Bacteria, Archaea, and Viruses

Domains

• Bacteria
  • Archaea
  • Eukarya

Eukaryotes

• Possibly multicelled
  • Nucleus
  • Branch off of archaea
  • Membrane-bound organelles

Endosymbiosis theory

• Cyanobacteria
  • chloroplasts
  • Protobacteria
  • mitochondria
  • Phospholipid bi-layer
  • 

Protists

• Eukaryotes that are not plants, animals, or fungi
  • Acquiring organelles
  • Flexible cell surface that allows them to have infoldings
  • These folds make cell compartments, these compartments have specialization
  • Organelles are double membraned because when they entered the protist they took some of the cell wall with them.
  • Mitochondria, used to detoxify O2
  • cyanobacterium enters a cell, chloroplast has two membranes
  • Eukaryote engulfs a green algae cell
    • Green algae cell becomes a chloroplast, has three membranes
  • Nuclear envelope - membrane infoldings
  • Cytoskeleton - cytoplasmic microtubules

Prokaryotes

• Single celled
  • DNA is in a ring
  • Plasmids add DNA
  • No mitosis
  • Binary fission
  • Cell wall, not cell membrane
  • No nucleus
  • No organelles
  • Bacteria are prokaryotes
  • Important decomposers

Nitrogen cycle

• Nitrogen fixers
  • Convert atmospheric N2 to ammonia
  • Air to ground
  • Nitrifiers
  • Ammonia to nitrate
  • Soil to soil
  • Nitrogen is now consumable by plants
  • Denitrifiers
  • Nitrate to N2
  • Soil to air
  • 
• Both
  • Ribosomes
  • Cell wall
  • Metabolic pathways
  • Respiration
  • Photosynthesis
  • ATP

Archaea

• Extremophiles
  • rRNA allows you to differentiate between Archaea and Bacteria
  • Common in soil or the ocean
  • Prokaryotic
  • No peptidoglycan
  • Lipid monolayer
  • Some are obligate anaerobes

Bacteria

Lateral Gene Transfer

• Bacteria transfer plasmids through “bridges” which donates genetic material to another bacteria
  • Plasmids are the smallest stretch of DNA
  • Have the ability to target the nucleus and alter DNA, GMO
  • Bacteria from environment
  • Common for antibiotic resistance
  • Makes it difficult to interpret genome analysis

Bacterial Cell Wall

• Peptidoglycan
  • Takes the place of cellulose
  • Gram positive
  • Thick outside layer of peptidoglycan
  • Stains purple, blue stain bonds to PepGly
  • Gram negative
  • Cell envelope, thin peptidoglycan in a phospholipid bilayer sandwich
  • Stains pink, stain does not bond

Shapes

• Coccus
  • Sphere
  • Cock and balls
  • Bacillus
  • Rod
  • Back should be straight rod
  • Spirillum
  • Spiral
  • Bacillus and Spirillum can form chains/clusters
  • Chains form during division when cells fail to separate
  • Branched filaments
  • Produce spores in order to reproduce

Endospores

• Nutrients scarce? Simply pack your genetic material into a cell wall package and wait for that package to be rehydrated!
  • Rest of the cell dies
  • Food poisoning

Cyanobacteria

• Single-celled, form colonies
  • Photosynthetic
  • Fix nitrogen
  • heterocyst
  • Big oxygen producers
  • Photosynthetic lamellae
  • Those little indents in the cell wall that allow for photosynthesis to take place
  • Works in place of a chloroplast
  • Origin of chloroplasts in Eukaryotes

Spirochaeta

• Internal flagella that allows them to move around
  • Syphilis, Lyme
  • Chlamydia
  • Obligate parasite
  • STDs, pneumonia

Protobacteria

• Where the mitochondria was derived from
  • Largest group of bacteria
  • Nitrogen fixers
  • Rhizobium, legumes
  • Escherichai coli

Biofilms

• Sticky polysaccharide matrix
  • Makes cells harder to kill, antibiotic resistance, environmental resistance
  • Dental plaque
  • Bacteria binds to a surface, a larger colony forms, the bacterial matrix forms

Quorum sensing

• Sending chemicals and establishing communication with other bacteria
  • Attracts more bacteria to the biofilm area

Human Microbiomes

• Important to our health
  • Antibiotics deplete them

Endotoxins

• Lyse: bacterial puncture/death
  • Rarely fatal
  • Salmonella

Exotoxins

• Released by living bacteria, continual proliferation
  • Highly toxic, often fatal
  • Black plague

Extremophiles

• Prokaryotic
  • Bacteria and archaea
  • Thrive under extreme conditions
  • Radiation, temperature, pH, salinity, heavy metals
  • Thermostable proteins that prevent denaturing
  • Not as abundant

Metabolic pathways

• Obligate anaerobes
  • Oxygen is poisonous
  • Those homies that live inside termites
  • Relic of prehistoric life
  • Facultative anaerobes
  • Both aerobic and anaerobic pathways
  • Obligate aerobes
  • Require oxygen
  • Photoautotrophs
  • Produce their energy from the sun, photosynthesise
  • Use CO2
  • Photoheterotrophs
  • Use the sun for energy but have to consume organic material in order to get carbon
  • Chemoautotrophs
  • Get energy from inorganic compounds
  • Use CO2 for carbon
  • Chemoheterotrophs
  • Get energy from organic compounds as well as their carbon
  • Humans

Viruses

• Infectious particles
  • Obligate parasites
  • Need a host to survive
  • DNA or RNA
  • This is not typical
  • Infect all forms of life
  • Grouped based on genome structure
  • Hard to classify based on physiological differences

What makes up a virus?

• Genetic material: RNA or DNA
  • A viral capsid
  • Protein around genetic material
  • Some have a membrane envelope and spike proteins
  • Similar to cell membrane
  • Virus can leave cell and steal membrane

Negative-sense

• Has negative-sense RNA that is not ready to be translated
  • Uses the host cell to create positive-sense RNA
  • RNA polymerase helps it convert from negative to positive

Positive-sense

• RNA ready to be translated
  • Doesn't need to bring its own RNA polymerase
  • Host already has it
  • Most abundant and diverse group
  • Covid
  • Mosaic viruses
    • Just genetic material and capsid