General Biology I: Foundational Concepts and Macromolecules

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CHAPTER 1: Introduction to Biology

Definitions and Scope of Biology

Biology is the scientific study of life and living organisms. It encompasses various subfields and concepts that help us understand the complexity and diversity of life.

Biology: The study of living things.
Cytology: The study of cells.
Homeostasis: The maintenance of a stable internal environment.
Genetics: The study of heredity and variation in organisms.
Ecology: The study of ecosystems and interactions among organisms and their environment.
Emergent Properties: New characteristics that arise at each level of biological organization due to the arrangement and interactions of parts as complexity increases.

Properties (Characteristics) of Life

All living organisms share several key properties that distinguish them from non-living matter.

Order: Living organisms have a highly ordered structure, such as the intricate arrangement of a flower's petals.
Evolutionary Adaptation: Organisms adapt to their environments over generations (e.g., pygmy seahorse camouflage).
Regulation: Maintenance of internal stability (e.g., jackrabbit regulates body temperature).
Energy Processing: Living beings use energy to perform activities (e.g., butterflies use nectar as fuel).
Growth and Development: Organisms grow and develop according to genetic instructions (e.g., oak seedling sprouting).
Response to Environment: Organisms respond to stimuli (e.g., Venus flytrap closing on a grasshopper).
Reproduction: Living things reproduce to ensure species continuation (e.g., giraffes producing offspring).

Theory and Law in Science

Scientific theories and laws are foundational to understanding natural phenomena.

Theory: A well-substantiated explanation of some aspect of the natural world, based on a body of evidence and repeated testing.
Law: A statement based on repeated experimental observations that describes some aspect of the world.

Scientific Naming and Taxonomy

Organisms are classified using a binomial nomenclature system.

Scientific Name: Consists of the genus and species (specific epithet), e.g., Felis catus for the domestic cat.
When writing, underline or italicize the genus and species. Always capitalize the genus, not the species.

Reasoning in Science

Scientific reasoning can be deductive or inductive.

Deductive Reasoning: Starts with general principles and applies them to specific cases.
Inductive Reasoning: Draws general conclusions from specific observations.

Species Concept

A species is a group of populations whose members can interbreed in nature and produce viable, fertile offspring.

Darwin's Theory of Evolution by Natural Selection

Darwin proposed that species evolve over time through natural selection.

Descent with Modification: Species change over generations.
Natural Selection: Individuals with advantageous traits survive and reproduce more successfully.

Levels of Biological Organization

Life is organized in a hierarchical manner, from atoms to the biosphere.

Atom: Basic unit of matter (e.g., H, C, N).
Molecule: Atoms bonded together (e.g., DNA, energy molecules).
Organelle: Structures within cells (e.g., nucleus, mitochondria).
Cell: Basic unit of life.
Tissue: Group of cells performing a specific function.
Organ: Structure composed of tissues performing one task.
Organ System: Group of organs working together.
Organism: Individual living entity.
Population: Group of organisms of the same species.
Community: Different populations in an area.
Ecosystem: Community plus its physical environment.
Biosphere: All ecosystems on Earth.

Domains and Kingdoms of Life

Life is classified into three domains and several kingdoms based on cellular structure and other characteristics.

Archaea: Prokaryotic, no membrane-enclosed organelles, often live in extreme environments.
Bacteria: Prokaryotic, no membrane-enclosed organelles, cell walls contain peptidoglycan.
Eukarya: Eukaryotic, membrane-bound organelles. Includes four kingdoms:
- Protista: Mostly unicellular, diverse nutrition modes.
- Fungi: Mostly multicellular, absorb nutrients.
- Plantae: Multicellular, autotrophic (photosynthetic).
- Animalia: Multicellular, ingest food.

Taxonomic Levels

Taxonomy organizes living things from broad to specific categories.

Domain → Kingdom → Phylum → Class → Order → Family → Genus → Species

Prokaryotic vs. Eukaryotic Cells

Cells are classified based on the presence or absence of a nucleus and organelles.

Prokaryotic Cells: No nucleus, no membrane-bound organelles (e.g., bacteria, archaea).
Eukaryotic Cells: Have a nucleus and membrane-bound organelles (e.g., plants, animals, fungi, protists).

The Scientific Method

The scientific method is a systematic approach to investigation.

Steps: Observe → Test (experiment) → Hypothesis → Results → Predict → Conclude

CHAPTER 2: Elements, Atoms, and Molecules

Basic Chemical Concepts

Chemistry underpins biological processes. Understanding atoms, molecules, and chemical bonds is essential.

Matter: Anything that has mass and occupies space.
Ion: Atom or molecule with a net electric charge.
Cation: Positively charged ion.
Anion: Negatively charged ion.
Isotope: Atoms of the same element with different numbers of neutrons.
Valence Electrons: Electrons in the outermost shell, involved in bonding.
Element: Substance that cannot be broken down by chemical means.
Compound: Substance formed from two or more elements.
Molarity: Concentration of a solution, measured in moles per liter.
Van der Waals Interactions: Weak attractions between molecules.

Atomic Structure and Notation

Atoms are represented by symbols, with subscripts and superscripts indicating atomic number and mass number.

Atomic Number (Z): Number of protons in the nucleus.
Mass Number (A): Number of protons plus neutrons.
Atomic Weight: Average mass of atoms of an element.

Example: Carbon (C) with atomic number 6 and mass number 13: 6 protons, 7 neutrons.

Formula:

Octet Rule

Atoms tend to gain, lose, or share electrons to achieve a full set of eight valence electrons.

Major Elements in Living Things

Carbon (C)
Hydrogen (H)
Oxygen (O)
Nitrogen (N)

Chemical Bonds

Atoms combine through different types of chemical bonds.

Ionic Bond: Transfer of electrons between atoms.
Covalent Bond: Sharing of electrons between atoms.
Hydrogen Bond: Weak attraction between a hydrogen atom and an electronegative atom.

Bond Polarity

Nonpolar Covalent Bond: Electrons shared equally.
Polar Covalent Bond: Electrons shared unequally, creating partial charges.
Ionic Bond: Complete transfer of electrons.

CHAPTER 3: Water, Acids, and Bases

Properties of Water and Solutions

Water is essential for life due to its unique chemical and physical properties.

Polar: Molecule with uneven distribution of charge.
Nonpolar: Molecule with even distribution of charge.
Solvent: Substance that dissolves other substances.
Solute: Substance dissolved in a solvent.
Solution: Homogeneous mixture of solute and solvent.
Aqueous Solution: Solution where water is the solvent.
Buffer: Substance that minimizes changes in pH.
Emulsifier: Substance that stabilizes mixtures of oil and water.
Electronegativity: Atom's ability to attract electrons.
Hydrophilic: Water-attracting.
Hydrophobic: Water-repelling.

pH Scale and Acids/Bases

The pH scale measures hydrogen ion concentration, ranging from 0 (acidic) to 14 (basic).

Acid: Substance that increases hydrogen ion concentration (pH < 7).
Base: Substance that decreases hydrogen ion concentration (pH > 7).
Neutral: pH = 7.

Formula:

Cohesion and Adhesion

Cohesion: Water molecules stick to each other.
Adhesion: Water molecules stick to other surfaces.

Hydrogen Bonding and Water's Properties

Water's polarity allows it to form hydrogen bonds, leading to high cohesion, adhesion, and surface tension.

Acids, Bases, and Buffers

Acids and bases affect the hydrogen ion concentration of solutions. Buffers help maintain stable pH.

CHAPTER 4: Functional Groups

Organic Chemistry and Functional Groups

Functional groups are specific groups of atoms within molecules that confer particular chemical properties.

Hydroxyl (-OH)
Carboxyl (-COOH)
Amino (-NH2)
Phosphate (-PO4)
Carbonyl (C=O)
Sulfhydryl (-SH)
Methyl (-CH3)

Isomers

Structural Isomers: Differ in covalent arrangement of atoms.
Enantiomers: Mirror images of each other.
Geometric Isomers: Differ in spatial arrangement around a double bond.

CHAPTER 5: Macromolecules

Macromolecules and Their Building Blocks

Macromolecules are large, complex molecules essential for life. They are formed from smaller units called monomers.

Polymer: Large molecule made of repeating monomers.
Monomer: Small molecule that can join to form polymers.
Hydrocarbon: Molecule made of only carbon and hydrogen.
Polyunsaturated Fat: Fat with multiple double bonds.
Unsaturated Fat: Fat with at least one double bond.
Saturated Fat: Fat with no double bonds.
Dipeptide: Two amino acids joined by a peptide bond.
Polypeptide: Chain of amino acids.
Denaturation: Loss of protein structure and function.
Dehydration Synthesis: Formation of a bond by removing water.
Hydrolysis: Breaking a bond by adding water.
Polymerization: Process of forming polymers.
Depolymerization: Breaking down polymers into monomers.
Reactants: Substances that start a chemical reaction.
Products: Substances formed from a chemical reaction.

Organic Macromolecules

Carbohydrates: Energy source and structural support.
Lipids: Energy storage, membrane structure.
Proteins: Catalysis, structure, transport, signaling.
Nucleic Acids: Information storage and transfer (DNA, RNA).

Carbohydrates

Monosaccharides: Simple sugars (e.g., glucose, empirical formula ).
Disaccharides: Two monosaccharides joined (e.g., maltose, sucrose, lactose).
Polysaccharides: Long chains of monosaccharides (e.g., starch, glycogen, cellulose, chitin).

Monosaccharide Classification

Type	Number of Carbons
Triose	3
Tetrose	4
Pentose	5
Hexose	6
Heptose	7

Polysaccharide Comparison

Polysaccharide	Function	Contains N?	Alternating -OH Groups?
Starch	Plant energy storage	No	No
Glycogen	Animal energy storage	No	No
Cellulose	Plant cell wall structure	No	Yes
Chitin	Fungal cell wall, exoskeletons	Yes	No
Amylose	Plant starch	No	No
Amylopectin	Plant starch	No	No

Lipids

Fat Molecule Composition: Glycerol + 3 fatty acids.
Phospholipids: Major component of cell membranes.

Proteins

Amino Acids: Building blocks of proteins, contain amino and carboxyl groups.
There are 20 naturally occurring amino acids.
Protein Structure:
- Primary: Sequence of amino acids.
- Secondary: Local folding (alpha helix, beta sheet).
- Tertiary: Overall 3D shape.
- Quaternary: Association of multiple polypeptides.
Denaturation: Loss of protein structure due to environmental changes.

Nucleic Acids

DNA: Deoxyribonucleic acid, stores genetic information.
RNA: Ribonucleic acid, involved in protein synthesis.
Purines: Adenine (A), Guanine (G).
Pyrimidines: Cytosine (C), Thymine (T, in DNA), Uracil (U, in RNA).
DNA vs. RNA: DNA is double-stranded, found in nucleus, stores information; RNA is single-stranded, found in cytoplasm, involved in protein synthesis.

Important Bonds in Macromolecules

Glycosidic Bond: Joins monosaccharides in carbohydrates.
Peptide Bond: Joins amino acids in proteins.
Phosphodiester Bond: Joins nucleotides in nucleic acids.

Additional info: Some details, such as the specific examples of adaptation and the full list of macromolecule functions, were expanded for clarity and completeness.