Taxonomy, Domains of Life, and Prokaryotes: Structured Study Notes

Biological Levels of Organization

Overview of Biological Hierarchy

Biology studies life at multiple levels of organization, from the smallest molecules to the entire biosphere. Understanding these levels helps clarify how living systems are structured and interact.

• Atoms → Molecules → Cells → Tissues → Organs → Organ Systems → Organism → Species → Communities → Population → Biosphere

Taxonomy and Classification

Definition and Purpose

Taxonomy is the branch of biology concerned with naming, describing, and classifying organisms. It provides a universal language for scientists and helps organize biological diversity.

• Species: The basic unit of classification; a group of organisms capable of interbreeding and producing fertile offspring.

• Genus: A group of closely related species.

• Binomial Nomenclature: Each species is given a unique two-part Latin name (Genus species), e.g., Homo sapiens.

• Genus name is capitalized and italicized; species name is lowercase and italicized.

• Example: Sialia sialis (Eastern bluebird)

Taxonomic Ranks

Organisms are classified into a hierarchy of ranks, from broadest to most specific.

• Domain

• Kingdom

• Phylum

• Class

• Order

• Family

• Genus

• Species

These ranks form a nested hierarchy, with each level including all levels below it.

Phylogenetic Trees and Systematics

Systematics is the study of evolutionary relationships among organisms. It uses phylogenetic trees to represent these relationships.

• Phylogenetic tree: Diagram showing evolutionary connections.

• Clade: A group consisting of an ancestor and all its descendants.

• Systematists reconstruct evolutionary history using genetic, morphological, and biochemical data.

Domains of Life

Three Domains

All living organisms are classified into three domains based on differences in cell structure and genetics.

• Bacteria: Prokaryotic, single-celled organisms with cell walls containing peptidoglycan.

• Archaea: Prokaryotic, single-celled organisms with unique cell membrane lipids and RNA machinery; often found in extreme environments.

• Eukarya: Organisms with eukaryotic cells (nucleus and organelles); includes plants, fungi, animals, and protists.

Comparison of Domains

Domain	Cell Type	Cell Wall Composition	Examples
Bacteria	Prokaryotic	Peptidoglycan	Escherichia coli, Cyanobacteria
Archaea	Prokaryotic	Unique lipids, no peptidoglycan	Halophiles, Thermophiles
Eukarya	Eukaryotic	Varies (cellulose in plants, chitin in fungi)	Humans, Mushrooms, Algae

Prokaryotes: Bacteria and Archaea

Characteristics

Prokaryotes are single-celled organisms lacking a nucleus and membrane-bound organelles. They are the most abundant and diverse life forms on Earth.

• Shapes: Cocci (spherical), Bacilli (rod-shaped), Spirilla (spiral)

• Cell wall composition: Bacteria have peptidoglycan; archaea have unique lipids.

• Gram staining: Differentiates bacteria based on cell wall structure.

• Motility: Many prokaryotes have flagella for movement.

• Biofilms: Communities of prokaryotes embedded in a protective matrix.

• Quorum sensing: Prokaryotes communicate and coordinate behavior based on population density.

Survival and Reproduction

Prokaryotes reproduce asexually, primarily by binary fission. They can survive harsh conditions by forming endospores.

• Binary fission: A cell divides into two identical daughter cells.

• Endospores: Resistant structures that allow survival in extreme environments.

Ecological Roles

Prokaryotes play essential roles in ecosystems and human health.

• Decomposition and nutrient cycling

• Symbiotic relationships (e.g., gut bacteria)

• Pathogenic effects (disease-causing)

Viruses, Viroids, and Prions

Definitions and Characteristics

Viruses, viroids, and prions are infectious agents but are not considered living organisms.

• Virus: Non-cellular particle composed of genetic material (DNA or RNA) and a protein coat; requires a host cell to replicate.

• Viroid: Infectious RNA molecule lacking a protein coat; affects plants.

• Prion: Infectious protein that can cause neurodegenerative diseases in animals.

Are Viruses Alive?

Most biologists do not consider viruses alive because they lack many characteristics of life:

• Cannot reproduce independently

• Do not carry out metabolism

• Are not composed of cells

Central Dogma of Molecular Biology

The flow of genetic information in cells is described by the central dogma:

• $\text{DNA} \rightarrow \text{(transcribed)} \ \text{RNA} \rightarrow \text{(translated)} \ \text{Protein}$

Viruses can disrupt this process, leading to diseases such as AIDS and certain cancers.

Examples and Applications

• Herpes virus: Can remain dormant in the body and cause periodic outbreaks.

• Viroids: Cause crop diseases like potato spindle tuber disease.

• Prions: Cause diseases such as kuru in humans, transmitted by ritual cannibalism.

Characteristics of Living Things

Key Features

To be considered alive, an entity must:

• Be able to evolve

• Be able to grow

• Be able to reproduce

• Be able to utilize energy

• Be able to maintain complexity

• Be able to respond to stimuli

Additional info:

• Systematics and taxonomy are foundational for understanding biodiversity and evolutionary relationships.

• Modern classification increasingly relies on genetic data to reconstruct phylogenies.

• Prokaryotes are crucial for biotechnology, medicine, and environmental science.