Enzymes

Biological Reactions

  - Biological reactions are generally slow.
  - However, they can be accelerated by the use of catalysts.

Introduction to Catalysis

  - Catalysis is considered one of the most fundamental functions of proteins.
  - Reactions occur when:
    - Reactants collide in a precise orientation.
    - Reactants possess enough kinetic energy to overcome the repulsion between electrons during bond formation.
  - Enzymes assist in overcoming these two challenges.

Functions of Enzymes

  - Enzymes perform two key functions:
    1. Bring substrates together in a precise orientation that allows for interaction of the electrons involved in the reaction.
    2. Lower the kinetic energy requirement needed for the reaction to proceed.

Activation Energy and Rates of Chemical Reactions

  - The activation energy ( E_a) of a reaction is defined as the amount of free energy required to reach the transition state (intermediate condition).
  - Reactions only occur when the reactants have enough kinetic energy to overcome this energy barrier.
  - The kinetic energy of molecules is temperature-dependent.
  - Thus, the rate of a reaction depends on:
    - The kinetic energy of the reactants.
    - The activation energy of the specific reaction (i.e., the free energy of the transition state).

Kinetic Energy of Atoms or Molecules

  - At low temperatures, most molecules have lower kinetic energy, with the majority detected at a certain energy level.
  - At higher temperatures, the energy level with the most atoms shifts due to increased kinetic energy.

Catalysts and Free Energy

  - A catalyst is any substance that:
    - Lowers the activation energy of a reaction, thereby increasing the reaction rate.
    - Is not consumed or permanently altered in the reaction process.

Characteristics of Enzymes

  - Enzymes are specific protein catalysts, usually catalyzing only one type of reaction.
  - Most biological chemical reactions require enzymes to achieve meaningful rates.
  - Major functions of enzymes include:
    - Bringing substrates together in specific orientations.
    - Stabilizing the transition states.
  - Enzymes can speed up reactions by factors of TRILLIONS.

Substrate Enzyme Interaction

  - Example:
    - Substrate (glucose) binds to enzyme (hexokinase).
    - This binding leads to a conformational change in the enzyme, termed "induced fit," resulting in a tighter connection between the substrate and the active site.

Mechanism of Enzyme Action

  - Enzymes work by:
    - Bringing substrates into specific positions that facilitate the reactions.
    - Undergoing conformational changes (induced fit) upon substrate binding.
    - Interacting with substrates to stabilize the transition state, lowering activation energy requirements.

Process of Enzyme Action

  - The model of enzyme action consists of three main stages:
    1. Initiation: Reactants bind to the active site in a specific orientation to form an enzyme-substrate complex.
    2. Transition State Facilitation: Interactions between the enzyme and substrate reduce the activation energy needed for the reaction.
    3. Termination: Reaction products are released from the enzyme, which remains unchanged post-reaction.

Regulation of Enzymes

  - Some enzymes require cofactors for normal function, which may include:
    - Metal ions (e.g., Zn²⁺, Mg²⁺, Fe²⁺)
    - Organic molecules known as coenzymes (e.g., NADH, FADH₂)
    - Prosthetic groups, which are non-amino acid molecules permanently attached to proteins.
  - Enzymes are regulated by molecules that do not form part of the enzyme itself.

Types of Enzyme Regulation

  - Competitive Inhibition:
    - Occurs when a regulatory molecule of similar structure competes with the substrate for the active site.
  - Allosteric Regulation:
    - A regulatory molecule binds to a different site on the enzyme, inducing a change in enzyme shape that can either activate or deactivate the enzyme.

Enzyme Catalysis Rates

  - Enzymes exhibit saturation; their activity is limited by substrate availability and enzyme concentration.
  - At low substrate concentrations, the reaction rate increases linearly.
  - As substrate concentration rises, the rate of increase slows until the maximum reaction speed is reached, where active sites cannot accept substrates any faster.

Physical Conditions Impacting Enzyme Activity

  - Enzymes function optimally under specific conditions of temperature and pH.
    - Temperature affects both enzyme and substrate movement.
    - pH influences enzyme shape and reactivity.

Optimal Conditions for Enzymes

  - Different organisms possess enzymes that function best under variable temperature and pH ranges:
    - Example data indicates enzymes from heat-loving bacteria thrive at elevated temperatures, while those from acidic environments show optimal activity at lower pH.

Summary of Rate Influencing Factors

  - The rate of enzyme-catalyzed reactions is governed by:
    - Substrate concentration
    - Intrinsic affinity of enzyme for the substrate
    - Optimal temperature
    - Optimal pH

Hypothesis on the Origin of Life

  - Inquiry into whether the first living entities were proteins based on:
    - The abundance of amino acids in primordial conditions.
    - The efficiency of proteins as catalysts.
    - The requirement for self-replicating molecules to catalyze the polymerization of copies.
  - However, the necessity for a template suggests that proteins alone might not have been the first self-replicators.