Foundations of General Biology: Scientific Method, Origins of Life, Macromolecules, Cells, and Evolution

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Introduction to Science and the Scientific Method

Definition and Nature of Science

Science is a systematic approach to understanding the natural world through observation, experimentation, and reasoning. The word science is derived from the Latin verb scire, meaning "to know." Scientific inquiry seeks to explain natural phenomena by identifying natural causes.

Objective analysis: Science relies on objective, repeatable observations and testable hypotheses.
Principles from observations: Scientific knowledge is built by determining principles from empirical evidence.
Process of inquiry: Involves repeatable observations and testable explanatory hypotheses.

The Scientific Process

The scientific process is a logical sequence of steps used to investigate phenomena and answer questions.

Observation: Gathering data about the world.
Quantification: Measuring and recording observations.
Hypothesis: Formulating a testable explanation for observations.
Prediction: Making predictions based on the hypothesis.
Experiment: Testing predictions through controlled experiments.
Analysis: Using statistical tests to determine significance.

Reasoning in Science

Inductive reasoning: Specific observations yield general concepts (e.g., laws).
Deductive reasoning: General concepts lead to specific explanations and tests (e.g., hypothesis testing).

Controlled Experiments

Controlled experiments are designed to determine causality by manipulating one variable while keeping others constant.

Independent variable: Manipulated by the experimenter.
Dependent variable: Measured by the experimenter.
Extraneous variables: Not of interest, but must be controlled.
Control group: Subjects with the independent variable "zeroed" to cancel out extraneous variables.

Evaluating Science: Good vs. Bad Science

Sources: Primary (journal articles), secondary (web pages, news).
Peer review: Research should be reviewed by experts.
Controlled experiments: Explanatory and reliable.
Correlation vs. causation: Correlation does not prove causation.
Logical consistency and plausibility: Findings should be supported by data and statistics.

Origins of Life

History of Earth and Life

Earth is approximately 4.5 billion years old. The earliest definitive fossils date to about 3.5 billion years ago, and life likely originated between 3.5 and 3.8 billion years ago.

Early Earth conditions: No oxygen, high carbon dioxide, extreme volcanic activity, lightning storms, ultraviolet radiation.
Raw ingredients for life: Amino acids, nucleotides, carbohydrates, lipids.

Miller-Urey Experiment

The Miller-Urey experiment simulated early Earth conditions and demonstrated that organic molecules such as amino acids and nucleotides could be synthesized abiotically.

Significance: Showed that life's building blocks could form under prebiotic conditions.

Steps in the Origin of Life

Abiotic synthesis: Formation of organic molecules near hydrothermal vents or other energy sources.
Polymerization: Organic molecules joined to form macromolecules (e.g., amino acids to polypeptides).
Protocells: Macromolecules formed droplets, possibly leading to primitive cell-like structures capable of metabolism and reproduction.
Darwinian evolution: Diversity and complexity of life arose through evolutionary processes.

Domains of Life

All living organisms are classified into three domains:

Bacteria: Prokaryotic, lacking a nucleus.
Archaea: Prokaryotic, distinct from bacteria.
Eukarya: Eukaryotic, possessing a nucleus and organelles.

Macromolecules

Overview of Macromolecules

Macromolecules are large organic molecules essential for life. They are typically polymers made from repeating monomer units.

Organic molecules: Contain at least one C-H bond.
Types: Carbohydrates, lipids, proteins, nucleic acids.

Carbohydrates

Carbohydrates are polymers of monosaccharides (simple sugars).

Monosaccharides: Glucose (C6H12O6), can be linear or cyclic.
Polysaccharides: Starch (storage), cellulose (structural in cell walls).

Lipids

Lipids are hydrophobic molecules, not true polymers.

Triglycerides: Glycerol + 3 fatty acids; energy storage.
Saturated fatty acids: No double bonds; solid fats.
Unsaturated fatty acids: One or more double bonds; liquid oils.
Phospholipids: Glyceride with a phosphate group; amphipathic, forms bilayers (basis of cell membranes).
Steroids: Cholesterol-based hormones (testosterone, estrogen, progesterone).

Proteins

Proteins are polymers of amino acids, with 20 different kinds.

Structure: Determined by sequence and folding (primary, secondary, tertiary, quaternary).
Function: Enzymes, structural components, signaling.
Enzymes: Have active sites specific to substrates; shape is crucial for function.
Prions: Misfolded proteins that can cause disease (e.g., mad cow disease, Creutzfeld-Jacob disease).

Nucleic Acids

Nucleic acids (DNA and RNA) are polymers of nucleotides.

Nucleotide structure: Phosphate group, 5-carbon sugar (ribose or deoxyribose), nitrogenous base (A, T, C, G, U).
DNA: Double-stranded helix, complementary base pairing, information storage.
RNA: Information transmission between DNA and proteins.

Cell Structure and Function

Cell Theory

All living organisms are composed of cells, which are the smallest units of life. Organisms may be unicellular or multicellular.

Prokaryotic cells: Lack a nucleus and organelles; include Bacteria and Archaea.
Eukaryotic cells: Possess a nucleus and organelles; include Eukarya.

Prokaryotic Cell Structure

Shape: Spherical (cocci), rod-shaped (bacilli), spiral.
Chromosome: Single ring of DNA, 1500+ genes.
Internal compartments: Generally absent, but may have infolded plasma membrane for metabolic functions.

Plasma Membrane

The plasma membrane is a selectively permeable barrier composed of a phospholipid bilayer and embedded proteins.

Permeability: Nonpolar molecules (O2, CO2) diffuse freely; polar molecules require transport proteins.
Osmosis: Movement of water across the membrane; solutions can be hypertonic, isotonic, or hypotonic.
Active transport: Movement against concentration gradient (e.g., sodium-potassium pump).
Endocytosis: Only in eukaryotes; plasma membrane forms vesicles to engulf substances (phagocytosis).

Eukaryotic Cell Organelles

Nucleus: Contains genetic material; nuclear envelope with pores regulates traffic.
Endoplasmic reticulum (ER): Rough ER synthesizes proteins; smooth ER synthesizes lipids and detoxifies.
Golgi apparatus: Modifies, sorts, and ships proteins and lipids.
Lysosomes: Contain digestive enzymes; involved in recycling and breakdown (e.g., Tay-Sachs disease, asbestosis).
Mitochondria: Site of cellular respiration; contains its own DNA; inherited maternally.
Chloroplasts: Site of photosynthesis in plants and algae.
Cytoskeleton: Provides structural support, movement (actin, myosin, tubulin, dynein, keratin).

Endomembrane System

The endomembrane system includes the nucleus, ER, Golgi apparatus, lysosomes, and vesicles, which are interconnected for transport and processing of cellular materials.

Cell Division and Inheritance

Prokaryotic Cell Division

Binary fission: Produces two genetically identical daughter cells.

Eukaryotic Cell Division

Mitosis: Produces two genetically identical daughter cells.
Meiosis: Reduces chromosome number, produces genetically non-identical daughter cells (gametes).
Fertilization: Restores chromosome number.

Metabolism

Metabolic Pathways

Metabolism encompasses all chemical reactions that transform energy in cells.

Catabolic pathways: Break down complex molecules to release energy.
Anabolic pathways: Consume energy to build complex molecules.

Example: Cellular Respiration

Cellular respiration is the catabolic breakdown of glucose to generate ATP.

Response to Environment and Homeostasis

Response to Stimuli

Plants: Detect light and gravity, respond with growth hormones.
Bacteria: Move toward nutrients or away from toxins; can sense magnetic fields.
Animals: Use sense organs and nervous system for integration and response.

Homeostasis

Homeostasis is the maintenance of a relatively constant internal environment.

Negative feedback: A change is offset by a response in the opposite direction (e.g., insulin lowers blood glucose).
Body temperature: Maintained at ~37°C in humans.
Water regulation: Managed by organ systems.

Evolution

Natural Selection and Adaptation

Charles Darwin's theory of evolution by natural selection explains how species change over time.

Variation: Exists among individuals due to mutation.
Selection: Environment determines whether mutations are beneficial, harmful, or neutral.
Antibiotic resistance: Bacteria evolve resistance through mutation and selection pressure.

Inheritance and Mutation

DNA: Molecule of inheritance; mutation is the source of variation.
Types of mutations: Neutral (most common), harmful, beneficial (rare).
Sickle cell anemia: Mutation in hemoglobin gene; one copy confers resistance to malaria.

Evidence for Evolution

Fossil record: Documents changes over time (e.g., origin of whales).
Homology: Similarity due to common ancestry.
Analogy: Similarity due to convergent evolution, not common ancestry.

Summary Tables

Domains of Life

Domain	Cell Type	Key Features
Bacteria	Prokaryotic	No nucleus, peptidoglycan cell wall
Archaea	Prokaryotic	No nucleus, distinct biochemistry
Eukarya	Eukaryotic	Nucleus, organelles

Macromolecules: Monomers and Polymers

Macromolecule	Monomer	Polymer
Carbohydrates	Monosaccharide	Polysaccharide (e.g., starch, cellulose)
Proteins	Amino acid	Polypeptide
Nucleic acids	Nucleotide	DNA, RNA
Lipids	Fatty acid, glycerol	Triglyceride, phospholipid

Levels of Protein Structure

Level	Description
Primary	Amino acid sequence
Secondary	Initial folding (alpha helices, beta sheets)
Tertiary	Three-dimensional folding
Quaternary	Multiple polypeptides interacting

Types of Cell Transport

Type	Energy Required	Direction	Example
Diffusion	No	Down gradient	O2, CO2
Facilitated diffusion	No	Down gradient	Glucose via transport protein
Active transport	Yes	Against gradient	Sodium-potassium pump
Osmosis	No	Water down gradient	Water movement

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