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I. WHAT ARE ENZYMES MADE OF? Defining Terms

• Enzyme: A biomolecule that catalyzes a specific biochemical reaction.
• Catalysis: The process of increasing biochemical reaction rates using a molecule (catalyst) that is not part of the reaction itself.
• Active Site: The specific region on an enzyme responsible for substrate binding and chemical catalysis.
• Substrate: The molecule that undergoes a chemical change, which can be understood as the reactant. The binding of the substrate is reversible.

I. WHAT ARE ENZYMES MADE OF? Defining Terms

• Cofactor: An inorganic ion required for enzymatic activity.
• Coenzyme: An organic molecule required for enzymatic activity.

II. THERMODYNAMIC BASIS OF REACTION RATES

Does Free Energy Determine Rate?

• Example Reaction: $C<em>{12}H</em>{22}O<em>{11}(s) + 12O</em>2(g) \rightarrow 12CO<em>2(g) + 11H</em>2O(g)$
• Change in Free Energy ($\Delta G$): $\Delta G < -5000 kJ/mol$

Kinetics of Molecules

• Kinetically Stable: A term describing a molecule that has a long half-life or slow rate of breakdown; same reaction as above applies with $\Delta G < -5000kJ/mol$.

What Does Determine Rate?

• Rate Constant: A proportionality constant relating the rate of a reaction to the concentration of reactants; reflects the probability that a reaction will occur.
• Mathematical Expression: $A \quad k<em>1 \quad \frac{d[X]}{dt} = v</em>0 = k_1[A]$

Determinants of Rate Constant Magnitude

• Two Key Factors:
  1. Activation Energy
  2. Temperature
• Transition State (‡): A chemical species that is neither a reactant nor product but represents an activated form of the molecule during which electron redistribution from reactant to product is only partially accomplished.
• Activation Energy ($\Delta G^{‡}$): The energy required for a reactant to form the transition state.

III. ENZYMES: BIOLOGICAL CATALYSTS

Building a Framework

• Concepts illustrated through diagrams showing:
  • Free energy ( extit{G}) changes for substrate ( extit{S}), enzyme-substrate complex ( extit{ES}), transition state, and product ( extit{P}).

Induced Fit

• Induced Fit: Refers to conformational changes in both the macromolecule and substrate/ligand that lead to greater complementarity, enhancing the binding efficiency and catalytic activity.

Binding Energy (ΔGB)

• Binding Energy ($\Delta G_B$): The energy derived from non-covalent interactions when an enzyme or protein binds its substrate (transition state) or ligand. This can also be viewed as transition state stabilization.

III. ENZYMES: BIOLOGICAL CATALYSTS

Specific Catalytic Mechanisms

• Reaction Intermediates: Chemical species that are neither product nor reactant, found in the reaction pathway with a finite lifetime.
• Example reaction pathway:
  • $E + S \rightarrow ES \rightarrow ES^* \rightarrow E + P$

Acid/Base Catalysis

• Acid/Base Catalysis: A catalytic mechanism where an enzymatic functional group donates (acts as an acid) or accepts (acts as a base) a proton from the substrate, facilitating the reaction.

Covalent Catalysis

• Covalent Catalysis: A catalytic mechanism in which an enzymatic functional group acts as a nucleophile and forms a covalent bond with the substrate during the reaction.

Metal Ion Catalysis

• Metal Ion Catalysis: Involves the use of a metal ion by an enzyme's active site to achieve several functions, including:
  1. Stabilizing charged intermediates.
  2. Promoting a redox reaction or acid/base catalysis.
  3. Producing strong nucleophiles at physiological pH.

IV. EXAMPLES OF SPECIFIC ENZYMATIC MECHANISMS

Serine Protease

• Illustrated by structure diagrams showing key residues involved in catalysis:
  • Key amino acids include: His 57, Asp 102, and Ser195.
  • Presence of oxyanion hole facilitating transition state stability.

Enolase

• Catalytic mechanism involving:
  • Key residues: Lys 345, Glu 211.
  • Formation of enzyme-substrate (ES) complex and enolic intermediate.
  • Transition to enzyme-product (EP) complex.

Summary of Mechanisms

• Each enzymatic mechanism described provides specific catalytic efficiencies and is often dependent on the precise configuration of active site residues, the presence of cofactors, and the particular substrate being acted upon. Such details highlight the intricate nature of enzyme function and its significant role in biochemistry.