Bio Final

Virology

The study of viruses and viral diseases.

SEQ Evolution by Natural Selection

A process involving heritable variation in traits, environmental pressure, differential survival and reproduction, and changes in allele frequency over generations.

Heritable Variation in Traits

Genetic variation that must be present for evolution to occur.

Environmental Pressure

Factors such as limited resources and predators that affect survival and reproduction.

Differential Survival & Reproduction

The concept that individuals with beneficial traits survive and reproduce more effectively.

Frequency of Beneficial Traits

The increase in the prevalence of advantageous traits in a population over time.

Evolution

The change in allele frequencies in a population over generations.

Parts of a Phylogenetic Tree

Components such as root, nodes, basal taxon, and sister taxa that illustrate evolutionary relationships.

Root

The base of a phylogenetic tree representing the common ancestor of all taxa in the tree.

Node

A point in a phylogenetic tree where a lineage diverges from a common ancestor.

Basal Taxon

A lineage that diverges early in the evolutionary history of a group.

Sister Taxa

Two taxa that share an immediate common ancestor.

Polytomy

A branch point in a phylogenetic tree where more than two groups emerge, indicating uncertainty.

Monophyletic Group

A group consisting of a common ancestor and all its descendants.

Paraphyletic Group

A group that includes a common ancestor and some, but not all, of its descendants.

Polyphyletic Group

A group that does not include the most recent common ancestor of its members.

PSC (Phylogenetic Species Concept)

The smallest group of organisms that share an evolutionary history.

Dichotomies

Two-way branch points in a phylogenetic tree.

Branch Points / Nodes

Points that represent divergence from a common ancestor.

SEQ General Viral Replication Cycle (Lytic)

The process by which a virus replicates and assembles new viruses, leading to the destruction of the host cell.

Lytic Cycle

A viral replication cycle where the host cell is destroyed.

Lysogenic Cycle

A viral replication cycle where the virus integrates into the host genome and replicates with the host.

Host Cell Fate in Lytic Cycle

The host cell is destroyed (lysed).

Host Cell Fate in Lysogenic Cycle

The host cell survives while the virus integrates into the host bacterial chromosome.

Transmission in Lytic Cycle

Horizontal transmission from host to host.

Transmission in Lysogenic Cycle

Vertical transmission passed to daughter cells or host offspring.

Viral DNA Status in Lytic Cycle

Active replication occurs immediately after entry.

Viral DNA Status in Lysogenic Cycle

Viral DNA integrates into the host genome and becomes a prophage.

Virus Type in Lytic Cycle

Virulent phages that are only capable of the lytic cycle.

Virus Type in Lysogenic Cycle

Temperate phages that can perform both lytic and lysogenic cycles.

Conditions for Lytic Cycle

Triggered by stress or poor host conditions.

T4 bacteriophage

Lambda phage (λ)

Prokaryotes

Cells that lack a nucleus and membrane-bound organelles.

Eukaryotes

Cells that have a nucleus and membrane-bound organelles.

Nucleus

A membrane-bound structure that contains the cell's genetic material.

Cell Size

Prokaryotes are smaller (~1-10 micrometers) while Eukaryotes are larger (~10-100 micrometers).

Cell Wall

Prokaryotes often have a cell wall with peptidoglycan; Eukaryotes have cell walls made of cellulose or chitin.

Gram +

Bacteria with a thick peptidoglycan wall that stains purple in gram stain and are less likely to cause serious disease.

Gram -

Bacteria with a thin peptidoglycan wall that stains pink in gram stain and are more likely to cause serious disease.

Cell Type

Prokaryotes are unicellular ONLY; Eukaryotes can be unicellular or multicellular.

Ribosomes

Prokaryotes have smaller ribosomes; Eukaryotes have larger ribosomes.

Flagellum

A structure used by prokaryotes for locomotion, powered by a proton gradient.

DNA Structure

Prokaryotes have circular DNA; Eukaryotes have linear chromosomes.

Modes of Reproduction

Prokaryotes reproduce asexually via binary fission; Eukaryotes can reproduce sexually or asexually.

Domains

Prokaryotes are classified into Bacteria and Archaea; Eukaryotes are classified into Eukarya.

Binary fission

A rapid (under optimal conditions), asexual reproduction method in prokaryotes resulting in identical offspring.

Mutation

Spontaneous changes in DNA during replication that occur in both prokaryotes and eukaryotes.

Genetic Recombination

The exchange of genetic material from different sources, occurring in both prokaryotes and eukaryotes.

Transformation

The uptake of foreign DNA from the environment by a cell.

Transduction

A process where a virus accidentally grabs bacterial DNA and transfers it to a new bacterium.

Conjugation

Direct DNA transfer via pilus from F- to F+ bacteria.

Energy Source / Carbon Source

Prokaryotes can be autotrophs (inorganic) or heterotrophs (organic).

Obligate aerobes

Organisms that require oxygen for survival.

Obligate anaerobes

Organisms that are poisoned by oxygen and use fermentation or anaerobic respiration.

Facultative anaerobes

Organisms that use oxygen when available but can switch to anaerobic methods when it is not.

Bacteria

Prokaryotic organisms that have peptidoglycan in their cell walls.

Archaea

Prokaryotic organisms that do not have peptidoglycan in their cell walls.

Eukaryotic Cells

Cells characterized by the presence of a nucleus and membrane-bound organelles.

Size of Eukaryotic Cells

Eukaryotic cells range from 10-100 micrometers.

Cytoskeleton

Well-developed (helps w/ structure + enables shape & asymmetry)

Cell Type

Unicellular or multicellular

Reproduction

Mitosis or Meiosis

DNA Structure

Linear chromosomes in nucleus

Ancestral Archaean

Anaerobic organism that engulfs aerobic alpha-proteobacterium

Eukaryote with mitochondria

Result of Primary Endosymbiosis - phagocytosis of bacterium by larger cell

Photosynthetic Eukaryote

E.g., Green Alga; formed from engulfing cyanobacterium

Eukaryote with Secondary Plastid

Result of Secondary Endosymbiosis - bigger heterotrophic eukaryote engulfs smaller autotrophic eukaryotic

Cellularity

Mostly unicellular; some colonial or multicellular

Nutrition Types

Heterotrophs, photoautotrophs, mixotrophs (does photosynthesis + consumes other organisms)

Relevance

First eukaryotic cells (~1.8 BYA); evolved ~1 billion years before plants, fungi, animals

Organization

Complex internal structures despite often being unicellular.

Morphology

Highly diverse (amoebas, algae, etc.)

Evolutionary Term

"Protist" = outdated and paraphyletic, but still commonly used.

Archaeplastida

Primary plastids (from cyanobacteria); includes red algae, green algae, land plants

SAR

Secondary plastids from red algae (via secondary endosymbiosis)

Stramenopiles

Hairy + smooth flagella; includes diatoms, golden algae, brown algae

Alveolates

Alveoli (flattened vesicles just inside the plasma membrane that support the membrane); includes dinoflagellates, apicomplexians, ciliates

Rhizarians

Genetic traits, shells made of calcium/silica

Amoebozoa

Love/tube-shaped pseudopodia; includes slime molds, entamoebas

Opisthokonta

Posterior flagellum, diverse group, related to fungi/animals; includes animals, fungi, choanoflagellates, nucleariids

Euglenids

A type of protist

Trypanosomes

A type of protist

Discoba

Crystalline rod in flagella, some have 2º plastids from green algae → mixotrophic

Eukaryotes

Organisms with complex cells that have a nucleus.

SAR Supergroup

Includes groups with secondary plastids from red algae via secondary endosymbiosis.

Stramenopiles

Includes Diatoms, Golden Algae, Brown Algae (hairy + smooth flagella).

Alveolates

Includes Dinoflagellates, Apicomplexans, Ciliates (membrane-bound sacs).

Rhizarians

Includes Radiolarians, Foraminiferans, Cercozoans (calcium-based shells).

Archaeplastida

Includes groups with primary plastids from cyanobacteria.

Red Algae

Multicellular, red pigment, found in deep water.

Green Algae

Includes Chlorophytes (mostly freshwater, unicellular or colonial) and Charophytes (sister group to land plants).

Land Plants

Not algae; evolved later from Charophytes.

Unikonta

Includes Amoebozoans and Opisthokonta.

Amoebozoans

Characterized by lobe-shaped pseudopodia.

Opisthokonta

Includes Nucleariids (sister group to fungi), Fungi, Choanoflagellates (sister group to animals), and Animals.

Fungi

Ancient lineage; absorptive heterotrophs.

Nucleariids

Amoeba-like; filose pseudopodia.

Chytrids

Primitive fungi; flagellated spores.

Hyphae

Long threadlike structures that make up the main body of fungus; filamentous.

Aerial hyphae

Special structures that reach up & release spores into the air.