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thermodynamics

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What is the relationship between anabolic and catabolic reactions in the concept of metabolism?

Metabolism is the sum of all anabolic and catabolic reactions in a cell, connected in a network of reaction pathways.

What are the defining characteristics of anabolic reactions?

Anabolic reactions synthesize or 'build' molecules with more bonds, making higher free energy products; they also use or store energy (endergonic), reduce entropy, and are non-spontaneous.

How do catabolic reactions differ from anabolic reactions?

Catabolic reactions degrade or 'break' molecules to make lower free energy products with fewer bonds; they also increase entropy and release energy (exergonic), and are spontaneous.

What is the relationship between the First and Second Laws of Thermodynamics and the concept of free energy?

The First and Second Laws of Thermodynamics state that energy is transformed in many ways, but always at cost of energy lost through entropy that is not available to do work. Free energy (G) is chemical energy available to do work and is expressed as the difference between enthalpy (total energy) and entropy.

How does the change in free energy, $\Delta G$, determine the direction of a reaction?

Any reaction involves a change in free energy, $\Delta G$, between reactants and products. The direction of change in free energy tells if it is positive or negative $\Delta G$ (anabolic or catabolic).

What is the primary role of enzymes in chemical reactions?

Enzymes are proteins that reduce the activation energy of a reaction.

How does the structure of an enzyme relate to its specificity and function?

Enzyme specificity and function are the result of the structure (shape) of the protein.

Describe the interaction between an enzyme and its substrate at the active site.

Substrates interact with enzymes at the active site, forming an enzyme-substrate complex with a close interaction through induced fit.

How do anabolic reactions differ from catabolic reactions in terms of energy changes?

Anabolic reactions use or store energy (endergonic), while catabolic reactions release energy (exergonic).

What is the relationship between entropy and the spontaneity of a reaction?

Anabolic reactions reduce entropy and are non-spontaneous, while catabolic reactions increase entropy and are spontaneous.

What is the role of allosteric effectors in enzyme regulation?

Allosteric effectors bind to a site other than the active site (called the allosteric site) and alter the shape of the enzyme protein to either inhibit or activate its function.

How can metabolic pathways be regulated at different steps?

Metabolic pathways can be regulated at different steps depending on the demands of the cell, allowing the cell to fine-tune its metabolism.

What is the purpose of negative feedback (or feedback inhibition) loops in metabolic pathways?

Negative feedback loops use the product of a metabolic pathway to inhibit an enzyme at the beginning of the pathway, providing a way to regulate pathway activity in response to the cell's needs.

Explain the concept of reaction coupling and how it is used to accomplish positive $\Delta$G reactions in cells.

Positive $\Delta$G reactions are accomplished through reaction coupling, which combines a positive $\Delta$G reaction with a negative $\Delta$G reaction (such as ATP hydrolysis) to give a new net negative $\Delta$G for the combined reactions. This allows the cell to harness the energy released from the negative $\Delta$G reaction to drive the positive $\Delta$G reaction.

Describe the role of ATP in coupled reactions and the continuous cycling of ATP in cells.

The hydrolysis of ATP, yielding a $\Delta$G = -7.3 kcal/mole, is commonly used to generate phosphorylated intermediate molecules of higher energy. ATP is continuously used and regenerated from ADP + P$_i$ in the cell's metabolism.

Explain the concept of redox reactions and the role of electron carriers like NADH and NADPH in metabolism.

Redox reactions transfer electrons between molecules, with oxidation being the loss of electrons and reduction being the gain of electrons. NADH (or NADPH) is a commonly used high-energy electron carrier in metabolism that captures high-energy electrons from organic molecules and holds them for later use when the energy from those electrons can be extracted through an electron transport chain.

State the first and second laws of thermodynamics and explain how they relate to energy transformations in cellular processes.

The first law of thermodynamics states that energy can be transformed but not created or destroyed. The second law states that the entropy (disorder) of an isolated system not in equilibrium will tend to increase over time, approaching a maximum value at equilibrium. These laws govern the energy transformations and changes in entropy that occur in cellular processes.

Describe the relationship between enthalpy, entropy, and free energy in chemical reactions, and how this relates to the spontaneity of reactions.

The free energy ($\Delta$G) of a reaction is determined by the changes in enthalpy ($\Delta$H) and entropy ($\Delta$S) according to the equation $\Delta$G = $\Delta$H - T$\Delta$S. Reactions with a negative $\Delta$G are spontaneous, while those with a positive $\Delta$G are non-spontaneous. Enzymes help drive positive $\Delta$G reactions by lowering the activation energy barrier.

Distinguish between anabolic and catabolic reactions in terms of change in free energy, change in entropy, spontaneity, and whether they are endergonic or exergonic.

Anabolic reactions are biosynthetic, building larger molecules from smaller ones, and have a positive $\Delta$G, decreasing entropy, are non-spontaneous, and are endergonic. Catabolic reactions are degradative, breaking down larger molecules into smaller ones, and have a negative $\Delta$G, increasing entropy, are spontaneous, and are exergonic.

Explain the function of enzymes in relation to their structure and their role in negative $\Delta$G reactions, and discuss how enzymes are regulated in cells.

Enzymes lower the activation energy barrier of reactions, allowing negative $\Delta$G reactions to occur more readily. Enzyme structure, with an active site that binds substrates, is key to their catalytic function. Enzymes can be regulated allosterically, where effector molecules bind to sites other than the active site and alter the enzyme's shape to inhibit or activate it, or through covalent modification like phosphorylation.

Study Notes

Enzyme Regulation

  • Allosteric effectors bind to the allosteric site, altering the protein shape to inhibit or activate enzyme function.
  • Metabolic pathways are regulated at different steps depending on the cell's demands.

Reaction Coupling

  • Positive ∆G reactions are accomplished by combining a positive ∆G reaction with a negative ∆G reaction to achieve a net negative ∆G.
  • The most common means of reaction coupling is to use the hydrolysis of ATP, yielding a ∆G = -7.3 kcal/mole, to generate phosphorylated intermediate molecules of higher energy.
  • ATP is continuously used and regenerated from ADP + Pi.

Redox Reactions

  • Oxidation is the loss of electrons, while reduction is the gain of electrons by molecules.
  • NADH (or NADPH) is a high-energy electron carrier that captures high-energy electrons from organic molecules and holds on to them for later use.

Thermodynamics

  • The First and Second Laws of Thermodynamics state that energy is transformed, but always at the cost of energy lost through entropy.
  • Free energy (G) is the chemical energy available to do work, expressed as the difference between enthalpy (total energy) and entropy.
  • Any reaction involves a change in free energy, ∆G, between reactants and products.

Anabolic and Catabolic Reactions

  • Anabolic reactions synthesize or "build" molecules with more bonds, increasing free energy, reducing entropy, and are non-spontaneous (endergonic).
  • Catabolic reactions degrade or "break" molecules to make lower free energy products with fewer bonds, increasing entropy, releasing energy, and are spontaneous (exergonic).

Enzymes

  • Enzymes are proteins that reduce the activation energy of a reaction.
  • Enzyme specificity and function result from the structure (shape) of the protein.
  • Substrates interact with enzymes at the active site, forming an enzyme-substrate complex with a close interaction through induced fit.
  • Enzymes can be regulated by allosteric effectors, negative feedback loops, and reaction coupling.

Explore the concept of metabolism, which encompasses all anabolic and catabolic reactions within a cell. Understand the difference between anabolic and catabolic reactions, their energy requirements, and how they contribute to the overall functioning of biological systems.

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