Metabolism and Bioenergetics Flashcards

The Energy of Life

• The living cell functions as a miniature chemical factory containing thousands of simultaneous reactions.
• Cells extract energy from their surroundings and apply that energy to perform various types of work.
• Energy conversion is a universal requirement for life; some organisms even convert energy into light, a process known as bioluminescence.
• Metabolism and metabolic processes are fundamentally driven by energy transformations.

Metabolism and Metabolic Pathways

• Metabolism is defined as the totality of an organism’s chemical reactions.
• It is considered an emergent property of life, arising from the complex and specific interactions between molecules within the cell.
• A metabolic pathway is a sequence that begins with a specific starting molecule and concludes with a specific product.
• Every individual step in a metabolic pathway is catalyzed by a specific enzyme.
• Catabolic pathways release energy by breaking down complex molecules into simpler compounds.
  • This released energy becomes available to perform cellular work.
  • A primary example is cellular respiration, where glucose and other organic fuels are broken down into $CO_2$ and $H_2O$.
• Anabolic pathways, also referred to as biosynthetic pathways, consume energy to build complex molecules from simpler ones.
  • An example of this is the synthesis of proteins from amino acids.
• Bioenergetics is the specific study of how energy flows through living organisms.

Forms of Energy and Work

• Energy is defined as the capacity to cause change.
• Energy exists in various forms, though not all forms can be used to perform work.
• Work is defined as the movement of matter against opposing forces, including gravity and friction.
• Kinetic energy is the energy associated with the motion of objects.
• Thermal energy is a specific type of kinetic energy associated with the random movement of atoms or molecules.
• Heat is the term used for thermal energy in transfer from one object to another.
• Light is another form of energy that can be captured and harnessed to perform work.
• Potential energy is the energy that matter possesses due to its specific location or structure.
• Chemical energy is a form of potential energy that is available for release during a chemical reaction.
• Energy is not static and can be converted from one form to another.

The Laws of Energy Transformation

• Thermodynamics is the study of energy transformations that occur in a collection of matter.
• An open system is one where energy and matter can be freely transferred between the system and its surroundings.
• An isolated system is one where no exchange can occur with the surroundings.
• Organisms are characterized as open systems.
• The First Law of Thermodynamics, also known as the principle of conservation of energy, states that the energy of the universe is constant.
  • Energy can be transferred or transformed, but it cannot be created or destroyed.
• The Second Law of Thermodynamics states that every energy transfer or transformation increases the entropy of the universe.
• Entropy is a scientific measure of molecular disorder.
  • Disorder describes how dispersed energy is within a system and how many energy levels are present.
• During energy transfers, some energy is inevitably lost to the surroundings as heat, which increases the disorder (entropy) of the surroundings.

Biological Order and Disorder

• Spontaneous processes are those that occur without an input of energy; they can happen quickly or very slowly.
  • For a process to be spontaneous, it must result in an increase in the entropy of the universe.
• Nonspontaneous processes lead to a decrease in entropy and require the supply of energy to occur.
• Biological systems create ordered structures from less organized starting materials (increasing local order).
• Conversely, organisms replace ordered forms of matter and energy with less ordered forms.
• On an ecosystem scale, energy enters in the form of light and eventually exits in the form of heat.
• The evolution of complex organisms does not violate the second law of thermodynamics because while local entropy (within a system) may decrease, the total entropy of the universe always increases.
• Organisms are described as "islands of low entropy" within an increasingly random universe.

Free-Energy Change ($\Delta G$)

• Biologists use the concept of free energy to understand the chemical reactions of life and predict whether they occur spontaneously.
• Free energy constitutes the portion of a system's energy that can perform work when temperature and pressure are uniform throughout a system, such as in a living cell.
• The change in free energy ($\Delta G$) is calculated as the difference between the free energy of the final state and the initial state:
  • $\Delta G = G_{\text{final state}} - G_{\text{initial state}}$
• Only reactions with a negative $\Delta G$ ($\Delta G < 0$) are spontaneous.
• Free energy serves as a measure of a system’s instability and its tendency to move toward a more stable state.
  • Unstable systems (high $G$) tend to change into more stable states (low $G$).
  • During a spontaneous change, free energy decreases and the stability of the system increases.
• At chemical equilibrium, the forward and reverse reactions occur at the same rate, representing a state of maximum stability.
• A process is only spontaneous and capable of performing work when it is moving toward equilibrium.

Exergonic and Endergonic Reactions

• An exergonic reaction involves a net release of free energy and is spontaneous; its $\Delta G$ is negative.
  • The magnitude of $\Delta G$ for an exergonic reaction represents the maximum amount of work the reaction can perform.
• An endergonic reaction absorbs free energy from the surroundings and is nonspontaneous; its $\Delta G$ is positive.
  • The magnitude of $\Delta G$ for an endergonic reaction is the exact quantity of energy required to drive that reaction.

Equilibrium and Cellular Metabolism

• Hydroelectric systems serve as an analogy: reactions in isolated systems eventually reach equilibrium and can then do no work.
• Cells are open systems that maintain a constant flow of materials in and out; therefore, they are not in equilibrium.
• A defining feature of life is that metabolism as a whole is never at equilibrium.
• Catabolic pathways in cells release free energy through a series of reactions rather than a single step.
• By making the product of one reaction the reactant for the next, the system is prevented from reaching equilibrium.

ATP: Structure and Energy Coupling

• Cells perform three main types of work:
  • Chemical work
  • Transport work
  • Mechanical work
• To manage energy resources, cells use energy coupling, which is the use of an exergonic process to drive an endergonic one.
• Most energy coupling in cells is mediated by ATP (Adenosine Triphosphate).
• ATP is composed of:
  • Ribose (a sugar molecule)
  • Adenine (a nitrogenous base)
  • A chain involving three phosphate groups
• Beyond energy coupling, ATP is a building block used to synthesize RNA.
• The bonds between the phosphate groups of ATP can be broken via hydrolysis.
• ATP hydrolysis releases a significant amount of energy because of the repulsive force between the three negatively charged phosphate groups.
  • The triphosphate tail of ATP is likened to a compressed spring.
  • The energy released comes from the chemical change to a state of lower free energy, not from the phosphate bonds themselves.

Mechanisms of ATP Work and Regeneration

• ATP hydrolysis powers chemical work by driving endergonic reactions.
• ATP drives these reactions through phosphorylation: the transfer of a phosphate group to another molecule (the reactant).
• The recipient molecule post-transfer is called a phosphorylated intermediate.
• Once coupled, the overall reactions become exergonic.
• Transport and mechanical work also rely on ATP hydrolysis, which often induces a change in a protein's shape and its binding ability.
  • This can occur through phosphorylated intermediates or noncovalent bonding between ATP and the protein.
• ATP is a renewable resource regenerated by adding a phosphate group back to ADP (Adenosine Diphosphate).
• The energy required to phosphorylate ADP comes from catabolic reactions.
• The ATP cycle acts as a "revolving door" facilitating energy transfer from catabolic to anabolic pathways.

Enzymes and Activation Energy

• A catalyst is a chemical agent that increases the rate of a reaction without being consumed by it.
• An enzyme is a macromolecule (usually a protein) acting as a catalyst; an example is sucrase, which catalyzes the hydrolysis of sucrose.
• Every chemical reaction involves both bond breaking and bond forming.
• Activation energy ($E_A$) is the initial energy required to start a reaction by breaking the bonds in reactant molecules.
• Activation energy is often sourced as heat absorbed from the surroundings.
• While heat can speed up reactions, it is nonselective and high temperatures can denature proteins.
• Organisms use catalysis to selectively speed up reactions.
• Enzymes lower the $E_A$ barrier, allowing reactions to occur faster.
• Substantively, enzymes do not change the $\Delta G$ of a reaction; they only accelerate reactions that would have eventually occurred anyway.

Enzyme Specificity and the Active Site

• The substrate is the specific reactant molecule upon which an enzyme acts.
• The enzyme binds to its substrate to form an enzyme-substrate complex.
• Most enzyme names end in the suffix "-ase".
• The active site is the specific region of the enzyme where the substrate binds.
• Specificity is determined by the complementary fit between the shape of the active site and the substrate.
• Enzymes undergo an induced fit, where chemical interactions cause the enzyme to change shape, bringing the active site's chemical groups into the correct position for catalysis.
• Substrates are held in the active site by weak interactions, such as hydrogen bonds.
• The active site converts substrates to products and then releases them, becoming available for new substrate molecules.
• The active site lowers $E_A$ through four mechanisms:
  1. Orienting substrates correctly for reaction.
  2. Straining the bonds within the substrate.
  3. Providing a favorable microenvironment.
  4. Forming brief covalent bonds with the substrate.

Factors Affecting Enzyme Activity

• Increasing substrate concentration generally speeds up the reaction rate.
• An enzyme is considered saturated when all available enzyme molecules in a solution are bonded with substrate.
  • At the point of saturation, the reaction speed can only be increased by adding more enzyme.
• Enzyme activity is sensitive to environmental factors:
  • Temperature: Each enzyme has an optimal temperature.
  • pH: Each enzyme has an optimal pH.
• Cofactors are nonprotein molecules that assist in processes difficult for amino acids.
  • Cofactors can be inorganic (metal ions) or organic.
  • An organic cofactor is specifically called a coenzyme (e.g., vitamins).
• Enzyme inhibitors regulate activity:
  • Competitive inhibitors: Bind to the active site, physically blocking the substrate.
  • Noncompetitive inhibitors: Bind to a different site, changing the enzyme's shape and making the active site less effective.
• Reversible inhibitors bind via weak interactions; irreversible inhibitors (like many toxins and poisons) form covalent bonds.

Regulation and Evolution of Metabolism

• Enzymes are encoded by genes; mutations in these genes can lead to changes in amino acid composition.
• Altered enzymes may gain novel activities or bind to different substrates, which may be favored under specific environmental conditions.
• Cells regulate metabolic pathways by:
  1. Switching the genes for specific enzymes on or off.
  2. Regulating the activity of enzymes after they have been formed.
• Allosteric regulation occurs when a regulatory molecule binds to a protein at one site and affects the function at a different site (can be inhibitory or stimulatory).
• Feedback inhibition occurs when the final product of a metabolic pathway acts as an inhibitor to an enzyme early in the pathway.
  • This prevents the cell from wasting resources by over-synthesizing products.
• Enzymes are structurally organized within the cell to provide order:
  • Some act as structural components of membranes.
  • In eukaryotes, specific enzymes are localized in organelles (e.g., cellular respiration enzymes in the mitochondria).