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 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 Zuckerkandl and Pauling

Flow of information in a cell…

• When DNA is

transcribed

, the result is an RNA molecule

DNA molecule Gene 1 Gene 2 Gene 3 DNA strand Transcription RNA Translation Codon Polypeptide Amino acid

Figure 10.10

• When DNA is

transcribed

, the result is an RNA molecule • RNA is then

translated

into a sequence of amino acids

DNA molecule Gene 1 Gene 2 Gene 3 DNA strand Transcription RNA Translation Codon Polypeptide Amino acid

Figure 10.10

Ribosomal Function

A typical prokaryotic cell may 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. 2013 Using 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

Archaea Differ 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

• Halobacteria Euryarchaeota • 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