Biology: Viruses, Prokaryotes, Protists, Plants, and Fungi

A comprehensive vocabulary review set covering viral replication and hypotheses, bacterial structure and metabolisms, protistan supergroups, land plant adaptations and anatomy, and fungal phyla and reproductive cycles.

Virus

An infectious particle consisting of genes packed in a protein coat that occasionally has an outer membrane or envelope and requires a host to replicate.

Progressive Hypothesis

A hypothesis on viral origins stating that viruses arose from genetic elements that gained the ability to move between cells.

Regressive Hypothesis

A hypothesis on viral origins asserting that viruses are remnants of cellular organisms.

Virus-First Hypothesis

A hypothesis on viral origins proposing that viruses predate or coevolved with current cellular hosts.

Viral Genome

The genetic material of a virus, which can be either DNA or RNA as a single linear or circular molecule containing between $3$ and $2{,}000$ genes.

Capsid

The protein shell enclosing the viral genome, built from protein subunits called capsomeres.

Viral Envelope

A membrane structure derived from host cell membranes that surrounds the capsid in some viruses, such as influenza.

Bacteriophages

Viruses that infect bacteria by injecting their DNA.

Host Range

The limited number of species that a particular virus is capable of infecting.

Lytic Cycle

A phage replicative cycle that culminates in the death of the host cell by breaking open the cell wall to release progeny viruses.

Virulent Phage

A bacteriophage that replicates exclusively through a lytic life cycle.

Lysogenic Cycle

A viral replicative cycle in which the phage genome replicates without destroying the host cell, incorporating the viral DNA into the host cell genome.

Temperate Phages

Bacteriophages that are capable of using both lytic and lysogenic cycles of replication.

Retroviruses

Viruses that utilize reverse transcriptase to copy their RNA genome into DNA so it can integrate into the host genome.

Provirus

Viral DNA resulting from retroviral reverse transcription that is integrated into the host cell's genome.

Pattern Recognition Receptors

Receptors situated on host cells that recognize and bind to structures that are unique to microbes as part of the innate immune system.

Interferon Response

An innate immune defense where special interferons are released by an infected host cell to prevent neighboring cells from becoming infected.

Epitopes

Specific regions on the surface of antigens with shapes complementary to antigen receptor binding sites.

Primary Immune Response

The adaptive immune response mounted upon the first exposure to a specific antigen.

Secondary Immune Response

The adaptive immune response mounted upon a second exposure to an antigen, which is typically faster than the primary response.

Prokaryotes

Small, usually unicellular organisms lacking membrane-enclosed organelles and a nucleus, containing a single circular chromosome with genes arranged in operons.

Gram-Positive Bacteria

Bacteria that possess simple cell walls composed of a large amount of peptidoglycan.

Gram-Negative Bacteria

Bacteria that possess less peptidoglycan in their cell wall and have a second outer membrane containing lipopolysaccharides.

Capsule

A dense and well-defined layer or slime layer surrounding the bacterial cell wall that provides adherence to substrates or other bacteria.

Fimbriae

Hairlike appendages on prokaryotes that allow them to adhere to their substrate or other surroundings.

Pili

Longer surface appendages compared to fimbriae that pull cells together to enable DNA transfer.

Endospores

Multilayered, resistant structures formed around a duplicated chromosome in times of environmental distress to preserve DNA.

Taxis

The directed movement of an organism toward or away from a stimulus, typically accomplished via flagella.

Nucleoid

A non-membrane-enclosed region in a prokaryotic cell where the single circular chromosome is located.

Plasmids

Small, independently replicating rings of DNA in prokaryotes that carry additional survival genes.

Transformation

A process of genetic recombination in which a prokaryote takes up foreign DNA from its surroundings due to competence or increased membrane permeability.

Transduction

A process of genetic recombination where bacteriophages transfer prokaryotic genes from one host cell to another.

Conjugation

A mechanism of horizontal gene transfer in which a pilus pulls two prokaryotes together to transfer DNA, dependent on an F factor.

Catabolic Pathways

Metabolic pathways that release energy by breaking down complex molecules into simpler compounds, such as in cellular respiration.

Anabolic Pathways

Metabolic pathways that consume energy to build complex molecules from simpler ones, such as in photosynthesis.

Chemoautotrophs

Organisms that carry out an anabolic process using inorganic energy sources to synthesize larger molecules, with most living in extreme conditions.

Photoautotrophs

Organisms that trap light energy and convert it to chemical energy either with or without oxygen through an anabolic process.

Obligate Aerobes

Organisms that require $\text{O}_2$ for cellular respiration.

Obligate Anaerobes

Organisms that are poisoned by $\text{O}_2$ and survive via fermentation or by utilizing substances other than $\text{O}_2$.

Facultative Anaerobes

Organisms that can switch between metabolizing energy with $\text{O}_2$ or without $\text{O}_2$.

Photoheterotrophs

Organisms that break down organic molecules from other organisms to obtain carbon and energy while also retaining the ability to harvest energy from light.

Metagenomics

A DNA sequencing approach used to analyze the collective genomes of prokaryotic communities directly, including uncultured species.

Proteobacteria

A diverse bacterial lineage of gram-negative photoautotrophs, chemoautotrophs, and heterotrophs that include potential pathogens.

Chlamydias

A phylum of obligate parasitic, gram-negative bacteria whose cell walls lack peptidoglycan.

Spirochetes

Helical, gram-negative heterotrophic bacteria that move through their environment via rotating internal filaments.

Cyanobacteria

Gram-negative photosynthetic autotrophs responsible for generating oxygen and causing the Great Oxidation Event.

TACK

An archaeal supergroup composed of multiple closely related clades of Archaea.

Lokiarchaeotes

A recently discovered group of Archaea distinct from the TACK supergroup.

Symbioses

Long-term biological relationships between two different species living in close physical or physiological contact.

Nitrogen Fixing

The biological transformation of atmospheric nitrogen into forms accessible to other organisms, performed by prokaryotes.

LECA

Last Eukaryotic Common Ancestor; the ancestral lineage from which all modern eukaryotic organisms descended.

Plastids

Plant and algal organelles that originated via the endosymbiotic engulfment of a photosynthetic cyanobacterium by a heterotrophic eukaryote.

Protists

An informal term describing all eukaryotic organisms outside of the kingdoms Plantae, Animalia, and Fungi.

Excavata

A major eukaryotic protist group characterized by the presence of a specialized cytoskeleton.

Euglenozoans

A diverse clade of Excavata that includes predatory heterotrophs, autotrophs, mixotrophs, and parasites characterized by a spiral or crystalline rod inside their flagella.

SAR

A large eukaryotic supergroup composed of Stramenopiles, Alveolates, and Rhizarians.

Stramenopiles

Photosynthetic protists characterized by possessing both a hairy flagellum and a smooth flagellum.

Diatoms

Unicellular photosynthetic algae possessing a unique two-part, glass-like wall (frustule) composed of $\text{SiO}_2$.

Brown Algae

The largest and most complex multicellular algae; foundational species that exhibit alternation of generations.

Alternation of Generations

A life cycle that alternates between multicellular haploid (gametophyte) and multicellular diploid (sporophyte) stages.

Alveolates

Protists defined by membrane-enclosed sacs (alveoli) located directly underneath the plasma membrane.

Dinoflagellates

Alveolate protists possessing two flagella located in perpendicular grooves within armor-like cellulose plates.

Archaeplastida

A eukaryotic supergroup that includes red algae, green algae, and land plants.

Opisthokonts

A clade containing animals, fungi, and related protists whose motile cells are propelled by a single posterior flagellum.

Choanoflagellates

Free-living unicellular and colonial flagellated eukaryotes that are the closest living relatives of animals.

Holdfast

A root-like structure that anchors multicellular algae to hard substrates.

Stipe

A stem-like supporting structure found in multicellular algae.

Blade

A flattened, leaf-like photosynthetic structure found in multicellular algae.

Embryophytes

Land plants that possess specialized adaptations for life in terrestrial environments.

Tracheophytes

Plants possessing specialized vascular tissues (xylem and phloem).

Mycorrhizae

Symbiotic associations between fungi and plant roots that acted as the first root structures on early land plants.

Gametophyte

The multicellular haploid generation in the plant life cycle that produces haploid gametes.

Sporophyte

The multicellular diploid generation in the plant life cycle that produces spores capable of developing without fertilization.

Apical Meristems

Localized regions of cell division at the tips of roots and shoots that sustain continuous indeterminate growth.

Cuticle

A waxy exterior covering on the epidermis of land plants that prevents desiccation and water loss.

Stomata

Microscopic pores in the epidermis of plants that facilitate gas exchange between internal tissues and the external air.

Bryophytes

A non-monophyletic group of non-vascular land plants that depend on water for survival and spend the majority of their life cycle as gametophytes.

Xylem

Vascular tissue responsible for the unidirectional transport of water and dissolved minerals from roots upward.

Phloem

Vascular tissue responsible for the bidirectional transport of sugars, amino acids, and other organic solutes.

Microphylls

Small leaves supported by a single unbranched strand of vascular tissue, which evolved as outgrowths of stems.

Megaphylls

Leaves with a highly branched vascular system that evolved through the webbing together of flattened branch systems.

Pollen Grain

A structure consisting of the male gametophyte enclosed within a protective pollen wall.

Ovule

A structure composed of a megaspore, megasporangium, and protective integuments that develops into a seed following fertilization.

Gymnosperms

Vascular seed plants whose seeds are exposed on modified leaves called sporophylls rather than enclosed in ovaries.

Angiosperms

Vascular seed plants that produce reproductive structures known as flowers and fruits.

Fruits

Mature, thickened ovary walls of flowering plants that enclose seeds and facilitate their dispersal.

Fungi

Monophyletic, absorptive heterotrophic eukaryotes characterized by the absence of phagotrophy and the presence of cell walls composed of chitin.

Green Theory

A hypothesis proposing that ancestral fungi were strictly dependent on green plants for their colonization of land.

Brown Theory

A hypothesis proposing that zoosporic fungi acquired saprotrophic habits and colonized sediments or damp land by evolving hyphal morphology.

White Theory

A hypothesis stating that zoosporic fungi adapted to frozen environments to serve as evolutionary intermediates between aquatic and terrestrial habitats.

Septa

Cross-walls dividing fungal hyphae into cells, perforated by pores that permit the movement of organelles and cytoplasm.

Coenocytic Fungi

Fungi that lack septa and consist of a continuous cytoplasmic mass containing multiple nuclei.

Mycelium

The densely branched vegetative network of thread-like hyphae that absorbs nutrients from the environment.

Plasmogamy

The fusion of the cytoplasm of two parent mycelia without the immediate fusion of their nuclei.

Heterokaryon

A fungal mycelium that contains two or more genetically distinct, coexisting haploid nuclei per cell.

Karyogamy

The fusion of two haploid nuclei within a fungal heterokaryon to form a diploid zygotic nucleus.

Cryptomycetes

A basal, globally distributed soil lineage of unicellular fungi that produce flagellated spores.

Microsporidians

Unicellular parasitic basal fungi possessing reduced mitochondrial remnants and extremely compact genomes with infectious spores.

Chytridiomycota

The simplest true fungal phylum, predominantly aquatic, characterized by flagellated spores termed zoospores.

Ascomycota

A true fungal phylum characterized by septate hyphae with pores and the production of sexual spores inside microscopic saclike structures called asci.