Study guide: Metabolism and Bioenergetics

📋 Course Outline

1. Metabolism and Energy Flow
2. Energy Forms and Thermodynamics
3. Entropy and Biological Order
4. Gibbs Free Energy and Reactions
5. ATP and Cellular Work
6. Enzyme Catalysis and Pathways
7. Enzyme Activity and Regulation

📖 1. Metabolism and Energy Flow

🔑 Key Concepts & Definitions

• Metabolism: The totality of an organism’s chemical reactions and an emergent property of life arising from orderly molecular interactions.

• Metabolic pathway: A series of defined steps in which a specific molecule is altered to produce a product, with each step catalyzed by a specific enzyme.
• Bioenergetics: The specialized study of how energy flows through living organisms.

★ Must-know

📌 Catabolic pathways release energy by breaking complex molecules into simpler compounds, whereas anabolic pathways consume energy to build complex molecules from simpler ones.

Further detail

📐 Formula - Cellular respiration is represented by $\mathrm{C_6H_{12}O_6 + 6O_2 \rightarrow 6CO_2 + 6H_2O + energy}$, converting glucose and oxygen into carbon dioxide, water, and energy.

📐 Formula - Photosynthesis is represented by $\mathrm{6CO_2 + 6H_2O + sunlight\ energy \rightarrow C_6H_{12}O_6 + 6O_2}$.

💡 Memory Hook

Catabolism breaks down; anabolism builds up.

📖 2. Energy Forms and Thermodynamics

🔑 Key Concepts & Definitions

• Energy: The ability to do work and exists in many forms.
• Chemical energy: Potential energy stored in the structural arrangement of molecules and available for release during a chemical reaction.
• Thermal energy: The kinetic energy associated with the random movement of atoms or molecules.
• Heat: Thermal energy transferred from one object to another.
• Thermodynamics: The specialized study of energy transformations within a collection of matter.

★ Must-know

• Energy exists in two states: potential energy and kinetic energy.

📌 Energy cannot be created or destroyed, but it can be converted from one form to another.

📌 An isolated system exchanges neither energy nor matter with its surroundings, whereas an open system can transfer both energy and matter with its surroundings.

• Living organisms are open systems that absorb energy from light or food and release heat and metabolic wastes such as CO2 to their surroundings.

📌 The First Law of Thermodynamics states that the total energy of the universe is constant because energy can be transferred and transformed but not created or destroyed.

Further detail

• All work carried out by living organisms involves transforming potential energy into kinetic energy.

• Complex organic molecules such as glucose contain high chemical energy because significant energy is liberated as they break down into simpler products.

📖 3. Entropy and Biological Order

🔑 Key Concepts & Definitions

• Entropy: A scientific measure of molecular disorder or randomness.

★ Must-know

• The Second Law of Thermodynamics states that every energy transfer or transformation increases the entropy of the universe.

• Spontaneous processes occur without energy input and increase the entropy of the universe, whereas nonspontaneous processes decrease entropy and require energy input.

• The local increase in order within living systems does not violate the Second Law because catabolic breakdown releases heat and small molecules into the environment.

Further detail

• Living organisms increase the disorder of their surroundings through metabolism, including when complex food molecules are broken down into heat and small molecules such as CO2.

• Living cells create ordered structures from less-organized materials, such as assembling amino acids into ordered polypeptide chains.

• Energy enters ecosystems continuously as light and exits permanently as heat.

💡 Memory Hook

Catabolic breakdown releases heat and small molecules, balancing local biological order.

📖 4. Gibbs Free Energy and Reactions

🔑 Key Concepts & Definitions

• Free energy: The portion of a system’s energy available to do work inside a living cell at uniform temperature and pressure.

★ Must-know

📐 Formula - The change in free energy is the final free energy minus the initial free energy: $\Delta G = G_{final} - G_{initial}$.

📌 A negative ΔG means a reaction loses free energy, becomes more stable, and is spontaneous, whereas a positive ΔG means it gains free energy, becomes less stable, and is nonspontaneous.

• A system at equilibrium is maximally stable and can do no work; a process can perform work only while spontaneously moving toward equilibrium.

📌 An exergonic reaction releases free energy to its surroundings, whereas an endergonic reaction absorbs free energy from its surroundings.

Further detail

• A system with high free energy is unstable and has potential energy ready to change, whereas a system with low free energy is more stable and has less available energy.

📌 Cells harness reactions with negative ΔG to power cellular processes, while reactions with positive ΔG require an input of cellular energy.

💡 Memory Hook

Negative ΔG releases energy; positive ΔG requires energy input.

📖 5. ATP and Cellular Work

🔑 Key Concepts & Definitions

• ATP: Adenosine triphosphate (ATP) is the cell’s energy currency and consists of a sugar, an adenine nucleobase, and a chain of three phosphate groups.

★ Must-know

• Cells perform three kinds of work:
  • Chemical work drives energy-consuming reactions
  • Transport work pumps substances across membranes against their gradient
  • Mechanical work powers movement such as muscle contraction or cilia beating

📌 Energy coupling uses an exergonic, energy-releasing process to drive an endergonic, energy-consuming process, and ATP is the primary mediator of this coupling.

• ATP hydrolysis releases energy when water is added and the terminal phosphate bond is broken.

• ATP is regenerated by adding a phosphate group to ADP, using free energy from exergonic catabolic breakdown reactions.

• ATP transfers its terminal phosphate group to another molecule to power an endergonic reaction, forming a phosphorylated intermediate that is less stable, has more free energy, and is highly reactive.

Further detail

• The three negatively charged phosphate groups in ATP repel one another, making its triphosphate tail a compressed spring of potential energy.

📌 Coupling ATP hydrolysis to an energy-consuming reaction can make the coupled reaction net exergonic.

• During transport and mechanical work, ATP transfers a phosphate group to a motor or transport protein, changing its shape and binding ability to drive cellular movement.

• Photosynthesis converts sunlight energy into ATP that is used to make sugars, while cellular respiration breaks down the potential energy in sugars and converts it into ATP.

💡 Memory Hook

ATP’s negatively charged phosphate tail is a compressed spring that can transfer a phosphate to power work.

📖 6. Enzyme Catalysis and Pathways

🔑 Key Concepts & Definitions

• Enzyme: A macromolecule, almost always a protein, that acts as a biological catalyst.
• Activation energy: The initial energy investment needed to break chemical bonds and start a reaction.
• Catalyst: A chemical agent that drastically speeds up a reaction without being altered or consumed in the process.
• Transition state: The highly unstable peak reached when reactants absorb enough energy to break their bonds.
• Active site: The area of an enzyme that binds a substrate.
• Induced fit: The tight fit formed when an enzyme and substrate bind together as a complex.

★ Must-know

📌 Enzymes selectively lower activation energy so reactions can proceed rapidly at normal body temperature, whereas adding heat can denature proteins and speed up reactions indiscriminately.

📌 An enzyme changes reaction speed but cannot change ΔG or turn a nonspontaneous reaction into a spontaneous one.

• In a biochemical pathway, the product of one reaction becomes the substrate for the next reaction until a final product is produced.

Further detail

• Sucrase drives the breakdown of sucrose into glucose and fructose in seconds, whereas the same solution can take years to break down naturally.

• Most enzyme names end in -ase, and enzymes are reused and specific to a subset of molecules.

📖 7. Enzyme Activity and Regulation

🔑 Key Concepts & Definitions

• Cofactor: A non-protein helper required by many enzymes to function properly; it may bind permanently or attach loosely with the substrate.
• Feedback inhibition: The product of a reaction acts as a repressor.
• Allosteric regulation: A regulatory molecule binds to a protein at one site and affects its function at another site.

★ Must-know

• Increasing temperature can denature enzymes, and changing pH can also denature them.

• Competitive inhibitors compete with the substrate and block the active site, whereas noncompetitive inhibitors bind to an allosteric site and change the active-site shape so the substrate cannot bind.

• A repressor inhibits an enzyme when bound, whereas an activator changes the enzyme’s shape so it can bind substrate.

Further detail

📌 Inorganic cofactors are typically metal ions such as zinc, iron, and copper, whereas coenzymes are organic cofactors.

• Most vitamins function directly as coenzymes or supply the raw materials cells need to manufacture coenzymes.

• Poisons can act as irreversible enzyme inhibitors; sarin binds the active site of acetylcholinesterase, and pesticides and antibiotics are other inhibitor examples.

💡 Memory Hook

Competitive inhibitors block the active site; noncompetitive inhibitors alter it from an allosteric site.

📊 Synthesis Tables

Catabolic and Anabolic Pathways

Pathway	Effect	Energy
Catabolic	Breaks complex molecules down	Releases energy
Anabolic	Builds complex molecules	Consumes energy