Ch 24: Bacteria, Archaea, Viruses

For Biol 130

Antonie van Leeuwenhoek

• father of microbiology

• discovered bacteria

• 1st microscopist & microbiologist

What are the 3 domains of life?

Bacteria, Archaea, Eukarya

ALL domains have… (3 things)

1. plasma membranes & ribosomes

2. common set of metabolic pathways

3. use DNA to encode proteins, same genetic code & similar DNA sequences

What do the shared features of the 3 domains help support?

the idea that all living organisms share a common ancestor & show monophyly of life

3 characteristics of prokaryotes 

1. divide by binary fission

2. DNA not enclosed in a membrane (circular molecule)

3. no membrane-enclosed organelles

3 characteristics of Bacteria

• membrane-enclosed nucleus - absent

• Membrane-enclosed organelles - few

• peptidoglycan in cell wall - present

3 characteristics of Archaea

• membrane-enclosed nucleus - absent

• Membrane-enclosed organelles - absent

• peptidoglycan in cell wall - absent

3 characteristics of Eukarya

• membrane-enclosed nucleus - present

• Membrane-enclosed organelles - many

• peptidoglycan in cell wall - absent

Does the gram stain method do?

it separates bacteria through stains

What color are gram-POSITIVE bacteria?

they retain violet dye

What color are gram-NEGATIVE bacteria?

they retain red dye

Why do gram-positive & gram-negative stain differently?

they stain differently due to the structure of their cell walls

What are the 3 bacteria cell shapes?

Spiral, rod, sphere

What are the 3 forms of bacterial spiral cells?

Vibrio, spirillum, spirochete

What are the 4 types of bacterial groupings?

Diplococcus - pair

Staphylococcus - clusters

Streptococcus - chain

Tetracoccus - 4 in 2 planes to make squares of four

How are evolutionary relationships clarified?

by sequencing rRNA genes

3 important details of rRNA

1. rRNA is evolutionary ancient

2. in all free-living organisms

3. evolved slowly, similarities easily found

What is lateral/horizontal gene transfer?

lateral gene transfer is when genes from one species become incorporated into the genome of another.

• “moving sideways in a tree”

True or false? Lateral gene transfer can occur between domains?

True

Why are prokaryotes so diverse/abundant?

• prokaryotes are most successful in terms of # of individuals

• 8 groups of bacteria have broadest phylogenetic support

Explain what biofilms are

Biofilms 

• formed by many microbial communities

• difficult to kill cells in biofilm - many be impenetrable to antibiotics

• bacteria in biofilms communicate using chemical signals

How is Archaea separated?

rRNA sequencing

True or false? Much is known about the shapes of Archaea.

False - little is known of Archaea shapes, many never been seen and only known from DNA samples

What are the known Archaea species?

cocci, bacilli, triangular, square

Where do Archaea grow?

on surfaces 

What is the environment of Archaea? (3)

• Many are extremophiles

• some not extremophiles (common in soil)

• many live in ocean depths

What are some traits of Archaea?

• lack peptidoglycan in cell walls

• liquids in cell membranes using ether linkages

What are the categories of Archaea?  (4)

• Methanogens - energy from H₂ - produces methane as waste & poisoned by O₂

• Extreme halophiles - salt tolerant to salt dependent 

• Extreme thermophiles - hot environments, metabolism based on sulfur

• Nonextreme Archaea - same environment as bacteria - soil

Why are prokaryotes important to health? (3 ideas)

• many prokaryotes live in/on organisms

• human health depends on microbiome health

• every surface of body covered with bacteria

What is a microbiome?

bacterial communities that live in & on our bodies

What are pathogens?

pathogenic prokaryotes shown to cause disease

True or false? Majority of bacteria are pathogens.

False - minority of bacteria are pathogens

What are Koch’s postulates? 4 rules.

set of rules to establish a particular organisms that causes a disease

1. microorganism always found in infected person

2. can be taken from host and grown in pure culture

3. sample of culture causes disease in a new host

4. new host also yields a pure culture

What is required for an organism to become a pathogen? (5 steps)

1. arrive at body of surface of a host

2. enter hosts body

3. evade hosts defenses

4. multiply inside host

5. infect new host

Explain what the consequences of the host depend on. (2)

• Invasiveness of pathogen (its ability to multiply in host)

• toxinogenicity (ability to produce toxins)

When are endotoxins & exotoxins released? How fatal are they?

• Endotoxins  - released when lysed (rarely fatal)

• Exotoxins - released by living bacteria (often fatal)

List and describe the 4 prokaryotic metabolic pathways.

• Obligate anaerobe - poisoned by oxygen

• Facultative anaerobes - shift between anaerobic & aerobic

• Aerotolerant anaerobes - not damaged by oxygen, but don’t use oxygen for cellular respiration

• Obligate aerobes - have to use oxygen to survive

Nutritional categories of prokaryotes (4)

1. Photoautotrophs - use photosynthesis for energy

2. Photoheterotrophs - use light energy & get carbon from compounds made by other organisms (carbohydrates, fatty acids, alcohols)

3. Chemoautotrophs - get energy by oxidizing inorganic compounds & use energy to fix CO₂

4. Chemoheterotrophs - obtain both energy & carbon from complex organic compounds that were synthesized by other organisms

How do prokaryotes impact environments? (3 kinds)

• decomposers - metabolize organic compounds in dead organisms & other organic materials 

• denitrifiers - use ntirate as an electron receptor in anaerobic conditions & N into the atmosphere N₂

• Nitrifiers  - chemoautotrophic bacteria (fix nitrogen for plant use, important for plant growth)

Are viruses cellular?

• viruses are NOT cellular

  • derived from other cells

  • DNA & RNA

  • infect all cellular forms of life

Why is virus phylogeny difficult? (4)

• viral genomes are tiny (restricts analyses)

• no known viral fossils

• diverse and may have evolved rapidly

• raid mutation rate/evolution clouds evolutionary relationships

How do retroviruses reproduce? Explain the process.

Reverse transcriptase

• in host nucleus, viral reverse transcriptase produces cDNA from the viral RNA genome

• cDNA is replicated to produce double-stranded DNA

• Viral integrase catalyzes the integration of the new double stranded DNA

• viral genome is replicated along w the host cell’s DNA

Viral genome is replicated along with the host cell’s DNA; the integrated retroviral DNA is known as a ____

Provirus

Is HIV a retrovirus?

Yes

What happens when cells are infected with retrovirus

they undergo uncontrolled replication

• associated with some forms of cancer

How do retrovirus’ infect other cells?

by inserting their genome into the host genome 

Humans have about ______ fragments of endogenous viruses

100,000

What are DNA viruses? (3)

• start with double-stranded DNA

• polyphyletic (many independent origins)

• many common phage (bacteriophage)

What is phage therapy?

bacteriophage viruses have been used to fight bacterial infections in humans

What replaced phage therapy?

antibiotics

What is the issue to antibiotics & bacteria? What do we do about it?

bacteria evolve resistance to antibiotics, so research in phage therapy continues

What diseases are DNA viruses? (3)

smallpox, HPV, Herpes