Introduction to Classification, Evolution, and Plant Biology

Taxonomy

Science of describing, naming, & classifying organisms.

Phylogeny

Evolutionary history of a species or group of related species.

Species

Basic level of classification.

Nested Hierarchy

Groups from Broad to narrow are: Domain to Species.

Taxon

General name for group at any level.

Evolution

Change in ALLELES over time.

Natural Selection

Differential survival and adaptation.

Diversity

Three types of diversity: Genetic, Species, Community and Ecosystem.

Phylogeny (in context)

Represents an evolutionary hypothesis.

Monophyletic

A group that consists of an ancestor and all its descendants.

Paraphyletic

A group that includes an ancestor but not all its descendants.

Polyphyletic

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

Branch point

Where lineages diverge in a phylogenetic tree.

Sister taxa

Groups that share a most recent common ancestor.

Basal taxon

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

Polytomy

A branch point from which more than two descendant groups emerge.

Extant species

Species that are not extinct.

Obligate intracellular parasites

Viruses that require a host cell to replicate.

Capsid

Protein coat that surrounds DNA/RNA in viruses.

Host range

The specific species that a virus can infect.

Lytic Cycle

Viral replication cycle that kills the host at the end.

Lysogenic Cycle

Viral replication cycle where virus DNA hides in hosts as a prophage.

Virulent phage

Phage that kills the host at the end of the cycle.

Temperate phage

Phage that can use either the lytic or lysogenic cycle.

Prophage

Virus DNA that hides in hosts during the lysogenic cycle.

Prokaryotes

Organisms that lack a nucleus and membrane-bound organelles.

Probiotic Soup

Hypothesis about how life first originated.

Iron-sulfur

Another hypothesis about the origin of life.

DNA location in prokaryotes

Prokaryotes put their DNA in the nucleoid region.

Nucleoid

Single haploid chromosome found in prokaryotes.

Prokaryotes

Organisms that lack a membrane-bound nucleus and have a simpler internal organization.

Cell Wall Functions

Protection, maintain cell shape, and prevents bursting in hypotonic solution.

Peptidoglycan

A component found in the cell wall of bacteria, varying in amounts between species.

Gram Staining

A two-step process using crystal violet and safranin to identify bacteria.

Gram Positive

Bacteria that appear purple due to thick cell walls that hold the violet stain.

Gram Negative

Bacteria that appear pink due to a thin peptidoglycan layer that does not hold the violet stain.

Motility

The ability of some prokaryotes to move.

Taxis

Movement of an organism in response to a stimulus, can be positive or negative.

Flagella

A structure used for movement, found in all domains but analogous in structure due to convergent evolution.

Binary Fission

A method of asexual reproduction in prokaryotes that produces identical copies.

Genetic Diversity

Variability in genetic characteristics within a population, promoted by rapid reproduction and mutation.

Mutation Rate

The chance of a mutation occurring in a gene is 1 in 10 million.

E. coli Mutations

E. coli populations can have about 9 million mutations per day in a human host.

Vertical Gene Transfer

Transfer of genetic material from parent to offspring.

Horizontal Gene Transfer

Transfer of genetic material not from parent to offspring.

Transformation

A form of horizontal gene transfer where DNA from the surroundings is incorporated into a bacterium.

Transduction

A process where phages transfer bacterial DNA between bacteria.

Conjugation

A process where DNA is shared between two individuals, involving a pilus.

Phototrophs

Organisms that obtain energy from light.

Chemotrophs

Organisms that obtain energy from chemical reactions.

Cyanobacteria

Photoautotrophs that obtain energy from sunlight.

Autotroph

An organism that uses CO2 as a carbon source.

Heterotroph

An organism that obtains carbon from food.

Clostridium botulinum

A chemoheterotroph that gets energy from chemical reactions and carbon from food.

Obligate Aerobe

needs oxygen (like you!)

Obligate Anaerobe

oxygen will kill, must have none

Facultative Anaerobe

can live with or without oxygen

Obligate

required

Facultative

helps but not needed

Aer

Greek for air

An

as prefix means none

Prokaryotic Diversity

Divides prokaryotes into 2 domains

Bacterial Diversity

Includes mitochondria & other mutualistic bacteria

Cyanobacteria

Photoautotrophs

Cyanobacteria

Most gram negative

Cyanobacteria

Phytoplankton

Cyanobacteria

Ancestors of chloroplasts

Archaea Diversity

Prokaryotes

Extremophiles

Organisms that thrive in extreme environments

Cell walls but No peptidoglycan

Characteristic of Archaea

Halophiles

high salt environments

Thermophiles

very hot environments

Methanogens

unique to Archaea

Marsh gas

methane from Archaea

Eukaryotic Cell Structures

The root of Eukarya is not known

Polytomy

We are not sure who is the ancestor of whom

Endosymbiosis

a cell was engulfed by another cell and they now live together

Endosymbiont theory

Mitochondria and Chloroplasts were bacteria

Primary Endosymbiosis

a bacteria is engulfed

Serial Endosymbiosis

is when this happens in series

Plastids

organelles that result from Secondary endosymbiosis

Protists

A general word for all Eukaryotes but traditionally does not include the Plants, Animals, or Fungus

Archaeplastida

Ancient Plastids

Red Algae

Red color pigment phycoerythrin

Green Algae

Closely related to land plants

Chlorophytes

One of the two main groups of green algae.

Charophytes

The second main group of green algae.

SAR

A clade that includes Stramenopiles, Alveolates, and Rhizarians.

Shared derived traits

Characteristics that are unique to a particular clade.

Stramenopiles

A group characterized by long 'hairy' flagella and shorter 'smooth' flagella.

Photosynthetic algae

Algae that have chloroplasts and can perform photosynthesis.

Diatoms

A type of algae that contributed to the potato famine.

Brown Algae

Multicellular algae, such as kelp.

Alveoli

Flattened vesicles just inside the plasma membrane that support it.

Apicomplexans

A group of mostly parasitic organisms.

Malaria

A disease that killed over 384,000 people in 2019.

Rhizarians

A group characterized by a skeletal structure of calcium or silica.

Foraminiferans

A group of Rhizarians known as forams.

Tests

Porous shells made of calcium carbonate.

Amoebozoa

A group characterized by derived characteristics and genetic similarities.