Prokaryotes and Viruses Overview

- **Classification**: Prokaryotic cells belong to two primary domains: - **Bacteria**: These organisms are the most commonly known prokaryotes, with a wide variety of shapes, sizes, and metabolic capabilities. They are characterized by their peptidoglycan-rich cell walls. - **Archaea**: These organisms are often found in extreme environments and share similarities with both bacteria and eukaryotes; however, their cellular structure is distinctly different, lacking peptidoglycan.

#### Characteristics of Archaea - **Types**: - **Methanogens**: - Produce methane as a metabolic byproduct, especially in anaerobic environments. - Found in settings like swamps, marshes, and the intestines of ruminants. - Play a crucial role in the global carbon cycle by decomposing organic matter. - **Halophiles**: - Thrive in saline environments such as salt lakes and salt mines. - Possess unique adaptations to manage osmotic pressure, including specialized proteins. - Often exhibit bright pigmentation, which aids in protecting them from UV radiation. - **Thermophiles**: - Flourish in extremely hot environments, typically above 45°C (113°F). - Found in locations such as hot springs and hydrothermal vents. - Have enzymes that remain stable at high temperatures, useful for industrial applications. - **Psychrophiles**: - Adapted to cold temperatures, typically below 15°C (59°F). - Key players in polar ecosystems, often found in glaciers and deep-sea environments. - Help decompose organic materials in cold habitats, contributing to nutrient cycling.

#### Bacterial Structure and Function - **Key Structures**: - **Pili**: - Thin, hair-like appendages that enhance adhesion to surfaces and promote genetic exchange during conjugation. - Facilitate movement on surfaces in some bacteria (twitching motility). - **Capsule**: - A gelatinous layer surrounding the cell wall that prevents desiccation (water loss). - Protects the cell from phagocytosis by immune cells and helps bacteria adhere to surfaces. - Composed of polysaccharides or polypeptides, contributing to virulence in pathogenic bacteria. - **Cell Wall**: - Mainly composed of peptidoglycan, providing structural support and protection against osmotic pressure. - Differences in cell wall composition help classify bacteria into Gram-positive or Gram-negative groups; the latter has an additional outer membrane. - **Cell Membrane**: - A phospholipid bilayer that serves as a selectively permeable barrier, regulating import and export of substances. - Contains proteins that aid in transport processes and signal transduction. - **Chromosome**: - A single, circular strand of DNA located in the nucleoid region, containing essential genes for cellular functions and replication. - Chromosomal DNA is often coiled and supercoiled to fit within the prokaryotic cell. - **Plasmid**: - Small, circular DNA molecules that may carry genes beneficial for survival, such as antibiotic resistance. - Can replicate independently of chromosomal DNA, facilitating gene transfer through conjugation. - **Ribosome**: - Composed of RNA and proteins, these are the sites of protein synthesis, translating messenger RNA into proteins. - Prokaryotic ribosomes are smaller (70S) than eukaryotic ribosomes (80S). - **Flagellum**: - Long, whip-like structures that provide motility, allowing bacteria to swim toward nutrients and away from harmful substances. - Typically composed of the protein flagellin, and movement is powered by rotation. - **Cytoplasm**: - A jelly-like substance that fills the cell, housing various organelles and facilitating biochemical reactions necessary for life. - Contains enzymes, nutrients, and the cytoskeleton, which helps maintain cell shape.

#### Bacterial Shapes and Classification - **Shapes**: - **Coccus** (Round): - **Diptococcus**: Pairs of cocci, can lead to infections if pathogenic. - **Streptococcus**: Chains of cocci, often associated with diseases like strep throat. - **Staphylococcus**: Clusters resembling grapes, can be pathogenic (e.g., *Staphylococcus aureus*). - **Bacillus** (Rod-shaped): - **Diplobacillus**: Pairs of bacilli; can differ in pathogenic potential. - **Streptobacillus**: Chains of bacilli, some are linked to diseases like bacillary dysentery. - **Spirillum**: - Spiral-shaped bacteria, often free-moving, associated with certain illnesses such as leptospirosis. - **Gram Classification**: - **Gram-positive**: - Have a thick peptidoglycan layer that retains the crystal violet stain, appearing purple under a microscope. - Generally more susceptible to antibiotic treatments targeting cell wall synthesis. - **Gram-negative**: - Possess a thinner peptidoglycan layer and an outer membrane that does not retain the violet dye, appearing pink. - More resistant to many antibiotics due to the protective outer membrane.

#### Reasons for Prokaryotic Success 1. **Metabolic Diversity**: - **Autotrophic**: - Capable of producing organic molecules from inorganic sources, utilizing sunlight or chemical reactions (e.g., photosynthetic bacteria). - Examples include cyanobacteria, which perform oxygenic photosynthesis. - **Heterotrophic**: - Obtain energy by decomposing organic materials, obtaining nutrients from dead organisms (saprotrophs). - Include a variety of organisms that feed on living hosts (parasites) or on organic compounds (saprotrophs). 2. **Oxygen Utilization**: - **Obligate Aerobes**: - Require oxygen for survival and for carrying out cellular respiration to produce energy. - **Facultative Anaerobes**: - Capable of surviving with or without oxygen, switching their metabolic pathways based on availability, allowing adaptability to fluctuating environments. - **Obligate Anaerobes**: - Poisoned by oxygen; thrive only in anaerobic environments, such as the intestines, where they play essential roles in digestion. 3. **Ecological Niche Occupation**: - Occupy diverse habitats including extreme conditions such as geothermal vents, deep-sea environments, and highly variable terrains, reflecting a wide range of ecological roles. - Act as primary producers, decomposers, and play crucial roles in symbiotic relationships with other organisms. 4. **Endospore Formation**: - In adverse environmental conditions, specific bacteria can form endospores, dormant and resilient structures that enable survival through extreme heat, desiccation, and nutrient depletion. - Endospores can remain viable for years and can germinate when conditions become favorable again.

#### Evolution of Classification - **History**: - **Antonie van Leeuwenhoek** (1600s): - The first to effectively use microscopes to observe microorganisms, laying the foundation for microbiology. - **Ernst Haeckel** (1866): - Introduced the **Protist Kingdom**, expanding the classification framework to accommodate a broader range of life forms. - **1900s**: - The formal introduction of the **Bacteria** and **Fungi** kingdoms further refined classifications based on unique characteristics and ecological roles. - **Modern Classification**: - Living organisms are now classified into six kingdoms and three domains, based on cellular structure, genetic makeup, modes of reproduction, and nutritional strategies, reflecting evolutionary relationships.

#### Key Definitions - **Autotroph**: - Organisms that synthesize their own food from inorganic sources, including plants and certain bacteria, critically important in ecosystems as producers. - **Heterotroph**: - Organisms that derive energy and nutrients by consuming other organisms, playing essential roles in food webs as consumers. - **Photosynthetic**: - Organisms capable of converting sunlight into usable chemical energy through the process of photosynthesis. - **Terrestrial**: - Referring to living organisms that dwell on land, contrasting with **Aquatic**, which includes organisms living in water.

#### Differences Between Prokaryotic and Eukaryotic Cells - **Prokaryotic**: - Lacks a membrane-bound nucleus. - Absence of membrane-bound organelles. - Generally simpler in structure, predominantly unicellular. - Primarily reproduces through binary fission, a form of asexual reproduction. - **Eukaryotic**: - Contains a true nucleus enclosed by a nuclear membrane. - Possesses membrane-bound organelles that compartmentalize functions for enhanced efficiency. - Can exist as unicellular organisms (like yeast) or multicellular organisms (like plants and animals). - Reproduces through mitosis (asexual) or meiosis (sexual), allowing for genetic variation.

#### Methods of Bacterial Reproduction 1. **Asexual Reproduction**: **Binary Fission** leads to the production of two genetically identical daughter cells. - This method allows rapid population growth under favorable conditions, enabling quick colonization of environments. 2. **Sexual Reproduction**: - **Conjugation**: - Involves the transfer of genetic material, such as plasmids, between two bacterial cells through direct cell-to-cell contact, promoting genetic diversity. - **Transformation**: - Refers to the process where a competent bacterium uptakes naked DNA from its surroundings, allowing it to acquire novel traits.

#### Viruses Overview - **Classification**:

- Viruses are classified as non-living entities, lacking cellular structure and metabolic processes; they are technically not classified in any kingdoms due to their inability to reproduce independently. - **Reproduction**: - Viral reproduction is completely dependent upon host cells; they invade host cells to replicate. - **Lytic Cycle**: - Rapidly results in the destruction of the host cell while generating numerous viral particles, often leading to cell lysis. - **Lysogenic Cycle**: - Involves the integration of viral DNA into the host genome, where it can remain dormant (lysogeny) and can reactivate to enter the lytic cycle when conditions change.

#### Gene Therapy and Pathogens - **Gene Therapy Types**: - **Somatic Gene Therapy**: - Aimed at treating non-reproductive cells, offering potential cures for genetic diseases in patients without affecting descendants. - **Germline Gene Therapy**: - Targets reproductive cells, enabling genetic alterations that can be inherited by future generations, raising significant ethical and safety considerations. - **Virulence Factors**: - Specific attributes that enable certain bacteria and viruses to become pathogenic, including the production of toxins, secretory proteins that enhance their ability to invade host tissues and various mechanisms that evade host immune responses.

#### Classification of Protists - **General Characteristics**: - A highly diverse group, predominantly unicellular, primarily aquatic, capable of both sexual and asexual reproduction, and exhibiting nutritional strategies as either autotrophic (photosynthetic) or heterotrophic depending on species. - **Eukaryotes**: - The first eukaryotic cells are believed to have evolved from prokaryotic ancestors via the processes described in the endosymbiotic theory, where certain organelles originated from engulfed prokaryotic cells.

##### Classification of Living Organisms - Living organisms are categorized into various domains and kingdoms based on cell structure, metabolism, genetics, and evolutionary history. The primary domains include: - **Bacteria** - **Archaea** - **Eukarya**

##### 1. **Domain Bacteria** - **General Characteristics**: - Composed of prokaryotic cells that are unicellular and devoid of membrane-bound organelles, exhibiting outstanding metabolic diversity. - Exhibit various metabolic pathways that allow survival in a wide range of environments, often including extreme habitats. - Primarily reproduce through binary fission, which enables rapid population increases under optimal conditions. - **Kingdom Eubacteria**: - **Characteristics**: - Their cell walls often contain peptidoglycan, crucial for structural integrity and protecting against osmotic pressure. - Classified as Gram-positive or Gram-negative based on cell wall characteristics, which affect susceptibility to antibiotics. - Include both pathogenic species that can cause diseases and beneficial bacteria involved in processes like digestion (gut flora) and nutrient cycling. - - **Examples**: - *Escherichia coli* (commonly found in the intestine and some strains can cause food poisoning), - *Staphylococcus aureus* (linked to skin infections and more serious conditions), - *Streptococcus pneumoniae* (responsible for pneumonia and meningitis).

##### 2. **Domain Archaea** - **General Characteristics**: - Prokaryotic cells that are genetically and biochemically distinct from bacteria; they often have unique metabolic pathways that enable survival in hostile environments. - Typically thrive in extreme environments, known as extremophiles, such as hot springs or salt lakes. - Their cell walls lack peptidoglycan, distinguishing them from bacteria, which provides resistance to extreme conditions. - **Kingdom Archaebacteria**: - **Types**: - **Methanogens**: - Produce methane gas, predominantly found in anaerobic environments such as wetlands and within the digestive systems of certain animals. - **Halophiles**: - Thrive in high-salt concentrations, utilizing specialized adaptations to maintain cellular function in such environments; can produce compatible solutes to balance osmotic pressure. - **Thermophiles**: - Organisms adapted to high-temperature environments, with enzymes that remain stable and functional at elevated temperatures, making them valuable for industrial processes. - **Psychrophiles**: - Cool-adapted organisms capable of thriving in freezing temperatures, contributing to nutrient cycling in polar ecosystems; some species can remain active at sub-zero temperatures, impacting nutrient dynamics.

##### 3. **Domain Eukarya** - **General Characteristics**: - Comprises eukaryotic cells that feature a nucleus and membrane-bound organelles, which vastly increases cellular complexity. - Exists as unicellular organisms, like yeast, or multicellular organisms with varied structures and functions. - **Kingdom Protista**: - **Characteristics**: - Primarily unicellular, though some multicellular forms exist (e.g., certain algae). - Utilizes both autotrophic (through photosynthesis) and heterotrophic modes of nutrition depending on species. - **Examples**: - *Amoeba* (heterotrophic, known for its pseudopodia), - *Paramecium* (heterotrophic, uses cilia for movement), - *Euglena* (mixotrophic, capable of both photosynthesis and heterotrophy), and various algae like *Chlamydomonas* and *Spirulina*.

- **Kingdom Fungi**: - **Characteristics**: - Eukaryotic and primarily multicellular (with the exception of yeasts); absorb nutrients from their environment through external digestion. - Play indispensable roles as decomposers in ecosystems, breaking down organic materials and recycling nutrients back into the environment. - The structure of their cell walls is composed of chitin, which distinguishes them from the cellulose structures found in plant cell walls. - **Examples**: - Common edible mushrooms (e.g., *Agaricus bisporus*), various molds, and yeasts (e.g., *Saccharomyces cerevisiae* used in baking and brewing).

- **Kingdom Plantae**: - **Characteristics**: - Composed of multicellular organisms that are primarily autotrophic, conducting photosynthesis to convert solar energy into chemical energy. - Possess cell walls made primarily of cellulose, providing mechanical support and rigidity, essential for erect growth. - **Examples**: - Trees, flowering plants, ferns, and mosses, all of which play critical roles as primary producers in ecosystems.

- **Kingdom Animalia**: - **Characteristics**: - Comprised of multicellular, heterotrophic organisms that do not possess cell walls, allowing mobility and interaction with their environment. - Animals exhibit a high degree of complexity and diversity, with various adaptations to occupy diverse habitats. - **Examples**: - Mammals (e.g., humans and whales), birds (e.g., eagles), reptiles (e.g., snakes), amphibians (e.g., frogs), and various invertebrates such as insects (e.g., ants).

##### Summary of Major Domains and Their Kingdoms - **Domain Bacteria**: - Kingdom Eubacteria - **Domain Archaea**: - Kingdom Archaebacteria - **Domain Eukarya**: - Kingdom Protista - Kingdom Fungi - Kingdom Plantae - Kingdom Animalia