Chapter 3 Bioenergetics, enzymes and metabolism (Cell Biology)

Bioenergetics: The study of the various types of energy transformations that occur in living organisms.
Energy: Defined as the capacity to do work, i.e., the capacity to change or move something.
Thermodynamics: The study of the changes in energy that accompany events in the universe.
- Predicts whether energy input is required but does not indicate the rate of specific processes.

Statement: The law of conservation of energy: Energy can neither be created nor destroyed but can be converted from one form to another.
Cells are capable of:
- Energy transduction
- Energy storage
- Energy transport
Types of energy conversion in cells:
- Conversion of mechanical energy to electrical energy.
- Storage of electrical energy in chemical form (e.g., ATP).
- Conversion of electrical energy to mechanical energy.
Chemical energy is notably stored in biological molecules such as ATP.
Energy transduction examples:
- Conversion of sunlight into chemical energy through photosynthesis.
- Animals (e.g., fireflies) converting chemical energy back into light.
- Muscle contraction involves the release of heat through the conversion of chemical energy to mechanical energy.

System: The subset of the universe under study.
Surroundings: Everything outside the system.
Internal Energy (E): The energy of the system; change during a transformation is expressed as ΔE.
Equation: ΔE = Q – W
- Where Q = heat energy, W = work energy.
Exothermic reactions lose heat; endothermic reactions gain heat.
The first law of thermodynamics does not predict if a change will be positive or negative.

Statement: Events in the universe tend to proceed from a state of higher energy to a state of lower energy.
- These events are termed spontaneous and can occur without external energy.
A loss of available energy during a process results from an increase in randomness (or disorder).
Entropy: A measure of randomness or disorder; every event increases the entropy of the universe.

Justus von Liebig: Studied fermentation, highlighting alcohol as a common organic reaction.
Louis Pasteur: Noted fermentation only occurs in the presence of yeast cells.
Hans Buchner: Introduced the concept of "yeast juice" capable of fermentation, indicating an intracellular catalyst.
Enzymes: Proteins that act as mediators of metabolism, responsible for nearly every reaction.
- 1926: James Sumner crystallized the enzyme urease from jack beans.
- Enzymes are conjugated proteins and can contain non-protein components called cofactors (organic or inorganic).

Spontaneity of a Reaction:
- ΔG < 0: reaction is spontaneous and exergonic (releases energy).
- ΔG > 0: reaction is endergonic and requires energy input.
Reactions tend toward equilibrium represented by K_{eq} = \frac{[C][D]}{[A][B]}.
Free energy changes in reactions under standard conditions are represented by:
- \Delta G^{\circ'} = -RT \ln K_{eq},
- Not representative of cellular conditions but useful for comparison.

An organism, such as an amoeba, maintains nutrient intake to sustain metabolic pathways at a steady state, differing from equilibrium.
- Upon death, concentrations of ATP and other metabolites shift toward equilibrium ratios.

Activation Energy (EA): Minimum energy needed for a chemical transformation to occur.
- Reactants must reach a transition state to proceed.
Catalytic Efficiency: Enzymes facilitate more substrates reaching the transition state quicker.
Enzymes lower activation energy by stabilizing the transition state, thus increasing reaction rates.

Enzymes interact with substrates to form enzyme-substrate (ES) complexes at active sites with complementary shapes for specificity.
Binding at the active site occurs through noncovalent interactions (ionic, hydrogen bonds).

Maintaining Precise Substrate Orientation: Correct alignment of substrates boosts catalysis.
Changing Substrate Reactivity: Substrate's electrostatic configuration is modified by amino acid side chains in the active site.
Inducing Strain in the Substrate: Structural conformation changes of the enzyme create tension in substrate bonds, facilitating the transition state formation.

Enzyme Inhibitors: Substances that decrease enzymatic reaction rates.
- Irreversible Inhibitors: Bind tightly and permanently to enzymes.
- Reversible Inhibitors: Bind loosely; competitively mimic substrates for active sites potentially overcome with excess substrate.

Antibiotics target bacterial enzymes without harming human hosts, focusing on:
- Enzymes in bacterial cell wall synthesis (e.g., penicillin as an irreversible inhibitor of transpeptidases).
- Sulfa drugs mimic endogenous PABA, crucial for folic acid synthesis.
- Resistance mechanisms arise through mutations (e.g., b-lactamase opens the lactam ring in penicillin).
Antibiotic resistance issue extends beyond bacteria to viruses as well, indicated in diseases like AIDS due to rapid mutation rates.

Metabolism: Collection of biochemical reactions occurring in cells, with metabolic pathways defining sequences converting substrates into end products through intermediates.
- Catabolic Pathways: Breakdown complex molecules to simpler ones, generating energy.
- Anabolic Pathways: Synthesize complex products from simple substrates, requiring energy (ATP, NADPH).
Metabolic Pathway Stages:
1. Hydrolysis of macromolecules to building blocks.
2. Further degradation into common metabolites.
3. Production of ATP from degradation of small metabolites (e.g., acetyl-CoA).

ATP generated during catabolic reactions and hydrolysis powers synthetic reactions, mechanical work, or light production (e.g., fireflies).
High energy of ATP hydrolysis arises from:
1. Resonance stabilization of products.
2. High solvation energy of products.

Studies show caloric restriction (10-30% less intake) in various organisms may increase lifespan and slow aging.
- Mechanisms involve specific genes influenced by caloric intake timing.
Conflicting studies on caloric restriction effects observed in rhesus monkeys; health indicators improved regardless of lifespan increase.