Tree of Life

Overview of the Three Domains

The Tree of Life is a model that illustrates the evolutionary relationships among all living organisms. It is divided into three major domains: Bacteria, Archaea, and Eukarya. Each domain contains distinct groups of organisms with unique cellular structures and genetic characteristics.

• Bacteria: Includes gram-positive bacteria, Thermoproteus, Pyrodictium, and Aquifex.

• Archaea: Includes Methanobacterium, Methanococcus, Halobacterium, Thermoplasma, Methanopyrus, and Thermococcus.

• Eukarya: Includes Entamoebae, slime molds, fungi, plants, animals, and protists.

Common ancestor: All three domains diverged from a single common ancestor.

Prokaryotes: Bacteria and Archaea

Defining Prokaryotes

Prokaryotes are unicellular organisms that lack a membrane-bound nucleus. Their genetic material is located in a region called the nucleoid. Prokaryotes include both Bacteria and Archaea.

• No membrane-bound nucleus: DNA is found in the nucleoid.

• Cell wall composition: Bacteria have cell walls made of peptidoglycan; Archaea have cell walls made of glycoprotein or other polymers, but not peptidoglycan.

• Comparison: Plant and fungal cell walls are made of cellulose or chitin, respectively.

Ecological Impact and Diversity

Prokaryotes are among the most diverse, abundant, and ubiquitous organisms on Earth. They play critical roles in ecosystems and have a long evolutionary history.

• Fossil record: Bacteria fossils date back 3.5 billion years; Archaea appear later.

• Abundance: Billions of microbes exist in soil and seawater; prokaryotes under the ocean make up about 10% of the world's total biomass.

• Diversity: Prokaryotes inhabit nearly every environment, including extreme habitats such as hydrothermal vents and under Arctic ice.

• Research significance: Studying extremophiles helps explain the origins of life and guides the search for extraterrestrial life.

Prokaryotic Cell Structure

Prokaryotic cells have several key structural features that distinguish them from eukaryotic cells.

• Nucleoid: Region containing the cell's DNA.

• Plasmid: Small, circular DNA molecules that can carry additional genes.

• Cell wall: Provides structural support and protection.

• Cell membrane: Controls the movement of substances in and out of the cell.

• Pili and fimbriae: Hair-like structures for attachment and genetic exchange.

• Flagella: Used for motility.

Gram Staining and Cell Wall Composition

Gram-Positive vs. Gram-Negative Bacteria

The Gram stain is a dyeing system used to classify bacteria based on their cell wall structure.

• Gram-positive bacteria: Appear purple under the microscope; have a thick peptidoglycan layer.

• Gram-negative bacteria: Appear pink; have a thin peptidoglycan layer and an outer lipid bilayer.

Metabolic Diversity in Prokaryotes

Energy Acquisition Strategies

Prokaryotes exhibit a wide range of metabolic strategies to obtain energy and carbon.

• Phototrophs: Use light energy to excite electrons.

• Chemoorganotrophs: Oxidize organic molecules with high potential energy.

• Chemolithotrophs: Oxidize inorganic molecules with high potential energy.

Oxygen and Photosynthesis

Molecular oxygen was absent for much of Earth's history. The evolution of oxygenic photosynthesis by certain bacteria transformed the atmosphere and enabled aerobic respiration.

• Oxygenic photosynthesis: First performed by photosynthetic bacteria, producing oxygen as a byproduct.

• Impact: Allowed for the development of aerobic respiration, which uses oxygen as the final electron acceptor in the electron transport chain.

Equation for aerobic respiration:

Nitrogen Fixation

Nitrogen is essential for the synthesis of proteins and nucleic acids, but most organisms cannot use atmospheric nitrogen directly. Certain bacteria, known as nitrogen-fixing bacteria, convert atmospheric nitrogen into usable forms.

• Process: Conversion of to , , or .

• Ecological importance: Critical for nutrient cycling in ecosystems.

Antibiotics and Resistance

Antibiotics

Antibiotics are chemicals that kill bacteria or inhibit their growth. They are produced naturally by some soil bacteria and fungi.

• Discovery: First discovered in 1928; widespread use began in the 1940s.

• Resistance: Overuse, especially in animal feed, has led to the evolution of antibiotic-resistant strains of pathogenic bacteria.

Biofilms

Biofilms are bacterial colonies enmeshed in a polysaccharide-rich matrix that shields bacteria from antibiotics and environmental stress.

Endospores

Formation and Function

Some bacteria can form endospores in response to stressful conditions. Endospores are highly resistant cells that can survive dehydration, nutrient deprivation, and other harsh environments.

• Process: DNA is copied and surrounded by a tough coat; metabolism slows.

• Survival: Endospores can remain dormant until conditions improve.

Bioremediation

Environmental Applications

Bioremediation uses bacteria and archaea to clean up polluted environments by breaking down organic and inorganic toxins.

• Methods: Encouraging growth of existing microbes or adding specific species to contaminated sites.

• Applications: Used to treat oil spills, industrial waste, and other pollutants.

Microbiome

Human Microbiome

The microbiome refers to the community of microbes that naturally inhabit the human body. Maintaining a healthy balance of microbial species is important for overall health.

• Locations: Skin, gut, feet, and other body parts.

• Function: Supports digestion, immunity, and other physiological processes.

Major Groups of Eukaryotes

Protista, Plantae, and Animalia

Eukaryotes are organisms with membrane-bound nuclei and organelles. Major groups include Protista, Plantae, and Animalia.

• Protista: Diverse group including algae and protozoa.

• Plantae: Multicellular, photosynthetic organisms (plants).

• Animalia: Multicellular, heterotrophic organisms (animals).

Table: Comparison of Bacteria, Archaea, and Eukarya

Additional info:

• Extremophiles are a hot area of research for understanding life's origins and for biotechnology applications.

• Biofilms contribute to antibiotic resistance and are important in medical and industrial contexts.

• Endospores are a survival mechanism for bacteria facing harsh conditions.