Metabolic Pathways and Thermodynamics

Introduction to Metabolism

• Metabolism transforms matter and energy, following the laws of thermodynamics.
• The free-energy change determines if a reaction occurs spontaneously.
• ATP powers cellular work by linking exergonic and endergonic reactions.
• Enzymes accelerate metabolism by reducing energy barriers.
• Metabolic regulation is aided by enzymes.

Energy and Matter Transformation

• Living cells are like chemical factories where many reactions take place.
• Cells extract energy from sugars and other organic molecules to do work.
• Organisms like Antarctic krill convert energy to light via bioluminescence for defense.

Metabolic Pathways

• Metabolism is the sum of an organism's chemical reactions.
• Metabolism is a unique property of life because interactions between molecules in cells.
• Metabolic pathways involve a specific molecule as a substrate or reactant at the start and end with a product.
• Each step is catalyzed by a specific enzyme i.e. the enzymes regulate traffic in the cell.

Anabolism and Catabolism

• Catabolic pathways release energy by breaking down complex molecules into simpler ones.
• Cellular respiration is an example of catabolism, where glucose is broken down with oxygen.
• Anabolic pathways use energy to build complex molecules from simpler ones.
• Protein synthesis from amino acids is an example of anabolism.
• Bioenergetics is the study of how organisms manage their energy.

Energy

• Energy is what enables change and exists in different forms for doing work.
• Energy can be converted from one form to another.
• Kinetic energy is energy associated with the movement.
• Heat is a type of kinetic energy that results from the random motion of atoms or molecules.
• Potential energy is the energy matter has due to its location or structure.
• Chemical energy is a type of potential energy available for release in a chemical reaction.

Thermodynamics

• Thermodynamics is the study of energy transformations.
• An isolated system cannot exchange energy or matter with its surroundings (e.g., liquid in a thermos).
• A closed system can exchange energy but not matter with its surroundings (e.g., soup in a closed container).
• An open system can exchange both energy and matter with its surroundings.
• Organisms function as open systems.

First Law of Thermodynamics

• According to the first law of thermodynamics, the amount of energy in the universe is constant.
• Energy can be transferred and transformed, but it cannot be created or destroyed.
• The first law is also known as the principle of conservation of energy.
• Plants convert sunlight to chemical energy, acting as energy transformers, not producers.
• A bear converts its food into energy for biological processes using energy conversion

Second Law of Thermodynamics

• During energy transfer or transformation, some energy becomes unusable and turns into heat.
• Heat increases the disorder of energy in the universe.
• Entropy measures the degree of disorder or randomness.
• Second law of thermodynamics state that every energy transfer or transformation raises the entropy of the universe.
• Energy transformations result in unusable energy, often released as heat for example when a bear converts its food to kinetic energy.

Energy Flow and Biological Disorder

• Living cells convert organized energy into heat.
• Energy enters an ecosystem as light and exits as heat.
• Processes always increase entropy but complex structures still exist.

Biological Order

• Cells create ordered structures from less ordered materials.
• Structural organization(biological order) is one of the characteristics of a living thing.
• Energy input is required to maintain this order.
• When an animal eats it breaks down complex food molecules back into simplier molecules like CO2.

Free Energy

• Spontaneous processes occur without needing energy input.
• Processes that occur without energy input raise the entropy of the universe.
• Biologists determine energy changes in chemical reactions to know which reactions happen spontaneously and which require energy.
• The change in free energy (ΔG) is related to changes in total energy and entropy as well temperature.
• Living systems' free energy is energy that can do work, the formula for which is: ΔG = ΔH - TΔS.

Free Energy and System Stability

• Only processes with a negative ΔG (change in free energy) are spontaneous.
• Spontaneous processes can be harnessed for work.
• Stability increases, and free energy decreases during a spontaneous change.
• Free energy is a measure of a system's instability.
• Equilibrium is a state of maximum stability.
• Processes perform work spontaneously when moving toward equilibrium.

Exergonic and Endergonic Reactions

• The chemistry of life's processes can be defined by free energy.
• Chemical reactions, metabolic ones as well, are either exergonic or endergonic based how free energy changes.
• Exergonic reactions release free energy and occur spontaneously.
• Endergonic reactions absorb free energy and are nonspontaneous.

Exergonic and Endergonic Reactions

• Reactions in a closed system eventually reach equilibrium and then do no work.
• Cells are open systems with a constant flow of energy and matter, thereby are not in equillibrium.
• Being not at equilibrium is what defines life.
• A catabolic pathway in a cell releases free energy through many reactions.

Cellular Work

• There are three kinds of cellular work:
  • Chemical work is like building polymers from monomers.
  • Transport work is like pumping ions.
  • Mechanical work is like muscle movement.

ATP: The Cell's Energy Shuttle

• Cells manage energy resources by energy coupling, using an exergonic process to drive an endergonic one.
• Energy coupling in cells is from ATP (adenosine triphosphate), which is the cell's energy shuttle.
• An ATP molecule is composed of adenosine, a five carbon sugar(ribose), and three phosphate groups.

ATP Hydrolysis

• ATP can have bonds between its phosphate groups broken by hydrolysis.
• When ATP reacts with water it yields inorganic phosphate (Pi) and ADP and releases energy.
• Energy is released when the terminal phosphate bond of ATP is broken.
• Energy release comes from the chemical change to a lower energy state and not the phosphate bonds.

How ATP Powers Endergonic Reactions

• The three types of cellular work are powered by ATP hydrolysis.
• Energy from the exergonic reaction of ATP hydrolysis can drive an endergonic reaction.
• Coupled reactions are exergonic overall.
• ATP drives endergonic reactions by phosphorylation.
• Phosphorylation transfers a phosphate group to another molecule now called a phosphorylated intermediate.
• Chemical work: Glutamine synthesis from glutamic acid is endergonic but the reaction is not spontaneous.

How ATP Powers Endergonic Reactions

• ATP hydrolysis and protein phosphorylation leads to a shape change in a transport protein allowing it to transport a solute(transport work).
• ATP binds noncovalently to motor proteins and ATP hydrolysis releases the energy for a shape change for said protein(mechanical work).

The Regeneration of ATP

• ATP becomes ADP and then recyles as ATP through a process regenerates it
• ATP is a sustainable source of energy
• Phosphorylating ADP energy comes from catabolic reactions

Enzymes and Energy Barriers

• Catalysis speeds up synthetic reaction i.e. an enzyme that can do this is a biological catalyst.
• A catalyst is a chemical agent that speeds up a reaction without being consumed.
• An enzyme is a catalytic protein.
• Hydrolysis of sucrose by use of the sucrase enzyme breaks the sucrose molecule down.

Activation Energy Barrier

• Every chemical reaction requires initial activation energy for the bond breaking involved.
• The initial start energy is the free energy of activation, or activation energy (EA).
• Activation energy is mainly the thermal energy that absorbs into reactants.

Role of Enzymes

• Enzymes lower the activation energy barrier for chemical reactions.
• Enzymes catalyze reactions by lowering the EA barrier.
• Enzymes instead speed up reactions that eventually occur.

Enzymes and Their Substrates

• An enzyme acts on a reactant called a substrate or a molecule.
• Enzymes combine to form an enzyme-substrate.
• An enzyme catalysed substrate/reactant is very specific.
• The active region is wheee the substrate links.
• Induced fit of a substrate enhances its capability to catalyse reaction.

The Catalytic Cycle of an Enzyme

• The substrate joins the active enzyme site during an enzymatic reaction.
• Active sites minimise activation energy barrier by:
  • Correctly orienting substrates.
  • Straining substrate bonds.
  • Providing a favorable microenvironment.
  • Bonding covalently to the substrate.
• Enzymes can therefore catalyse both forward and backward reactions to attain equilibrium.

Cofactors and Coenzymes

• Cofactors help enzymes but are non protein helpers, this can either be inorganic or organic.
• Metal or ionic components can be cofactors.
• Organic cofactors are called coenzymes, and include vitamins.

Effects of Local Conditions on Enzyme Activity

• Enzyme activity can be reduced or increased by;
  • General temperature and pH conditions.
  • Special chemicals.
• Optimal environment favors active enzyme shape or conformation.

Enzyme Inhibitors

• Competitive inhibitors function by mimicking an intended substrate.
• Noncompetitive inhibitors cause an enzyme alteration and hence less effiectve at binding as active sites are altered.
• Examples of inhibitors include toxins, poisons, pesticides, and antibiotics.

Regulation of Metabolism

• Chemical chaos comes about from incorrectly managed cell pathways.
• Cells ensure metabolic regulation by;
  • Switching on/off certain genes.
  • Regulating enzyme activity.

The Evolution of Enzymes

• Allosteric regulation can repress or activate an enchyme.
• Allosteric regulation happens when one molecule binds to a protein, which affects where the said protein functions.
• Multi-unit polypeptides come in large amounts on regulated enzymes.
• Bindings of activators stabilises a live shape.
• Bindings of inhibitors ensure non avtive shape.

Cooperativity

• Cooperativity represents a type of allosteric regulation used to improve enzyme operations.
• One substrate can cause more substrates to act on one enzyme.
• Subtrates affects catalysis as it brings a specific chain to action more favourably.

Feedback Inhibition

• Feedback inhibition occurs when pathway-end products prevent metabolic pathways from being metabolised any further i.e the whole end product halts the initial process.
• Preventative methods include; preventing too much chemical discharge by creating less than its required product

Specific Location of Enzymes

• Metabolic pathways become better arranged given ordered structures surrounding their pathways.
• Many membrane enzymes are made of structural parts.
• Many eukaryotic cells are based off of mitochondrial enzymes like ones for cellular respiration

Explore the relationship between catabolic and anabolic pathways, cellular respiration, and protein synthesis. Understand enzymes, kinetic vs potential energy, and bioenergetics. Learn about the laws of thermodynamics and spontaneous processes.