Taxonomy & Phylogeny
Taxonomy – the classification & naming of organisms
Phylogeny – evolutionary history of a group of organisms
5 – Kingdom Classification System
Developed by Robert Whittaker in 1969
- Monenra (bacteria) (No longer used)
- Protista (algae, protozoa, etc.) (No longer used)
Domain System – Developed by Carl Woes in 1978, based on similarities in rRNA
◊Note – There are no Kingdoms in Bacteria & Archaea (Prokaryotes)
Bacterial Species – population of cells w/ similar characteristics
Strains – sub-species ex. 0157-H7
- Extreme halophiles (Halobacterium): Salt environments
- Hyperthermophiles (pyrodictium): Hot environments
- Acidophiles (sulfolobus): Acidic environments
Methanogens (Methanobacterium) → Methane generating archaea CH4
Phylum Proteobacteria Characteristics:
- Largest, most diverse group of bacteria
- Proteo- meaning “many forms”
- Obligate intracellular parasite
- Transmitted by vector – tick (Dermacenter)
- Infects endothelial cells, including those of capillaries & lyces cells which creates the red spots.
- Symptoms: Fever, headache, chills, nausea & spotted non-itchy rash.
Orientia tsutsugamushi – Scrub typhys
- Vector is chiggers (mites)
- endemic to Eastern Asia, Australia, Western Pacific Islands
- Symptoms – Muscle pain
Neisseria gonorrhoeae – Gonorrhea”the clap” (term came from french word for brothel – Clapoir)
- Humans are only host/reservoir
- Virulence Factors – fimbriae & capsules that cause the bacteria to adhere to mucous membranes of host.
Bordetella pertusis – Whooping Cough
- Virulence factors – bacteria attached to lipids in cytoplasmic membranes of tracheal cells via adhesions such as pertussis toxin & hemagglutinin. This causes increased mucus production while paralyzing the cilia of tracheal cells.
- Survives in phagocytes & can travel to other parts of body.
Vibrio Cholerae – Cholera
- Humans become infected by ingesting contaminated food or water
- Virulence factor – causes secretion of water & electrolytes in host
- Environment of human body causes toxins in genes to be expressed → toxins cause intestinal cells to secrete water & electrolytes.
Legionella pneumophila – Legionaire’s Disease
- Got name from outbreak at American legion meeting in Philly in 1970
- Common in water, including condensation in air conditioning units & water towers. Live inside protozoa in fresh water such as rivers.
- Exposure route – Inhalation.
Haemophilus influenzae – Meningitis, pneumoniae
- Obligate intracellular parasite
- colonizes mucus membranes
- Capsules that evade phagocytes
- Type B causes most problems in humans.
pseudomonas auruginosa –
- Opportunistic pathogen, common in soil
- green pigment
Francisella tularensis – tularemia
- intracellular parasite
- reservoirs – rabbits, ticks
- symptoms include buboes, dry cough
Yersina pestis – Plague
- buboes (swollen lymph nodes)
- vector – flea; reservoir – rodents
- 2 types: Bubonic plague & pneumonic plague
- 14th century it killed 1/3 of Europeans & mid 500s AD – late 1700s AD killed 40 million people.
Virulence Factor Definition – characteristics of a pathogenic organism that causes harm to the host
Note – Archaea & Eukarya have histones (proteins associated w/ DNA) Bacteria do not.
Ex Credit: Lichen – fungus & algae &/or cyanobacteria, crusty material found on branches or rocks.
3 Types of Symbiotic Relationships:
- Parasitic – one organism is harmed
- Commensalistic – one organism is neutral
- Mutualistic – both organisms benefit
Microbial Nutrition & Growth
Elements Essential for Growth:
- + Magensium, Calcium, Iron, Zinc (co-factors for enzymes)
- + some other trace elements → used in “membrane pumps” (proteins that transfer ions. Also, used to maintain water balance.)
Oxygen Requirement Terms:
Obligate aerobes – must have oxygen in order to conduct metabolic RXNs, such as respiration. (These would be found at the top of a broth tube)
Obligate anaerobes – must live in an environment w/ no oxygen in order to conduct metabolic RXNs (ex. Clostridium botulinum)
Facultative anaerobes – prefer/live best in aerobic environments but can maintain metabolic processes in anaerobic environment. (ex. yeast)
Aerotolerant anaerobes – same as obligate anaerobes but oxygen doesn’t kill them.
Microphiles – Requires a little oxygen.
Toxic Form of Oxygen:
Singlet Oxygen 1O2 : Molecular oxygen that has been boosted to a higher energy state making it extremely reactive.
Superoxide Radical O2− : formed in small amounts during aerobic respiration, highly toxic.
Peroxide anion O2 2-: Produced during RXN beneath. The Superoxide Radical O2 – acts as the catalyst for the reaction.
- Formation of hydrogen peroxide by superoxide dismutase (SOD)
Hydroxyl radical: OH−
Important enzymes that react with the toxic forms of Oxygen listed above, to detoxify the Oxygen radical/ion.
(Note: Brahce said to focus more on the enzymes that react with the oxygen’s rather than the oxygen structures)
- Superoxide dismutase: Detoxifies superoxide radical
- Peroxidase: Detoxifies hydrogen peroxide (H2O2) and Superoxide Radical (O2 2¯)
- Catalase: Also helps the superoxide dismutase remove the superoxide radical by catalyzing the reaction for peroxide anion. (confusing)
Organism Temperature Requirements:
- Psychrophiles – “Cold-loving” (near freezing temps.)
- Mesophiles – “Middle-temp-loving” (room temps)
- Thermophiles – “Heat-loving” (Hot environments)
- Hyperthermophiles – “Extreme-heat-loving” (near boiling temps)
Other Requirements for growth:
pH: most human pathogens grow best around neutral pH (buffers added to growth media to maintain pH)
Note – Fungi grows best in somewhat acidic conditions (6-7 pH range)
Osmotic pressure: most human pathogens grow best in isotonic conditions exceptions include Staphylococcus
◊ Growth of a bacteria population is exponential: meaning as time continues so does cell growth.
Bacteria Life Phases:
Lag Phase: bacterial cells are preparing for growth by replicating chromosomes & making extra cell material (peptidoglycan, etc) for splitting in 1/2 (binary fission)
Log Phase: most of the growth occurs; binary fission occurs (1 cell → 2 cell)
Stationary Phase: amount of cell reproduction is equal to the amount of death.
Death Phase: # of cells dying is > (is greater) than # of cells being produced (this is due to lack of nutrients and waste buildup)
Eukaryotic cells w/ walls:
- plants (cellulose)
- fungi (chiten)
Nuclear envelope – Has 2 membranes w/ pores for communication
Cytoplasmic membrane- composed of phospholipid bilayer
Endoplasmic Reticulum – Rough & Smooth
- Rough – function is to synthesize (make) proteins & enclose them in vesicles to send out
- Smooth – makes lipids that help repair cells, also to be sent out in vesicles
Golgi Body – “shipping center” where proteins & lipids get modiified & sent to other locations
- Cis – “front” location where vesicles are recieved
- Trans – “back” where vesicles are secreted by the cell enclosed in another membrane.
Mitochandria – respiration …makes ATP (I may have missed some stuff here)
- Has outer membrane
- has an inner membrane that is folded into structures called cristae
- 70s ribosomes, 1 circular chromosome, divides by binary fission
Chloroplasts – Found in plant cells and algae cells (photosynthetic organisms) as the dark green color
- thylakoid membranes stacked into grana (dense areas)
- thylakoid contain photosynthetic pigments
- 70s ribosomes, 1 circular chromosome, divides by binary fission
Free ribosomes – make (synthesize) proteins that will remain in the cell
- lysosomes (in animal cells) – digest cell waste
- vacuoles (ex. central part of plant) – stores water in plant cells or a contractile vacuole which maintains the water level coming in by pushing out excess preventing the cell from bursting do to hyper or hypotonic conditions.
- peroxisomes – contain enzymes that degrade metabolic wastes such as H & O
Eukaryote External Structures: (Not all eukaryotic structures have these structures)
Glycocalyx Functions: (Not part of cells that have a cell wall)
- Helps evade the immune system
- transmit messages (think biofilms)
- helps to adhere to eachother &/or inanimate objects.
Cytoplasmic membranes –
- Some contain steroid lipids such as cholesterol
- Most have sugars attached to cell surface : glycolipids (attach to head of phospholipid) or glycoproteins (attach to protein channels) – One function of glycolipids and glycoproteins is self-recognition
- Surrounded by cytoplasmic membrane
- composed of microtubules in a 9+2 arrangement (microtubules contain protein called tubulin)
- moves in an undulating (wave-like) fashion
Cilia – Short “hair-like” projections, used for motility. Also have 9+2 arrangement of the microtubules (move like oars)
(Prokaryotes do not have cillia)
Exocytosis – secretion of material from inside to outside of eukaryotic cells in a vesicule
Endocytosis – bringing in material from outside to inside the cell in a vesicle.
- Phagocytosis – “to eat” (larger of dry materials)
- Pinocytosis – “to drink” (liquids)
Cytoskeleton – composed of various sizes/shapes of protein filaments /tubules for movement & structure
Ribosomes – composed of polypeptides + rRNA & make protein
Centrosomes – Area near nucleus involved in forming the mitotic spindle during mitosis.
Centrioles – found in animal cells withing the centrosome area; bundles of microtubules that are perpendicular to one another.
- Plants, algae, cyanobacteria use water to reduce carbon dioxide producing oxygen as a biproduct
- Green sulfur bacteria & purple nonsulfur bacteria, some archaea
- Hydrogen, sulfur, & nitrifying bacteria, some archae
- Green nonsulfur bacteria & purple nonsulfur bacteria, some archae
- aerobic respiration, most animals, fungi, protozoa, bacteria & archae
Also has trichomes, & a glycocalyx slimelayer
Single cells with glycocalyx caspules
Special Structures –
Heterocysts – Contain enzymes for conducting nitrogen fixation. Nitrogen fixation is the process of bacteria capturing N in gas form w/ enzymes in their body.
Akinetes– It serves as a survival structure. It is a resting cell of cyanobacteria and unicellular and filamentous green algae. Under magnification, akinetes appear thick walled with granular-looking cytoplasms.
Trichomes – Stacks of cells
Most are multicellular but some are unicellular
Nutrition – Release digestive enzymes into environment & then absorb nutrients from broken down organic material.
3 Major groups:
- Molds (filamentous)
- Fleshy fungi
- yeasts (unicellular)
Domain – Eukarya
Kingdom – Fungi
Phylum – Oomycota
1st image – oogonium w/ sexual oospores
2nd image – asexual sporangiospores