THE PROKARYOTES

Systematics• Focus on animals and plants

– History limited to 20% of evolutionary time

• How to classify prokaryotes?

Limited in morphological characters

Carl Richard Woese

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

Carl Woese and George Fox

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

Flow of information in a cell…

• 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

• 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

Ribosomal Function

A typical prokaryotic cellmay have

10,000+ ribosomes

Where does rRNA enter the picture?

Ribosomal Structure

Two subunits

Ribosomal subunits=rRNA molecules + proteins

Prokaryotes Eukaryotes

What’s the ‘S’?

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

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

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

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

Shape AND size determine sedimentation rate…

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?

Ribosomal Function

• PROTEIN SYNTHESIS

• Not much room for error!

• Disruption of ribosome structure likely to disrupt protein synthesis…

Life threatening!

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???

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

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

Ciniglia et al. 2004

Lang et al. 2013Using 24 genes and 3000 taxa

Gram Stain and Structure

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)

Proteobacteria

• Disparate functional groups joined by molecular sequences

• Likely the source of mitochondria

Alphaproteobacteria• Rikettsias (typhus Rocky

Mtn spotted fever

• Rhizobias (N-fixing bacteria)

• Likely the ancestor of mitochondria was from this group

Gammaproteobacteria• Usually small rods or

cocci• Causative agents of

Bubonic Plague, Tuleremia, Legioner’s Disease, Cholera

• Includes Escherichia coli

Spirochaetae

Spirochaetae• Spiraled with internal

flagella• Many are free-living• Causative agents of

Lyme disease, syphilis, yaws, and relapsing fever

Cyanobacteria

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

Firmicutae• Lack second outer

membrane of Eubacteria

• Gram positive

Aphragmabacteria• Tiny, smallest

genome of any non-virus

• No walls• Obligate parasites • One causes

pneumonia; many plant pathogens

Anoxybacteria• Obligate anaerobes

• Causative agents of botulism and tetanus

• Botox

• Common in soil and animal digestive systems

Endosporobacteria• Produce resistant spores

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

• Includes Lactobacillus

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

Deinococcobacteria• Thermophiles

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

• Thermus, found at Yellowstone, enzymes used for PCR

ArchaeaDiffer from the Eubacteria

– Form of ribosomes– No murein– Different lipids– Different RNA polymerase

Crenarchaea• These are the

hyperthermophiles

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

Euryarchaeota• Halobacteria

• Methanobacteria

• Thermoplasmobacteria

Viruses• Non-cellular• Usually nucleic acid

and protein• Types

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

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)

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