General-purpose Programming Quiz

Bioenergetics

• Bong Carlo N. Remillion prepared the material
• The objectives include understanding thermodynamics of cellular functions, describing biological oxidation-reduction reactions, explaining the structural basis of energy content of compounds, and solving problems related to bioenergetics.

Metabolism

• Metabolism is a coordinated cellular activity with multi-enzyme systems (metabolic pathways) to obtain chemical energy, convert nutrients, polymerize precursors into biomolecules, synthesize, and degrade biomolecules needed for cellular functions.
• Metabolism is composed of catabolism (breaking down biochemical fuels to extract energy) and anabolism (building up biomolecules for life).

ΔH and ΔS

• Neither ΔH nor ΔS alone can predict the direction of the chemical reaction.
• Combining ΔH and ΔS gives us free energy (G).

Gibbs' Free Energy

• Developed by Josiah Willard Gibbs, Gibbs free energy (ΔG) is a measure of the energy available to do work, mathematically defined as ΔG = ΔH - TΔS.
• ΔH represents change in enthalpy; ΔS represents change in entropy; and T represents absolute temperature.

Gibbs' Free Energy - Spontaneity of Reactions

• A negative ΔG indicates an exergonic (spontaneous) reaction, releasing free energy.
• A positive ΔG indicates an endergonic (non-spontaneous) reaction, requiring energy input.
• A ΔG of zero indicates a reaction in equilibrium.

Standard Free Energy Change

• Designated as ΔG°, experimentally measured at 25°C and 1 atm.
• Used to relate to the equilibrium constant, Keq.
• Keq= [C]^c[D]^d / [A]^a[B]^b

ΔG° & Keq

• ΔG = ΔG°' + RTlnKeq
• This formula relates the standard free-energy change to the actual free energy change, the equilibrium constant, the gas constant and the temperature.

Determining ΔG°' in an Experiment

• ΔG°'= ΔG - RT In Q
• If [reactants]=[products], ΔG= ΔG°'

Sample Problem

• Given an example problem on calculating ΔG°' at equilibrium for a reaction involving glucose and phosphate. Key data in the problem are provided for the calculation.

Metabolic Redox Reactions

• Redox reactions involve electron transfer. Examples of redox reactions are provided in diagrams.

Standard Reduction Potential, E°'

• Represents the tendency of a substance to gain electrons.
• The more positive E°', the greater the tendency to gain electrons. Examples are shown: NAD⁺ + H⁺ + 2e^-= NADH and FAD + 2H⁺ + 2e^-= FADH₂.

Overall/Net Potential, ΔE°'

• The sum of the potentials of the half reactions.

Exercise and Examples

• Instructions from Sir Bong regarding the determination of the overall net potential.
• Example question regarding the calculation of ΔE°' associated as a pair of electrons passes from NADH to O2.

ΔG°' of a Redox Reaction

• The formula for calculating the change in Gibbs free energy (ΔG°') is given by ΔG°' = -n F ΔE°', where n is the number of electrons transferred, F is Faraday's constant and ΔE°' is the overall cell potential.

Sample Problem (2)

• Includes a calculation of how much free energy is required for a pair of electrons to move from NADH to O₂ given the appropriate data and formulas.

Keq derivation

• Formulas are shown relating ΔG° and Keq.

Sample Problem (3)

• includes the calculation of Keq when a pair of electrons is passed from NADH to O₂.

Co-enzymes in Biological Oxidation

• Co-enzymes function as activated carriers, making metabolism more efficient.
• Active carriers play roles in fuel oxidation and reductive biosynthesis, and transfer of small fragments. Active carriers provide a framework for metabolism to be manageable and comprehensive.
• NAD⁺/NADH and NADP⁺/NADPH; FAD/FADH₂, FMN/FMNH₂; Ubiquinone ; cytochromes are presented as examples.

ATP - The Energy Currency of the Cell

• Adenosine triphosphate (ATP) is the cell's primary energy currency
• Hydrolytic cleavage of ATP releases energy.
• This release of energy from the bonds is coupled with energy-requiring (non-spontaneous) reactions, making cellular work possible.

Hydrolysis of ATP

• Hydrolysis of ATP into ADP and phosphate releases a significant amount of free energy.

The ATP Cycle

• ATP is synthesized from ADP and phosphate using energy from catabolic (energy releasing) processes
• ATP is hydrolyzed into ADP and phosphate to release energy for use in cellular processes

Coupling of Reactions

• Coupling unfavorable reactions with favorable ones allows unfavorable reactions to proceed.
• The overall free energy change of a chemically coupled series of reactions is the sum of the individual reactions' free energy changes.

Example Coupling of Reactions

• Detailed example of reaction coupling involving glutamate, ammonia, ATP, ADP, and phosphate.

How do cells make ATP?

• ATP is mostly synthesized through phosphorylation.
• Autotrophic metabolism, heterotrophic metabolism (aerobic and anaerobic), substrate level phosphorylation, and oxidative phosphorylation are some of the processes involved in creating ATP.

Other High Phosphate Compounds

• Various high energy phosphate compounds, including phosphoenol pyruvate, 1,3-bisphosphoglycerate, 3-phosphoglycerate, and creatine phosphate, are presented. Their hydrolysis yields energy. The values for their energy changes are included in the table of data.

Sample Problem (Challenge)

• A practical problem is presented on how to determine if other energy compounds can replace ATP in a previous reaction.
• Relevant energy values for different compounds are included in the problem to facilitate calculation and solution

Reminders

• The user is reminded to complete an exercise from the lecture booklet.

Electron Transport Chain and Oxidative Phosphorylation

• Objectives include understanding how energy is extracted from food molecules through cellular respiration, and describing the electron transport chain, its inhibitors, and its physiological significance. 
• Objectives also include explaining the chemiosmotic theory.
• An overview of the Electron Transport Chain, the role of the protein complexes and the generation of ATP. The steps of the electron transport chain are outlined, and the roles of protein complexes I, II, III, and IV are detailed. Data for calculating the Net ATP Yield is included.

Pentose Phosphate Pathway

• Discusses the enzymes, co-factors, regulation, and significance of the Pentose Phosphate Pathway. 
• The different stages are discussed: Oxidative and Non-Oxidative stages.
• Modes of the Pentose Phosphate Pathway, (including when both NADPH and Ribose-5-P are needed, when only Ribose-5-P is needed, and when only NADPH is needed) are discussed.

Glutathione and Pentose Phosphate Pathway

• Discusses the significance of glutathione and the role of the Pentose Phosphate Pathway in glutathione activity and cellular detoxification processes. Shows some chemical structures for glutathione, and redox reactions for the detoxification of peroxides.
• Discusses a deficiency of Glc-6-P dehydrogenase, which leads to insufficient NADPH and thus insufficient GSH for cellular detoxification.

ATP Accounting

• A summary of how much ATP is produced from the different stages of cellular respiration (glycolysis, Krebs cycle, and electron transport chain), taking into account the different shuttle mechanisms (glycerol-3-phosphate shuttle, malate-aspartate shuttle) ATP data for various compounds is included to facilitate calculations.
• Sample problems involving calculations are included to help demonstrate calculation methods.

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