General Biology Study Notes: Scientific Process, Chemistry of Life, and Biological Molecules

Process of Science, Diversity of Life, Unifying Themes in Biology, Taxonomy, and Nomenclature

Introduction

This section introduces the foundational concepts of biology, including the scientific method, the diversity of life, and the principles that unify biological study. It also covers taxonomy and the system of naming organisms.

Learning Objectives

• Understand the process used to study scientific phenomena.

• Explore characteristics that unify and differentiate organisms.

• Explain the different levels of biological organization and emergent properties.

• Explain why evolution is the central paradigm of biology.

Key Terms

• Scientific Method

• Structure and Function

• Community

• Diversity

• Emergent Properties

• Evolution

• Hypothesis

• Molecules

• Organism

• Metagenomics

• Bioinformatics

• Biological Organization

• Prediction

• Population

• Taxonomy

• Tissues

• Analogy

• Phylogeny

• Reductionism

The Scientific Method

The scientific method is the process by which scientific knowledge is accumulated and tested. It involves:

• Descriptive Inquiry: Observation and data collection to generate general principles.

• Scientific Method (Hypothesis-based Inquiry): Deductive reasoning to explain causes of observed phenomena.

Scientific questions must be predictive, testable, and potentially falsifiable. A hypothesis can never be proven absolutely true, but it can be disproved.

Influences on the Process of Science

• Exploration and Discovery

• Community Analysis and Feedback

• Societal Benefits and Outcomes

Levels of Biological Organization

Life is organized hierarchically from the biosphere down to molecules:

• Biosphere

• Ecosystems

• Communities

• Populations

• Organisms

• Organs and Organ Systems

• Tissues

• Cells

• Organelles

• Molecules

• Atoms

Emergent properties arise at each level that are not present at the previous level. Reductionism is the approach of reducing complex systems to simpler components for study.

Taxonomy, Classification, and Nomenclature

• Taxonomy: The science of classifying organisms based on similarities and differences.

• Binomial Nomenclature: Each species is given a two-part scientific name: Genus species.

Diversity of Life: The Three Domains

• Bacteria: Prokaryotes (e.g., cyanobacteria, enterics)

• Archaea: Prokaryotes (e.g., extreme halophiles, high salt environments)

• Eukarya: Eukaryotes (e.g., protists, animals, plants, fungi)

Unifying Themes in Biology

• Emergent properties at each level of organization

• Structure and function are correlated

• Cells are the basic unit of structure and function

• Continuity of life is based on heritable information in DNA

• Organisms interact with their environment

• Evolution is the core theme of biology

Basic Chemistry and Water

Introduction

This section covers the chemical basis of life, including the structure of atoms, elements, ions, molecules, and compounds, as well as the properties of water and its importance to life.

Key Terms

• Element

• Atom

• Proton

• Neutron

• Electron

• Isotope

• Compound

• Covalent Bond

• Ionic Bond

• Hydrogen Bond

• van der Waals Interactions

• pH

• Buffer

• Hydrophilic

• Hydrophobic

Elements and Atoms

• Element: A substance that cannot be broken down into simpler substances by chemical means. About 25 elements are essential to life.

• Atom: The smallest unit of an element, consisting of protons, neutrons, and electrons.

• Isotope: Atoms of the same element with different numbers of neutrons.

Electron Shells and Chemical Bonds

• Electrons occupy specific energy levels (shells).

• Electron configuration determines chemical behavior.

• Chemical Bonds: Interactions between atoms that hold them together in molecules and compounds.

Types of Bonds

• Covalent Bond: Sharing of electron pairs between atoms.

• Ionic Bond: Transfer of electrons from one atom to another, resulting in oppositely charged ions.

• Hydrogen Bond: Weak bond between a hydrogen atom and an electronegative atom (e.g., oxygen).

• van der Waals Interactions: Weak attractions between molecules in close proximity.

pH and Buffers

• pH: Measures the concentration of hydrogen ions in solution.

$\text{pH} = -\log_{10}[\text{H}^+]$

• pH scale: 0 (acidic) to 14 (basic); 7 is neutral.

• Buffer: Substance that minimizes changes in pH by accepting or donating hydrogen ions.

Water and Its Properties

• Water is a polar molecule, forming hydrogen bonds with other water molecules.

• Water's emergent properties are essential for life.

Emergent Properties of Water

1. Cohesion and Adhesion: Water molecules stick to each other (cohesion) and to other surfaces (adhesion), resulting in high surface tension.

2. Moderation of Temperature: Water has a high specific heat and high heat of vaporization, helping to stabilize temperatures.

3. Ice Floats: Solid water (ice) is less dense than liquid water, so it floats.

4. Versatility as a Solvent: Water dissolves a wide variety of substances, making it the "universal solvent."

Chemical Composition of Organisms and Biological Molecules

Introduction

This section explores the chemical basis of life, focusing on the versatility of carbon, the structure and function of macromolecules, and the synthesis and breakdown of polymers.

Key Terms

• Monomer

• Polymer

• Carbohydrate

• Lipid

• Protein

• Nucleic Acid

• Condensation (Dehydration) Reaction

• Hydrolysis

• Isomer

• Functional Group

Organic Chemistry: Carbon at the Center

• Carbon can form four covalent bonds, allowing for a diversity of stable organic molecules.

• Carbon skeletons can be straight, branched, or ring-shaped.

• Functional groups (e.g., hydroxyl, carboxyl, amino, phosphate, sulfhydryl) confer specific properties to molecules.

Polymers and Their Synthesis/Breakdown

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

• Hydrolysis: Breaks a covalent bond by adding a water molecule.

Biological Molecules

Carbohydrates

• Functions: Fuel, energy storage, structural components, protection, cell surface properties.

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

• Disaccharides: Two monosaccharides joined (e.g., sucrose).

• Polysaccharides: Long chains of monosaccharides (e.g., starch, cellulose, glycogen, chitin).

Proteins

• Functions: Enzymes, transport, structural components, contractile molecules, hormones, protective coats.

• Structure: Polymers of amino acids joined by peptide bonds.

• Levels of Structure:

  • Primary: Linear chain of amino acids

  • Secondary: Alpha helices and beta-pleated sheets (hydrogen bonds)

  • Tertiary: 3D structure (hydrogen bonds, ionic bonds, covalent bonds, hydrophobic interactions, disulfide bridges)

  • Quaternary: Association of multiple polypeptides

• Protein Folding: Chaperonins assist in proper folding by providing a hydrophilic environment.

Nucleic Acids

• Functions: Storage, replication, and transmission of genetic information; energy carrying (e.g., ATP).

• Structure: Polymers of nucleotides (nitrogenous base, sugar, phosphate).

• Phosphodiester bonds link nucleotides.

Lipids

• Functions: Energy storage, structural components (membranes), hormones, protective coats.

• Structure: Fatty acids (hydrophobic tails, hydrophilic heads), can be saturated or unsaturated.

Summary Table: Major Biological Molecules

Class	Monomer	Bond Type	Function
Carbohydrates	Monosaccharide	Glycosidic linkage	Energy, structure
Proteins	Amino acid	Peptide bond	Enzymes, structure, transport
Nucleic Acids	Nucleotide	Phosphodiester bond	Genetic information
Lipids	Fatty acid, glycerol	Ester linkage	Energy storage, membranes

Additional info: These notes are expanded and clarified for academic completeness and to ensure self-contained study utility.