Metabolism, Energy, and Life

Metabolism Overview

Metabolism encompasses all chemical reactions occurring within a cell or organism. These reactions are organized into pathways that either break down or build up molecules, facilitating energy flow and matter transformation.

• 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 different forms and is governed by the laws of thermodynamics. Organisms are open systems, exchanging energy and matter with their environment.

• Kinetic energy: Energy of motion.

• Potential energy: Stored energy based on position or structure (e.g., chemical bonds).

• Open system: Exchanges energy and matter with surroundings.

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

• Second law of thermodynamics: Every energy transfer increases the entropy (disorder) of the universe; some energy becomes less available, often as heat.

Free Energy and Reaction Types

Free energy change determines whether a reaction is spontaneous. Entropy and enthalpy are key components in this calculation.

• 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 three main types of work, powered by ATP hydrolysis. ATP is a nucleotide that stores and transfers energy.

• 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

• ATP hydrolysis: Removes terminal phosphate, forming ADP + Pi and releasing energy

Enzymes: Catalytic Proteins

Enzyme Function and Specificity

Enzymes are biological catalysts that speed up reactions by lowering activation energy. Their specificity is determined by the structure of their active site.

• Enzyme: Biological catalyst; not consumed in the reaction

• Activation energy: Initial energy required to start a reaction

• Active site: Region of enzyme where substrate binds

• Induced-fit model: Active site changes shape to fit substrate more closely upon binding

Mechanisms and Regulation of Enzyme Activity

Enzymes lower activation energy through various mechanisms and are regulated by multiple factors.

• Mechanisms: Orient substrates, strain bonds, create favorable environments, form temporary bonds

• Substrate concentration: Increases reaction rate until saturation

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

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

Cellular Respiration

Redox Reactions and Electron Carriers

Cellular respiration involves redox reactions, transferring electrons and energy. NAD+ is a key electron carrier.

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

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

• NAD+: Accepts electrons and hydrogen, becoming NADH

Stages of Cellular Respiration

Cellular respiration occurs in three main stages, each in specific cellular locations.

• Glycolysis: Cytosol; glucose (6C) split into two pyruvate (3C)

• Pyruvate oxidation: Mitochondrial matrix; pyruvate → acetyl-CoA + CO2 + NADH

• Citric acid cycle: Mitochondrial matrix; acetyl-CoA → CO2 + NADH + FADH2 + ATP

• Oxidative phosphorylation: Inner mitochondrial membrane; ETC and ATP synthase

ATP Production and Electron Transport Chain

ATP is produced by substrate-level and oxidative phosphorylation. The ETC creates a proton gradient used by ATP synthase.

• Substrate-level phosphorylation: Direct transfer of phosphate to ADP

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

• ETC: Electrons from NADH/FADH2 pass through membrane proteins, pumping H+ into intermembrane space

• ATP synthase structure: F0 (membrane channel/rotor), F1 (catalytic head), central stalk

ATP Yield Table

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

Photosynthesis: The Process That Feeds the Biosphere

Autotrophic vs. Heterotrophic Nutrition

Organisms obtain energy and carbon through different nutritional strategies.

• 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 the site of photosynthesis, containing specialized membranes and compartments.

• Outer and inner envelope membranes: Surround the chloroplast

• Stroma: Fluid where 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

Photosynthesis Pathways

Photosynthesis Equation and Redox

Photosynthesis converts light energy into chemical energy, producing sugars and oxygen.

• Equation:

• Water is oxidized: Releases electrons and O2

• CO2 is reduced: Incorporated into sugars using electrons from NADPH

Stages of Photosynthesis

Photosynthesis consists of light reactions and the Calvin cycle, each occurring in distinct chloroplast regions.

• Light reactions: Thylakoid membrane; produce ATP, NADPH, O2

• Calvin cycle: Stroma; uses ATP and NADPH to fix CO2 into G3P (carbohydrate)

Pigments and Light Absorption

Photosynthetic pigments absorb light at specific wavelengths, driving photosynthesis and protecting cells.

• Action spectrum: Measures effectiveness of wavelengths for photosynthesis

• Absorption spectrum: Measures pigment light absorption

• Accessory pigments: Chlorophyll b, carotenoids broaden action spectrum

• Carotenoids: Absorb excess light, dissipate energy, reduce reactive oxygen species

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

Photosystems and Electron Flow

Photosystems are complexes that capture light and transfer electrons through linear or cyclic pathways.

• Photosystem components: Light-harvesting antenna, 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

Calvin Cycle Phases

The Calvin cycle fixes carbon and produces carbohydrates, using ATP and NADPH.

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

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

• Regeneration: ATP helps regenerate RuBP from G3P

• ATP: Provides energy and phosphate

• NADPH: Provides reducing power (electrons)

Photorespiration and Adaptations

Photorespiration occurs when rubisco binds O2 instead of CO2, reducing photosynthetic efficiency. Plants have adaptations to minimize this process.

• Photorespiration: Rubisco binds O2, uses energy, releases CO2, reduces sugar production

• C4 plants: Spatial separation; initial CO2 fixation in mesophyll, Calvin cycle in bundle-sheath cells

• 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 purposes.

• Glucose and other sugars: Energy storage and transport

• Starch: Storage in plants

• Sucrose: Transported in phloem

• Cellulose: Structural component

• Cellular respiration: G3P can enter glycolysis

Quick Reminders

• ATP: Immediate energy-transfer molecule

• NADH and FADH2: Electron carriers for respiration

• NADPH: Electron carrier for Calvin cycle

• Cellular respiration: Releases energy from sugar

• Photosynthesis: Stores light energy in carbohydrates