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Thermodynamic and Energy Principles of Biochemistry Notes

Introduction

  • All living things require energy, obtained either from the sun or by consuming other organisms, establishing an energy flow in nature.
  • Cells have evolved efficient mechanisms to couple energy from sunlight or fuels to energy-consuming processes.

Biology and Energy

  • Open System: A living organism is an open system that exchanges both energy and matter with its surroundings.
    • A system is defined as all reactants, products, solvent, and the immediate atmosphere involved in a chemical reaction.
    • Isolated system: No exchange of energy or matter.
    • Closed system: Exchanges energy but not matter.
    • Open system: Exchanges both energy and matter.

Bioenergetics

  • Bioenergetics: The study of energy flow within living organisms.
  • Exergonic Reactions: Reactions that release energy.
  • Endergonic Reactions: Reactions that consume energy.

Metabolism

  • Metabolism encompasses all chemical reactions in the body, including nutrient processing and energy distribution.
    • Nutrients: Amino acids, vitamins, minerals, and sugars.
    • Substances can also include toxins.

Catabolism and Anabolism

  • Catabolism: Metabolic pathways that break down molecules into smaller units, releasing energy (energy-yielding metabolism).
    • Energy sources are broken down, releasing heat and utilizable energy (ATP).
  • Anabolism: Metabolic pathways that construct molecules from smaller units, requiring energy (biosynthetic metabolism).
    • Biopolymers are synthesized from smaller intermediates, using ATP.
  • Energy-yielding reactions are part of catabolism.

Energy Sources for Organisms

  • Organisms obtain energy by:
    • Taking up chemical fuels.
    • Absorbing energy from sunlight.
  • Producers: Plants.
  • Consumers: Animals.
  • Decomposers: Fungi, bacteria, worms.
  • All organisms release heat.

Energy Classes of Microorganisms

  • Chemotrophs: Conserve energy from chemicals.
    • Chemoorganotrophs: Obtain energy from organic chemicals.
    • Chemolithotrophs: Obtain energy from inorganic chemicals.
  • Phototrophs: Convert light energy into chemical energy.

Nitrogen Cycle Examples

  • Chemolithotrophs: Examples in the nitrogen cycle include:
    • Nitrosomonas: Convert ammonium (NH4+) to nitrites (NO2-).
    • Nitrobacter: Convert nitrites (NO2-) to nitrates (NO3-).

Heterotrophs and Autotrophs

  • All cells require carbon to create new cell materials (anabolism).
  • Autotrophs (Primary Producers): Obtain cell carbon from carbon dioxide (CO2).
  • Heterotrophs: Obtain cell carbon from other organic carbon sources.
  • Chemoorganotrophs are heterotrophs.
  • Most chemolithotrophs and phototrophs are autotrophs.
  • Exceptions: Purple and green non-sulfur bacteria can be photoheterotrophs.

Summary of Energy and Carbon Sources

  • Chemoorganotrophs: Energy from organic compounds, carbon from organic compounds (Heterotrophs).
  • Chemolithotrophs: Energy from inorganic compounds, carbon from CO2 (Autotrophs)
  • Phototrophs: Energy source is light, carbon source is CO2 (Autotrophs).

Laws of Thermodynamics

  • First Law: Energy is neither created nor destroyed.
  • Second Law: The entropy (disorder) of the universe is always increasing.

Entropy (Disorder)

  • Entropy expresses the randomness or disorder of a chemical system.
  • Increasing entropy is thermodynamically favorable.
  • Heat flows spontaneously from hot to cold due to this principle.

Measuring and Expressing Entropy

  • Entropy (S) is a measure of disorder, measured in Joules per Kelvin (J/K).
  • Change in entropy (\Delta S) expresses changes in the randomness of a system.
  • \Delta S is positive when randomness increases.
  • However, \Delta S alone cannot determine the spontaneity of a process.

Enthalpy

  • Enthalpy (H): H = U + PV, where U is the internal energy, P is pressure, and V is volume.
  • Change in enthalpy (\Delta H) indicates the change in heat due to changes in chemical bonds.

Enthalpy and Spontaneity

  • Exothermic reactions (release heat) have a negative \Delta H and tend to be spontaneous.
  • However, \Delta H alone cannot determine the spontaneity of a process.

Gibbs Free Energy

  • Gibbs Free Energy (G) is the energy available to do work, expressed in kilojoules (kJ).
  • The change in free energy during a reaction (\Delta G) is expressed as \Delta G^0', indicating standard conditions:
    • pH 7
    • Temperature = 25°C
    • Pressure = 1 atmosphere
    • Reactants and products at 1 mole/L concentration

Gibbs Free Energy and Spontaneity

  • \Delta G < 0: Exergonic reaction, spontaneous.
  • \Delta G > 0: Endergonic reaction, non-spontaneous.
  • \Delta G = 0: Reaction is at equilibrium.

Gibbs Free Energy Equation

  • \Delta G = \Delta H - T\Delta S
  • Energetically favorable: \Delta H is negative (-).
  • Entropically favorable: \Delta S is positive (+).
  • If \Delta H is negative and \Delta S is positive, the reaction is always spontaneous.
  • If \Delta H is positive and \Delta S is negative, the reaction is never spontaneous.
  • If \Delta H and \Delta S are both positive, the reaction is spontaneous at high temperatures.
  • If \Delta H and \Delta S are both negative, the reaction is spontaneous at low temperatures.

Catalysis and Enzymes

  • Free energy calculations indicate the energy released or required but not the reaction rate.
  • Energy-favorable reactions can occur slowly due to the need to break existing bonds (activation energy, Ea).
  • Enzymes catalyze reactions by lowering the activation energy, increasing the reaction rate.
  • Most cellular reactions occur slowly without enzymes.

Coupling of Biochemical Reactions

  • Biosynthetic reactions (endergonic) are coupled with exergonic reactions to provide the necessary energy.
  • Overall free-energy change for a coupled series of reactions is the sum of the free-energy changes of the individual steps.

Example of Coupled Reactions

  • Reaction 1: A → B (\Delta G^0 = +21 kJ/mol) (Endergonic)
  • Reaction 2: ATP → ADP + Pi (\Delta G^0 = -34 kJ/mol) (Exergonic)
  • Coupled Reaction: Glucose + ATP → Glucose-6-phosphate + ADP

Energy Currency: ATP

  • Energy is stored in compounds like ATP.
  • ATP stores energy from exergonic reactions and provides energy for endergonic reactions.

ATP Cycle

  • ATP + H2O → ADP + Pi (\Delta G^0' = -30.5 kJ/mol)
  • ATP is the shared chemical intermediate linking energy-releasing and energy-requiring cell processes.
  • ATP is produced in exergonic reactions and consumed in endergonic reactions.

Coupled Reactions: Process

  • Exergonic reaction: A → B + 15 kcal (energy is released).
  • Endergonic synthesis: X + Y → X~Y - 8 kcal (energy is stored).
  • Overall reaction: A + X + Y → B + X~Y + 7 kcal (7 kcal is wasted).
  • Complex molecule synthesis: C + D → C-D (requires 5 kcal).
  • Energy supplied by trapped energy in X~Y: X~Y → X + Y + 8 kcal.
  • Overall biosynthesis: C + D + X~Y → C-D + X + Y + 3 kcal (3 kcal wasted).
  • Energy efficiency: 5/15 or 33%.

Electron Donors and Acceptors

  • Catabolic reactions release energy.
  • Energy can be conserved by synthesizing ATP.
  • Reactions that release sufficient energy for ATP synthesis are often oxidation-reduction (redox) reactions.
  • Oxidation: Removal of an electron from a substance.
  • Reduction: Addition of an electron to a substance.

Redox Tower

  • Illustrates the redox potentials of various half-reactions.
  • The more negative the redox potential, the better the substance is as an electron donor.
  • The more positive the redox potential, the better the substance is as an electron acceptor.
    Examples
  • H2 + fumarate → succinate (\Delta G^0' = -86 kJ)
  • H2 + NO3- → NO2- + H2O (\Delta G^0' = -163 kJ)
  • H2 + ½ O2 → H2O (\Delta G^0' = -237 kJ)

Redox Potential

  • Redox potential (E0) measures the tendency of a chemical species to acquire electrons.
  • Example: HOCl + H+ + 2e- → Cl- + H2O E0(V) = 1.482
  • Example: Fe3+ + e- → Fe2+ E0(V) = 0.771
  • Hypochlorous acid is a stronger oxidizer than Fe3+ because it has a higher redox potential.

NAD+/NADH: Electron Carrier

  • Nicotinamide adenine dinucleotide (NAD+/NADH) serves as an intermediary in redox reactions.
  • Constant recycling allows for a lot of work to be done by a low concentration of NAD+/NADH

Other Carriers

  • Other activated carriers in metabolism include:
    • ATP (Phosphoryl).
    • NADH and NADPH (Electrons).
    • FADH2 (Electrons).
    • Coenzyme A (Acyl).

Fermentation and Respiration

  • Fermentation: Metabolic process that releases energy from a sugar or other organic molecule, does not require oxygen or an electron transport system, and uses an organic molecule as the final electron acceptor.
  • Respiration: (Krebs cycle, electron transport, oxidative phosphorylation) involves transferring electrons to an external electron acceptor.

Aerobic Respiration

  • Aerobic electron acceptor: oxygen (O2).

Anaerobic Respiration

  • Under anoxic conditions, alternative electron acceptors support respiration in certain prokaryotes:
    • Nitrate (NO3-) to nitrite (NO2-) or nitrogen (N2).
    • Fe3+ to Fe2+.
    • SO42- to H2S.
    • CO32- to CH4 or acetate.

Energy Yield in Anaerobic Respiration

  • Alternative electron acceptors result in a lower energy yield than O2.
  • In environments where O2 is limited or absent, anaerobic respiration is a vital means of energy production.

Table 1 - Reductive Reaction Employed by Bacteria

  • Lists various half-reactions employed by bacteria under aerobic and anaerobic conditions, including sample enzymes, processes and species.
  • The substrates of these reactions are terminal electron acceptors.