Prokaryotes, Eukaryotes, Bacteria, Archaea & Viruses Lecture Notes

The Three Domains of Life

• The Domain is the highest rank of biological classification, sitting above the Kingdom level.

• There are three primary domains used to categorize all life on Earth:

  • Archaea: Composed entirely of prokaryotic microorganisms.

  • Bacteria: Composed entirely of prokaryotic microorganisms.

  • Eukarya: Includes all life forms that possess a nucleus and membrane-bound organelles. This domain encompasses the majority of multicellular life, including all plants and animals.

• Note on Non-Cellular Life: None of the three domains include viruses, as they are considered non-cellular life forms.

• Evolutionary Relationships: Evidence suggests that Eukaryotes are more closely linked to Archaea than they are to Bacteria.

Comparison of Prokaryotes and Eukaryotes

• Prokaryotes (Bacteria, Archaea):

  • Appearance: Emerged approximately $3.5 \times 10^9$ years ago = 3,500,000,000.

  • Size: Characteristically small, ranging from $1-10\,\mu\text{m}$.

  • Genetic Structure: DNA is circular and not bound by a nuclear membrane; typically consists of one single chromosome.

  • Cell Division: Primarily through binary fission.

  • Reproduction: Asexual reproduction is common.

  • Multicellularity: Multicellular forms are rare.

  • Organelles: Mitochondria and other membrane-bound organelles are absent.

  • Metabolism: Many are anaerobic (do not require oxygen).

  • Etymology: Derived from "pro" (before) and "karyon" (nucleus), reflecting their simple structure.

• Eukaryotes (Protists, Plants, Fungi, Animals):

  • Appearance: Emerged approximately $1.5 \times 10^9$ years ago = 1,500,000,000.

  • Size: Significantly larger, ranging from $100-1000\,\mu\text{m}$.

  • Genetic Structure: Linear DNA located within a nucleus, bound by a membrane; organized into several chromosomes.

  • Cell Division: Occurs via mitosis and meiosis.

  • Reproduction: Sexual reproduction is common.

  • Multicellularity: Most organisms in this group are multicellular.

  • Organelles: Mitochondria and other complex organelles are present to facilitate energy production and specialized functions.

  • Metabolism: Most are aerobic (require oxygen).

The Theory of Endosymbiosis and Eukaryotic Evolution

• Definition of Endosymbiosis: A type of internal symbiosis where one organism takes up permanent residence inside another, eventually evolving into a single lineage.

• General Theory: Evidence suggests eukaryotes are descendants of separate prokaryotic cells that joined in a symbiotic union.

• Process of Early Evolution:

  • A free-living bacterium was engulfed by another larger host cell.

  • Mutual Benefit: The host cell profited from the chemical energy produced by the internal bacterium (the proto-mitochondrion), while the bacterium benefited from protection and a nutrient-rich environment.

  • Over time, this relationship led to the evolution of modern eukaryotic cells.

• Evidence for Endosymbiosis (Mitochondria and Chloroplasts):

  • Membranes: Mitochondria possess their own cell membranes, similar to those of prokaryotic cells.

  • DNA: Each mitochondrion has its own circular DNA genome, independent of the cell’s nuclear genome. This DNA is passed directly from a mitochondrion to its offspring.

  • Reproduction: Mitochondria multiply by pinching in half, which is the same process (binary fission) used by bacteria. Every new mitochondrion must be produced from a parent mitochondrion.

Domain Bacteria: Characteristics and Ecological Roles

• Prevalence: Bacteria surround us in the air, soil, water, and on our skin. Their total numbers exceed those of all other forms of life.

• Structure: They are prokaryotes that mostly live as single cells, though some produce colonies, chains, or filaments.

• Utility: Only approximately $1\%$ of bacteria are "bad" (pathogenic). They are vital for ecosystems (e.g., the nitrogen cycle) and food production (vinegar, cheese, butter, yogurt).

• Atmospheric Impact: Early Earth was uninhabitable due to a lack of oxygen. Some bacteria began producing oxygen via photosynthesis using sunlight. This oxygen buildup eventually allowed plants and animals to develop.

• Fossil Record: Bacterial fossils have been found dating back $3 \times 10^6$ years.

• Movement Mechanisms:

  • Flagella: Tail-like structures that rotate like propellers to move through liquids.

  • Bacterial Gliding: The secretion of slime to ooze over surfaces.

  • Twitching Motility: Specialized movement to cross surfaces.

Bacterial Classification and Reproduction

• Classification by Shape:

  • Spherical (Cocci): From the Greek for "berries." Example: Staphylococcus aureus (can cause food poisoning).

  • Rod-shaped (Bacilli): From the Latin for "stick." Example: Capnocytophaga sputigena (can cause blood poisoning, gum disease, and meningitis).

  • Spiral-shaped (Spirochetes): From the Greek for "long hair." Example: Leptospira (can cause liver and kidney disease).

• Reproduction and Genetic Mixing:

  • Binary Fission: Asexual division producing two genetically identical cells. Allows for rapid population growth but no genetic recombination.

  • Transformation: Bacterial cells take up fragments of free DNA from the surrounding environment (often from dead bacteria).

  • Conjugation: Two bacterial cells join via a "mating bridge" of cytoplasm and directly exchange genetic material, usually involving plasmids.

  • Transduction: Viruses that infect bacteria carry genes from one cell and inject them into another.

• Classification Challenges: Classification is difficult because bacteria swap genes readily and undergo rapid genetic mutation, leading to significant differences within a few generations.

• Metabolic Classifications:

  • Photoautotrophs: Obtain all energy from sunlight.

  • Photoheterotrophs: Obtain energy from sunlight and the environment.

  • Chemoautotrophs: Use inorganic energy sources to produce carbon.

  • Chemoheterotrophs: Use organic energy sources and cannot make their own carbon.

Bacterial Communication: Quorum Sensing

• Definition: Quorum sensing (q.s.) is chemical communication used by bacteria to synchronize coordinated activities, such as attacks on a host.

• Mechanism: Based on population density. Bacteria release communication molecules. In small populations, these molecules float away. In large, dense populations, the molecules build up to a threshold level that signals the bacteria they are surrounded.

• Molecule Types: One universal molecule is used for general community information, while specialized molecules are used for within-species communication.

• Vibrio fischeri Case Study: These bacteria use q.s. molecules to sense when their population is large enough to switch on their bioluminescence. They live symbiotically in an organ of the Hawaiian bobtail squid. The light they produce prevents the squid from casting a shadow on moonlit nights, helping it avoid predators.

Domain Archaea: The Extremophiles

• General Traits: Extreme-loving prokaryotic microorganisms that can live without oxygen (anaerobic).

• Metabolism:

  • Some produce methane.

  • Autotrophs: Obtain energy from inorganic molecules or light.

  • Chemoautotrophs: Mostly get energy from chemicals in the environment.

  • Heterotrophs: Require organic compounds for growth.

• Unique Features:

  • Cell Walls: Lack peptidoglycan, a polymer found in most bacterial cell walls.

  • Cell Membranes: Contain unusual ether-linked lipids not found in any other group of organisms. These lipids are stable at high temperatures.

  • Genetic Structure: Structure and function of genes (and RNA) are more similar to eukaryotes than to bacteria.

• Classifications of Archaea:

  • Methanogens: Produce methane; live in oxygen-free environments like swamps or sewage plants.

  • Halophiles: Thrive in highly saline (salt-loving) environments.

  • Thermoacidophiles: Thrive in heat and acid (hot sulfur springs, volcanoes, deep-sea vents). Grow best at temperatures above $80\,^{\circ}\text{C}$.

Viruses: Structure and Characteristic Properties

• Nature of Viruses: Non-living infectious agents that replicate only inside the living cells of other organisms. They are dormant outside of a host cell.

• Non-Cellular Status: They lack cytoplasm, cell membranes, and membrane-bound organelles.

• Composition: Consist of genetic material (DNA or RNA) wrapped in a protective protein coat called a capsid (which accounts for $95\%$ of the virus total and determines shape).

• Antigens: Extensions on the virus that allow it to identify, attack, and enter a target host.

• Host Range: The specific number of species, tissues, or cells a virus can infect. Viruses are highly selective.

• Bacteriophage: A specific type of virus that infects bacteria.

• Genetics:

  • DNA: Found in the nucleus; contains sugar deoxyribose and bases A, T, C, G.

  • RNA: Found in the nucleus and cytoplasm; contains sugar ribose and bases A, U, C, G.

• Shapes: Rods, filaments, crystals, helixes, polyhedrons, and spheres with extensions (most human viruses are nearly spherical).

Viral Reproduction Cycles

• Lytic Cycle:

  • 1. Virus particle attaches to a host cell.

  • 2. Genetic instructions are released into the host.

  • 3. Viral material recruits host enzymes.

  • 4. Enzymes manufacture parts for new viruses.

  • 5. Parts assemble into new virus particles.

  • 6. The host cell lyses (breaks open), destroying the cell and releasing new viruses.

  • Replication Location: Occurs in the host cell's cytoplasm; viral DNA exists separately from host DNA.

• Lysogenic Cycle (The "Sleeping" Virus):

  • The viral DNA integrates into the host cell’s chromosome, becoming a provirus.

  • The host cell lives and reproduces normally, copying the viral DNA along with its own.

  • Latency: Effects may not be immediate (e.g., HIV). The virus can stay dormant for years.

  • Activation: A stimulus (environmental change like temperature, pH, or nutrient availability) can trigger the lytic cycle, leading to virus production.

Human Viral Diseases and Vaccines

• Lytic Cycle Example (Cold/Flu): Inhaled virus particles attach to sinus cells, reproduce rapidly, and cause cells to break. This results in fluid flow (runny nose), throat cell attacks (sore throat), and muscle cell attacks (aches).

• Vaccines: Liquid preparations of dead or weakened viral or bacterial cells. They work by "pre-infecting" the body so it can produce antibodies immediately upon real exposure.

• Genetic Variation: Viruses reproduce so quickly that they frequently undergo slight genetic changes. This alters their protein coat, which is why a vaccine from one year may not be effective the next.

Table: Examples of Human Viral Diseases