Foundations of General Biology: Scientific Method, Chemistry of Life, Macromolecules, and Cell Structure

Science and the Scientific Process

Definition and Nature of Science

Science is the systematic study of how the world works, relying on observation, experimentation, and evidence-based reasoning. It is distinct from other forms of learning, such as rote memorization or experiential learning, by its emphasis on the scientific method and critical analysis.

• Scientific literacy: The ability to read, understand, and critically evaluate scientific information, including research papers and data.

• Biology: The scientific study of life and living organisms.

Fundamental Properties of Life

All living things share certain fundamental properties that distinguish them from non-living matter.

• Reproduction: The ability to produce offspring, either sexually or asexually.

• Growth and development: Increase in size and complexity over time.

• Energy use: Metabolism, including the transformation and use of energy.

• Regulation (homeostasis): Maintenance of stable internal conditions.

• Response to the environment: Ability to sense and react to stimuli.

• Cells: The smallest unit of life; all living things are composed of one or more cells.

Levels of Biological Organization

Life is organized into hierarchical levels, each with emergent properties not present at lower levels.

• Biosphere → Ecosystems → Communities → Populations → Organisms → Organs → Tissues → Cells → Organelles → Molecules → Atoms

• Emergent properties: New functions or characteristics that arise at each level of organization due to the arrangement and interaction of parts.

• Structure-function correlation: The structure of a biological component determines its function (e.g., red blood cell shape maximizes oxygen transport).

Domains of Life

All life is classified into three domains based on cellular organization and genetics:

• Bacteria: Prokaryotic, unicellular organisms.

• Archaea: Prokaryotic, often extremophiles, genetically distinct from bacteria.

• Eukarya: Eukaryotic organisms, including plants, animals, fungi, and protists.

Unifying Themes in Biology

• Organization, energy, and matter: Biological systems are highly organized and require energy and matter to maintain structure and function.

• Information: Genetic information (DNA) is stored, expressed, and transmitted to future generations.

• Transfer and transformation of energy and matter: Energy flows through ecosystems (e.g., light to chemical energy), and matter is recycled (e.g., carbon, nitrogen cycles).

• Interactions: Organisms interact with each other and their environment (e.g., mutualism, predation).

• Diversity and unity: Life shows both diversity (many forms) and unity (common ancestry, shared genetic code).

The Scientific Method

Steps of the Scientific Method

The scientific method is a systematic approach to investigating natural phenomena.

• Theory: Broad explanation supported by a large body of evidence.

• Hypothesis: Testable, proposed explanation for a specific phenomenon.

• Null hypothesis: States no effect or difference; used as a baseline for testing.

• Experimentation: Testing hypotheses through controlled experiments.

• Observation and data collection: Gathering evidence to support or refute hypotheses.

Chemistry of Life

Atoms and Elements

All matter is composed of atoms, which consist of protons, neutrons, and electrons.

• Isotopes: Atoms of the same element with different numbers of neutrons; some are radioactive and decay spontaneously.

• Electron shells: Electrons occupy energy levels around the nucleus; the outermost shell (valence shell) determines chemical reactivity.

• Octet rule: Atoms are most stable when they have eight electrons in their valence shell.

Chemical Bonds

Atoms form chemical bonds to achieve stability, resulting in molecules with new properties.

• Ionic bonds: Involve the transfer of electrons from one atom to another, creating charged ions (cations and anions) that attract each other.

• Covalent bonds: Form when atoms share pairs of electrons. Can be single, double, or triple bonds depending on the number of shared electron pairs.

• Polar covalent bonds: Unequal sharing of electrons due to differences in electronegativity (e.g., water).

• Nonpolar covalent bonds: Equal sharing of electrons (e.g., O2).

• Hydrogen bonds: Weak attractions between a hydrogen atom in one molecule and an electronegative atom in another molecule (important in water and DNA structure).

Properties of Water

Water's unique properties are essential for life and result from its polarity and hydrogen bonding.

• Cohesion: Water molecules stick to each other (surface tension).

• Adhesion: Water molecules stick to other substances.

• High specific heat: Water absorbs and retains heat, moderating temperature changes.

• Ice floats: Solid water is less dense than liquid water due to hydrogen bonding.

• Solvent properties: Water dissolves polar and ionic substances (hydrophilic), but not nonpolar substances (hydrophobic).

Acids, Bases, and pH

The pH scale measures the concentration of hydrogen ions (H+) in a solution.

• Acid: Increases H+ concentration (pH < 7).

• Base: Decreases H+ concentration (pH > 7).

• Neutral: Equal concentrations of H+ and OH- (pH = 7).

• Each pH unit represents a tenfold difference in H+ concentration.

Example: A solution with pH 5 has 10 times more hydrogen ions than a solution with pH 6.

Molecular Diversity of Life

Functional Groups

Functional groups are specific groups of atoms within molecules that determine the chemical properties and reactions of those molecules.

Macromolecules

There are four major classes of biological macromolecules, each with distinct structures and functions.

• Carbohydrates: Sugars and polymers of sugars. Main functions: energy storage and structural support.

• Lipids: Hydrophobic molecules including fats, phospholipids, and steroids. Main functions: energy storage, membrane structure.

• Proteins: Polymers of amino acids. Main functions: catalysis (enzymes), structure, transport, signaling.

• Nucleic acids: DNA and RNA, polymers of nucleotides. Main function: storage and transmission of genetic information.

Monomers and Polymers

• Monomer: Small, repeating unit that serves as a building block for polymers (e.g., glucose, amino acid, nucleotide).

• Polymer: Large molecule made of many monomers joined together.

• Dehydration synthesis: Reaction that joins monomers by removing water.

• Hydrolysis: Reaction that breaks polymers into monomers by adding water.

Carbohydrates

• Monosaccharides: Simple sugars (e.g., glucose, fructose).

• Disaccharides: Two monosaccharides joined by a glycosidic bond (e.g., sucrose, lactose).

• Polysaccharides: Long chains of monosaccharides. Functions include energy storage (starch in plants, glycogen in animals) and structural support (cellulose in plants, chitin in fungi and arthropods).

Example: Cellulose is the most abundant organic compound on Earth but is indigestible to humans without the proper enzyme.

Lipids

• Fats (triglycerides): Composed of glycerol and three fatty acids. Used for long-term energy storage.

• Saturated fatty acids: No double bonds; maximum number of hydrogen atoms; solid at room temperature.

• Unsaturated fatty acids: One or more double bonds; fewer hydrogen atoms; liquid at room temperature.

• Phospholipids: Glycerol, two fatty acids, and a phosphate group. Hydrophilic head and hydrophobic tails; form cell membranes.

• Steroids: Lipids with four fused carbon rings (e.g., cholesterol).

Proteins

• Amino acids: Building blocks of proteins; 20 different types in humans.

• Polypeptide: Chain of amino acids linked by peptide bonds.

• Primary structure: Linear sequence of amino acids.

• Secondary structure: Local folding into alpha helices and beta sheets due to hydrogen bonding.

• Tertiary structure: Overall 3D shape due to interactions among R groups.

• Quaternary structure: Association of multiple polypeptide chains (if present).

• Denaturation: Loss of protein shape (and function) due to changes in pH, temperature, or other environmental factors.

Example: Hemoglobin transports oxygen in the blood; sickle-cell disease is caused by a single amino acid substitution in hemoglobin.

Nucleic Acids

• Nucleotides: Building blocks of nucleic acids; each consists of a phosphate group, a five-carbon sugar, and a nitrogenous base.

• DNA (deoxyribonucleic acid): Double-stranded helix; stores genetic information; bases are A, T, C, G; sugar is deoxyribose.

• RNA (ribonucleic acid): Single-stranded; involved in protein synthesis; bases are A, U, C, G; sugar is ribose.

• Base pairing: In DNA, A pairs with T, and C pairs with G via hydrogen bonds.

Example: The complementary strand for 5'-CCGGTACCTGGAACTGG-3' is 3'-GGCCATGGACCTTGACC-5'.

Feature	DNA	RNA
Sugar	Deoxyribose	Ribose
Strands	Double	Single
Bases	A, T, C, G	A, U, C, G
Function	Genetic information storage	Protein synthesis, gene expression

Cells: The Fundamental Unit of Life

Cell Theory

Cells are the basic unit of structure and function in all living organisms. All cells arise from pre-existing cells and carry out essential life processes.

• Prokaryotic cells: Lack membrane-bound organelles; include Bacteria and Archaea; generally smaller and simpler.

• Eukaryotic cells: Contain membrane-bound organelles (e.g., nucleus, mitochondria); include plants, animals, fungi, and protists.

Common Features of All Cells

• Plasma membrane: Selective barrier that controls entry and exit of substances.

• Cytoplasm: Jelly-like substance containing organelles.

• DNA: Genetic material.

• Ribosomes: Sites of protein synthesis.

Cell Membranes

The plasma membrane is composed of a phospholipid bilayer with embedded proteins, providing selective permeability and structural support.

• Fluid mosaic model: Describes the dynamic and flexible nature of the membrane.

• Membrane fluidity: Influenced by temperature and the composition of fatty acids (more unsaturated fatty acids increase fluidity).

Organelles in Eukaryotic Cells

• Nucleus: Contains DNA; site of RNA synthesis.

• Ribosomes: Synthesize proteins.

• Endomembrane system: Includes the endoplasmic reticulum (ER), Golgi apparatus, lysosomes, and plasma membrane; involved in synthesis, modification, and transport of proteins and lipids.

• Rough ER: Studded with ribosomes; synthesizes and processes proteins.

• Smooth ER: Synthesizes lipids and detoxifies chemicals.

• Golgi apparatus: Modifies, sorts, and packages proteins and lipids for secretion or delivery to other organelles.

• Lysosomes: Contain digestive enzymes; break down macromolecules and recycle cellular components.

• Mitochondria: Site of cellular respiration and ATP production; "powerhouse" of the cell.

• Chloroplasts: Site of photosynthesis in plants and algae.

• Cytoskeleton: Network of protein filaments that provide structural support, cell movement, and transport within the cell.

Comparison of Prokaryotic and Eukaryotic Cells

Feature	Prokaryotic Cells	Eukaryotic Cells
Nucleus	Absent	Present
Membrane-bound organelles	Absent	Present
Size	Small (1-5 μm)	Larger (10-100 μm)
Examples	Bacteria, Archaea	Plants, Animals, Fungi, Protists

Additional info:

• Some context and terminology were clarified and expanded for academic completeness.

• Tables were inferred and formatted for clarity based on the original notes.

• Some chemical and biological processes (e.g., dehydration synthesis, hydrolysis, denaturation) were explained in more detail for self-contained understanding.