Chapter 24: Photosynthesis: Light-independent reactions

Learning Objectives

• Explain the general role of ATP in the cell.
• Explain what it means for two chemical reactions to be coupled.
• Explain why a large change in free energy level occurs when an enzyme or substrate is phosphorylated (adding two tightly packed negative charges).
• Given a graph showing free energy changes: Label reactants, activation energy, transition state, and products.
• Describe and annotate how an enzyme affects the energy curve.
• Determine if a reaction is exergonic or endergonic.
• Explain why enzymes increase reaction rates but don't make endergonic reactions exergonic.
• Create a model describing how plants fix carbon from the air to create sugars, including CO2, thylakoid, stroma, rubisco, NADP+/NADPH, ADP/ATP, Calvin Cycle, glucose, reduction, and oxidation.
• Predict the consequences for ATP and NADPH production if a component in the photosynthesis pathway is altered.

Introduction

• Light-dependent reactions convert light energy into chemical energy (ATP and NADPH).
• ATP and NADPH are unstable and not suitable for long-term storage.
• Light-independent reactions use ATP and NADPH to synthesize stable carbohydrates.
• Carbohydrates can be moved, stored, and broken down for energy.

Types of Energy

• Energy is the capacity to do work and exists in various forms (electrical, light, heat).
• Understanding energy flow in biological systems requires knowledge of different energy types.

Kinetic Energy

• Energy associated with motion is kinetic energy.
• Examples: Airplane in flight, wrecking ball, speeding bullet, walking person, molecule movement (heat), electromagnetic radiation (light).

Potential Energy

• Energy associated with the potential to do work is potential energy.
• Example: A wrecking ball suspended above the ground.
• Objects transfer energy between kinetic and potential forms.
  • A motionless wrecking ball has 0% kinetic and 100% potential energy.
  • As it releases, its kinetic energy begins to increase and potential energy decreases.
  • Midfall: 50% kinetic and 50% potential energy.
  • Just before impact: nearly 100% kinetic energy.
• Other examples: water behind a dam, a person about to skydive.
• Potential energy is associated with both location and structure.
  • Examples: compressed spring, stretched rubber band.

Chemical Energy

• Living cells rely heavily on structural potential energy.
• Chemical bonds holding molecules together have potential energy.
• Metabolic pathways:
  • Anabolic pathways: synthesize complex molecules from simple ones; require energy.
  • Catabolic pathways: break down complex molecules; release energy.
• Food molecules store potential energy in their bonds.
• This energy originates from photosynthesis, converting sunlight into chemical energy in carbohydrates.
• Chemical energy is the potential energy within chemical bonds.

Gibbs Free Energy

• Gibbs free energy (G) quantifies energy transfers in chemical reactions.
• It represents the usable energy available after accounting for entropy (energy lost as heat, according to the second law of thermodynamics).
• Every chemical reaction involves a change in free energy, denoted as delta G ($\Delta G$).

Endergonic Reactions and Exergonic Reactions

• If energy is released during a chemical reaction, \Delta G < 0. This indicates the products have less free energy than the reactants.
• Exergonic reactions (or spontaneous reactions) have a negative $\Delta G$ and release free energy.
• Exergonic reactions can be harnessed to perform work inside the cell.
• Spontaneous reactions don't necessarily occur immediately; rusting iron is a slow spontaneous reaction.
• Free energy diagrams illustrate energy profiles for reactions.
• If a chemical reaction requires energy input, $\Delta G$ is positive, and the products store more energy than the reactants.
• Endergonic reactions are non-spontaneous and require energy input to occur.
• Anabolic processes (building complex molecules) involve endergonic reactions, while catabolic processes (breaking down molecules) involve exergonic reactions.
• Cells couple endergonic reactions with exergonic reactions to provide the required energy; ATP hydrolysis is a common exergonic reaction used for this purpose.

Activation Energy

• Even exergonic reactions require an initial energy input called activation energy ($E_a$).
• During chemical reactions, bonds break and new ones form which requires molecules to be contorted into a transition state.
• The transition state is a high-energy, unstable state.
• Activation energy ($E_a$) is always positive, regardless of whether the reaction is exergonic or endergonic.
• The activation energy determines the reaction rate; higher activation energy means a slower reaction.
• Burning fuels requires sufficient heat to overcome activation energy.

Enzymes Catalyze Reactions

• Enzymes lower the activation energy for cellular reactions; this process is called catalysis.
• Enzymes bind to reactant molecules, stabilizing them and making it easier to reach the transition state.
• Enzymes speed up reactions by lowering activation energy but do not affect the energy levels of reactants or products and, subsequently, do not change whether a reaction is exergonic or endergonic.

Enzyme Active Site and Substrate Specificity

• Substrates are the chemical reactants that bind to an enzyme.
• The active site is the location within the enzyme where the substrate binds.
• The active site contains a unique combination of amino acid side chains that create a specific chemical environment, characterized by size, charge, polarity, or acidity/basicity.
• Enzymes are known for their specificity due to the precise match between the active site and the substrate.
• The induced fit model describes a dynamic interaction between enzyme and substrate, where the enzyme's structure shifts to confirm an ideal binding arrangement.
• When an enzyme binds its substrate, it forms an enzyme-substrate complex, which lowers the reaction's activation energy.
• Enzymes promote reactions by bringing substrates together in an optimal orientation or creating an optimal environment within the active site.
• After catalyzing a reaction, the enzyme releases its product(s).

Energy stored in usable form as ATP in Living Systems

• Cells store usable potential energy in the form of Adenosine Triphosphate (ATP).
• ATP is the "energy currency" of the cell and can be used to fill any energy need of the cell.
• ATP consists of three phosphate groups attached to an adenosine molecule.
• Adenosine monophosphate (AMP) is at the heart of ATP, consisting of an adenine base, a ribose molecule, and a single phosphate group.
• Phosphate groups are negatively charged and repel each other, giving ATP a high amount of potential energy.
• A large amount of energy is released when ATP is dephosphorylated (removal of the terminal phosphate group).
• The released phosphate often binds to another molecule, increasing its potential energy.
• When the terminal phosphate is removed, ATP becomes Adenosine Diphosphate (ADP).
• ADP can be "recharged" by adding a third phosphate group in a process called phosphorylation.
• Kinases are enzymes that catalyze phosphorylation reactions.
• ATP hydrolysis (using water to break apart) produces ADP, an inorganic phosphate ion ($P_i$), and free energy.
• ADP is continuously regenerated into ATP by reattaching a third phosphate group.

Light-Independent Reactions (Calvin Cycle)

• Light-dependent reactions convert solar energy into chemical energy, temporarily stored in ATP and NADPH.
• Light-independent reactions use ATP and NADPH to build carbohydrate molecules for long-term energy storage.
• Carbon dioxide ($CO_2$) from the atmosphere provides the carbon atoms for these carbohydrates, entering the leaves through stomata.
• In mesophyll cells, $CO_2$ diffuses into the stroma of chloroplasts, where the Calvin cycle takes place.
• The Calvin cycle's reactions can be organized into three basic stages: fixation, reduction, and regeneration.

Calvin Cycle Phase 1: Carbon Fixation

• In the stroma, two components are present to initiate the light-independent reactions: RuBisCO and ribulose bisphosphate (RuBP).
• RuBisCO catalyzes a reaction between $CO_2$ and RuBP to form two molecules of 3-phosphoglycerate (3-PGA).
• This process is called carbon fixation, where $CO_2$ is converted from a gaseous, inorganic form into organic molecules.
• Carbon progresses from its most oxidized state as $CO_2$ to a more reduced, higher energy state in 3-PGA.