Category: Week 3

Thursday Notes

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

  1. Monenra (bacteria) (No longer used)
  2. Protista (algae, protozoa, etc.) (No longer used)
  3. Fungi
  4. Plantae
  5. Animalia

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

Domain Archaea


  • Extreme halophiles (Halobacterium): Salt environments
  • Hyperthermophiles (pyrodictium): Hot environments
  • Acidophiles (sulfolobus): Acidic environments

Methanogens (Methanobacterium) → Methane generating archaea CH4

Domain Bacteria

Phylum Proteobacteria Characteristics:

  • Gram-Negative
  • Largest, most diverse group of bacteria
  • Proteo- meaning “many forms”


  • Alphaproteobacteria
  • Betaproteobacteria
  • Gammaproteobacteria
  • Deltaproteobacteria
  • Epsilonproteobacteria

Class: Alphaproteobacteria:

Rickettsia rickettsiiRocky Mountain Spotted Fever:

  • 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

Class: Betaproteobacteria

Neisseria gonorrhoeae – Gonorrhea”the clap” (term came from french word for brothel – Clapoir)

  • STD
  • 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.

Class: Gammaproteobacteria

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

  • Capsules
  • 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.

Extra Notes

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:

  1. Parasitic – one organism is harmed
  2. Commensalistic – one organism is neutral
  3. Mutualistic – both organisms benefit




Wednesday Notes

Microbial Nutrition & Growth

Elements Essential for Growth:

  • Carbon
  • Oxygen
  • Nitrogen
  • Hydrogen
  • Phosphorus
  • Sulfur
  • + 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.

\mathrm{2\ O_2 ^-\ +\ 2\ H^+\ \xrightarrow {SOD}\ \ H_2O_2 +\ O_2}
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)

  1. Superoxide dismutase: Detoxifies superoxide radical
  2. Peroxidase: Detoxifies hydrogen peroxide (H2O2) and Superoxide Radical (O2 2¯)
  3. Catalase: Also helps the superoxide dismutase remove the superoxide radical by catalyzing the reaction for peroxide anion. (confusing)

Organism Temperature Requirements:

  1. Psychrophiles – “Cold-loving” (near freezing temps.)
  2. Mesophiles – “Middle-temp-loving” (room temps)
  3. Thermophiles – “Heat-loving” (Hot environments)
  4. 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)




Tuesday Notes

Eukaryotic Cells…

Eukaryotic cells w/ walls:

  • plants (cellulose)
  • algae
  • fungi (chiten)

Membranous Organelles of Eukaryotic cells:

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


Membranous Sacs:

  1. Vesicles
  2. lysosomes (in animal cells) – digest cell waste
  3. 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.
  4. 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)

  1. Helps evade the immune system
  2. transmit messages (think biofilms)
  3. helps to adhere to eachother &/or inanimate objects. 

Cytoplasmic membranes –

  1. Some contain steroid lipids such as cholesterol
  2. 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

Flagella – 

  • 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)


Vesicular Transport

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)

Nonmembranous Organelles

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.


Microbial Growth


  • 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

Taxonomy & Images of Organisms


Domain: Bacteria

Kingdom: N/A

Phylum: Cyanobacteria


Possesses trichomes



Also has trichomes, & a glycocalyx slimelayer


Genus: Gloeocapsa

Single cells with glycocalyx caspules


Genus: Anabaena


Genus: Spirulina









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.[2] Under magnification, akinetes appear thick walled with granular-looking cytoplasms.

Trichomes – Stacks of cells


Eurkaryotic 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:

  1. Molds (filamentous)
  2. Fleshy fungi
  3. yeasts (unicellular)

Domain – Eukarya

Kingdom – Fungi

Phylum – Oomycota

Albugo bliti

Albugo blitiAlbugo bliti

Sexual oospores




Saprolegnia Saprolegnia

1st image – oogonium w/ sexual oospores

2nd image – asexual sporangiospores

Phylum: Zygomycota

Rhizopus stolonifer

Rhizopus stolonifer – sporangium w/ asexual sporangiospores

Rhizopus stolinifer –  Sexual zygospore