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Thermodynamics in Biological Systems: Fundamentals and Applications

This chapter provides an overview of basic thermodynamic concepts and their significance in biological systems, including pH, concentration, coupled processes, high-energy biomolecules, and entropy. It also explores the laws of thermodynamics and their applications in understanding biochemical reactions and energy transfer.

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Thermodynamics in Biological Systems: Fundamentals and Applications

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  1. Chapter 3 Thermodynamics of Biological Systems to accompany Biochemistry, 2/e by Reginald Garrett and Charles Grisham All rights reserved. Requests for permission to make copies of any part of the work should be mailed to: Permissions Department, Harcourt Brace & Company, 6277 Sea Harbor Drive, Orlando, Florida 32887-6777

  2. Outline • Basic Thermodynamic Concepts • Physical Significance of Thermodynamic Properties • pH and the Standard State • The Effect of Concentration • Coupled Processes • High-Energy Biomolecules

  3. Basic Concepts • The system: the portion of the universe with which we are concerned • The surroundings: everything else • Isolated system cannot exchange matter or energy • Closed system can exchange energy • Open system can exchange either or both

  4. The First LawThe total energy of an isolated system is conserved. • E (or U) is the internal energy - a function that keeps track of heat transfer and work expenditure in the system • E is heat exchanged at constant volume • E is independent of path • E2 - E1 = E = q + w • q is heat absorbed BY the system • w is work done ON the system

  5. Enthalpy A better function for constant pressure • H = E + PV • If P is constant, H = q • H is the heat absorbed at constant P • Volume is approx. constant for biochemical reactions (in solution) • So H is approx. same as E

  6. The Second Law • Systems tend to proceed from ordered to disordered states • The entropy change for (system + surroundings) is unchanged in reversible processes and positive for irreversible processes • All processes proceed toward equilibrium - i.e., minimum potential energy

  7. Entropy • A measure of disorder • An ordered state is low entropy • A disordered state is high entropy • dSreversible = dq/T

  8. The Third Law • The entropy of any crystalline, perfectly ordered substance must approach zero as the temperature approaches 0 K • At T = 0 K, entropy is exactly zero • For a constant pressure process: Cp = dH/dT

  9. Free Energy • Hypothetical quantity - allows chemists to asses whether reactions will occur • G = H - TS • For any process at constant P and T: G = H - TS • If G = 0, reaction is at equilibrium • If G < 0, reaction proceeds as written

  10. G versus Go’ • How can we calculate the free energy change for rxns not at standard state? • Consider a reaction: A + B  C + D • Then: G = Go’ + RT ln ([C][D]/[A][B])

  11. Energy Transfer A Crucial Biological Need • Energy acquired from sunlight or food must be used to drive endergonic (energy-requiring) processes in the organism • Two classes of biomolecules do this: • Reduced coenzymes (NADH,FADH2) • High-energy phosphate compounds - free energy of hydrolysis larger than -25 kJ/mol)

  12. High-Energy Biomolecules Study Table 3.3! • Note what's high - PEP and 1,3-BPG • Note what's low - sugar phosphates, etc. • Note what's in between - ATP! • Note difference (Figure 3.8) between overall free energy change - noted in Table 3.3 - and the energy of activation for phosphoryl-group transfer!

  13. ATP An Intermediate Energy Shuttle Device • PEP and 1,3-BPG are created in the course of glucose breakdown • Their energy (and phosphates) are transferred to ADP to form ATP • But ATP is only a transient energy carrier - it quickly passes its energy to a host of energy-requiring processes

  14. Phosphoric Acid Anhydrides Why ATP does what it does! • ADP and ATP are examples of phosphoric acid anhydrides • Note the similarity to acyl anhydrides • Large negative free energy change on hydrolysis is due to: • electrostatic repulsion • stabilization of products by ionization and resonance • entropy factors

  15. Phosphoric-Carboxylic Anhydrides • These mixed anhydrides - also called acyl phosphates - are very energy-rich • Acetyl-phosphate: G°´ = -43.3 kJ/mol • 1,3-BPG: G°´ = -49.6 kJ/mol • Bond strain, electrostatics, and resonance are responsible

  16. Enol Phosphates • Phosphoenolpyruvate (PEP) has the largest free energy of hydrolysis of any biomolecule • Formed by dehydration of 2-phospho-glycerate • Hydrolysis of PEP yields the enol form of pyruvate - and tautomerization to the keto form is very favorable

  17. Ionization States of ATP • ATP has five dissociable protons • pKa values range from 0-1 to 6.95 • Free energy of hydrolysis of ATP is relatively constant from pH 1 to 6, but rises steeply at high pH • Since most biological reactions occur near pH 7, this variation is usually of little consequence

  18. The Effect of Concentration Free energy changes are concentration dependent • We will use the value of -30.5 kJ/mol for the standard free energy of hydrolysis of ATP • But at non-standard-state conditions (in a cell, for example), the G is different! • Equation 3.12 is crucial - be sure you can use it properly • In typical cells, the free energy change for ATP hydrolysis is typically -50 kJ/mol

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