Basic Thermodynamics and Water Properties

Basic Thermodynamics

• Basic thermodynamics encompasses the quantitative study of energy transformations in living cells.
• The laws of thermodynamics apply to all energy conversions, including those in biological systems.
• Small molecules, macromolecules, and supramolecular structures undergo continuous synthesis and breakdown, implying constant mass and energy fluxes.

Water and Its Properties

• Water's properties, including dissociation and association constants, pH, buffers (like pKa, Henderson-Hasselbalch equation), are crucial aspects.
• Implications of these concepts are important to understand.
• Basic thermodynamics, including the concepts of Gibbs free energy (ΔG), enthalpy (ΔH), and entropy (ΔS), are discussed.

A Simple Thought Experiment

• This experiment models the behavior of a single E. coli cell in different conditions.
• It showcases the differing outcomes concerning glucose uptake, cell proliferation, and metabolism variations.
• Variables like the number and concentration of cells, the presence and amounts of nutrients (glucose, (NH4)SO4, and trace elements), and the duration of the experiment are crucial.

Interdependence of Cells

• In a cyclical process, photoautotrophs like plants use solar energy to produce glucose from CO2 and H2O.
• This also produces oxygen, which acts as a crucial byproduct for the hetero-trophic ecosystem to function.
• This cycle involves the continuous exchange of oxygen, glucose, water, and carbon dioxide, fostering a balanced ecosystem.

Energy Flow in Metabolism

• Organisms use catabolism to break down energy-rich nutrients (carbohydrates, fats, proteins).
• These processes produce ATP, NADPH and other energy-carrying molecules.
• The process of catabolism is exergonic (releasing energy). Subsequently, anabolism utilizes these energy-carrying molecules to synthesize complex biomolecules resulting in growth and maintenance of the overall system like the cells.

Catabolic Pathways

• Complex macromolecules (proteins, polysaccharides, lipids) are broken down into simpler building blocks like amino acids, sugars, and fatty acids.
• These processes are often associated with the conversion of energy stored in metabolic bonds to chemical energy.
• The citric acid cycle plays a central role in converging the breakdown of macromolecules into a common product known as Acetyl-CoA, ultimately fueling oxidative phosphorylation for ATP production.

Connection between Catabolic and Anabolic Pathways

• Catabolic and anabolic pathways are interconnected via shared metabolic intermediates.
• There are converging and diverging pathways which create common metabolic intermediates thereby acting as a central hub in the metabolic network.
• Pathways converge during catabolism, sharing common pathways and intermediates for the degradation of various macromolecules. During anabolism, pathways diverge to synthesize various biomolecules using precursor molecules which are common intermediates.

Features of Metabolism

• Anabolic and catabolic pathways are reciprocally regulated so they do not run at the same time
• Catabolic and anabolic pathways using the same end points have at least one step catalyzed by different enzymes.
• Paired catabolic and anabolic pathways, such as fatty acid synthesis and degradation, often occur in different cellular compartments.

Physical Foundations in Biological Chemistry

• Energy is constantly extracted, channeled, and utilized in the cell.
• Energy transformations adhere to thermodynamic laws.
• Processes like cellular energy conversions occur in a dynamic steady state that's far from equilibrium to maintain homeostasis.

Bioenergetics and Thermodynamics

• Bioenergetics quantifies transformations of energy within biological entities.
• First Law of Thermodynamics: Energy remains constant and cannot be created or destroyed.
• Second Law of Thermodynamics: Entropy tends towards an increase.

Driving Forces for Natural Processes

• Energy systems move toward a decreased energy state in a quest for stability (enthalpy).
• Systems tend toward maximized randomness (entropy).

Enthalpy and Bond Strength

• Enthalpy (ΔH) elucidates the total energy change in a reaction under constant pressure.
• The enthalpy change is a negative value if heat is released (exothermic) and positive if heat is absorbed (endothermic).
• Measuring 1 cal = 4.18 joule

Entropy and Randomness

• Entropy (S) signifies the level of randomness within a system.
• Increased randomness implies an increase in entropy (+ ΔS).
• A decrease in entropy implies a decrease in randomness (- ΔS).

System definitions

• A system is a defined region or space.
• The surroundings encompass everything else outside the system that interacts with the system.
• An isolated system is one which exchanges neither matter nor energy with its surroundings.
• A closed system exchanges only energy with its surroundings, not matter. An open system exchanges energy and matter with its surroundings

Cells and Organisms: Open Systems

• Cells and organisms continually exchange matter and energy with their surroundings to maintain their function.
• Organisms absorb energy from sunlight or extract from chemical fuels for biological needs (catabolism) and release waste products (CO2, water, and ammonia into the surroundings.

1st Law of Thermodynamics

• Energy conservation.
• Energy conversion.
• Example, light-driven reduction of CO2.

2nd Law of Thermodynamics

• Total entropy in the universe increases in spontaneous processes.
• Cells can decrease entropy, but the surroundings must see an increase in total entropy.

Enthalpy, Entropy, and Gibbs Free Energy

• Gibbs free energy (ΔG) combines enthalpy and entropy to determine spontaneity.
• Gibbs free energy change (ΔG) helps determine if a reaction will occur spontaneously, and the driving force.
• ΔG = ΔH - TΔS

Standard State and ΔG°

• Standard states, like pressure and temperature, are defined and important factors in thermodynamic calculations and reactions analysis. Defined values facilitate precise quantification and comparison of various reactions or processes.

Biochemical Conventions: ΔG°'

• Most biochemical reactions operate at a pH of 7 in an aqueous environment.
• Simplification for ΔG° and Keq. [H+] = 10-7 M, [H2O]=1

Relationship of ΔG to ΔG°

• ΔG is the actual free energy change for reactions in various solution conditions.
• The equation shows how ΔG depends on the standard free energy change and the actual concentrations.

Relationship Between ΔG°' and K'eq

• At equilibrium, ΔG=0
• The relationship of ΔG to K'eq determines direction of a reaction or its spontaneity.

Table 13 - 3

• A table showing the relationships between equilibrium constant (Keq) and the free energy change (ΔG°'). -Predicting spontaneity of chemical reaction based on equilibrium constant and standard free energy change.

Relationship Between K'eq and ΔG°'

• This table correlates values of K'eq to their corresponding values of Gibbs free energy change.
• The direction of a chemical reaction can be determined using the data to predict the spontaneity of each chemical reaction with the provided equilibrium constant values.

Will a Reaction Occur Spontaneously?

• Spontaneity is determined by Gibbs free energy (ΔG) – a negative ΔG indicates that a process will tend to occur, while a positive ΔG indicates that a reaction will not tend to occur spontaneously under given conditions.
• The change in Gibbs free energy under certain conditions allows for prediction of the tendency toward spontaneity and possible equilibrium characteristics or positions of the process.

A Caution About ΔG°

• Even with a large, negative ΔG°, the reaction may not occur quickly, emphasizing the importance of kinetics, which studies reaction rate.
• The understanding of enzymes helps demonstrate how enzymes help speed up reactions without changing their equilibrium constants or spontaneity.

ΔG° is Additive (State Function)

• ΔG° values for individual steps can be added to determine the ΔG° of multiple steps in a reaction pathway.
• The overall free energy change is determined by using the sum of ΔG degree values from individual reactions or steps.
• This characteristic of ΔG is relevant since it allows for predictions in complex multi-step reactions or pathways or even multi-reaction sequences or multi-step processes

The Flow of Electrons Provides Energy for Organisms

• Nearly all organisms derive energy either directly or indirectly from sunlight through photoautotrophs and the subsequent energy transfer between organisms.
• Illustrates how light-driven splitting of water in photosynthesis plays a crucial role in energy transfer.
• The flow of electrons facilitates the transfer of energy.

Creating and Maintaining Order Requires Work and Energy

• Maintaining order (or low entropy) in biological systems requires energy input.
• The concepts of entropy, enthalpy, and free energy are important for describing equilibrium or non-equilibrium, spontaneous and non-spontaneous reactions
• Reactions and processes tend to proceed naturally in directions that increase total entropy.

Actual Free Energy Changes

• Actual free energy changes are dependent on the concentrations of both reactants and products, not just the standard state conditions.
• By using the equation ΔG = ΔG° + RT ln ([C][D]/ [A][B]), we can account for the changes in concentration from the standard state conditions.

Coupling Reactions

• Biochemical reactions are frequently coupled to produce a favorable overall free energy change.
• A favorable exergonic process can drive an unfavorable endergonic process. This is essential for biological systems.
• Coupled reaction provides free energy to accomplish work such as synthesis of complex biomolecules, like proteins, or even movement. This is especially important since many biological processes may need energy to run which may involve unfavorable conditions.

Enzymes Promote Sequences of Chemical Reactions

• Enzymes markedly and substantially increase the rate of biological reactions.
• Enzymes promote sequences of chemical reactions or reactions and thus enhance the overall rate of biochemical reaction sequences.
• Enzymes do so by lowering the activation energy needed for reactants to transition to products.

Energy Changes During a Chemical Reaction

• Reactions proceed spontaneously, and enzymes can catalyze the reactions.
• Activation Energy (ΔG‡) depicts the energy required for reactants to transition to the transition state, which is then converted to reaction products.
• Enzymes lower the activation energy and increase reaction rates.