Energy in Biological Systems

Definitions and Types of Energy

Energy is the capacity to do work, move, or elicit change in biological systems. It exists in various forms and is fundamental to all cellular processes.

• Enthalpy (H): Internal system energy.

• Potential Energy: Stored energy due to location or chemical structure (e.g., chemical bonds, gradients).

• Kinetic Energy: Energy of motion (e.g., heat, molecular movement).

• Thermal Energy: A type of kinetic energy responsible for temperature; heat is a flow of thermal energy.

Thermodynamics in Biology

Thermodynamics describes how energy is transferred and transformed in biological systems.

• First Law of Thermodynamics: Energy cannot be created or destroyed, only converted from one form to another.

• Second Law of Thermodynamics: Energy will always become more spread out and increase in disorder (entropy) in spontaneous processes.

• Entropy (S): Measure of disorder/randomness; increases in spontaneous processes.

Free Energy and Spontaneity

Free energy determines whether a reaction can occur spontaneously.

• Gibbs Free Energy (G): Portion of a system's energy available to do work.

• Change in Free Energy (ΔG): Determines if a reaction is spontaneous.

• Exergonic Reaction: Releases energy, occurs spontaneously.

• Endergonic Reaction: Requires energy input, non-spontaneous.

Enzymes and Metabolism

Role and Mechanism of Enzymes

Enzymes are biological catalysts that lower activation energy and speed up chemical reactions without being consumed.

• Activation Energy (Ea): Minimum energy required to start a reaction (reach transition state).

• Substrate: Reactant molecule that binds to an enzyme's active site.

• Active Site: Region on enzyme where substrate binds and reaction occurs.

• Induced Fit: Enzyme changes shape slightly to better fit substrate.

Mechanisms of Enzyme Action

• Binds to substrates at active site.

• Promotes substrate reaching transition state.

• Releases products as products have less affinity for active site.

Factors Affecting Enzyme Activity

• Temperature: Too high = denaturation; too low = slowed activity.

• pH: Extreme pH alters enzyme structure and function.

• Concentration of Substrate/Enzyme: More substrate = faster reaction until saturation; more enzyme = higher rate.

• Presence of Cofactors/Coenzymes: Required for proper activity.

• Inhibitors/Regulators: Competitive, non-competitive, allosteric regulation.

Enzyme Regulation

• Competitive Inhibition: Substrate and inhibitor compete for active site; can be overcome by more substrate.

• Non-Competitive Inhibition: Inhibitor binds allosterically; lowers activity regardless of substrate amount.

• Feedback Inhibition: End product shuts down pathway at an early step (prevents waste, regulates balance).

• Protein Modifications: Phosphorylation or cleavage can activate/deactivate enzymes.

ATP & Metabolism

ATP Structure and Function

ATP (adenosine triphosphate) is the universal energy currency in cells, coupling exergonic and endergonic reactions.

• Structure of ATP: Adenine + ribose + 3 phosphate groups.

• ATP Hydrolysis:

• Exergonic: Used to power cellular processes.

Anabolism and Catabolism

• Anabolism (Anabolic Pathways): Build complex molecules; require energy (endergonic).

• Catabolism (Catabolic Pathways): Break down molecules; release energy (exergonic).

Molecules of Life & Cell Parts

Cell Theory and Evolution

All life is composed of one or more cells, and cells are the basic unit of life. Evolution is a change in characteristics of a population over time, often driven by natural selection.

• Phylogenetics: Explores relationships among different species.

Macromolecules

Cells are built from four major types of macromolecules:

• Nonpolar covalent bonds: Atoms have no charge (e.g., hydrogen & methane).

• Polar covalent bonds: Atoms have partial charge (e.g., ammonia & water).

• Ionic bonds: Atoms have full charge (e.g., sodium chloride).

Protein Structure

• Primary structure: Sequence of amino acids.

• Secondary structure: Alpha helices, beta sheets.

• Tertiary structure: 3D folding, hydrophobic interactions, hydrogen bonds, ionic bonds, disulfide bonds.

• Quaternary structure: Arrangement of multiple polypeptide chains (subunits) into one functional protein (e.g., hemoglobin).

Cell Structure and Function

Domains of Life

• Bacteria: Prokaryotes (no membrane-bound nucleus).

• Archaea: Prokaryotes (no membrane-bound nucleus, unique membrane and metabolism).

• Eukarya: Eukaryotes (membrane-bound nucleus).

Energy Sources for Cells

Structural Features of Eukaryotic Cells

• Compartmentalization: Making efficient use of limited space; large area of internal membranes (endomembrane system) facilitates manufacturing and transport.

• Organelles: Specialized structures with specific functions (e.g., Golgi apparatus, lysosomes).

• Energy Generation: Mitochondria (power generation), chloroplasts (sugar manufacturing in plants and algae).

Cell Surface Structures

• Flagella: Used for motility (movement), made from rigid helical proteins.

• Fimbriae & Pili: Shorter than flagella, different proteins, made for attachment.

• Capsule: Polysaccharide layer for protection and attachment.

Cell Size and Volume

• Surface area to volume ratio is important for exchange of nutrients and waste.

• Smaller cells have higher surface area to volume ratio, allowing more efficient exchange.

Internal Cell Structures

• Nucleus: Contains DNA, controls cell activities.

• Chromatin: Eukaryotic DNA complexed with proteins.

• Nuclear Envelope: Double membrane, controls transport of molecules through nuclear pores.

• Smooth ER: Synthesizes lipids, detoxifies, stores calcium, makes steroid sex hormones.

• Rough ER: Studded with ribosomes, synthesizes proteins for export.

• Lysosomes: Digestion and recycling, hydrolytic enzymes break down macromolecules.

• Vacuoles: Storage, digestion, recycling (large in plant cells).

Pathways to Lysosome

• Endocytosis: Cell grabs molecules from outside using receptors, forms vesicle, sends it to lysosome.

• Phagocytosis: Cell swallows big particles or smaller cells, makes a phagosome, fuses with lysosome to digest.

• Autophagy: Cell wraps up its damaged parts in a membrane, forms an autophagosome, fuses with lysosome to recycle.

Theory of Endosymbiosis

• Mitochondria evolved from ingested aerobic bacteria.

• Chloroplasts evolved from ingested cyanobacteria.

Summary Table: Key Terms and Definitions

Example: Hemoglobin is a protein with quaternary structure, composed of four subunits, and transports oxygen in blood.

Additional info: Some context and definitions have been expanded for clarity and completeness, including the summary tables and explanations of cell structure and enzyme regulation mechanisms.