Chapter 8 — Metabolism, Energy, and Life

Metabolism: Overview and Pathways

Metabolism encompasses all chemical reactions within a cell or organism, enabling life by managing energy and molecular transformations.

• Metabolism: The sum of all chemical reactions in a cell or organism.

• Catabolic pathways: Break down complex molecules into simpler ones, releasing energy (e.g., hydrolysis).

• Anabolic pathways: Build complex molecules from simpler ones, requiring energy input (e.g., dehydration synthesis).

• Hydrolysis: Adds water to break bonds; typically catabolic.

• Dehydration synthesis: Removes water to form bonds; typically anabolic.

Energy Types and Thermodynamics

Energy exists in various forms and is governed by fundamental laws of thermodynamics, which dictate biological processes.

• Kinetic energy: Energy of motion (e.g., movement of molecules).

• Potential energy: Stored energy due to position or structure (e.g., energy in chemical bonds).

• Open system: Organisms exchange energy and matter with their environment.

• First law of thermodynamics: Energy cannot be created or destroyed, only transformed.

• Second law of thermodynamics: Every energy transfer increases the entropy (disorder) of the universe.

Free Energy and Reaction Types

Free energy change determines whether a reaction is spontaneous and how energy is utilized or released.

• Free-energy equation:

• ΔG: Change in free energy

• ΔH: Change in enthalpy (total heat energy)

• T: Absolute temperature (Kelvin)

• ΔS: Change in entropy (disorder)

• Exergonic reactions: Release free energy;

• Endergonic reactions: Require energy input;

Cellular Work and ATP

Cells perform work by coupling energy-releasing reactions to energy-requiring processes, primarily using ATP.

• Three types of cellular work:

  • Chemical work: Building molecules

  • Transport work: Moving substances across membranes

  • Mechanical work: Movement (e.g., muscle contraction)

• ATP (adenosine triphosphate): A nucleotide composed of adenine, ribose, and three phosphate groups; serves as the cell's energy currency.

• ATP hydrolysis: Removes the terminal phosphate, forming ADP + Pi and releasing energy for cellular work.

Chapter 8 — Enzymes Are Catalytic Proteins

Enzyme Function and Specificity

Enzymes are biological catalysts that accelerate reactions by lowering activation energy, with specificity determined by their structure.

• Enzymes: Proteins that catalyze biological reactions without being consumed.

• Activation energy: The initial energy required to start a reaction.

• Active site: Region of the enzyme where substrate binds; determines specificity.

• Induced-fit model: Enzyme active site changes shape to fit substrate upon binding.

Mechanisms and Regulation of Enzyme Activity

Enzymes facilitate reactions through various mechanisms and are regulated to maintain cellular homeostasis.

• Mechanisms to lower activation energy:

  • Orienting substrates

  • Straining substrate bonds

  • Providing a favorable microenvironment

  • Forming temporary bonds with substrate

• Substrate concentration: Increases reaction rate until enzyme saturation.

• Factors affecting activity: Temperature, pH, substrate/enzyme concentration, salt, cofactors.

• Regulation: Competitive/noncompetitive inhibitors, allosteric regulation, feedback inhibition, covalent modification.

Chapter 9 — Cellular Respiration

Redox Reactions and Electron Carriers

Cellular respiration involves redox reactions, transferring electrons and energy to produce ATP.

• Oxidation: Loss of electrons (OIL: Oxidation Is Loss)

• Reduction: Gain of electrons (RIG: Reduction Is Gain)

• NAD+: Electron carrier; reduced to NADH during glycolysis, pyruvate oxidation, and citric acid cycle.

Stages of Cellular Respiration

Cellular respiration occurs in three main stages, each with distinct locations and products.

• Glycolysis: Occurs in cytosol; glucose (6C) split into two pyruvate (3C); produces ATP and NADH.

• Pyruvate oxidation: Occurs in mitochondrial matrix; pyruvate converted to acetyl-CoA, CO2 released, NADH produced.

• Citric acid cycle: Occurs in mitochondrial matrix; acetyl-CoA oxidized to CO2; produces NADH, FADH2, ATP.

• Oxidative phosphorylation: Occurs in inner mitochondrial membrane; ETC creates H+ gradient, ATP synthase produces ATP.

ATP Production and Electron Transport Chain

ATP is generated by substrate-level and oxidative phosphorylation, with the ETC playing a central role.

• Substrate-level phosphorylation: Direct transfer of phosphate to ADP during glycolysis and citric acid cycle.

• Oxidative phosphorylation: Uses H+ gradient from ETC to drive ATP synthase.

• ETC: Electrons from NADH/FADH2 pass through membrane proteins, pumping H+ to create a gradient.

• ATP synthase structure:

  • F0: Membrane channel/rotor

  • F1: Catalytic head in matrix

  • Central stalk

  • Membrane channel

ATP Yield Table

Additional info: Exact ATP yield varies due to transport costs, proton leak, and efficiency differences.

Chapter 10 — The Process That Feeds the Biosphere

Autotrophic vs. Heterotrophic Nutrition

Organisms obtain energy and carbon through different nutritional strategies, impacting their ecological roles.

• Autotrophs: Produce organic molecules from inorganic sources (e.g., CO2).

• Heterotrophs: Obtain organic molecules by consuming other organisms.

• Photoautotrophs: Use light energy (e.g., plants, algae, cyanobacteria).

• Chemoautotrophs: Use energy from inorganic chemical reactions (e.g., nitrifying bacteria).

Chloroplast Structure and Function

Chloroplasts are specialized organelles for photosynthesis, with distinct compartments for different reactions.

• Outer and inner envelope membranes: Surround the chloroplast.

• Stroma: Fluid where the Calvin cycle occurs.

• Thylakoids: Flattened membrane sacs containing chlorophyll, photosystems, ETC, and ATP synthase.

• Grana: Stacks of thylakoids.

• Thylakoid lumen: Stores H+ during light reactions.

Chapter 10 — The Pathways of Photosynthesis

Photosynthesis Equation and Redox Roles

Photosynthesis transforms light energy into chemical energy, involving redox reactions and distinct stages.

• Photosynthesis equation:

• Water: Oxidized, releasing electrons and O2.

• CO2: Reduced, incorporated into sugars via NADPH.

Stages and Components of Photosynthesis

Photosynthesis consists of light reactions and the Calvin cycle, each with specific locations and functions.

• Light reactions: Occur in thylakoid membrane; produce ATP, NADPH, O2.

• Calvin cycle: Occurs in stroma; uses ATP and NADPH to fix CO2 into G3P (carbohydrate).

Pigments and Light Absorption

Photosynthetic pigments absorb light, with accessory pigments broadening the action spectrum and protecting cells.

• Action spectrum: Measures effectiveness of wavelengths for photosynthesis.

• Absorption spectrum: Measures light absorbed by chlorophyll a.

• Accessory pigments: Chlorophyll b, carotenoids absorb additional wavelengths.

• Carotenoids: Protect cells by dissipating excess light energy.

• Effective wavelengths: Blue-violet and red; green is least effective.

Photosystems and Electron Flow

Photosystems organize pigments and proteins to capture light and transfer electrons, driving ATP and NADPH production.

• Photosystem components:

  • Light-harvesting antenna pigments

  • Reaction center (special chlorophyll a)

  • Primary electron acceptor

• Linear electron flow: H2O → Photosystem II → ETC → Photosystem I → NADP+ (forms NADPH); produces ATP and O2.

• Cyclic electron flow: Electrons cycle through Photosystem I and ETC; produces extra ATP, no NADPH or O2.

Photosynthetic Electron Flow Table

Calvin Cycle Phases and Regulation

The Calvin cycle fixes carbon and regenerates its starting molecule, with ATP and NADPH providing energy and reducing power.

• Carbon fixation: Rubisco attaches CO2 to RuBP, forming 3-PGA.

• Reduction: ATP and NADPH convert 3-PGA to G3P.

• Regeneration: ATP rearranges G3P to regenerate RuBP.

• ATP: Supplies energy and phosphate.

• NADPH: Supplies high-energy electrons.

Photorespiration and Adaptations

Photorespiration reduces photosynthetic efficiency, but C4 and CAM plants have evolved mechanisms to minimize its effects.

• Photorespiration: Rubisco binds O2, leading to energy loss and CO2 release.

• C4 plants: Spatial separation of CO2 fixation and Calvin cycle.

• CAM plants: Temporal separation; CO2 uptake at night, Calvin cycle during day.

Fates of Photosynthetic Products

G3P produced by the Calvin cycle can be used for various biosynthetic and metabolic pathways.

• Converted to glucose and other sugars

• Stored as starch

• Transported as sucrose

• Used to build cellulose and other organic molecules

• Can enter cellular respiration

Quick Reminders

• ATP: Immediate energy-transfer molecule in cells.

• NADH and FADH2: Carry electrons to respiratory ETC.

• NADPH: Supplies electrons for Calvin cycle.

• Cellular respiration: Releases energy from sugar.

• Photosynthesis: Stores light energy in carbohydrates.

Additional info: Enzyme names are not required for exam; focus on inputs and products of each stage.