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THE PROKARYOTES
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THE PROKARYOTES. Systematics Focus on animals and plants –History limited to 20% of evolutionary time How to classify prokaryotes? Limited in morphological.

Dec 25, 2015

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Page 1: THE PROKARYOTES. Systematics Focus on animals and plants –History limited to 20% of evolutionary time How to classify prokaryotes? Limited in morphological.

THE PROKARYOTES

Page 2: THE PROKARYOTES. Systematics Focus on animals and plants –History limited to 20% of evolutionary time How to classify prokaryotes? Limited in morphological.

Systematics• Focus on animals and plants

– History limited to 20% of evolutionary time

• How to classify

prokaryotes?

Limited in

morphological

characters

Page 3: THE PROKARYOTES. Systematics Focus on animals and plants –History limited to 20% of evolutionary time How to classify prokaryotes? Limited in morphological.

Carl Richard Woese

1928-2012, USA; Developed system based on 16S rRNA in 1977

Page 4: THE PROKARYOTES. Systematics Focus on animals and plants –History limited to 20% of evolutionary time How to classify prokaryotes? Limited in morphological.

Carl Woese and George Fox

Page 5: THE PROKARYOTES. Systematics Focus on animals and plants –History limited to 20% of evolutionary time How to classify prokaryotes? Limited in morphological.

rRNA

Zuckerkandl and Pauling

Emile Zuckerkandl (1922-2013); Austria & USA. Molecular biology and molecular clock

Linus Carl Pauling (1901-1994) USA Founder of fields like quantum chemistry and molecular biology

Suggested that a tree of life might be generated by comparing sequences of biopolymers like RNA

Page 6: THE PROKARYOTES. Systematics Focus on animals and plants –History limited to 20% of evolutionary time How to classify prokaryotes? Limited in morphological.

Flow of information in a cell…

Page 7: THE PROKARYOTES. Systematics Focus on animals and plants –History limited to 20% of evolutionary time How to classify prokaryotes? Limited in morphological.

• When DNA is transcribed, the result is an RNA molecule

Figure 10.10

DNA molecule

Translation

Polypeptide

Gene 1

Gene 2

Gene 3

DNA strand

Transcription

RNA

Codon

Amino acid

Page 8: THE PROKARYOTES. Systematics Focus on animals and plants –History limited to 20% of evolutionary time How to classify prokaryotes? Limited in morphological.

• When DNA is transcribed, the result is an RNA molecule

• RNA is then translated into a sequence of amino acids

Figure 10.10

DNA molecule

Translation

Polypeptide

Gene 1

Gene 2

Gene 3

DNA strand

Transcription

RNA

Codon

Amino acid

Page 9: THE PROKARYOTES. Systematics Focus on animals and plants –History limited to 20% of evolutionary time How to classify prokaryotes? Limited in morphological.

Ribosomal Function

A typical prokaryotic cellmay have

10,000+ ribosomes

Page 10: THE PROKARYOTES. Systematics Focus on animals and plants –History limited to 20% of evolutionary time How to classify prokaryotes? Limited in morphological.

Where does rRNA enter the picture?

Page 11: THE PROKARYOTES. Systematics Focus on animals and plants –History limited to 20% of evolutionary time How to classify prokaryotes? Limited in morphological.

Ribosomal Structure

Two subunits

Page 12: THE PROKARYOTES. Systematics Focus on animals and plants –History limited to 20% of evolutionary time How to classify prokaryotes? Limited in morphological.

Ribosomal subunits=rRNA molecules + proteins

Page 13: THE PROKARYOTES. Systematics Focus on animals and plants –History limited to 20% of evolutionary time How to classify prokaryotes? Limited in morphological.

Prokaryotes Eukaryotes

Page 14: THE PROKARYOTES. Systematics Focus on animals and plants –History limited to 20% of evolutionary time How to classify prokaryotes? Limited in morphological.

What’s the ‘S’?

• Svedberg units: a measure of how quickly particles sediment in an ultracentrifuge

Page 15: THE PROKARYOTES. Systematics Focus on animals and plants –History limited to 20% of evolutionary time How to classify prokaryotes? Limited in morphological.

What’s the ‘S’?

• Svedberg units: a measure of how quickly particles sediment in an ultracentrifuge

• Larger the particle, the greater its S value

• Smaller subunit of a ribosome sinks slower than the larger subunit

Page 16: THE PROKARYOTES. Systematics Focus on animals and plants –History limited to 20% of evolutionary time How to classify prokaryotes? Limited in morphological.

Why then does 5S + 23S = 50S?

Page 17: THE PROKARYOTES. Systematics Focus on animals and plants –History limited to 20% of evolutionary time How to classify prokaryotes? Limited in morphological.

Why then does 5S + 23S = 50S?

Shape AND size determine sedimentation rate…

Page 18: THE PROKARYOTES. Systematics Focus on animals and plants –History limited to 20% of evolutionary time How to classify prokaryotes? Limited in morphological.

Ribosomal RNA Molecules

• Components of the ribosomes of ALL ORGANISMS

• Changes in nucleotide sequence indicative of evolutionary history

• “highly conserved molecules”…

What does this mean?

Page 19: THE PROKARYOTES. Systematics Focus on animals and plants –History limited to 20% of evolutionary time How to classify prokaryotes? Limited in morphological.

Ribosomal Function

• PROTEIN SYNTHESIS

• Not much room for error!

• Disruption of ribosome structure likely to disrupt protein synthesis…

Life threatening!

Page 20: THE PROKARYOTES. Systematics Focus on animals and plants –History limited to 20% of evolutionary time How to classify prokaryotes? Limited in morphological.

Practical applications…

• Some antibiotics (e.g. erythromycin and streptomycin) work by targeting the 70S ribosomes

• Alter shape and prevent bacteria from synthesizing proteins needed to survive

• Why are our own ribosomes not affected by the same drugs???

Page 21: THE PROKARYOTES. Systematics Focus on animals and plants –History limited to 20% of evolutionary time How to classify prokaryotes? Limited in morphological.

A modification of Woese from Brock et al. (1994).

Page 22: THE PROKARYOTES. Systematics Focus on animals and plants –History limited to 20% of evolutionary time How to classify prokaryotes? Limited in morphological.

Two different supertrees generated by ML methods for complete genomes of 45 taxa. Daubin et al. 2002

Page 23: THE PROKARYOTES. Systematics Focus on animals and plants –History limited to 20% of evolutionary time How to classify prokaryotes? Limited in morphological.

Ciniglia et al. 2004

Page 24: THE PROKARYOTES. Systematics Focus on animals and plants –History limited to 20% of evolutionary time How to classify prokaryotes? Limited in morphological.

Lang et al. 2013Using 24 genes and 3000 taxa

Page 25: THE PROKARYOTES. Systematics Focus on animals and plants –History limited to 20% of evolutionary time How to classify prokaryotes? Limited in morphological.

Gram Stain and Structure

Page 26: THE PROKARYOTES. Systematics Focus on animals and plants –History limited to 20% of evolutionary time How to classify prokaryotes? Limited in morphological.

Eubacteria

• >9 Kingdoms• Same type of ribosomes• Polysaccharide of outer

wall made of murein• Most groups involved in

global nutrient cycling• Many of economic

importance• Disease• Other functions (e.g.

antibiotic producers)

Page 27: THE PROKARYOTES. Systematics Focus on animals and plants –History limited to 20% of evolutionary time How to classify prokaryotes? Limited in morphological.

Proteobacteria

• Disparate functional groups joined by molecular sequences

• Likely the source of mitochondria

Page 28: THE PROKARYOTES. Systematics Focus on animals and plants –History limited to 20% of evolutionary time How to classify prokaryotes? Limited in morphological.

Alphaproteobacteria

• Rikettsias (typhus Rocky Mtn spotted fever

• Rhizobias (N-fixing bacteria)

• Likely the ancestor of mitochondria was from this group

Page 29: THE PROKARYOTES. Systematics Focus on animals and plants –History limited to 20% of evolutionary time How to classify prokaryotes? Limited in morphological.

Gammaproteobacteria

• Usually small rods or cocci

• Causative agents of Bubonic Plague, Tuleremia, Legioner’s Disease, Cholera

• Includes Escherichia coli

Page 30: THE PROKARYOTES. Systematics Focus on animals and plants –History limited to 20% of evolutionary time How to classify prokaryotes? Limited in morphological.

Spirochaetae

Page 31: THE PROKARYOTES. Systematics Focus on animals and plants –History limited to 20% of evolutionary time How to classify prokaryotes? Limited in morphological.

Spirochaetae

• Spiraled with internal flagella

• Many are free-living• Causative agents of

Lyme disease, syphilis, yaws, and relapsing fever

Page 32: THE PROKARYOTES. Systematics Focus on animals and plants –History limited to 20% of evolutionary time How to classify prokaryotes? Limited in morphological.

Cyanobacteria

Page 33: THE PROKARYOTES. Systematics Focus on animals and plants –History limited to 20% of evolutionary time How to classify prokaryotes? Limited in morphological.

Cyanobacteria• Like free-living chloroplast • Group from which chloroplasts

appeared• Form filaments, colonies• Very large for bacteria• Some produce toxins• Many are nuisance algae in

over-fertilized waters• Source of most atmospheric

oxygen, especially prior to eukaryotes

Page 34: THE PROKARYOTES. Systematics Focus on animals and plants –History limited to 20% of evolutionary time How to classify prokaryotes? Limited in morphological.

Firmicutae

• Lack second outer membrane of Eubacteria

• Gram positive

Page 35: THE PROKARYOTES. Systematics Focus on animals and plants –History limited to 20% of evolutionary time How to classify prokaryotes? Limited in morphological.

Aphragmabacteria

• Tiny, smallest genome of any non-virus

• No walls• Obligate parasites • One causes

pneumonia; many plant pathogens

Page 36: THE PROKARYOTES. Systematics Focus on animals and plants –History limited to 20% of evolutionary time How to classify prokaryotes? Limited in morphological.

Anoxybacteria

• Obligate anaerobes

• Causative agents of botulism and tetanus

• Botox

• Common in soil and animal digestive systems

Page 37: THE PROKARYOTES. Systematics Focus on animals and plants –History limited to 20% of evolutionary time How to classify prokaryotes? Limited in morphological.

Endosporobacteria

• Produce resistant spores

• Many major human pathogens, including anthrax, staph (including methicillin-resistant Staphylococcus aureus), strep

• Includes Lactobacillus

Page 38: THE PROKARYOTES. Systematics Focus on animals and plants –History limited to 20% of evolutionary time How to classify prokaryotes? Limited in morphological.

Actinobacteria

• Many are slow-growing and fungus-like

• Antibiotic sources (e.g. streptomycin, actinomycin)

• Causative agents of leprosy and tuberculosis; diptheria

• Bacteria which cause holes in Swiss cheese

• Bifida, a necessary commensal in our lower bowel

Page 39: THE PROKARYOTES. Systematics Focus on animals and plants –History limited to 20% of evolutionary time How to classify prokaryotes? Limited in morphological.

Deinococcobacteria

• Thermophiles

• Deinococcus withstands 6,000 rads (and up to 1500 megarads)

• Thermus, found at Yellowstone, enzymes used for PCR

Page 40: THE PROKARYOTES. Systematics Focus on animals and plants –History limited to 20% of evolutionary time How to classify prokaryotes? Limited in morphological.

Archaea

Differ from the Eubacteria– Form of ribosomes– No murein– Different lipids– Different RNA polymerase

Page 41: THE PROKARYOTES. Systematics Focus on animals and plants –History limited to 20% of evolutionary time How to classify prokaryotes? Limited in morphological.

Crenarchaea

• These are the hyperthermophiles

• They tend to inhabit very hot environments that are rich in sulfur

Page 42: THE PROKARYOTES. Systematics Focus on animals and plants –History limited to 20% of evolutionary time How to classify prokaryotes? Limited in morphological.

Euryarchaeota

• Halobacteria

• Methanobacteria

• Thermoplasmobacteria

Page 43: THE PROKARYOTES. Systematics Focus on animals and plants –History limited to 20% of evolutionary time How to classify prokaryotes? Limited in morphological.

Viruses

• Non-cellular• Usually nucleic acid

and protein• Types

– DNA (ss & ds)– RNA (ss & ds)– DNA RT– RNA RT– Prions

Page 44: THE PROKARYOTES. Systematics Focus on animals and plants –History limited to 20% of evolutionary time How to classify prokaryotes? Limited in morphological.
Page 45: THE PROKARYOTES. Systematics Focus on animals and plants –History limited to 20% of evolutionary time How to classify prokaryotes? Limited in morphological.

Some Human Viral Diseases• Herpes• Smallpox• Hepatitis (B, C, D)• Yellow Fever• Dengue fever• West Nile• HIV• Ebola• Rabies• Chicken Pox

/Shingles

• Rubella (German Measles)• Influenza• Polio• Mumps• Measles• Epstein-Barr• Hemorrhagic fever• Rota • Rhinovirus• Transmissible spongiform

encephalopathy (TSE)

Page 46: THE PROKARYOTES. Systematics Focus on animals and plants –History limited to 20% of evolutionary time How to classify prokaryotes? Limited in morphological.

Theories on Origin of Viruses

• Regressive Hypothesis: cellular parasites of larger cells that became simplified

• Cellular Origin Hypothesis: pieces of living cells that can replicate (e.g. strands of nucleic acids like plasmids or transposons)

• Coevolution Hypothesis: evolved together with the first cells as their parasites