_m + [S]}$

where $V$ is the reaction rate, $[S]$ is substrate concentration, $V_{max}$ is the maximum rate, and $K_m$ is the Michaelis constant.

Enzyme Concentration

Increasing enzyme concentration increases the reaction rate, provided substrate is not limiting.

• Directly proportional relationship between enzyme concentration and reaction rate at constant substrate concentration.

Temperature

Enzyme activity is sensitive to temperature. Each enzyme has an optimal temperature at which it functions most efficiently.

• Increasing temperature generally increases reaction rate up to the optimum.

• Above the optimum, enzyme structure (and thus activity) declines due to denaturation.

• Different organisms have enzymes adapted to their environmental temperatures.

pH

Enzyme activity is also affected by pH, with each enzyme having an optimal pH range.

• Changes in pH can alter the ionization state of amino acids, affecting enzyme structure and function.

• Enzymes from different organisms or cellular compartments have different pH optima.

Example: Pepsin (stomach enzyme) functions best at low pH, while trypsin (intestinal enzyme) functions best at neutral to slightly basic pH.

pH and Amino Acid Ionization

The ionization state of amino acids in the enzyme can change with pH, affecting enzyme structure and activity.

Example: The charge state of amino acids such as lysine or glutamic acid changes as pH shifts from acidic to basic, altering protein folding and function.

Regulation of Enzyme Activity

Non-covalent Regulation

• Competitive Inhibition: An inhibitor molecule competes with the substrate for binding to the active site. This type of inhibition is concentration dependent and can be overcome by increasing substrate concentration.

• Non-competitive (Allosteric) Regulation: A regulatory molecule binds to a site other than the active site (allosteric site), causing a conformational change that increases or decreases enzyme activity.

Example: Penicillin acts as a competitive inhibitor of the enzyme that synthesizes bacterial cell walls (peptidoglycan).

Covalent Modifications

• Changes to Amino Acid Sequence (Primary Structure): Some enzymes are synthesized as inactive precursors (zymogens) and activated by cleavage of specific peptide bonds (e.g., trypsinogen to trypsin).

• Modification of Specific Amino Acids: Enzyme activity can be regulated by the addition or removal of chemical groups (e.g., phosphorylation, methylation) to specific amino acids.

Example: Phosphorylation by kinases can activate or deactivate enzymes; dephosphorylation by phosphatases reverses this modification.

Effect of Structural Changes

Changes in primary structure or covalent modification of amino acids can alter the enzyme's shape and thus its activity.

• Phosphorylation can cause conformational changes that activate or inhibit enzyme function.

Feedback Inhibition

Many metabolic pathways are regulated by feedback inhibition, where the end product of a pathway inhibits an enzyme that acts early in the pathway. This prevents the overaccumulation of the product and conserves resources.

• Example: In amino acid biosynthesis, the final product often inhibits the first enzyme in the pathway.

Summary Table: Factors Affecting Enzyme Activity

Factor	Effect on Enzyme Activity	Example
Substrate Concentration	Increases rate up to saturation (Vmax)	Glucose phosphorylation by hexokinase
Enzyme Concentration	Increases rate linearly if substrate is not limiting	Digestive enzymes in the gut
Temperature	Increases rate to optimum, then decreases due to denaturation	Thermophilic vs. mesophilic enzymes
pH	Optimal range for each enzyme; extremes denature enzyme	Pepsin (pH 2), Trypsin (pH 8)
Cofactors	Required for activity of some enzymes	Zn2+ in carbonic anhydrase
Inhibitors/Regulators	Decrease or increase activity via competitive, allosteric, or covalent mechanisms	Penicillin, phosphorylation

Additional info: The notes above integrate and expand upon the provided slides and text, adding definitions, examples, and context for clarity and completeness. The Michaelis-Menten equation is included as a standard model for enzyme kinetics.