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