THE PROKARYOTES
Feb 24, 2016
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