Viruses, Prokaryotes, and Protista Exam Review

General Characteristics of Viruses

• Definition: Viruses are non-cellular infectious agents.

• Structural Composition:     * They consist of a protein coat (capsid) surrounding a core of genetic material, which can be either DNA or RNA.     * They possess no ribosomes or other metabolic machinery of their own.

• Replication and Evolution:     * Viruses replicate only within a living host cell.     * They evolve via natural selection and are characterized by a high mutation rate.

• Specific Examples and Types:     * Tobacco Mosaic Virus: A nonenveloped plant virus characterized by protein subunits of the coat surrounding viral RNA.     * Herpesvirus: An enveloped animal virus featuring an envelope (derived from a bit of the host's membrane) and a protein coat beneath that envelope surrounding viral DNA and enzymes.     * Retrovirus: An RNA virus that utilizes the enzyme reverse transcriptase to produce viral DNA inside a host cell. Its structure includes:         * Lipid envelope with proteins.         * Viral glycoproteins that bind to host proteins.         * Viral coat proteins.         * Two identical strands of viral RNA.

Viral Diseases and Pathogenesis

• Pathogenic Nature: Viral diseases are caused by pathogenic viruses.

• Symptom Expression: Symptoms are usually mild, but some viruses persist in the body for long periods (latent infections), such as the herpes virus.

• Transmission: Some viruses require vectors for transmission, such as the West Nile virus.

• Long-term Health Impacts: Certain viruses increase the risk of cancer; for example, the Human Papillomavirus (HPV) is the primary cause of cervical cancer.

• Genetic Plasticity:     * RNA viruses exhibit particularly high mutation rates.     * Viral Recombination: This occurs when viral genomes exchange genes if two different viruses infect a single host cell simultaneously.

Overview of Prokaryotes: Bacteria and Archaea

• General Physical Traits:     * Prokaryotes are unicellular organisms.     * They are very small, typically ranging from $1-5\,\mu\text{m}$ in size, which is approximately $\frac{1}{10}$ the size of eukaryotic cells.

• Ubiquity and Biomass:     * Prokaryotes are found everywhere on Earth.     * Their total biological mass is at least $10\times$ that of all eukaryotes combined.

• Ecological Roles:     * They play crucial roles in the biosphere as photosynthetic organisms and decomposers.     * While a minority cause disease in humans, the majority are essential for life.

Prokaryotic Traits and Anatomy

• Table 19.1: Universal Prokaryotic Traits:     1. Absence of a nucleus, endoplasmic reticulum, and Golgi bodies.     2. Possess a single chromosome (a circular DNA molecule); many species also contain smaller DNA loops called plasmids.     3. Most species have a cell wall.     4. Ribosomes are distributed freely in the cytoplasm.     5. Reproduction occurs asexually through binary fission.     6. Capacity for gene exchange among existing cells via conjugation, transduction, and transformation.

• Structural Components:     * DNA: Circular genetic material.     * Cytoplasm: Contains ribosomes.     * Plasma Membrane: Inner boundary.     * Cell Wall: Provides structure.     * Capsule: Outer protective layer.     * Flagellum: Tail-like structure for movement.     * Pilus: Hair-like appendages for attachment or gene transfer.

Identification and Classification of Bacteria

• Cell Shapes:     * Cocci: Spherical shape.     * Bacilli: Rod shape.     * Spirochete: Spiral shape.

• Cell Wall Composition:     * The bacterial cell wall is composed of Peptidoglycan, a polymer of sugars cross-linked by short polypeptides.

• Gram Staining Differences:     * Gram-positive Bacteria: Feature a thick peptidoglycan layer above the plasma membrane.     * Gram-negative Bacteria: Feature a thinner peptidoglycan layer situated between the plasma membrane and an outer membrane containing lipopolysaccharides and proteins.

Reproduction and Gene Exchange in Bacteria

• Vertical Gene Transfer (Binary Fission):     1. The bacterium has one circular chromosome attached to the inside of the plasma membrane.     2. The cell duplicates the chromosome, attaches the copy beside the original, and adds membrane and wall material between them.     3. When the cell nearly doubles in size, new membrane and wall materials are deposited across the midsection.     4. The process results in two genetically identical cells.

• Horizontal Gene Transfer:     * Conjugation: Transfer of DNA between cells through direct contact (often via a pilus).     * Transformation: The introduction and uptake of foreign DNA from the environment (e.g., Streptococcus pneumonia).     * Transduction: The process by which DNA is transferred from one bacterium to another by a viral vector.

Specific Bacterial Lineages and Human Impact

• Cyanobacteria:     * Photosynthetic cells often found in partnerships with fungi to form lichens.     * They contain nitrogen-fixing cells that convert atmospheric nitrogen into ammonia ($NH_3$).     * Evolutionary significance: Chloroplasts in eukaryotes evolved from ancestral cyanobacteria.

• Bacteria and Human Health:     * Normal Flora: Normally harmless or beneficial microorganisms living in or on the body. Examples include E. coli (produces Vitamin K) and Lactobacillus sp. (produces Vitamin B).     * Pathogenic Bacteria: Specifically cause disease.

Archaea and Extremophiles

• Evolutionary Context: Archaea constitute a distinct domain of prokaryotes that share a common ancestor with eukaryotes, forming a closer clade to eukaryotes than bacteria do in some phylogenetic models.

• Specialized Groups:     * Extreme Halophiles: Salt-loving organisms.     * Extreme Thermophiles: Heat-loving organisms.     * Methanogens: Methane-producing organisms.

Kingdom Protista: Overview and Nutrition *eukaryotic organism that cannot be classified as plant, animal, or fungus

• Complexity: Protists exhibit a high level of cellular complexity and undergo both mitosis and meiosis.

• Taxonomic Status: Taxonomical relationships are not well understood; the kingdom is considered a collection of lineages, some of which are only distantly related.

• Modes of Nutrition:     * Autotrophy: Self-feeding via photosynthesis (e.g., Caulerpa, a green alga).     * Heterotrophy: Consuming other organisms (e.g., Giardia, a parasite).     * Mixotrophy: Capable of both photosynthesis and heterotrophy (e.g., Euglena).

Animal-like Protists (Protozoans)

• Flagellates:     * Example: Trypanosoma. Characterized by a single large mitochondrion. It is a blood parasite causing sleeping sickness, transmitted by the tsetse fly.

• Ciliates:     * Example: Paramecium. Use hair-like cilia to move and sweep food into mouth. Structures include food vacuoles, contractile vacuoles (filled and empty states), and a nucleus.

• Amoebas:     * Free-living and "test-free" (lack a hard shell).     * Some inhabit the guts of humans and animals.     * Use lobe-shaped pseudopodia for movement and feeding.

• Forams:     * Characterized by a calcium carbonate ( $CaCO_3$ ) shell.

• Choanoflagellates:     * Closest known protistan relatives of animals.     * Possess a flagellum surrounded by a "collar" of threadlike projections.     * Structure is similar to sponge cells; they live as single cells or in colonies.

Fungus-like Protists: Slime Molds

• General Nature: Known as "social amoebas"; animal signaling mechanisms may have originated in amoebozoan ancestors.

• Plasmodial Slime Molds:     * Form a plasmodium, which is one large mass of cytoplasm containing many nuclei (a single large cell).     * Found in moist environments with decaying organic material; often have brightly colored pigments.

• Cellular Slime Molds:     * Found on rotting logs and decaying matter.     * Exist as solitary amoeboid cells but form slug-like aggregates when food is scarce.     * The mobile, multicelled "slug" seeks a spot to differentiate into a fruiting body to disperse spores.

Plant-like Protists: Algae

• Dinoflagellates:     * Possess two flagella in perpendicular grooves, causing them to spin as they move.     * Have cellulose plates under the cell membrane.     * Coastal marine species can "bloom" in summer, creating "red tides" where water appears golden or red.

• Diatoms:     * Feature a two-part shell made of silica.     * Store food in the form of lipids.     * Their remains form diatomaceous earth, used as a filtering agent.

• Green Algae:     * Can be unicellular, multicellular, or colonial.     * Closely related to land plants; contain chlorophyll for photosynthesis and cellulose in cell walls.

• Multicellular Algae (Kelp):     * Mostly marine and plant-like in appearance, though they lack true roots, stems, or leaves.     * Contain the brown pigment fucoxanthin.     * Serve as a source of algins, which are used as thickeners and emulsifiers.