Lecture 2: Prokaryotes

Outline

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

II. What is a Prokaryote?

III. Basic Organizational Points.

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

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
Gymnosperms	360 million years	"naked seeds", conifers, etc.
Angiosperms	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

1. Plasma membrane / Cytoplasm
2. DNA, transcription to RNA via RNA polymerase, translation to protein via tRNAs and ribosomes
3. Replication / reproduction / genetic exchange
4. Many metabolic pathways, photosynthesis, glycolosis
5. Behavior - sex, chemo-orientation (e.g. for feeding)

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:

NO nuclear membrane (no nucleus), no organelles (mitochondria, chloroplasts), no introns in genome BUT they do "everything" we do... (Note: There are certainly differences between the three domains. For example, although DNA machinery is quite similar in each domain, there are consistent differences; for example bacteria use a different DNA polymerase for replication than do the Archaea or Eucarya.

....DNA sequences of mitochondria and chloroplasts are more similar to bacterial homologoues than to nuclear homologues - more latter)

Prebiotic Evolution: Oparin/Haldane

1. Small Molecules: Miller & Urey (+ enrichment from Space?)
2. Polymers: clays as catalysts
3. Self Replication: RNA - ribozymes
4. Protobionts - Energy trapping - selection
:
:
5. Prokaryotes

Prokaryotes are Cells!

A. Membrane: Semipermeable Barrier, separating IN from OUT

B. Metabolic Activity: Biosynthesis, Recycling, "Waste"

                    Proteins
Environmental       Nucleic Acids        controlled release
Chemicals    =====> ATP (energy) ======> of waste / toxics
                    lipids               osmotic regulation
                    etc.

C. ENERGY: ATP >>>Hypothesis (Fig. 27.8):

1. Cell concentrates FeS + H₂S
FeS + H₂S ==> FeS₂ + H₂ + energy Exergonic (spontaneous)reaction:(p. 88). Concentration increases probability of reaction.

2. Cell enzyme in membrane (Hydrogenase) breaks and separates H₂ to 2e^-(in) and 2H⁺(out)

- establishes concentration gradient for H⁺ across membrane.
Concentration gradient = POTENTIAL ENERGY. (probably requires e^- acceptor inside cell - invention of electron transport chain).

3. H⁺ allowed to leak into cell via protein that uses ENERGY to synthesze ATP.

ADP + Pi ===> ATP

D. PHOTOSYNTHESIS

1. Invent protein that captures light energy - PHOTOSYSTEM

• Bacteriorhodopsin - structurally related to our visual pigments.
• Absorbs light, uses energy to pump H⁺, converting light energy into potential energy of H⁺ concentration gradient.
• Controlled entry of H⁺ coupled to ATP synthesis.

2. Early prokaryotes - Photosystems drive e^- from H₂S to NADP⁺.
• Reaction used to "FIX" carbon in CO₂ (synthesize carbon based molecules).

D. OXYGEN ATMOSPHERE - ENVIRONMENTAL DISASTER

1. CYANOBACTERIA = Shift from H₂S to H₂O as e^- doner.
• Synthesize organic compounds from H₂O + CO₂. Liberate O₂.
• Evolved 2.5-3.4 billion years ago.
• Rust appears in rocks 2 billion years ago.
  
2. Oxygen Reactive, breaks chemical bonds TOXIC - WORLD POISONED!
3. Drove some organisms into anaerobic enviornments.
4. Drove invention of anti-oxidents.
5. May have driven selection of aerobic symbionts

MITOCHONDRIA <<>> EUKARYOTES

Differences between the three domains

From Campbell, p. 512:

CHARACTERISTIC	Bacteria (Prokaryote)	Archaea (Prokaryote)	Eukarya (Eukaryote)
Nuclear envelop	no	no	yes
Membrane-enclosed organelles	no	no	yes
Peptidoglycan in cell wall	yes	no	no
Membrane lipids	unbranched hydrocarbons	some branched hydrocarbons	unbranchced hydrocarbons
RNA polymerase	one gene	several genes	several genes
Start amino acid	formyl-Met	Met	Met
Introns	no	some species	yes
Sensitivity to antibiotics streptomycin and chloramphenicol	yes	no	no

Prokaryotic Biodiversity?

Numerous Major groups (sub-domains / Kingdoms, sub-kingdoms, etc.)
5000 named species
estimates from 400,000 - 4 million species (p. 503)
Differences can be difficult to recognize because of relatively simple "body" plan. There are only so many different ways a single cell can appear or have gross molecular uniqueness (phenotypic differences). Must rely on DNA analysis (genotypic differences).

Diversity Within the Three Domains

                       BACTERIA
               |---------------------------Thermotagales
               |
            |==|  |------------------------Green non-sulfer bacteria
            |  |  |
            |  |--|  |---------------------Flavobacteria
            |     |  |
            |     |  |  |------------------Cyanobacteria (Nostoc)
            |     |--|  |                  (chloroplasts)
            |        |  |
            |        |--|  |---------------Purple bacteria (E. coli)
            |           |--|               (Agrobacterium,mitochondria)
            |              |
Earliest    |              |---------------Gram Positive Bacteria (TB)
Common------|                                
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
                                    |  |
                                    |--|---Animals
                                       |
                                       |---Fungi (yeast, mushrooms, etc)

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.

Classification

Kingdom
Phylum
Class
Order
Family
Genus
species

     Upper case-V    V-lower case 
                Homo sapien
                                   italics
                Manduca sexta

                Genus species

Digression... What is a species?

"...a species [is] a population or group of populations whose members have the potential to interbreed with one another in nature to produce viable, fertile offspring, but who cannot produce viable, fertile offspring with members of another species."

"...a species is the largest unit of population in which genetic exchange is possible, and that is genetically isolated from other such populations."

"Members of a biological species are united by being reproductively compatible, at least potentially."

"...the biological species concept hinges on reproductive isolation, with each species isolated by factors (barriers) that prevent interbreeding, thereby blocking genetic mixing with other species."

1. Species consist of groups of interbreeding populations.

2. Species are fundamental unit of evolution.

3. Species share a distinguishing characteristic, which is evolutionary independence. Evolution independence occurs when mutation, selection, migration, and drift operate on each species separately. This means that species form a boundary for the spread of alleles. Consequently, different speices follow independent evolutionary tragectories.

III. Basic Organizational Points for all organisms.

1. Form / Body Plan / Support
2. Nutrition / Excretion / Digestion
3. Circulation / Transport
4. Respiration
5. Communication: External / External (hormones, nervous system)
6. Motility / Behavior
7. Reproduction
8. Genetics

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

semi-permeable - restricts what can leak out of cell
hydrophillic along inner and outer surfaces, but hydrophobic in the interior
...molecules that are water soluble (hydrophilic) have difficulty passing through membrane
...because the hydrophobic interior is a barrier.

some bacteria: internal membranes, inner folds of plasma membrane (Campbell, fig 27.6)

water, ions (Na+, K+, Cl-, Ca++, Mg++), amino acids & proteins, nucleotides and nucleic acids (DNA, RNA), sugars, lipids, etc.

protein + sugar (plants also have cell walls, but of cellulose)
Gram positive bacteria: Plasma membrane + thick cell wall
Other bacteria (Gram-neg.): Plasma membrane + thin cell wall + second outer
"plasma membrane" inner and outer lipid bilayer membranes, separated by layer of peoptidoglycan

Purpose? Protection. (Campbell, p. 505)
"Among pathogenic, or disease-causing, bacteria, gram negative species are generally more threatening that gram-positive species. The lipopolysaccharides on the walls of gram-negative bacteria are often toxic, an dthe outer membrane helps protect the pathogens against the defenses of their hosts. Furthermore, gram-neg. bacteria are commonly more resistant than gram-pos. species to antibiotics because the outer membrane imbedes entry of the drugs." Penicillin (and many other antibiotics: disrupt peptidoglycan structure, esp. in gram-pos. species (and are thus bacteria specific). Lysozyme c (in animals' tears, saliva and nasal mucus) is an enzyme that destroys cell walls of bacteria.

Capsule: in many bacteria, gelatenous outer covering, sticky attachment and further protection
Pili (pilus): surface "appendages", for attachment

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

Requirements:
protein and nucleic acids require: carbon, nitrogen, phosphorous, sulfer
lipids, sugars require: carbon
also water, ions, etc.
energy source for driving energy dependent reactions (biosynthesis, membrane transport, motility)

Extracellular Digestion: secretion of enzymes, transport of small molecules (amino acids rather than proteins.

Sources of energy:

Autotrophic
1. Phototrophs - light energy (photosynthesis) Earth had no O2 until photosynthesis evolved.
2. Chemotrophs - inorganic chemicals in the environment

Heterotrophic - organic chemicals (something other organisms have produced)

from Campbell, p. 509...

Mode of Nutrition	Energy Source	Carbon Source
Autotroph ....Photoautotroph ....Chemoautotroph	Light Inorganic Chemicals	CO2 CO2
Heterotroph ....Photoheterotroph ....Chemoheterotrophic	Light Organic Compounds	Organic Compounds Organic Compounds

Nitrogen Metabolism (refer to fig. 54.11):
Bacteria evolved matabolic pathways for transfering nitrogen from N2 to organic molecules
Nitrogen fixing bacteria: N2 > NH3
Nitrifying bacteria: NH3 > NO2- (nitrites) > NO3- (nitrates) > assimilation
Denitifying bacteria: NO2- or NO3- > N2
Nitrogen fixing bacteria in certain plant roots (e.g. legumes) - symbiosis

Photosynthesis, Glycolysis: Solar Energy to sugar, sugar to ATP


There was NO molecular oxygen (O2) until photosynthesis had evolved
Cyanobacteria can photosynthesize (chloroplasts evolved from CB)

Energy Bio-Conversion: A Prokaryotic Invention:

                    LIGHT
                      V
                      V
        >>>>>>> PHOTOSYNTHESIS >>>>>>>>>
        ^       (chloroplasts)          v
        ^                               v
        ^                               v
    CO2 + H2O                 ORGANIC MOLECULES + O2
        ^                               v 
        ^                               v 
        ^ GLYCOLYSIS / ELECTRON TRANSPORT
                 (mitochondria)
                      V
                      V
                     ATP

Aerobic vs. anaerobic bacteria
Oxygen is used to accept electrons during electron transport -
production of ATP from organic molecules (fig. 9-15)
ATP can be produced less effeciently, in glycolysis, without using O2 (p. 162-4)
So, ATP can be produced aerobically, and anaerobically
anaerobic metabolism frequently occurs in our muscles under exercise - with painful buildup of lactic acid

Bacteria can be:
obligate aerobes
obligate anaerobes
facultative anaerobes (can switch)

3. Circulation / Transport:

Single cell - Easy movement / diffusion through cytoplasm.
transmembrane transport mechanisms to move molecules into and out of cell

4. Respiration

Single cell - Easy diffusion of CO2, O2 across cell membrane. l

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

1. Single Cell: metabolic / biochemical pathways
2. "Homeostasis" regulate internal enviornemnt in context of external environment:
Faculatative anaerobes can sense the environment and respond by adjusting their
metabolic pathways to accomodate aerobic or anaerobic needs.
Can sense food source (amino acids) available and regulate expression of
appropriate enzymes for metabolizing these molecules.
Water balance, ionic ballance

6. Behavior: sex, chemo-orientation

1. Motility: rotary flagella (see figure 27.5)
2. Taxes
a. chemotactic: tumble and run
b. phototactic
c. magnetotactic
3. Behavior:
1. chemosensory receptors detect "food"
2. biochemical decision making
3. communication of decision to flagellar motor
4. expression of appropriate behavior

7. Reproduction

1. Simple Division
2. Conjugation
a. genetic transfer of plasmid DNA (extrachromosomal circle)
b. cross over, exchanging chromosomal DNAs through recombination
3. Endospore: protective resting/dormant stage
a. harsh environmental conditions
b. no metabolic activity
c. 2000 year mummies

8. Genetics - self replication / reproduction

DNA - stored information: ~3,000 genes (vertebrates have about 100,000 genes)
double stranded, circular
universal codon usage (bacteria use a few codons differently than the Archaea/Eucarya)
transcription: RNA polymerase
translation: ribosomes (small and large rRNAs), tRNAs
no introns

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

Viruses

A. Intracellular parasites; categorized by host specificity.
1. tobacco mosaic virus, tomato virus
2. herpes, cold, HIV, T-cell leukemia, papilloma virus
B. Structure.
1. 2 parts: RNA or DNA inside a protein coat.
a. plant: RNA viruses
b. animal RNA and DNA viruses
2. small: 0.05 - 0.2 um
3. genome: ca. 50,000 bp long; several genes
C. Reproduction:
1. attach to cell
2. inject DNA or RNA
3. express protein to redirect cell metabolism
a. RNA > DNA > integration or DNA > integration
b. synthesize multiple copies of self using cell machinery; blow out cell

Viroids

A. Structure: RNA only, no coat protein
B. Pathogenicity: plant.

Prions

A. Pathogenicity: Mad Cow disease, scrapie
B. Reproduction
1. No DNA or RNA
2. mutant protein complexes with normal protein from host
normal protein is modified (protease activity) to irregular fold
modified normal protein mutates more normal proteins