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Bio 102 Syllabus

Lecture 2: Prokaryotes


I. History -- Geological History <<>> Biological History


Age of Earth

4.5 billion years

radioisotopic dating of meteorites formed during formation of solar system

Earliest Common Ancestor

3.5-4 billion years

formation of solid crust vs. observation of oldest fossils; carbon isotopes indicate 3.8by metebolic activity (Greenland)

Oldest Prokaryotic Fossils

3.5 billion years

possible cyanobacteria bacteria (autotrophic - photosynthetic). Western Austrailia stromatolites (Fig 26.1)

Oldest Eukaryotic Fossils

2.1 billion years

possible eukarytic algae, Michigan (Han & Runnegar, 1992, Science 257:232)
Giardia - "intermediate form"
...two nuclei, no mitochondria

Multicellular Eukaryotes

1-1.2 billion years

projected from on DNA sequence analysis

Cambrian "Explosion" (Animals)

500 million years

Burgess Shale Fossils
Many of current animal phyla (echinoderms, annelids, arthropods, chordates). appearance of skeletons thought to be in response to predation. Summary of animal evolution: Fig. 32.3. Summary of chordate evolution: Fig. 34.6.

Origins of Plants from green algae

460 million years

Fossil Record
Summary of Plant evolution: Fig. 29.3.

Vascular Plants

400 million years  



360 million years

"naked seeds", conifers, etc.  


130 million years

"contained seeds", flowering plants

Oldest Vertebrates

500 million years

jawless, fishlike, fig. 34-36

Oldest Jawed Vertebrates

500 million years

Hox gene duplications

Oldest Bony Fishes

425-450 million years


Oldest Amphibians

365 million years

fig. 34-36

Oldest Reptiles

300 million years

fig. 34-36

Oldest Birds

150 million years

fig. 34-36

Oldest Mammals

220 million years

fig. 34-36

Homo erectus

1-2 million years

fig. 34.30, 34.33

Homo sapien

100,000 years

fig. 34.30, 34.33

II. What is a Prokaryote?

Single Cell, but No Nucleus, No Organelles

Three Domains: (small subunit rRNAs)

             |------- Bacteria < PROKARYOTES
             |                  NO Nucleus, No Organelles
Earliest     |
Common ------|   |--- Archaea  < PROKARYOTES
Ancestor     |   |            (extreme: thermophyles, etc.)
                 |--- Eucarya  < EUKARYOTES (Nucleus, organelles)
                               Microsporidia, Diplomonads,
                               Trichomonads, Flagellates,
                               Entamoebae, Slime molds,
                               Cilliates, Fungi,
                               Plants, Animals 

Major Events:

1. Prokaryotic cell organization: membrane, DNA, protein synthesis, metabolic activities
2. Eukaryotic cell organization: nucleus, organelles (endosymbionts)
3. Multicellularity, specialization.

Prebiotic Evolution: Oparin/Haldane

Prokaryotes are Cells!

Differences between the three domains

From Campbell, p. 512:


Bacteria (Prokaryote)

Archaea (Prokaryote)

Eukarya (Eukaryote)

Nuclear envelop




Membrane-enclosed organelles




Peptidoglycan in cell wall




Membrane lipids

unbranched hydrocarbons

some branched hydrocarbons

unbranchced hydrocarbons

RNA polymerase

one gene

several genes

several genes

Start amino acid






some species


Sensitivity to antibiotics streptomycin and chloramphenicol




Prokaryotic Biodiversity?

Diversity Within the Three Domains

The following phylogenetic tree is based on comparisons of small rRNA sequences, from Freeman S & Herron JC (1998) Evolutionary Analysis. Prentice Hall, Upper Saddle River; taken from Woese CR (1996) Phylogenetic trees: Wither microbiology? Current Biology 6:1060.

            |==|  |------------------------Green non-sulfer bacteria
            |  |  |
            |  |--|  |---------------------Flavobacteria
            |     |  |
            |     |  |  |------------------Cyanobacteria (Nostoc)
            |     |--|  |                  (chloroplasts)
            |        |  |
            |        |--|  |---------------Purple bacteria (E. coli)
            |           |--|               (Agrobacterium,mitochondria)
            |              |
Earliest    |              |---------------Gram Positive Bacteria (TB)
Ancestor    |              
            |        |---------------------Pyrodictium
            |     |--|    Crenarchaeota
            |     |  |---------------------Thermoproteus    TEMPERATURE
            |     |
            |  |==|       ARCHAEA
            |  |  |                                
            |  |  |  |---------------------T. celer
            |  |  |  |    Euryarchaeota
            |  |  |--|  |------------------Methanococcus
            |  |     |  |
            |  |     |--|  |---------------Methanobacterium  METHANE
            |  |        |  |                                
            |==|        |--|  |------------Methanosarcina
               |           |--|
               |              |------------Haloarchaea       SALT 
               |          EUCARYA
               |  |------------------------Microsporidia
               |  |
               |==|  |---------------------Diplomonads (Giardia,fig.26.2)
                  |  |
                  |--|  |------------------Trichomonads
                     |  |
                     |--|  |---------------Flagellates (Euglena)
                        |  |
                        |--|  |------------Entamoebae
                           |  |
                           |--|  |---------Slime molds (Dictyostelium)
                              |  |
                              |--|  |------Ciliates (Paramecium)
                                 |  |
                                 |--|  |---Plants
                                    |  |
                                       |---Fungi (yeast, mushrooms, etc)

Note on Gram-positive bacteria and bacteria taxonomy: One hears a lot about "gram positive" and "gram negative" bacteria. The above tree should illustrate that gram-positive bacteria represent only one of several major divisions of extant bacteria. Gram positive refers to the cell-wall phenotype of these bacteria, the presence of which can be recognized by a "Gram stain" named for the person (Christian Gram) who developed the stain. Mycobacterium tuberculosis (TB) and Mycoplasma pneumoniae (walking pneumonia) are both gram-positive bacteria.

Taxonomy vs. Phylogeny Microbiologists have many techniques for characterizing bacterial groups; these techniques may distinguish bacterial groups which are phylogenetically distinct, but the techniques are not based on phylogeny (and are therefore taxonomic). Techniques include relative sensitivities to different antibiotics, antibodies, or more recently DNA sequence analysis (which are phylogenetically based). Taxonomy organizes "things" by convenient and at times unreliable markers (e.g. does the insect have yellow or red wings?). Phylogeny organizes organisms based on their evolutionary relatedness and hence directly or indirectly by genetic markers.


Digression... What is a species?

From Campbell, (p. 446): 4 different ways of putting it... From Freeman & Herron (1998) Evolutionary Analysis, Prentice Hall, Upper Saddle River. p. 314. NOTE - genetic exchange between species: these imply that hybrid offspring (product of mating between members of two species) can not themselves mate and produce viable offspring. However, there are documented cases where hybrid offspring successfully mate with members of one or the other species of their parents. In this case, the offspring will likely be viable. This is one example where genes from one species can be transferred to a second species (in general, a closely related species). Another mechanisms of genetic exchange between species involve retroviral transfer, where a retrovirus will integrate into a host genome, pick up some host genetic material, then later leave and infect another host (often a different species) and so transfer genetic material between species.

III. Basic Organizational Points for all organisms.

1. Form / Body Plan / Support - Prokaryotes are Single Cell organisms

Cell Membrane - phospholipid bilayer - "Plasma membrane"
Cytoplasm - all the stuff inside the membrane - the inside of the cell Cell Wall: Peptidoglycan (see Campbell, p. 505)
Cell surface: attachment

2. Nutrition / Excretion / Digestion: Metabolism / Metabolic Reactions

from Campbell, p. 509...

Mode of Nutrition

Energy Source

Carbon Source


Inorganic Chemicals



Organic Compounds

Organic Compounds
Organic Compounds

Energy Bio-Conversion: A Prokaryotic Invention:

The majority of known metabolic pathways exist in one form or another in prokaryotes. Presumably, the Earliest Common Ancestor possessed many of these features, and the essence of cellular biochemistry evolved quite early.

3. Circulation / Transport:

4. Respiration

5. Communication: External / External (hormones, nervous system)

6. Behavior: sex, chemo-orientation

7. Reproduction

8. Genetics - self replication / reproduction

IV. Viruses, Viroids, Prions - Small, but what are they?