Thermodynamics II - Entropy Notes

GAE#1 Recap and Systems

• Laws of Conservation

  • Conservation of Matter: Molecules are recycled.
  • Conservation of Energy: Energy flows through life and is transformed.

Open vs. Closed vs. Isolated Systems

• Open System: Exchanges both energy and matter with its surroundings.
• Closed System: Exchanges energy but not matter with its surroundings.
• Isolated System: Exchanges neither energy nor matter with its surroundings.
• Cells and Organisms: These are examples of open systems.
• Earth: Considered a closed system because matter is recycled within or between organisms with no significant mass entering or leaving. However, energy does move in and out.

Earth's Energy Balance

• Energy arrives as light, some is transformed by life, and heat flows out.
• The flow of energy determines Earth's temperature.
• Visible light in = Infrared light (heat) out.
• Sunlight is absorbed, and infrared energy is radiated back to space.
• Earth warms until energy in equals energy out.

Earth's Energy Budget

• Includes processes like convection, conduction, latent heat, infrared radiation, evaporation, and absorption of solar radiation.

Equations for Energy Balance

• Energy In: $Energy\ in = L(1 - a)πR^2$
  • $L$ = Solar illumination
  • $a$ = Albedo (fraction of light reflected)
  • $πR^2$ = Cross-sectional area of Earth
• Energy Radiated: $Energy\ radiated = \epsilon \sigma T^4 4πR^2$
  • $\epsilon$ = Emissivity
  • $\sigma$ = Stefan-Boltzmann constant
  • $T$ = Earth's temperature
  • $4πR^2$ = Surface area

Earth's Temperature

• Without the atmosphere, Earth's temperature would be 254 K (-2.47°F).
• $L(1 - a)πR^2 = \epsilon \sigma T^4 4πR^2$ leading to $T = \sqrt[4]{\frac{L(1-a)}{4\epsilon \sigma}}$

Role of the Atmosphere

• The atmosphere warms Earth's surface.
• The outer edge of the atmosphere is at 254K, but the temperature increases towards the surface due to the greenhouse effect.
• Infrared energy is reflected back to Earth, warming it up.
• Average temperature = 287 K = 13.9°C = 57°F.
• The atmosphere acts as a blanket.
• Atmospheric CO2 has been increasing since the industrial revolution increasing the atmosphere's blanketing effect.

University Initiatives

• Committed to carbon neutrality by 2025 and fossil fuel-free status by 2035.
• Currently, 100% renewable electricity is purchased, accounting for 67% of campus electricity.

Useful Sources of Biological Energy

• Lightning, light, and chemical energy (ATP).
• Thermal energy.

Autotrophic vs. Heterotrophic Eukaryotes

• Autotrophic Eukaryotes (e.g., plants):
  • Chloroplasts perform photosynthesis: $CO<em>2 + H</em>2O → O_2 + Glucose$
• Heterotrophic Eukaryotes (e.g., animals):
  • Mitochondria perform cellular respiration: $Glucose + O<em>2 → CO</em>2 + H_2O$
• Both types use ATP for cellular work, converting ADP + Pi back to ATP.

Examples of Cellular Work

• Light.
• Heat.
• Chemical.
• ATP is used to do cellular work.
• Examples: Chemical work (Calvin Cycle), physical work (ion pumps).

Chemical Work

• Generating high energy molecules. Metabolites are transformed in metabolic reactions.
• The Calvin Cycle phosphorylates metabolites: 6 low-energy $CO_2$ converted to 1 high-energy glucose.

Physical Work

• Moving ions across a cell membrane by phosphorylating an ion pump, which changes its shape.

Types of Work Organisms Do

• Metabolic: generating high energy molecules (e.g., glucose).
• Structural: forming structural elements like nucleic acids and cytoskeleton.
• Mechanical: lifting or applying force (e.g., flagella).
• Transport: moving molecules from one place to another.
• Osmotic: resisting or facilitating the movement of water.
• Electrical: moving ions (e.g., neurons).

Laws of Thermodynamics

• Define rules for converting environmental energy into useful forms for sustaining life.
  • 1st Law: Energy is conserved.
  • 2nd Law: For a spontaneous reaction, the entropy of the universe must increase.
• Thermodynamics doesn't specify the reactions; genomes store the biological solutions.

1st Law of Thermodynamics: Energy Conservation

• The total energy in the universe is neither created nor destroyed; it is transformed.
• $Energy<em>{initial} = Energy</em>{final}$
• Example: Photosynthesis - Light + chemical energy taken in ($CO<em>2$, $H</em>2O$) = Chemical energy produced ($O_2$ + glucose) + heat.

Implications of the 1st Law

• $\Delta H = \Delta G + \Delta S$
  • $\Delta G$ is the energy available to do work.
  • $\Delta S$ is the disorder (entropy).
  • $\Delta H$ is heat.
• Organisms release heat, increasing the disorder of the surroundings; thus, \Delta S > 0.
• Energy transfer efficiency < 100%: Some energy is always lost as heat. Therefore, \Delta G < \Delta H.

2nd Law of Thermodynamics

• $\Delta H = \Delta G + T\Delta S$
• For a closed system, $\Delta H = 0$, thus $\Delta G = -T\Delta S$
• A spontaneous reaction requires \Delta S_{universe} > 0.
• Therefore, for a spontaneous reaction, \Delta G_{spont} < 0.
• Reactants have more free energy than products in a spontaneous reaction.

Spontaneity and Free Energy

• If a reaction is not spontaneous, it can become spontaneous if it incorporates another high energy reactant, such as ATP.

Conclusions from the 2nd Law

• Spontaneous reactions proceed in the direction that reduces free energy (\Delta G < 0).
• Example: $C<em>6H</em>{12}O<em>6 + 6O</em>2 → 6CO<em>2 + 6H</em>2O$ is spontaneous, while the reverse is not.
• Spontaneous reactions release unusable heat into the environment (T\Delta S > 0).

Reaction Rates and Activation Energy

• Not all spontaneous reactions happen instantly.
  • Example: $C<em>{12}H</em>{22}O<em>{11} + 12O</em>2 → 12CO<em>2 + 11H</em>2O$ with $\Delta G = -5640 kJ/mole$.
• Activation energy is needed to initiate a reaction, even if \Delta G < 0.

Catalysts and Enzymes

• Catalysts speed up reactions by lowering activation energy without being consumed.
• Enzymes are biological catalysts.
• Life transforms available molecules into useful products in the right place at the right time and stores the recipe for making useful enzymes in the genome.

Evolutionary Scenario for Metabolic Reactions

1. Early protolife used naturally occurring metallic ions and complexes as catalysts.
2. Evolutionary relics: Metallic co-factors are found at the active sites of many ancient enzymes.
   • Cytochrome c (Fe heme protein) in oxidative phosphorylation.
   • Chlorophyll a (Mg tetrapyrrole) in photosynthesis.
   • Nitrogenase (FeMo and FeS metaloprotein) in nitrogen fixation.
3. More recently evolved enzymes use only amino acids in their active sites.

Criteria for Metabolic Reactions

• Reactants available in the environment.
• Thermodynamic constraints:
  • Energy is conserved.
  • Reaction requires \Delta G < 0
  • May require energy input (e.g., ATP) or enzymes.
  • Releases heat to the environment; Evolve molecular solutions and store in genome.

How is Biological Order Achieved?

• Life spontaneously organizes itself despite the universal increase in entropy through membrane formation and protein folding.

Spontaneity and Disorder

• For a spontaneous process, the universe becomes more disordered over time (\Delta S_{universe} > 0).
• Organisms can drive biological order by increasing the entropy of their surroundings.

Membrane Formation

• Membranes are composed of phospholipids with hydrophilic head groups and hydrophobic tails (amphipathic).
• Lipid bilayers form spontaneously because assembling lipids releases ordered water molecules, increasing entropy.

Self-Assembly of Membranes

• Forms a bilayer charged outside (close to polar water molecules) and hydrophobic inside.
• Protobionts: Hydrophobic interactions drive the formation of lipid vesicles, separating life from non-life and maximizing universal disorder.

Protein Folding

• Driven by hydrophobic interactions.
• Polar water molecules squeeze hydrophobic regions together.

Entropy-Driven Protein Order

• Protein folding occurs because \Delta S_{universe} > 0.
• Unfolded state: various configurations with exposed hydrophobic amino acids (intermediate S).
• Folded state: active protein with hydrophobic amino acids inside (low S) and freely moving water molecules (very high S).

Examples of Entropy-Driven Self-Assembly

• Virus assembly.
• Bacterial ribosomes (54 proteins and 3 rRNAs).
• Large macromolecular complexes may need scaffolding proteins (chaperonins) to fold.

Thermodynamic Definition of an Organism

• Organisms are open systems that:
  1. Use thermodynamically favored processes to transform available energy and matter.
  2. Use high quality free energy (G) for life's processes.
  3. Release low quality energy (heat).
  4. Maintain ordered structures by increasing universal disorder.

Key Ideas

• What is conserved in life on Earth?
• What is the role of ATP?
• How do the first two laws of thermodynamics inform us about the types and directions of reactions, and the role of enzymes and chaperonins?
• How is biological order achieved, and what is the key exchange made?