2  Energy and Thermodynamics

2.1 Learning Objectives

By the end of this chapter, you should be able to:

1. State and explain the First and Second Laws of Thermodynamics in biological contexts
2. Define entropy, enthalpy, free energy, and equilibrium as they apply to living systems
3. Explain why living organisms must continuously acquire and transform energy
4. Calculate free energy changes (ΔG) for biological reactions and predict their spontaneity
5. Describe how ATP serves as the universal energy currency in cells
6. Compare and contrast different metabolic strategies used by organisms
7. Apply thermodynamic principles to explain biological phenomena at multiple scales

2.2 Introduction

All living systems, from single bacterial cells to complex ecosystems, must obey the fundamental laws of physics. Thermodynamics ~the study of energy transformations~ provides essential insights into how living systems obtain, transform, and utilize energy while maintaining organization in a universe that tends toward disorder. This chapter establishes the physical foundations that govern all biological energy transactions, explaining why organisms must constantly acquire energy and how they efficiently convert it into useful work.

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2.3 Energy: The Capacity for Work

Energy is defined as the capacity to do work or cause change. In biological systems, energy enables:

• Chemical synthesis (anabolism)
• Mechanical motion (muscle contraction, cell division)
• Active transport across membranes
• Information processing (nerve impulses, gene expression)

2.3.1 Forms of Energy Relevant to Biology

Kinetic Energy: Energy of motion

• Molecular motion: Thermal energy (heat)
• Cellular motion: Cytoplasmic streaming, muscle contraction

Potential Energy: Stored energy based on position or structure

• Chemical energy: Energy stored in molecular bonds
• Concentration gradients: Differences across membranes
• Electrical gradients: Charge differences across membranes

Energy Transformations in Living Systems:

Solar Energy → Chemical Energy → Mechanical Energy → Heat
    ↓            ↓                ↓
Photosynthesis Metabolism        Movement

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2.4 The Laws of Thermodynamics

2.4.1 First Law: Conservation of Energy

Statement: Energy cannot be created or destroyed, only transformed from one form to another.

Mathematical expression: ΔE = Q - W

• ΔE: Change in internal energy of system
• Q: Heat added to system
• W: Work done by system

Biological implications:

1. Organisms cannot create energy; they must capture it from their environment
2. The total energy in any biological process remains constant
3. Energy transformations are never 100% efficient; some energy is always lost as heat

Example: In cellular respiration:

Chemical energy in glucose → Chemical energy in ATP + Heat
     686 kcal/mol              ~263 kcal/mol   ~423 kcal/mol
                    (approximately 38% efficiency)

2.4.2 Second Law: The Entropy Principle

Statement: In any energy transformation, the total entropy of the universe increases.

Entropy (S): A measure of disorder or randomness in a system. - Ordered systems have low entropy - Disordered systems have high entropy

Mathematical expression: ΔS_universe = ΔS_system + ΔS_surroundings > 0

Biological implications:

1. Living systems create local order at the expense of increasing disorder elsewhere
2. Energy transformations are directional; they proceed spontaneously only toward increased total entropy
3. Maintaining biological organization requires continuous energy input

The apparent paradox: Living systems appear to defy the Second Law by becoming more ordered (developing complex structures). Resolution: Organisms are open systems that export entropy to their surroundings.

Example: A growing plant becomes more ordered (low entropy) by: - Absorbing ordered sunlight - Releasing disordered heat and waste products - Increasing total entropy of the universe

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2.5 Gibbs Free Energy: Predicting Reaction Direction

The Gibbs Free Energy (G) combines enthalpy (heat content) and entropy to predict whether a reaction will occur spontaneously under constant temperature and pressure.

2.5.1 The Gibbs Free Energy Equation

ΔG = ΔH - TΔS

Where:

• ΔG: Change in free energy (kJ/mol)
• ΔH: Change in enthalpy (heat content; kJ/mol)
• T: Absolute temperature (Kelvin)
• ΔS: Change in entropy (kJ/mol·K)

2.5.2 Interpreting ΔG Values

ΔG < 0 (Negative):

• Reaction is exergonic (energy-releasing)
• Occurs spontaneously
• Products have less free energy than reactants
• Example: ATP hydrolysis: ΔG ≈ -30.5 kJ/mol

ΔG > 0 (Positive):

• Reaction is endergonic (energy-requiring)
• Does not occur spontaneously
• Requires energy input to proceed
• Products have more free energy than reactants
• Example: Glucose synthesis: ΔG ≈ +686 kJ/mol

ΔG = 0:

• System is at equilibrium
• No net change occurs
• Forward and reverse reactions proceed at equal rates

2.5.3 Standard Free Energy Change (ΔG°′)

Biological standard conditions:

• Temperature: 25°C (298 K)
• Pressure: 1 atmosphere
• pH: 7.0
• Reactant concentrations: 1.0 M

Important: Actual ΔG in cells differs from ΔG°′ due to non-standard concentrations.

Relationship to equilibrium constant (K_eq): ΔG°′ = -RT ln K_eq

Where:

• R: Gas constant (8.314 J/mol·K)
• T: Temperature (K)
• K_eq: [Products]/[Reactants] at equilibrium

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2.6 ATP: The Cellular Energy Currency

Adenosine Triphosphate (ATP) serves as the primary energy carrier in all living cells.

2.6.1 Structure of ATP

• Adenine: Nitrogenous base
• Ribose: Five-carbon sugar
• Three phosphate groups: High-energy bonds

2.6.2 ATP Hydrolysis

ATP + H₂O → ADP + P_i + Energy

• ΔG°′ ≈ -30.5 kJ/mol
• Highly exergonic under cellular conditions

Why ATP hydrolysis releases energy:

1. Charge repulsion: Negative charges on phosphate groups repel each other
2. Resonance stabilization: Inorganic phosphate (P_i) is more stable than phosphate in ATP
3. Increased entropy: One molecule becomes two molecules

2.6.3 ATP Cycle in Cells

Energy from
catabolism    Energy for
    ↓        cellular work
    ↓            ↓
ATP ←──────────→ ADP + P_i
    Synthesis    Hydrolysis

ATP turnover rate: A typical mammalian cell hydrolyzes and resynthesizes its entire ATP pool every 1-2 minutes.

2.6.4 Other Energy Carriers

Electron Carriers:

• NAD⁺/NADH: Nicotinamide adenine dinucleotide
• FAD/FADH₂: Flavin adenine dinucleotide
• NADP⁺/NADPH: Nicotinamide adenine dinucleotide phosphate

Activated Carriers:

• Acetyl-CoA: Activated acetate
• UTP, GTP, CTP: Nucleotide triphosphates for specific syntheses

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2.7 Metabolic Pathways: Energy Flow in Cells

Metabolism: The sum of all chemical reactions in an organism.

2.7.1 Catabolic Pathways

Break down complex molecules into simpler ones, releasing energy.

Examples:

1. Glycolysis: Glucose → Pyruvate (net: 2 ATP + 2 NADH)
2. Citric Acid Cycle: Acetyl-CoA → CO₂ (net: 1 ATP + 3 NADH + 1 FADH₂ per acetyl-CoA)
3. Oxidative Phosphorylation: NADH/FADH₂ oxidation → ATP (major ATP source)

Energy yields (complete glucose oxidation):

• Theoretical maximum: 36-38 ATP
• Actual in cells: ~30 ATP (due to energy costs of transport, etc.)

2.7.2 Anabolic Pathways

Synthesize complex molecules from simpler ones, requiring energy input.

Examples:

1. Gluconeogenesis: Synthesis of glucose from non-carbohydrate precursors
2. Protein Synthesis: Amino acids → Polypeptides
3. Lipid Synthesis: Acetyl-CoA → Fatty acids

2.7.3 Regulation of Metabolic Pathways

Feedback Inhibition: End product inhibits early enzyme in pathway Example: ATP inhibits phosphofructokinase in glycolysis

Allosteric Regulation: Binding at sites other than active site modifies enzyme activity

Covalent Modification: Phosphorylation/dephosphorylation activates/deactivates enzymes

Compartmentalization: Separating opposing pathways in different cellular locations

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2.8 Bioenergetics of Different Organisms

2.8.1 Classification by Energy Source

Phototrophs: Capture energy from sunlight

• Photoautotrophs: Use CO₂ as carbon source (plants, algae, cyanobacteria)
• Photoheterotrophs: Use organic compounds as carbon source (some bacteria)

Chemotrophs: Obtain energy from chemical compounds

• Chemoautotrophs: Use inorganic compounds (H₂S, NH₃, Fe²⁺)
• Chemoheterotrophs: Use organic compounds (animals, fungi, most bacteria)

2.8.2 Classification by Carbon Source

Autotrophs: “Self-feeders”; synthesize organic compounds from inorganic carbon (CO₂)

• Examples: Plants, algae, some bacteria

Heterotrophs: “Other-feeders”; obtain organic compounds from other organisms

• Examples: Animals, fungi, most bacteria

2.8.3 Metabolic Efficiency Comparisons

Photosynthetic efficiency:

• Theoretical maximum: 11-12% of solar energy
• Typical plants: 3-6%
• Reasons for inefficiency: Light absorption limits, photorespiration, metabolic costs

Cellular respiration efficiency:

• Glucose to ATP: ~38%
• Compared to car engine: 20-30%
• Compared to fuel cell: 40-60%

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2.9 Energy Flow in Ecosystems

2.9.1 Trophic Levels

Primary Producers: Autotrophs (plants, algae, cyanobacteria)

Primary Consumers: Herbivores

Secondary Consumers: Carnivores that eat herbivores

Tertiary Consumers: Top carnivores

Decomposers: Break down dead organic matter

2.9.2 Ecological Pyramids

Energy Pyramid:

• Each level contains ~10% of energy from previous level (10% rule)
• Explains why food chains are typically limited to 4-5 levels
• Most energy is lost as heat at each transfer

Biomass Pyramid: Usually similar shape to energy pyramid

Numbers Pyramid: Shape varies depending on organism size

2.9.3 Human Impact on Energy Flows

Agriculture: Redirects energy flow to human consumption - Only ~10% of plant biomass becomes human food in grain-fed meat production

Fossil Fuels: Ancient stored photosynthetic energy - Formed over millions of years, consumed in centuries

Renewable Energy: Attempts to harness current photosynthetic output - Biofuels from crops, algae, or waste

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2.10 Thermodynamic Perspectives on Biological Organization

2.10.1 From Molecules to Ecosystems

Molecular Level: Bond energies determine reaction spontaneity

Cellular Level: Membrane potentials represent stored electrical energy

Organismal Level: Basal metabolic rate measures minimum energy requirement

Ecosystem Level: Net primary productivity measures energy capture by producers

2.10.2 Energy and Evolution

Energetic constraints shape evolutionary adaptations:

1. Surface area to volume ratio affects energy acquisition and loss
2. Metabolic rate correlates with body size (Kleiber’s Law: Metabolic rate ∝ Mass^3/4)
3. Energy efficiency influences competitive success
4. Energy availability limits population sizes

2.10.3 Energy and Information

Energy enables information processing:

• DNA replication: Requires energy to unwind helix and form bonds
• Protein synthesis: Requires ~4 ATP equivalents per peptide bond
• Neural signaling: Ion pumping maintains membrane potential
• Cellular signaling: Phosphorylation cascades require ATP

Information guides energy utilization:

• Gene expression controls enzyme production
• Metabolic regulation optimizes energy use
• Behavioral adaptations improve energy acquisition

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2.11 Chapter Summary

2.11.1 Key Principles

1. First Law of Thermodynamics: Energy is conserved; organisms transform but do not create energy
2. Second Law of Thermodynamics: Total entropy always increases; living systems maintain local order by increasing disorder elsewhere
3. Gibbs Free Energy (ΔG): Predicts reaction spontaneity; ΔG = ΔH - TΔS
4. ATP: Primary energy currency; hydrolysis (ATP → ADP + P_i) releases ~30.5 kJ/mol
5. Metabolism: Catabolic pathways release energy; anabolic pathways require energy
6. Metabolic classifications: Phototrophs vs. chemotrophs; autotrophs vs. heterotrophs
7. Ecological energy flow: ~10% transferred between trophic levels

2.11.2 Important Equations

1. First Law: ΔE = Q - W
2. Second Law: ΔS_universe > 0
3. Gibbs Free Energy: ΔG = ΔH - TΔS
4. Standard Free Energy: ΔG°′ = -RT ln K_eq
5. Kleiber’s Law: Metabolic Rate = k × Mass^3/4

2.11.3 Energy Transformations in Context

Level	Energy Form	Example Process	Efficiency
Molecular	Chemical	ATP hydrolysis	ΔG = -30.5 kJ/mol
Cellular	Electrical	Nerve impulse	Ion pumping: ~3 Na+/ATP
Organismal	Mechanical	Muscle contraction	20-25%
Ecological	Solar → Chemical	Photosynthesis	3-6% of incident light

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2.12 Review Questions

2.12.1 Level 1: Recall and Understanding

1. State the First and Second Laws of Thermodynamics in your own words.
2. Define entropy and explain its relationship to biological order.
3. What does a negative ΔG value indicate about a chemical reaction?
4. Describe the structure of ATP and explain why its hydrolysis releases energy.
5. Distinguish between catabolic and anabolic pathways.

2.12.2 Level 2: Application and Analysis

6. Calculate ΔG for a reaction with ΔH = -50 kJ/mol and ΔS = 0.1 kJ/mol·K at 37°C. Is it spontaneous?
7. Explain how a cell can synthesize glucose (endergonic) using energy from ATP hydrolysis (exergonic).
8. A bacterium is discovered that lives near deep-sea vents using hydrogen sulfide as an energy source. How would you classify it metabolically?
9. Why are food chains typically limited to 4-5 trophic levels? Use thermodynamic principles in your explanation.

2.12.3 Level 3: Synthesis and Evaluation

10. Critics sometimes claim that evolution violates the Second Law of Thermodynamics because it produces more complex organisms. Refute this claim using thermodynamic principles.
11. Compare the energy efficiencies of different metabolic strategies (aerobic vs. anaerobic respiration, photosynthesis types). What evolutionary advantages might lower efficiency provide in some environments?
12. Design an experiment to measure the metabolic rate of a small organism. What variables would you control, and what measurements would you take?
13. How might global climate change affect energy flows in ecosystems? Consider multiple trophic levels in your response.

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2.13 Key Terms

• Thermodynamics: The study of energy transformations
• First Law of Thermodynamics: Energy cannot be created or destroyed
• Second Law of Thermodynamics: Total entropy of the universe always increases
• Entropy (S): A measure of disorder or randomness
• Enthalpy (H): Heat content of a system
• Gibbs Free Energy (G): Energy available to do work at constant temperature and pressure
• Exergonic: Energy-releasing reaction (ΔG < 0)
• Endergonic: Energy-requiring reaction (ΔG > 0)
• ATP (Adenosine Triphosphate): Primary energy currency in cells
• Metabolism: Sum of all chemical reactions in an organism
• Catabolism: Breakdown of complex molecules, releasing energy
• Anabolism: Synthesis of complex molecules, requiring energy
• Phototroph: Organism that captures energy from sunlight
• Chemotroph: Organism that obtains energy from chemical compounds
• Autotroph: Organism that produces its own organic compounds from inorganic carbon
• Heterotroph: Organism that obtains organic compounds from other organisms
• Trophic Level: Position in a food chain determined by energy source

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2.14 Further Reading

2.14.1 Books

1. Atkins, P. W. (2007). Four Laws That Drive the Universe. Oxford University Press.
2. Harold, F. M. (2001). The Way of the Cell: Molecules, Organisms, and the Order of Life. Oxford University Press.
3. Nicholls, D. G., & Ferguson, S. J. (2013). Bioenergetics (4th ed.). Academic Press.

2.14.2 Scientific Articles

1. Brown, J. H., et al. (2004). Toward a metabolic theory of ecology. Ecology, 85(7), 1771-1789.
2. Lane, N. (2010). Why are cells powered by proton gradients? Nature Education, 3(9), 18.
3. Whitfield, J. (2004). Everything You Always Wanted to Know About Entropy (But Were Afraid to Ask). Nature News.

2.14.3 Online Resources

1. MIT OpenCourseWare: Thermodynamics of Biomolecular Systems
2. Khan Academy: Free Energy and Metabolism
3. Bioenergetics Educational Resources: ATP and Energy Coupling

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2.15 Quantitative Problems

1. Free Energy Calculation: The reaction A → B has ΔH = -25 kJ/mol and ΔS = 50 J/mol·K.
   1. Calculate ΔG at 25°C.
   2. At what temperature would the reaction be at equilibrium?
   3. Would increasing temperature make the reaction more or less spontaneous?
2. ATP Turnover: A typical human cell contains approximately 1 × 10⁹ ATP molecules and consumes 2 × 10⁷ ATP molecules per second.
   1. How long does it take for the cell to turn over its entire ATP pool?
   2. If the human body contains ~3 × 10¹³ cells, estimate total ATP consumption per day.
   3. Compare this to daily food intake (~2000 kcal). Note: 1 ATP hydrolysis ≈ 30.5 kJ/mol.
3. Ecological Efficiency: A grassland ecosystem receives 5 × 10⁶ kcal/m²/year of solar energy.
   1. If plants capture 1% of this energy, how much is available to primary producers?
   2. Assuming 10% transfer efficiency between trophic levels, calculate energy available to:
      • Primary consumers (herbivores)
      • Secondary consumers (carnivores)
      • Tertiary consumers (top carnivores)
   3. Why are there few top carnivores in most ecosystems?

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2.16 Case Study: Deep-Sea Vent Ecosystems

Background: Hydrothermal vents on the ocean floor support diverse ecosystems without sunlight. Bacteria use hydrogen sulfide (H₂S) from vent fluids as an energy source.

Questions:

1. What metabolic classification applies to these bacteria?
2. Write a simplified chemical equation for their energy-yielding reaction.
3. Compare the energy yield of H₂S oxidation to glucose oxidation.
4. How does energy flow differ between vent ecosystems and sunlit surface ecosystems?
5. What implications might vent ecosystems have for the search for extraterrestrial life?

Data for analysis:

• Reaction: H₂S + 2O₂ → SO_{42- + 2H⁺ (ΔG°′ = -798 kJ/mol)}
• Compare to: C₆H₁₂O₆ + 6O₂ → 6CO₂ + 6H₂O (ΔG°′ = -2870 kJ/mol)

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