Cellular Metabolism and Thermodynamics

Introduction to Metabolism

• Metabolism transforms matter and energy, and is subject to the laws of thermodynamics.
• The free-energy change of a reaction indicates whether a reaction occurs spontaneously.
• ATP powers cellular work by coupling exergonic reactions to endergonic reactions.
• Enzymes accelerate metabolic reactions by reducing energy barriers.
• The moderation of enzyme activity aids in the regulation of metabolism.

Energy and Matter Transformation

• Living cells serve as chemical factories where thousands of reactions occur.
• Cells derive energy from sugars and other energy-containing organic molecules to perform work.
• Some organisms, like Antarctic krill, convert energy to light, as seen in bioluminescence.

Metabolic Pathways

• Metabolism is the sum total of an organism's chemical reactions.
• Metabolism emerges as a property of life resulting from molecular interactions within cells.
• Metabolic pathways start with a specific molecule (substrate or reactant) and conclude with a product.
• Each step in a metabolic pathway is expedited by a specific enzyme.

Anabolism and Catabolism

• Catabolic pathways discharge energy by simplifying complex molecules into simpler compounds.
• An example of catabolism includes cellular respiration, the breakdown of glucose in the presence of oxygen.
• Anabolic pathways necessitate energy to construct complex molecules from simpler ones.
• Protein synthesis from amino acids exemplifies anabolism.
• Bioenergetics explores how organisms manage their energy resources.

Energy

• Energy signifies the capacity to induce change and can be converted from one form to another.
• Kinetic energy is the energy linked with motion.
• Heat (thermal energy) is kinetic energy related to the random movement of atoms or molecules.
• Potential energy is energy that matter holds due to its location or structure.
• Chemical energy is potential energy available for liberation in a chemical reaction.

Thermodynamics

• Thermodynamics is the study of energy transformations.
• An isolated system cannot exchange energy or matter with its surroundings, such as liquid in a thermos.
• A closed system can transfer energy, but cannot exchange matter with its surroundings, such as a cup of soup with a lid.
• An open system can transfer both energy and matter between the system and its surroundings.
• Living organisms represent open systems.

First Law of Thermodynamics

• The first law of thermodynamics states that the quantity of energy in the universe is constant.
• Energy can be transferred and transformed but cannot be created or destroyed.
• The first law of thermodynamics is also known as the principle of conservation of energy.
• By converting sunlight to chemical energy, plants function as energy transformers, not energy producers.
• A brown bear converts the chemical energy of organic molecules in food into kinetic and other energy forms.

Second Law of Thermodynamics

• The second law of thermodynamics dictates that during energy transfer or transformation, some energy becomes unusable, often dissipating as heat.
• Heat amplifies the dispersion of energy in an open system, thereby increasing disorder.
• Scientists quantify entropy as a measure of disorder or randomness.
• The second law of thermodynamics states that every energy transfer or transformation escalates the entropy of the universe.
• As the bear transforms chemical energy into kinetic energy, it amplifies environmental disorder.

Energy Flow and Biological Disorder

• Living cells inevitably transform organized energy forms into heat.
• Energy enters an ecosystem as light and exits as heat.
• Complex structures are assembled from simpler materials.

Biological Order

• Cells construct ordered structures from less ordered materials.
• This process needs energy input.
• Structural organization, or biological order, is a defining characteristic of living things.

Free Energy

• Spontaneous processes ensue without energy input, occurring either quickly or slowly.
• Processes occurring without energy input need to increase the entropy of the universe.
• Biologists seek to distinguish spontaneous reactions from those needing energy input, requiring the assessment of energy changes in chemical reactions.
• Free energy in a living system is energy usable for work at uniform temperature and pressure, such as within a living cell.
• The change in free energy (ΔG) relates to changes in total energy (enthalpy, ΔH), entropy (ΔS), and temperature in Kelvin (T).

Free Energy and System Stability

• Only processes featuring a negative ΔG are spontaneous and capable of performing work.
• During spontaneous changes, free energy diminishes while system stability increases, indicating a system's inclination towards a more stable state.
• Equilibrium represents a state of maximum stability, where processes are only spontaneous and able to work when heading towards it.

Exergonic and Endergonic Reactions

• The principle of free energy helps to comprehend life's chemical processes.
• Based on free energy modifications, chemical reactions, along with metabolic processes, can be classified as exergonic or endergonic.
• An exergonic reaction releases free energy and happens spontaneously.
• An endergonic reaction takes in free energy from its surrounding and is nonspontaneous.

Exergonic and Endergonic Reactions

• Reactions in closed systems reach equilibrium and cease to perform work.
• Cells exist in a non-equilibrium stat; they are open systems with a continuous stream of energy and matter.
• A defining characteristic of life: metabolism perpetually avoids equilibrium.
• Catabolic pathways in cells discharge free energy via reaction sequences.

Cellular Work

• There are three kinds of cellular work.
  • Chemical work enables non-spontaneous reactions like forming polymers from monomers.
  • Transport work includes pumping ions against their concentration gradients.
  • Mechanical work includes beating cilia and muscle movement

ATP: The Cell's Energy Shuttle

• To accomplish tasks, cells manage energy using energy coupling, leveraging exergonic processes to fuel endergonic ones.
• ATP (adenosine triphosphate) mediates energy coupling in cells.
• ATP constitutes adenosine, a five-carbon sugar (ribose), and three phosphate groups.

ATP Hydrolysis

• Hydrolysis can break the bonds between ATP's phosphate groups.
• The reaction between ATP and water produces inorganic phosphate (Pi) and ADP, releasing energy as the terminal phosphate bond of ATP breaks.
• Energy release arises from chemical state changes to a lower energy level, not from the phosphate bonds themselves.

How ATP Powers Endergonic Reaction

• ATP hydrolysis powers mechanical, transport, and chemical cellular work.
• Cells harness energy from exergonic ATP hydrolysis to drive endergonic reactions.
• ATP drives endergonic reactions by phosphorylation: transferring a phosphate group to another molecule. The recipient molecule is called a phosphorylated intermediate.
• Glutamine synthesis from glutamic acid (Glu) is endergonic.

How ATP Powers Endergonic Reactions

• ATP hydrolysis and protein phosphorylation change the shape of transport proteins enabling solute transport.
• ATP binds noncovalently to motor proteins causing movement alongside cytoskeletal tracks followed by the release of ADP and inorganic phosphate.

The Regeneration of ATP

• ATP regenerates from adenosine diphosphate (ADP).
• Energy for ADP phosphorylation comes from catabolic reactions.

Enzymes and Energy Barriers

• Enzymes accelerate reactions by reducing the Free Energy of Activation barrier.

Catalysis

• Enzymes are biological catalysts.
• Catalysts are chemical agents accelerating reactions without being consumed.
• An enzyme embodies a catalytic protein.
• Hydrolysis, the enzyme-catalyzed reaction of breaking down sucrose by sucrase, showcases them at work.

Activation Energy Barrier

• Every chemical reaction between molecules entails bond disruption and formation.
• Free energy of activation, or activation energy (EA), signifies the initial energy input for reactions.
• Thermal energy normally feeds into activation energy that reactant molecules absorb from their environments.

Role of Enzymes

• Enzymes catalyze reactions by reducing the EA barrier without affecting the change in free energy (∆G).
• Enzymes expedite reactions that would otherwise occur eventually

Enzymes and Their Substrates

• A substrate constitutes the reactant on which enzymes act.
• Enzymes bind to their substrate to form a enzyme-substrate complex
• Enzymes exhibit high specificity for the substrate they bind to, resulting in unique reactions.
• An active site composes of a region on the enzyme where the substrate binds.
• Induced fit occurs when a substrate prompts its active site to shift into positions improving the enzyme's capability to catalyze reactions.

The Catalytic Cycle of an Enzyme

• The substrate binds to the active site of the enzyme.
• The active site reduces the Activation Free Energy barrier.
  • Orienting substrates accordingly
  • Straining bonds in the substrate molecule
  • Providing a favourable micro environment
  • Covalently bonding to the substrate

Cofactors and Coenzymes

• Cofactors are non-protein enzyme helpers.
• Cofactors may be inorganic or organic (coenzymes), which include vitamins.

Effects of Local Conditions on Enzyme Activity

• An enzyme’s activity is impacted by environmental factors, chemicals and optimal conditions favour the enzyme's conformation/shape.

Enzyme Inhibitors

• A competitive inhibitor resembles the substrate, vying for the active site to prevent substrate binding.
• Noncompetitive inhibitors bind at a site separate from the active site, resulting in shape alteration and rendering the active site less effective.
• Examples of inhibitors: toxins, poisons, pesticides, and antibiotics.

Regulation of Metabolism

• Chemical chaos ensues if a cell's metabolic pathways lack stringent regulation.
• A cell modulates its metabolism through gene regulation and regulating enzyme activity.

The Evolution of Enzymes

• Allosteric regulation can either hinder or boost an enzyme's functionality.
• Binding molecules at one location alters a proteins function at a different protein location.
• Subunits define allosterically regulated enzymes.
• Enzymes exhibits both active and inactive states.
• The active form of an enzyme are stabilized when bound to activators.
• Binding of an inhibitor stabilizes enzymes inactive form.

Cooperativity

• Cooperativity amplifies enzymatic activity through allosteric regulation.
• One substrate molecule readies an enzyme for additional substrate molecules.
• Binding by a substrate on an active affects catalyzation in different active site rendering cooperativity as allosteric.

Feedback Inhibition

• Metabolic pathways are shut down by an end product in the process of feedback inhibition.
• Feedback inhibition safeguards cells against wasting resources and overproducing.

Specific Location of Enzymes

• Intracellular structures help arrange metabolic pathways.
• Some enzymes function as structural elements of membranes.
• Eukaryotic cells locate specific organelle such as mitochondrion with corresponding enzymes.
• This creates optimal biochemical environment for reaction catalyzation.

Delve into the functions of ATP, enzymes, and metabolic pathways. Explore energy transformation and the significance of free energy in cells. Understand thermodynamics, spontaneity, and bioluminescence.