Table of Contents
Overview of the Domain Eukarya
The domain Eukarya includes all organisms whose cells possess a “true” nucleus and a complex internal structure. It encompasses the familiar kingdoms Protista, Plantae, Fungi, and Animalia, which are treated in their own chapters. Here, the focus is on what unites these diverse organisms as eukaryotes and on some key differences from the other domains, Bacteria and Archaea.
At the most basic level, eukaryotes are characterized by:
- Cells with a membrane-bound nucleus containing the genetic material
- A system of membrane-bound organelles
- A cytoskeleton that organizes cell shape and movement
- Typically larger and more complex cells than those of prokaryotes
These features make possible a high degree of specialization within cells and, in many lineages, the development of multicellular organisms with tissues and organs.
Defining Cellular Features of Eukaryotes
The Eukaryotic Cell and Its Nucleus
The name “Eukarya” comes from Greek: “eu” (true) and “karyon” (nut, kernel; here: nucleus). The nucleus is the most distinctive feature of eukaryotic cells:
- The DNA is enclosed by a double membrane, the nuclear envelope.
- Nuclear pores regulate the exchange of molecules (e.g. RNA, proteins) between nucleus and cytoplasm.
- The DNA is organized into linear chromosomes associated with histone proteins.
- During cell division (mitosis and meiosis), chromosomes become visible and are precisely sorted into daughter cells.
This compartmentalization separates transcription (in the nucleus) from much of translation (in the cytoplasm), allowing elaborate regulation of gene expression.
Membrane-Bound Organelles and Compartmentalization
Eukaryotic cells contain a variety of organelles, each with its own membrane and specialized function. Key examples (discussed in detail elsewhere) include:
- Mitochondria: Sites of most ATP production by cellular respiration
- Chloroplasts (in plants and some protists): Sites of photosynthesis
- Endoplasmic reticulum (ER): Synthesis and processing of proteins and lipids
- Golgi apparatus: Modification, sorting, and packaging of proteins and lipids
- Lysosomes and vacuoles: Digestion, storage, and regulation of water balance
This compartmentalization allows different chemical environments and processes to coexist in a single cell. For example:
- Digestive enzymes are confined to lysosomes rather than being free in the cytoplasm.
- Oxidative breakdown of molecules in mitochondria is spatially separated from biosynthetic processes in the cytosol.
Functionally, this increases efficiency and enables complex metabolic networks.
The Cytoskeleton and Intracellular Transport
A prominent feature of eukaryotic cells is the cytoskeleton, a dynamic network of protein filaments:
- Microtubules (tubulin)
- Microfilaments (actin)
- Intermediate filaments (various proteins)
The cytoskeleton:
- Maintains cell shape and provides mechanical stability
- Enables intracellular transport of vesicles and organelles along “tracks”
- Is essential for cell division (mitotic spindle)
- Enables cell movement, including amoeboid movement and the beating of cilia and flagella
Eukaryotic cilia and flagella have a characteristic internal structure (the “9+2” arrangement of microtubules) and differ fundamentally from the simpler flagella of bacteria.
Genome Organization and Gene Regulation
Eukaryotic genomes are generally:
- Larger and more complex than prokaryotic genomes
- Distributed over multiple linear chromosomes
- Containing introns and exons in many genes
As a result, eukaryotes exhibit:
- Complex regulation of gene expression, including multiple levels of control (chromatin structure, transcription, RNA processing, translation)
- Extensive RNA processing, such as mRNA splicing, capping, and polyadenylation
This fine-tuned regulation allows for cell differentiation and the stable maintenance of different cell types in multicellular organisms.
Diversity of Cell Organization in Eukarya
Unicellular vs. Multicellular Eukaryotes
Within the domain Eukarya, we find a continuum from simple unicellular forms to highly complex multicellular organisms:
- Unicellular eukaryotes (often called protists) can be:
- Autotrophic (e.g. many algae)
- Heterotrophic (e.g. amoebae, ciliates)
- Mixotrophic (combining photosynthesis and ingestion)
- Colonial forms consist of many similar cells loosely or moderately connected, sometimes showing simple division of labor.
- Multicellular organisms (plants, fungi, animals, and some protists) have:
- Stable cell–cell adhesion
- Specialized cell types
- Tissues and often organs
Eukaryotic multicellularity evolved several times independently (e.g. in animals, land plants, brown algae, and fungi), illustrating the evolutionary flexibility of eukaryotic cells.
Nutritional Strategies
The domain Eukarya encompasses a wide spectrum of nutritional types. At a high level:
- Photoautotrophs: Perform photosynthesis using chloroplasts; common in plants and many algae.
- Chemoheterotrophs: Obtain both carbon and energy from organic compounds; most fungi and animals belong here.
- Mixotrophs: Combine autotrophic and heterotrophic nutrition; certain protists can both photosynthesize and ingest food particles.
This diversity in nutrition underlies many of the ecological roles eukaryotes play, from primary producers to decomposers and consumers.
Reproduction and Life Cycles
Eukaryotes are defined not only by their cells but also by characteristic modes of reproduction and life cycles:
- Asexual reproduction is widespread (e.g. mitotic cell division, budding, vegetative propagation).
- Sexual reproduction involves:
- Meiosis to produce haploid cells (gametes or spores)
- Fusion of haploid cells (syngamy) to restore the diploid state
Various life cycle patterns are found:
- Haploid-dominant (e.g. many fungi and protists)
- Diploid-dominant (e.g. most animals)
- Alternation of generations with distinct haploid and diploid multicellular stages (e.g. plants, many algae)
These life cycles contribute to genetic diversity through recombination and are a major evolutionary advantage of eukaryotes.
Eukarya in the Tree of Life
Relationship to Bacteria and Archaea
On the broadest scale, the domain Eukarya is one of three domains:
- Bacteria
- Archaea
- Eukarya
Important contrasts with prokaryotic domains include:
- Cell size: Eukaryotic cells are typically larger and more complex.
- Internal structure: Eukarya have extensive compartmentalization; prokaryotes lack membrane-bound organelles.
- Genetic organization: Eukaryotes have multiple linear chromosomes with histones; many bacteria have a single circular chromosome, and Archaea show some intermediate features.
- Transcription and translation: Eukaryotes separate these processes in space and time; in prokaryotes, they often occur simultaneously.
Modern research suggests a close evolutionary relationship between eukaryotes and certain archaeal lineages. According to many current models, eukaryotes evolved from an archaeal ancestor that entered into a symbiotic relationship with a bacterium that became the mitochondrion (endosymbiotic theory). This underscores that eukaryotes are, in a sense, composite organisms.
Major Lineages Within Eukarya
Traditional biology grouped eukaryotes into four kingdoms: Protista, Plantae, Fungi, and Animalia. Modern molecular studies have revealed a more complex pattern of relationships. While the classic kingdoms remain useful in teaching, they do not fully reflect current phylogenies.
Instead, biologists now recognize several large supergroups of eukaryotes (names and composition can vary among classifications). Important points for this chapter:
- Protista (in the classical sense) is not a single natural group; it includes diverse lineages that are only distantly related to each other.
- Plants, fungi, and animals are each embedded within larger supergroups of mostly unicellular relatives.
- The diversity of unicellular eukaryotes is much greater than that of the familiar multicellular forms.
Subsequent chapters on the four kingdoms focus on representative features and evolutionary innovations of each major lineage.
Ecological and Evolutionary Significance of Eukarya
Eukaryotes as Ecosystem Engineers
Members of the domain Eukarya occupy central roles in ecosystems:
- Primary producers: Land plants and many algae convert light energy into chemical energy, forming the base of most food webs.
- Decomposers: Fungi and many protists break down organic matter and recycle nutrients.
- Consumers: Animals and many protists feed on plants, fungi, or other animals, structuring food chains and food webs.
Eukaryotic activities have profoundly transformed the planet, for example:
- The colonization of land by plants altered climate and soil formation.
- Fungal–plant symbioses facilitated nutrient uptake and terrestrial ecosystems.
- Animal activities influence pollination, seed dispersal, and biogeochemical cycles.
Symbioses and Complexity
Complex symbiotic relationships are common in Eukarya:
- Lichens: Symbiosis of fungi with algae or cyanobacteria.
- Mycorrhizae: Associations between fungi and plant roots.
- Endosymbiotic algae in many protists and some animals (e.g. corals).
These interactions can lead to new ecological opportunities and sometimes even to new levels of organization. The origin of mitochondria and chloroplasts themselves is an example of symbiosis leading to a fundamental evolutionary innovation.
Summary: What Defines the Domain Eukarya?
The domain Eukarya is distinguished by:
- Cells with a membrane-bound nucleus and linear chromosomes
- Extensive compartmentalization with membrane-bound organelles
- A dynamic cytoskeleton enabling complex cell shapes, movements, and intracellular transport
- Diverse reproductive strategies, including sexual reproduction with meiosis
- A wide range of body plans, from unicellular organisms to highly complex multicellular forms
- Nutritional diversity, from photosynthetic autotrophs to heterotrophs and mixotrophs
- Central roles in ecosystems as producers, consumers, and decomposers
The subsequent kingdom-level chapters explore how these shared eukaryotic features are realized and modified in Protista, Plantae, Fungi, and Animalia.