Prokaryote and Eukaryote Diversity: Domains, Traits, and Protist Overview (Chapters 27 & 28)

Chapter 27: Prokaryote Diversity and the Three Domains of Life

Overview of the Three Domains

The three domains of life—Bacteria, Archaea, and Eukarya—represent the major evolutionary lineages. Each domain is defined by unique molecular and cellular traits.

• Bacteria: Prokaryotic cells lacking a nucleus and membrane-bound organelles.

• Archaea: Prokaryotic cells with distinct molecular characteristics, often found in extreme environments.

• Eukarya: Eukaryotic cells with a true nucleus and membrane-bound organelles.

Comparison of Key Traits Across Domains

The following table summarizes major cellular and molecular traits distinguishing the three domains:

Characteristic	Bacteria (A)	Archaea (B)	Eukarya (C)
Nuclear Envelope	Absent	Absent	Present
Membrane-bound Organelles	Absent	Absent	Present
RNA Polymerases	One	Several	Several
Introns in Genes	Very rare	Present	Present
Histone Proteins	Absent	Present	Present

Cladogram: Evolutionary Relationships

A cladogram visually represents evolutionary relationships among the three domains. Key derived traits such as introns, histones, multiple RNA polymerases, nuclear envelope, and organelles mark evolutionary divergences.

• Bacteria: Lack introns, histones, and have a single RNA polymerase.

• Archaea: Possess introns, histones, and several RNA polymerases.

• Eukarya: Have nuclear envelope, organelles, and share molecular traits with Archaea.

Genetic Recombination in Prokaryotes

Prokaryotes increase genetic diversity through several mechanisms of genetic recombination:

• Transformation: Uptake of foreign DNA from the environment. For example, a nonpathogenic bacterium may acquire a pathogenic allele via transformation.

• Transduction: Transfer of DNA between bacteria via bacteriophages (viruses that infect bacteria). This process is often accidental during viral replication.

• Conjugation: Direct transfer of DNA between two bacterial cells, typically via a pilus. DNA transfer is one-way, from donor to recipient.

Example: In Escherichia coli, genetic recombination can result in new combinations of alleles, contributing to adaptation and antibiotic resistance.

Antibiotic Resistance

Antibiotic resistance arises when bacteria acquire genes that confer survival advantages in the presence of antibiotics. This can occur through mutation or horizontal gene transfer (transformation, transduction, conjugation).

• Key Point: Overuse and misuse of antibiotics accelerate the spread of resistance genes.

• Example: Methicillin-resistant Staphylococcus aureus (MRSA) is a major clinical concern.

Major Nutritional Modes in Prokaryotes

Prokaryotes exhibit diverse nutritional strategies, classified by energy and carbon sources:

Mode	Energy Source	Carbon Source	Example Organisms
Photoautotroph	Light	CO2	Cyanobacteria
Chemolithoautotroph	Inorganic chemicals	CO2	Some Archaea (e.g., Sulfolobus)
Photoheterotroph	Light	Organic compounds	Unique to certain aquatic prokaryotes
Chemoheterotroph	Organic compounds	Organic compounds	Most prokaryotes, some plants and animals

Chapter 28: Protist Diversity and Eukaryote Supergroups

Kingdom Protista and Eukaryote Supergroups

Protists are a diverse group of mostly unicellular eukaryotes. Modern classification divides eukaryotes into several supergroups based on molecular and structural similarities.

• Excavata: Characterized by an "excavated" groove on one side; includes diplomonads, parabasalids, and euglenozoans.

• SAR: Monophyletic supergroup named for Stramenopiles, Alveolates, and Rhizarians.

• Archaeplastida: Includes red algae, green algae, and plants; plastids originated from cyanobacterial endosymbionts.

• Unikonta: Includes animals, fungi, and related protists (e.g., amoebozoans).

Protist Diversity: Movement and Reproduction

Protists exhibit varied modes of movement and reproduction:

• Movement: By pseudopodia (amoebas), flagella (euglenoids), or cilia (paramecia).

• Reproduction: Both asexual and sexual reproduction; some have complex life cycles with alternation of generations.

Example: Plasmodium, the apicomplexan that causes malaria, has a two-host life cycle involving both humans and mosquitoes.

Alternation of Generations

Some protists and plants exhibit alternation of generations, producing both haploid (n) and diploid (2n) multicellular forms.

• Key Point: This strategy increases genetic diversity and adaptation to changing environments.

Ecological Roles of Prokaryotes and Protists

Both prokaryotes and protists play essential roles in ecosystems:

• Prokaryotes: Decomposition, nutrient cycling, symbiotic relationships (e.g., nitrogen fixation in cyanobacteria).

• Protists: Primary producers (algae), pathogens (e.g., Plasmodium), and symbionts.

Summary Table: Eukaryote Supergroups

Supergroup	Key Features	Representative Organisms
Excavata	Excavated groove, modified mitochondria	Euglena, Giardia
SAR	Stramenopiles (hairy flagella), alveolates (membrane sacs), rhizarians (amoeboid movement)	Diatoms, Plasmodium, foraminiferans
Archaeplastida	Plastids from cyanobacteria, photosynthetic	Red algae, green algae, plants
Unikonta	Amoeboid movement, single flagellum	Amoebozoans, animals, fungi

Key Terms and Definitions

• Cladogram: Diagram showing evolutionary relationships.

• Introns: Non-coding regions within genes, present in Archaea and Eukarya.

• Histones: Proteins that package DNA, present in Archaea and Eukarya.

• RNA Polymerase: Enzyme for synthesizing RNA; multiple types in Archaea and Eukarya.

• Alternation of Generations: Life cycle with both haploid and diploid multicellular stages.

Formulas and Equations

• Genetic Recombination Rate (example):

$\text{Rate} = k[\text{Donor Cells}][\text{Recipient Cells}]$

• Photosynthesis (generalized):

$6CO_2 + 6H_2O \rightarrow C_6H_{12}O_6 + 6O_2$