General Biology: Core Themes and Foundations Study Guide

Themes of Biology

What Defines a Living Organism?

Biologists use specific criteria to distinguish living organisms from non-living matter. These criteria help us recognize and classify life forms.

• Key Characteristics: Organization, metabolism, growth, adaptation, response to stimuli, reproduction.

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

• Examples: Bacteria in hot springs, tardigrades in space.

Basic Organizing Principles of Living Things

Living organisms are organized at multiple levels, from cells to ecosystems. Classification systems help group organisms by similarities.

• General Types of Cells: Prokaryotic (no nucleus) vs. Eukaryotic (nucleus present).

• Taxonomic Hierarchy: 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 systems into parts for study.

• Emergent Properties: Consciousness, metabolism.

• Reductionism: Studying DNA to understand genetics.

Basics of Evolution & Deductive Reasoning

Evolution explains the diversity of life through changes in populations over time. Deductive reasoning is used to form hypotheses and predictions.

• Evolution: Change in genetic composition of populations over generations.

• Individuals vs. Populations: Individuals do not evolve; populations do.

How Science Works

Scientific inquiry involves observation, hypothesis formation, experimentation, and theory development.

• Observation: Gathering data using senses or instruments.

• Hypothesis: Testable explanation for observations.

• Prediction: Expected outcome if hypothesis is correct.

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

• Theories vs. Laws: Theories explain phenomena; laws describe them.

Chemistry Basics

Atoms, Subatomic Particles, and the Periodic Table

Atoms are the fundamental units of matter, composed of subatomic particles. The periodic table organizes elements by properties.

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

• Groups vs. Periods: Groups are columns (similar properties); periods are rows (energy levels).

• Common Biological Elements: Carbon, hydrogen, oxygen, nitrogen, phosphorus, sulfur.

Valence Structure & Bonding

Valence electrons determine bonding behavior and molecular structure.

• Electronegativity: Tendency of an atom to attract electrons.

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

• Polarity: Unequal sharing of electrons creates partial charges.

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

• Examples: NaCl (ionic), H2O (polar covalent, hydrogen bonding).

Hydrogen Bonding

Hydrogen bonds are weak attractions between a hydrogen atom and an electronegative atom (e.g., oxygen, nitrogen).

• Importance: Stabilizes DNA, proteins, water properties.

• Labeling: In H2O, hydrogen bonds form between the hydrogen of one molecule and the oxygen of another.

Thermodynamics

Metabolism and Chemical Reactions

Metabolism encompasses all chemical reactions in living organisms, including anabolic (building) and catabolic (breaking down) processes.

• Bonds: Chemical reactions involve breaking and forming bonds.

• Products & Reactants: Reactants are substances that start a reaction; products are formed.

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

Laws of Thermodynamics

Energy transformations in biology obey the laws of thermodynamics.

• First Law: Energy cannot be created or destroyed.

• Second Law: Entropy (disorder) increases; energy transformations are not 100% efficient.

• Types of Energy: Kinetic, potential, chemical.

• Entropy: Measure of disorder; living systems maintain order by expending energy.

Spontaneity & Gibbs Free Energy

Spontaneous reactions occur without input of energy; Gibbs free energy determines spontaneity.

• Gibbs Equation:

$\Delta G = \Delta H - T\Delta S$

• Equilibrium: Dynamic (forward and reverse reactions occur), static (no change).

• Spontaneous Reaction: Occurs when $\Delta G < 0$.

Water & Life

Emergent Properties of Water

Water exhibits unique properties essential for life due to its molecular structure and hydrogen bonding.

• Solvent: Dissolves many substances.

• Adhesive & Cohesive: Sticks to other substances and itself.

• Density: Ice is less dense than liquid water.

• Heat Capacity: Absorbs heat without large temperature change.

Physical States and Solutions

Water exists as solid, liquid, and gas; its polarity affects solution formation and interactions.

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

• Osmosis: Diffusion of water across a membrane.

• Tonicity: Relative concentration of solutes affects water movement.

Hydrogen Bonding in Water

Hydrogen bonds give water its high cohesion, surface tension, and other properties.

• Thermal Energy: Molecular movement increases with temperature.

pH, Buffers, and Biological Importance

pH measures hydrogen ion concentration; buffers stabilize pH in biological systems.

• pH Scale: $pH = -\log[H^+]$

• Buffers: Substances that minimize pH changes.

• Examples: Blood buffer system (bicarbonate).

Organic Chemistry

Carbon and Organic Molecules

Carbon's versatility allows for diverse organic molecules essential for life.

• Hydrocarbons: Compounds of hydrogen and carbon.

• Bonding: Single, double, triple bonds; affects strength and reactivity.

• Carbon Skeletons: Straight, branched, or ring structures.

Isomers

Isomers are molecules with the same formula but different structures.

• Structural Isomers: Different connectivity.

• Cis-trans Isomers: Different spatial arrangement around double bonds.

• Enantiomers: Mirror-image isomers; chiral molecules.

Functional Groups

Functional groups confer specific chemical properties to organic molecules.

• Examples: Hydroxyl (-OH), carboxyl (-COOH), amino (-NH2), phosphate (-PO4).

• Role: Affect reactivity, solubility, and biological function.

Polymer Basics

Polymers vs. Monomers

Polymers are large molecules made from repeating monomer units. Their diversity underlies biological complexity.

• Examples: Proteins (amino acids), nucleic acids (nucleotides), polysaccharides (sugars).

• Variability: Sequence and type of monomers determine function.

Synthesis vs. Degradation

Biological polymers are synthesized and degraded by specific reactions.

• Anabolic: Building polymers (e.g., protein synthesis).

• Catabolic: Breaking down polymers (e.g., digestion).

• Condensation/Dehydration: Removes water to form bonds.

• Hydrolysis: Adds water to break bonds.

Polymerization Mechanisms

Polymerization varies among biomolecules, but all involve covalent bond formation.

• Bond Types: Peptide (proteins), glycosidic (carbohydrates), phosphodiester (nucleic acids), ester (lipids).

The 4 Biomolecules

Overview and Comparison

Biological macromolecules include carbohydrates, proteins, nucleic acids, and lipids. Each has distinct monomers, structures, and functions.

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

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

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

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

• Levels of Structure: Primary, secondary, tertiary, quaternary (proteins).

• Alpha vs. Beta Bonds: Affect digestibility of carbohydrates.

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

• R Groups: Determine amino acid properties.

• Lipid Types: Fats, phospholipids, steroids.

Enzymes

Definition and Function

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

• Substrate: Molecule acted upon by enzyme.

• Active Site: Region where substrate binds.

• Products: Resulting molecules after reaction.

Mechanism and Specificity

Enzymes lower activation energy, increasing reaction rates. Specificity arises from enzyme structure.

• Endergonic vs. Exergonic: Endergonic requires energy; exergonic releases energy.

• Transition State: High-energy intermediate; enzymes stabilize this state.

• Activation Energy ($E_a$): Energy required to start a reaction.

• Rate Comparison: Catalyzed reactions are much faster than uncatalyzed.

• Form and Function: Protein structure determines enzyme activity.

• Lock & Key vs. Induced Fit: Models of substrate binding.

• Factors Affecting Activity: Temperature, pH, substrate concentration.

• Allosteric Regulation: Molecules bind outside active site to inhibit or activate enzyme.

Example: Digestive enzymes (amylase, protease) break down food into absorbable units.