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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

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

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