AS

Chapter 8: Introduction to Metabolism and Enzymes

Exam Logistics & Schedules

  • Chapter Coverage: Chapter 8 will be on the upcoming test, which is the last chapter covered for this exam.

  • Test Dates: Exams are scheduled for next Monday, Tuesday, and Wednesday. No class on Tuesday due to exams.

  • Upcoming Topics: Chapter 9 will be discussed beginning Thursday after the exams.

Membrane Permeability: Chloride vs. Glucose

  • Key Factor for Membrane Crossing: Charge, not size, is the predominant factor preventing molecules from crossing the lipid bilayer.

    • Chloride (Charged): Even though small, its single charge makes it virtually impossible to cross the hydrophobic membrane directly.

    • Glucose (Uncharged but Hydrophilic): Contains hydroxyl (-OH) groups, making it hydrophilic. It can cross the membrane very slowly on its own.

  • Necessity of Transporters: Despite slow passive diffusion, cells require specific glucose transporters to bring in sufficient glucose to sustain life.

  • Focus of Permeability: When discussing membrane permeability, the primary concern is usually the hydrophobic fatty acid tails of the phosphodipid bilayer, as these tails largely dictate what can and cannot pass, rather than the hydrophilic phosphorus heads.

Introduction to Metabolism

  • Scope: Metabolism encompasses how cells utilize and manage energy, alongside the mechanisms and regulation of enzymes.

  • Anabolic Metabolism:

    • Definition: Processes that involve building complex molecules from simpler ones.

    • Example: The body synthesizing amino acids that are not directly consumed in the diet.

  • Catabolic Metabolism:

    • Definition: Processes that involve breaking down complex molecules into simpler ones.

    • Example: Digestion of food.

  • Essential Amino Acids: The body can synthesize about half of the 20 necessary amino acids. The remaining approximately 8 amino acids are 'essential' because the body cannot produce them and they must be obtained through diet. This is a crucial consideration for strict vegetarians or vegans.

Second Law of Thermodynamics and Living Systems

  • Common Misconception: Living organisms, being highly organized, appear to violate the Second Law of Thermodynamics (which states that the entropy, or disorder, of an isolated system must increase over time).

  • Correction: Living organisms do not violate the Second Law.

    • While specific metabolic reactions in the body might involve a decrease in local entropy ( ext{negative entropy}), the overall system (the organism plus its surroundings) always experiences a net increase in the entropy of the universe.

    • Examples of Entropy Increase by Organisms: Giving off heat and exhaling CO_2 (carbon dioxide) contribute to increasing the disorder of the universe.

  • Life and Entropy (Philosophical Theory): Some physicists and physical biologists propose a theory that life itself is a mechanism for the universe to increase its entropy faster, suggesting that living organisms accelerate the process of the universe reaching a lower, more disordered energy state.

Free Energy (oldsymbol{ ext{Delta G or } oldsymbol{ ext{ ext{ ext{ ext{}}oldsymbol{ ext{ ext{}oldsymbol{ ext{ ext{}oldsymbol{ ext{ ext{}}oldsymbol{ ext{ ext{}}oldsymbol{ ext{ ext{}}oldsymbol{ ext{ ext{}}oldsymbol{ ext{ ext{}}oldsymbol{ ext{}}oldsymbol{ ext{}}}oldsymbol{ ext{}}}oldsymbol{ ext{}}}oldsymbol{ ext{}}oldsymbol{ ext{}}}oldsymbol{ ext{ ext{}}}oldsymbol{ ext{ ext{}}}oldsymbol{ ext{ ext{}}}oldsymbol{ ext{ ext{}}}oldsymbol{ ext{ ext{}}}oldsymbol{ ext{ ext{}}}oldsymbol{ ext{ ext{}}}oldsymbol{ ext{ ext{}}}oldsymbol{ ext{ ext{}}}oldsymbol{ ext{~}}oldsymbol{ ext{ ext{}oldsymbol{ ext{}}}}}}oldsymbol{ ext{~}}}}}}oldsymbol{ ext{}}}oldsymbol{}}oldsymbol{ ext{ ext{}}}oldsymbol{ ext{~}}}}}}}oldsymbol{ ext{G}})

  • Fundamental Energy Currency in Biology: Free energy (oldsymbol{ ext{ ext{}}}oldsymbol{ ext{}}}}}}oldsymbol{ ext{ ext{}}}oldsymbol{ ext{}}}}}}}}}oldsymbol{ ext{~}}oldsymbol{}oldsymbol{ ext{~}}}}}}oldsymbol{}oldsymbol{}oldsymbol{ ext{}}}oldsymbol{ ext{}}}oldsymbol{ ext{}}}oldsymbol{ ext{}}}oldsymbol{ ext{}}}oldsymbol{ ext{}}}oldsymbol{ ext{}}}oldsymbol{~}}}oldsymbol{}oldsymbol{ ext{~}}}oldsymbol{ ext{~}}}oldsymbol{}oldsymbol{~}}oldsymbol{~}}oldsymbol{ ext{~}}}oldsymbol{~}}}oldsymbol{ ext{~}}}oldsymbol{}oldsymbol{ ext{~}}}oldsymbol{ ext{~}}}oldsymbol{~}}}oldsymbol{})})): The most basic and fundamental form of energy used to discuss biological systems. It dictates whether a reaction is favorable or not.

    • **Negative oldsymbol{ ext{ ext{}}}oldsymbol{ ext{}}}}}}oldsymbol{ ext{ ext{}}}oldsymbol{ ext{}}}}}}}}}oldsymbol{ ext{~}}oldsymbol{}oldsymbol{ ext{~}}}}}}oldsymbol{}oldsymbol{}oldsymbol{ ext{}}}oldsymbol{ ext{}}}oldsymbol{ ext{}}}oldsymbol{ ext{}}}oldsymbol{ ext{}}}oldsymbol{ ext{}}}oldsymbol{ ext{}}}oldsymbol{~}}}oldsymbol{}oldsymbol{ ext{~}}}oldsymbol{ ext{~}}}oldsymbol{}oldsymbol{~}}oldsymbol{~}}oldsymbol{ ext{~}}}oldsymbol{~}}}oldsymbol{ ext{~}}}oldsymbol{}oldsymbol{ ext{~}}}oldsymbol{ ext{~}}}oldsymbol{~}}}oldsymbol{})}) (Exergonic): Indicates a favorable, spontaneous reaction that releases energy. This is represented graphically when product free energy is lower than reactant free energy.

    • **Positive oldsymbol{ ext{ ext{}}}oldsymbol{ ext{}}}}}}oldsymbol{ ext{ ext{}}}oldsymbol{ ext{}}}}}}}}}oldsymbol{ ext{~}}oldsymbol{}oldsymbol{ ext{~}}}}}}oldsymbol{}oldsymbol{}oldsymbol{ ext{}}}oldsymbol{ ext{}}}oldsymbol{ ext{}}}oldsymbol{ ext{}}}oldsymbol{ ext{}}}oldsymbol{ ext{}}}oldsymbol{ ext{}}}oldsymbol{~}}}oldsymbol{}oldsymbol{ ext{~}}}oldsymbol{ ext{~}}}oldsymbol{}oldsymbol{~}}oldsymbol{~}}oldsymbol{ ext{~}}}oldsymbol{~}}}oldsymbol{ ext{~}}}oldsymbol{}oldsymbol{ ext{~}}}oldsymbol{ ext{~}}}oldsymbol{~}}}oldsymbol{})}) (Endergonic): Indicates an unfavorable, non-spontaneous reaction that requires an input of energy to occur.

  • Relationship to other Energy Forms:

    • ATP: Adenosine triphosphate is considered the next step up from free energy in biological energy currency, readily usable for cellular processes.

    • Glucose: An energetic molecule that cells break down to derive energy.

    • **Entropy (oldsymbol{ ext{}}oldsymbol{ ext{}}oldsymbol{ ext{}}oldsymbol{ ext{}}oldsymbol{ ext{}}oldsymbol{~}}}}oldsymbol{ ext{}}oldsymbol{~}}}}}oldsymbol{ ext{}}oldsymbol{~}}}}oldsymbol{}oldsymbol{~}}}}}oldsymbol{ ext{~}}}}oldsymbol{ ext{}}oldsymbol{~}}}}oldsymbol{}oldsymbol{~}}}}oldsymbol{ ext{}}oldsymbol{~}}}}oldsymbol{}oldsymbol{~}}}}oldsymbol{ ext{~}}}}}oldsymbol{ ext{}}oldsymbol{~}}}}oldsymbol{}oldsymbol{~}}}}oldsymbol{ ext{}}oldsymbol{~}}}}oldsymbol{ ext{}}}oldsymbol{ ext{}}}oldsymbol{}oldsymbol{ ext{}}}oldsymbol{ ext{}}}oldsymbol{ ext{}}}}_{oldsymbol{ ext{S}}}): A measure of disorder or randomness in a system.

      • Analogy: A messy room tending towards disorder (though this is an oversimplification, as the room doesn't get messy on its own in the same way entropy increases).

      • Measurement: Entropy cannot be measured directly but is calculated from free energy and enthalpy.

    • **Enthalpy (oldsymbol{ ext{ ext{}}}oldsymbol{ ext{}}oldsymbol{ ext{}}oldsymbol{ ext{}}}oldsymbol{ ext{}}oldsymbol{ ext{}}}oldsymbol{ ext{}}}oldsymbol{ ext{}}}oldsymbol{ ext{}}}oldsymbol{ ext{}}}oldsymbol{}oldsymbol{ ext{}}}oldsymbol{ ext{}}}oldsymbol{ ext{}}}oldsymbol{ ext{}}}oldsymbol{ ext{}}}oldsymbol{ ext{}}}oldsymbol{}oldsymbol{ ext{}}}oldsymbol{ ext{}}}oldsymbol{ ext{}}}oldsymbol{ ext{}}}oldsymbol{ ext{}}}oldsymbol{}oldsymbol{ ext{}}}oldsymbol{}oldsymbol{ ext{}}}oldsymbol{}oldsymbol{ ext{}}}oldsymbol{}oldsymbol{}oldsymbol{}oldsymbol{ ext{}}}oldsymbol{~}}}}}_{oldsymbol{ ext{H}}}): Represents the heat content of a system. It is almost always equivalent to the heat released or absorbed by a reaction.

      • Measurement: Enthalpy can be measured directly (e.g., by tracking heat changes).

  • Free Energy Equation: Free energy is a combination of enthalpy and entropy, as described by the equation: oldsymbol{ ext{ ext{}}}oldsymbol{}oldsymbol{ ext{~}}}}}oldsymbol{ ext{}}}oldsymbol{}oldsymbol{~}}} oldsymbol{ ext{G}} = oldsymbol{ ext{}}oldsymbol{}oldsymbol{ ext{~}}} oldsymbol{ ext{H}} - ext{T}oldsymbol{ ext{}}oldsymbol{}oldsymbol{ ext{~}}} oldsymbol{ ext{S}} (where T is temperature in Kelvin; the temperature term regulates the contribution of entropy to free energy).

  • Predicting Reactions: Knowing only a reaction's entropy or enthalpy is insufficient to predict whether it will occur spontaneously. Only by combining both into free energy (oldsymbol{ ext{ ext{}}}oldsymbol{ ext{}}}oldsymbol{~} oldsymbol{ ext{G}}oldsymbol{ ext{}}oldsymbol{}oldsymbol{ ext{~}}}) can biological reactions be predicted for spontaneity.

ATP's Role in Cellular Energy Coupling

  • Primary Function (Most General): ATP's fundamental role is linking favorable reactions to unfavorable ones (energy coupling).

    • Mechanism: ATP hydrolysis (breaking off a phosphate group) is a highly favorable reaction, releasing a significant amount of free energy (typically between 7 ext{ to } 10 ext{ kcal/mol}, with 7.3 ext{ kcal/mol} being a common reference).

    • This released energy is then used to drive an unfavorable reaction ( ext{positive } oldsymbol{ ext{ ext{}}}oldsymbol{ ext{}}}oldsymbol{~} oldsymbol{ ext{G}}oldsymbol{ ext{}}oldsymbol{}oldsymbol{ ext{~}}}), making the overall coupled reaction energetically favorable ( ext{net negative } oldsymbol{ ext{ ext{}}}oldsymbol{ ext{}}}oldsymbol{~} oldsymbol{ ext{G}}oldsymbol{ ext{}}oldsymbol{}oldsymbol{ ext{~}}}).

    • Examples: ATP drives pumps (e.g., in membrane transport), and powers numerous reactions in cellular respiration (Chapter 9) and photosynthesis.

  • Other Roles: While true, these are less general definitions of ATP's universal function:

    • Energizing the cell.

    • Transporting molecules (e.g., via ATP-dependent pumps).

  • ATP Regeneration: ATP is not resynthesized from scratch after use. Instead, the phosphate group is re-added to ADP (Adenosine Diphosphate) to regenerate ATP. This process, known as phosphorylation, is a major goal of cellular respiration (discussed in Chapter 9).

  • Stable ATP Levels: The amount of ATP in the human body (around 50 ext{ to } 75 ext{ grams}) remains relatively constant. It cycles rapidly between ATP and ADP forms depending on energy supply and demand.

  • Other High-Energy Molecules: Other molecules like GTP (Guanosine Triphosphate) and creatine phosphate serve similar roles by undergoing phosphate hydrolysis to release energy for unfavorable reactions.

Enzymes: Catalysts of Life

  • Definition: Enzymes are biological catalysts, primarily proteins (though a small percentage are RNA molecules).

  • Function: Enzymes only change the speed (kinetics) of a reaction.

  • What Enzymes DO NOT Change:

    • The overall heat taken up or lost in a reaction (enthalpy, oldsymbol{ ext{ ext{}}}oldsymbol{}oldsymbol{ ext{~}}} oldsymbol{ ext{H}}).

    • The overall free energy (oldsymbol{ ext{ ext{}}}oldsymbol{}oldsymbol{ ext{~}}} oldsymbol{ ext{G}}) of the reaction (the difference between reactants and products).

    • The amount of ATP required for a reaction.

  • Mechanism of Action: Enzymes lower the activation barrier (also known as activation energy - E_a, or less commonly, **free energy of activation - oldsymbol{ ext{ ext{}}}oldsymbol{ ext{}}}oldsymbol{ ext{~}} oldsymbol{ ext{G}}^oldsymbol{ ext{ ext{}}oldsymbol{ ext{}}oldsymbol{ ext{}}oldsymbol{ ext{}}oldsymbol{ ext{}}oldsymbol{}oldsymbol{ ext{}}oldsymbol{}oldsymbol{}}oldsymbol{ ext{}}oldsymbol{ ext{}}oldsymbol{ ext{}}oldsymbol{}oldsymbol{ ext{}}oldsymbol{}oldsymbol{}oldsymbol{}oldsymbol{ ext{}}oldsymbol{}oldsymbol{ ext{}}oldsymbol{ ext{}}oldsymbol{ ext{}}}oldsymbol{ ext{}}oldsymbol{ ext{}}}oldsymbol{ ext{}}oldsymbol{}oldsymbol{ ext{}}oldsymbol{}oldsymbol{ ext{}}oldsymbol{}oldsymbol{}oldsymbol{}oldsymbol{}oldsymbol{}oldsymbol{}oldsymbol{ ext{}}oldsymbol{ ext{}}oldsymbol{ ext{}}}}}oldsymbol{}oldsymbol{ ext{}}oldsymbol{ ext{}}oldsymbol{ ext{}}oldsymbol{}oldsymbol{ ext{}}oldsymbol{}oldsymbol{ ext{}}oldsymbol{}oldsymbol{}oldsymbol{}oldsymbol{}oldsymbol{}oldsymbol{}oldsymbol{ ext{}}oldsymbol{ ext{}}oldsymbol{ ext{}}}}}oldsymbol{}oldsymbol{ ext{}}oldsymbol{}oldsymbol{ ext{}}oldsymbol{~}}}} ).

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