Taxonomy Pyramid from bottom to top

(Do Koalas Perfer Chocolate Or Fruit, Generally Speaking?)

Domain

Kingdom

Phylum

Class

Order

Family

Genus

Species

Biological Taxonomy

where classifications follow a specific hierarchy that gets increasingly refined as you work down the ranks

(top to bottom)

Secies

a group of organisms that are able to reproduce and produce viable offspring

Domains in Prokaryotes

bacteria, archaea

Domains in Eukaryotes

eukarya

Species Name

homo sapiens

Genus in the Species Name

homo

Specific Epithet in Species Name

sapiens

Monera

single referring to single-celled organisms

Three Characteristics of Prokaryotic Cells

- DNA is circular

- No membrane-bound nucleus

- No membrane-bound organelles

Extremophiles

a very old group of organisms that inhabit the more extreme environments

Characteristics of Domain Archaea

• No peptidoglycan in cell walls
• Unique lipid construction in plasma membrane
• May be more closely related to Eukaryotes than they are to other Prokaryotes
• Some contain introns – non-coding parts of a gene.

Introns

the non-coding parts of a gene

Domain Archaea: Extremophiles

• Methanogens
• Halophiles
• Thermoacidophiles

Methanogens

• Live below the mire (mud) in swamps
• “methane makers”
• Reduce carbon dioxide to methane (swamp gas)
• Poisoned by oxygen (obligate anaerobe)

Halophiles

• Live in very salty places (15-20% salinity; normal sea water is 3%)
• Color is due to the presence of a pigment called bacteriorhodopsin
• Have the simplest form of photophosphorylation
• - Uses light (but with carotenoids – so not called
  photosynthesis)
• Can be found in places such as Great Salt Lake or Dead Sea

Thermoacidophiles

• Live in areas with a pH of 2 and below & temps above 60° C
• Example: Picrophilus- grows at 0.7 pH and can tolerate 0.0 pH; will disintegrate at 4.0 pH
• Can be found in areas such as deep sea vents or hot sulfur springs

Gram (+)

where there's lot of peptidoglycan in cell wall; stains violet

Gram (-)

where there's very little peptidoglycan in wall; stains red/pink

Domain Bacteria Characteristics

• Most have peptidoglycan in their cell walls
• Have ribosomes that are different from in eukaryotic cells
• Have chemotaxis
• Have phototaxis
• No mitosis or meiosis; divide by binary fission
• Can have extra-chromosomal DNA in plasmids
• Some can form endospores (cells able to withstand harsh environmental conditions)
• Some have pilli (for attachment or conjugation)
• Have various morphologies and arrangements.

Flagella

composed of flagellin (protein)

Chemotaxis

movement in response to a chemical gradients (+ or -)

Phototaxis

movement in response to light (+ vs. -)

Bacillus's Shape

rod shape

Cocci's Shape

Round Shape

Spirilla's shape

spiral shape

Diplo-

paired arrangement

Strepto-

chained arrangement

Staph-

cluster arrangement

Mitosis

the process eukaryotes use to divide nuclear DNA during cell division

Cell Division

what is used to replace old cells and grow larger

Binary Fission

how bacteria reproduce

Plasmids

it's self-replicating circular chromosomes not associated with the bacteria's normal chromosome. assists in genetic recombination

The three types of Plasmids

• Conjugation
• Transformation
• Transduction

Gene Recombination

horizontal gene transfer

Conjugation

the transfer of DNA between two bacterial cells which are temporarily joined

Transformation

the process of taking in DNA from the external environment

Transduction

the transfer of DNA between prokaryotes by viruses

Bacteriophages

viruses that infect bacteria

also commandeers a cell’s resources to make more of it

Endospores

used to withstand harsh conditions in bacteria (domain)

Photoautotroph Energy Source

Light

Chemoautotroph Energy Source

Inorganic compounds

Photoheterotroph Energy Source

Light

Chemoheterotroph Energy Source

Organic compounds

Photoautotroph Carbon Source

CO2

Chemoautotroph Carbon Source

CO2

Photoheterotroph Carbon Source

Organic Compounds

Chemoheterotroph Carbon Source

Organic Compunds

Chemoheterotroph Example

A majority of b acteria

Saprobes

they feed of dead organisms

Parasites

they feed on a living host

Obligate Aerobe

requires oxygen

ex. most bacteria

Facultative Anaerobe

can grow with or without oxygen

usually grows faster with it

Obligate Anaerobe

poisoned by oxygen

must have oxygen free (anoxic) environment

Symbiosis

An ecological relationship between different species which are in direct contact with each other

Effects of Mutualism on Species A and B

both species benefit from it

Effects of Commensalism on Species A and B

Species A benefits from it

Species B is neither harmed nor gets benefits from it

Effects of Parasitism on Species A and B

Species A benefits from it

Species B is harmed by it

Effects of Ammensalism on Species A and B

Species A is neither harmed nor gets benefits from it

Species B is harmed by it

Example of Mutualism

the microbes in our guts

Species A: We give them a place to live and food (benefit)

Species B: They make vitamin K for us (benefit)

Example of Commensalism

a bird living in a hole in a tree

Species A: the tree already had a hole, so it is neither harmed nor benefitted

Species B: the bird gets a home, thus benefits from the relationship

Example of Ammensalism

you stepping on an ant you never saw

Species A: the ant is dead, thus is harmed

Species B: you are neither harmed nor benefitted from the interaction

Example of Parasitism

a tapeworm in your intestines

Species A: the tapeworm gets a home and nutrition (benefit)

Species B: you are harmed because it is taking nutrition you need

The 5 Kingdoms of Domain Bacteria

(Please, Can Spiders Get + Blue Cars?)

Kingdom Proteobacteria

Kingdom Chlamydia

Kingdom Spirochetes

Kingdom Gram + Bacteria

Kingdom Cyanobacteria

Kingdom Proteobacteria Subgroups

(ABGDE)

Alpha Proteobacteria

Beta Proteobacteria

Gamma Proteobacteria

Delta Proteobacteria

Epsilon Proteobacteria

Alpha Proteobacteria

Many species in this subgroup are symbiotic with plant

Mutualism

Ex: Rhizobium

Beta Proteobacteria

Many species in this subgroup are nutritionally diverse and oxidizes ammonia to nitrites (nitrogen recyclers)

Mutualism

ex. Neisserria gonorrhoeae – causes gonorrhea

Gamma Proteobacteria

Many species in this subgroup oxidizes hydrogen sulfide to sulfur

ex. Escherichia coli, Vibrio cholerae – Cholera, Salmonella, Legionella – Legionnaire's Disease

Delta Proteobacteria

Many species in this subgroup have slime Producing Myxobacteria

ex. Bdellovibrios that consume other bacteria

Epsilon Proteobacteria

Many species in this subgroup have pathogens to humans and various animals.

ex. Heliociobacter pylori – Stomach ulcers and Camphylobactor – Blood Poisoning and Intestinal inflammation

Kingdom Chlamydia Characteristics

this kingdom survives only in animal cells, steals ATP from inside animal cells (Parasitism), and has an odd cell wall that stains gram negative

ex. Chlydia trachomatis – Causes blindness and non-gonococcal urethritis (most common STI)

Kingdom Spirochetes Characteristics

this kingdom uses Flagella to “spiral” through an environment (bacterial Flagella made of Flagellum)

ex. Treponema pallidum – Syphilis and Borrelia burgdorferi – Lyme Disease

Kingdom Cyanobacteria Characteristics

this kingdom is photosynthetic, it uses photosystem 1 and 2 and contains chlorophyll a [does not have chloroplasts (or other membrane bound organelles) and has chlorophyll found in thylakoid membranes scattered throughout cell], it has organisms arranged in filaments, and some have heterocyst's which convert nitrogen to ammonia like alpha proteobacteria

ex. Anabaena

Kingdom Gram Positive Bacteria Characteristics

this kingdom contains 2 species of Actinomycetes which causes Tuberculosis and Leprosy, responsible for the “earthy” odor of rich soil, and some are sources of antibiotics; includes Mycoplasmas, the only bacteria that does not have a cell wall Still grouped with the gram positives, smallest of all bacteria, and one species causes “walking pneumonia”

Ammensalism

ex. Streptomyces – produces the antibotic streptomycin that can destroy other bacteria, Bacillus anthracis – produces anthrax, and Clostridium botulinum – botulism (paralysis, from contaminated food/water)

Gram Staining: + Charged Crystal Violet

Primary stain

positive=purple

Gram Staining: Iodine Binds to Crystal Violet

fixes the crystal violet

Gram Staining: Alcohol

shrinks peptidoglycan OR dissolves outer membrane

Gram Staining: + Charged Safranin

counterstain

negative=red/pink

Zone of Inhibition

where there's a clear spot around the dot. The bigger and clearer the clear area = the more effective the antibiotic is