Themes of Biology

What Defines a Living Organism?

Biology is the study of living organisms, which are defined by a set of shared characteristics and processes.

• Characteristics of Life: Living organisms exhibit organization, metabolism, homeostasis, growth, reproduction, response to stimuli, and adaptation through evolution.

• Extremophiles: Organisms that thrive in extreme environments (e.g., high temperature, salinity, or acidity).

Example: Thermus aquaticus is an extremophile bacterium found in hot springs.

Basic Organizing Principles of Living Things

• Types of Cells: Prokaryotic (no nucleus, e.g., bacteria) and Eukaryotic (nucleus present, e.g., plants, animals).

• Biological Classification: Organisms are organized into hierarchical categories: Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species (DKPCOFGS).

• Cell Theory: All living things are composed of cells; cells are the basic unit of life; all cells arise from pre-existing cells.

Emergent Properties vs. Reductionism

Emergent properties arise when individual components interact to produce new functions, while reductionism breaks down complex systems into simpler parts for study.

• Emergent Properties: The whole is greater than the sum of its parts (e.g., consciousness in the brain).

• Reductionism: Understanding biological systems by studying their components.

Basics of Evolution & Deductive Reasoning

• Evolution: Change in the genetic composition of populations over time; individuals do not evolve, populations do.

• Deductive Reasoning: Using general principles to predict specific outcomes.

How Science Works

• Observation: Gathering data through the senses or instruments.

• Hypothesis: A testable explanation for an observation.

• Prediction: A logical statement about what will happen if the hypothesis is correct.

• Variables: Independent (manipulated), dependent (measured), and controlled (kept constant).

• Theories vs. Laws: Theories explain phenomena; laws describe patterns in nature.

Chemistry Basics

Atoms, Subatomic Particles, and the Periodic Table

All matter is composed of atoms, which consist of subatomic particles and are organized in the periodic table.

• Subatomic Particles: Protons (positive, in nucleus), neutrons (neutral, in nucleus), electrons (negative, orbit nucleus).

• Groups vs. Periods: Groups are columns (similar properties); periods are rows (increasing atomic number).

Common Biological Elements

• Major Elements: Carbon, hydrogen, oxygen, nitrogen, phosphorus, sulfur (CHONPS).

• Valence Electrons: Electrons in the outer shell determine bonding behavior.

Bonding and Electronegativity

• Electronegativity: Tendency of an atom to attract electrons (e.g., O > N > C ≈ H).

• Ionization: Process of gaining or losing electrons to form ions.

• Types of Bonds: Ionic (transfer of electrons), covalent (sharing electrons), hydrogen bonds (attraction between polar molecules).

Example: NaCl forms via ionic bonding; H2O forms via polar covalent bonds and hydrogen bonding.

Hydrogen Bonding

• Definition: Weak attraction between a hydrogen atom covalently bonded to an electronegative atom (like O or N) and another electronegative atom.

• Importance: Stabilizes DNA, proteins, and gives water its unique properties.

Thermodynamics

Metabolism and Chemical Reactions

Metabolism encompasses all chemical reactions in living organisms, divided into anabolic (building) and catabolic (breaking down) pathways.

• Reactants and Products: Substances consumed and formed in a reaction.

• Anabolic Reactions: Build complex molecules; require energy.

• Catabolic Reactions: Break down molecules; release energy.

Laws of Thermodynamics

• First Law: Energy cannot be created or destroyed, only transformed.

• Second Law: Entropy (disorder) increases in spontaneous processes.

• Types of Energy: Kinetic, potential, chemical.

Spontaneity and Gibbs Free Energy

• Gibbs Free Energy Equation:

• Spontaneous Reactions: Occur without input of energy ().

• Equilibrium: Dynamic state where forward and reverse reactions occur at the same rate.

Water & Life

Emergent Properties of Water

Water's unique properties are essential for life and arise from its molecular structure and hydrogen bonding.

• Solvent: Dissolves many substances due to polarity.

• Cohesion & Adhesion: Water molecules stick to each other and to other surfaces.

• High Heat Capacity: Absorbs heat with little temperature change.

• Density: Ice is less dense than liquid water.

Solutions, Diffusion, and Osmosis

• Polarity: Water interacts with polar and ionic substances.

• Diffusion: Movement of molecules from high to low concentration.

• Osmosis: Diffusion of water across a selectively permeable membrane.

• Tonicity: Relative concentration of solutes affects water movement.

pH and Buffers

• pH Scale: Measures hydrogen ion concentration;

• Buffers: Substances that minimize changes in pH.

Example: Blood contains bicarbonate buffer to maintain pH.

Organic Chemistry

Carbon and Its Bonding Capabilities

Carbon's ability to form four covalent bonds makes it the backbone of organic molecules.

• Hydrocarbons: Molecules consisting only of carbon and hydrogen.

• Bond Types: Single, double, triple bonds affect molecule shape and reactivity.

• Carbon Skeletons: Can be straight, branched, or ring-shaped.

Isomers

• Structural Isomers: Differ in covalent arrangement.

• Cis-Trans Isomers: Differ in spatial arrangement around double bonds.

• Enantiomers: Mirror-image isomers; important in pharmaceuticals.

Functional Groups

• Definition: Groups of atoms that confer specific properties to molecules (e.g., hydroxyl, carboxyl, amino, phosphate).

• Example: Estradiol and testosterone differ only in functional groups, leading to different biological effects.

Polymer Basics

Polymers and Monomers

Polymers are large molecules made by joining many smaller units (monomers).

• Variability: Sequence and type of monomers determine polymer properties.

Synthesis and Degradation

• Dehydration (Condensation) Reaction: Joins monomers by removing water.

• Hydrolysis: Breaks polymers by adding water.

• Anabolic vs. Catabolic: Anabolic builds polymers; catabolic breaks them down.

The 4 Biomolecules

Overview and Comparison

Four major classes of biomolecules are essential for life: carbohydrates, lipids, proteins, and nucleic acids.

• Carbohydrates: Monomer: monosaccharide; Polymer: polysaccharide. Function: energy storage, structure.

• Lipids: Not true polymers; include fats, phospholipids, steroids. Function: energy storage, membranes, signaling.

• Proteins: Monomer: amino acid; Polymer: polypeptide. Function: enzymes, structure, transport.

• Nucleic Acids: Monomer: nucleotide; Polymer: DNA/RNA. Function: information storage, transmission.

Comparison Examples:

• Alpha vs. Beta Bonds: Alpha (digestible, e.g., starch); Beta (indigestible, e.g., cellulose).

• RNA vs. DNA: RNA has ribose sugar and uracil; DNA has deoxyribose and thymine.

• Lipid Types: Fats (energy), phospholipids (membranes), steroids (hormones).

Enzymes

Structure and Function

Enzymes are biological catalysts, mostly proteins, that speed up chemical reactions without being consumed.

• Substrate: The molecule upon which an enzyme acts.

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

• Products: Molecules produced by the reaction.

Mechanism and Specificity

• Lock & Key Model: Substrate fits exactly into the active site.

• Induced Fit Model: Active site changes shape to fit substrate.

• Transition State: Enzyme stabilizes the transition state, lowering activation energy ().

• Effect on Reactions: Enzymes lower activation energy, increasing reaction rate.

Factors Affecting Enzyme Activity

• Temperature, pH, Substrate Concentration: Each enzyme has optimal conditions; extremes can denature the enzyme.

• Inhibition & Activation: Allosteric interactions can inhibit or activate enzyme function.

Example: Digestive enzymes like amylase break down starch into sugars.