Energetics & Metabolism

Introduction to Metabolism

Cells are dynamic chemical factories where thousands of reactions occur every second. Metabolism refers to the totality of an organism's chemical reactions, and bioenergetics is the study of how organisms manage their energy resources.

• Metabolic pathways begin with a specific molecule and end with a product, with each step catalyzed by a specific enzyme.

• Pathways can be catabolic (breaking down molecules, releasing energy) or anabolic (building molecules, consuming energy).

• Example: Cellular respiration is a catabolic pathway; protein synthesis from amino acids is anabolic.

Forms of Energy

Energy is the capacity to cause change and exists in various forms:

• Kinetic energy: Energy of motion.

• Heat (thermal energy): Energy associated with random movement of atoms or molecules.

• Potential energy: Energy due to position or structure.

• Chemical energy: Potential energy available for release in a chemical reaction.

Thermodynamics in Biology

Basic Laws of Thermodynamics

Thermodynamics is the study of energy transformations. Biological systems are open systems, exchanging energy and matter with their surroundings.

• First Law of Thermodynamics: Energy can be transferred and transformed, but cannot be created or destroyed (principle of conservation of energy).

• Second Law of Thermodynamics: Every energy transfer increases the entropy (disorder) of the universe; some energy is lost as heat.

Order, Disorder, and Equilibrium

Organisms create ordered structures from less ordered materials, but the universe's total entropy increases. Free energy is an indicator of a system's instability and tendency to change to a more stable state.

• Spontaneous processes occur without energy input and increase stability.

• Equilibrium is a state of maximum stability; living systems are never at equilibrium.

Free Energy and Metabolic Reactions

Exergonic and Endergonic Reactions

The concept of free energy applies to biological processes:

• Exergonic reactions: Proceed with a net release of free energy; spontaneous.

• Endergonic reactions: Absorb free energy from surroundings; nonspontaneous.

Equations:

• for exergonic reactions (energy released)

• for endergonic reactions (energy required)

Energy Coupling and ATP

Cells manage energy resources by energy coupling, using exergonic processes to drive endergonic ones. ATP (Adenosine Triphosphate) is the main energy shuttle in cells.

• ATP is composed of ribose, adenine, and three phosphate groups.

• Energy is released when the terminal phosphate bond is broken.

• ATP hydrolysis:

Enzymes and Catalysis

Enzyme Function

Enzymes are catalytic proteins that speed up chemical reactions without being consumed.

• Each enzyme acts on a specific substrate, forming an enzyme-substrate complex.

• The active site is where the substrate binds; induced fit enhances catalysis.

• Enzymes lower the activation energy () barrier, but do not affect the overall change in free energy ().

Enzyme Specificity and Regulation

• Enzyme activity can be affected by temperature and pH; each enzyme has optimal conditions.

• Competitive inhibitors bind to the active site, competing with the substrate.

• Noncompetitive (allosteric) inhibitors bind elsewhere, changing enzyme shape and reducing activity.

• Allosteric regulation and cooperativity can amplify or inhibit enzyme activity.

• Feedback inhibition: End product of a pathway inhibits an earlier step.

Enzyme Cofactors

• Cofactors are non-protein helpers; may be inorganic (e.g., metal ions) or organic (coenzymes).

• Many vitamins function as coenzymes.

Redox Reactions and Cellular Respiration

Reduction and Oxidation

Transfer of electrons during chemical reactions releases energy stored in organic molecules, used to synthesize ATP.

• Oxidation: Substance loses electrons.

• Reduction: Substance gains electrons.

• Electron donor is the reducing agent; electron acceptor is the oxidizing agent.

• Redox reactions often involve transfer of hydrogen atoms.

Overview of Cellular Respiration

Cellular respiration includes both aerobic and anaerobic processes, breaking down organic fuels to produce ATP.

• Glycolysis: Breaks down glucose into two pyruvate molecules; occurs in cytosol.

• Krebs Cycle (Citric Acid Cycle): Completes glucose breakdown; produces ATP, NADH, FADH2.

• Oxidative Phosphorylation: Electron transport and chemiosmosis; accounts for most ATP synthesis.

Glycolysis

• Net reaction:

Krebs Cycle

• Pyruvate converted to acetyl CoA; cycle produces ATP, NADH, FADH2.

Oxidative Phosphorylation & Chemiosmosis

• Electron transport chain (ETC) creates a proton gradient; ATP synthase uses this gradient to produce ATP.

• Final electron acceptor is O2.

• Equation:

Fermentation and Anaerobic Respiration

• Occurs in O2-poor environments; uses other electron acceptors.

• Alcohol fermentation: Pyruvate converted to ethanol.

• Lactic acid fermentation: Pyruvate converted to lactate.

Photosynthesis

Introduction to Photosynthesis

Photosynthesis nourishes almost all living organisms, directly or indirectly. Autotrophs sustain themselves without eating other organisms.

• Photosynthesis uses electromagnetic energy (light) to convert CO2 and H2O into sugars.

• Visible light: Wavelengths from ~380 nm to 750 nm.

Pigments and Light Absorption

• Pigments absorb specific wavelengths of light; perceived color is reflected light.

• Chlorophyll a: Main green pigment.

• Chlorophyll b: Yellow-green pigment.

• Accessory pigments: Carotenoids (yellow/orange), anthophylls & anthocyanins (red).

Chloroplast Structure

• Found in mesophyll cells of leaves.

• Double outer membrane; internal thylakoid membranes form stacks called grana.

• Space between thylakoid and inner membrane is the stroma.

Stages of Photosynthesis

• Light-dependent reactions: Occur in thylakoid membranes; produce ATP and NADPH, release O2.

• Light-independent reactions (Calvin cycle): Occur in stroma; fix carbon from CO2 to produce carbohydrates.

Photosystems and Electron Flow

• Photosystem II (P680): Absorbs light at 680 nm; splits water to replace lost electrons.

• Photosystem I (P700): Absorbs light at 700 nm; transfers electrons to NADP+ to form NADPH.

• Electron flow creates a proton gradient for ATP synthesis (photophosphorylation).

• Cyclic electron flow: Only involves Photosystem I; generates ATP but not NADPH or O2.

Calvin Cycle

• Carbon fixation: CO2 attached to RuBP by rubisco; forms 3-phosphoglycerate.

• Reduction: 3-phosphoglycerate phosphorylated and reduced to G3P using ATP and NADPH.

• Regeneration: Remaining G3P molecules rearranged to regenerate RuBP.

Alternate Carbon Fixation Pathways

• Photorespiration: Occurs when rubisco adds O2 instead of CO2; consumes ATP and releases CO2 without producing sugar.

• CAM plants: Open stomata at night; fix CO2 into acids for later use.

• C4 plants: Use a high-affinity enzyme to fix CO2 into 4-carbon compounds; spatial separation of steps.

Table: Comparison of Metabolic Pathways

Additional info: Some details, such as the specific steps of the Calvin cycle and the structure of ATP and NAD+/NADP+, were expanded for clarity and completeness.