Biology lecture on 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 formation of solid crust vs. observation of oldest fossils possible cyanobacteria bacteria (autotrophic photosynthetic). Western Austrailia (Fig 24.1) possible eukarytic algae, Michigan (Han & Runnegar, 1992, Science 257:232) ..Giardia - "intermediate form" ..two nuclei, no mitochondria projected from on DNA sequence analysis Burgess Shale Fossils Many of current animal phyla (echinoderms, annelids, arthropods, chordates). Appearance of skeletons poss. in response to predation. Summary of animal evolution:

Earliest Common Ancestor Oldest Prokaryotic Fossils

3.5-4 billion years 3.5 billion years

Oldest Eukaryotic Fossils

2.1 billion years

Multicellular Eukaryotes Cambrian "Explosion" (Animals)

1-1.2 billion years 500 million years

Fig. 29.1. Summary of chordate evolution: Fig. 30.6. Origins of Plants from green algae Vascular Plants Gymnosperms Angiosperms Oldest Vertebrates Oldest Jawed Vertebrates Oldest Bony Fishes Oldest Amphibians Oldest Reptiles Oldest Mammals Homo erectus Homo sapien 460 million years Fossil Record Summary of Plant evolution: Fig. 27.3.

400 million years 360 million years 130 million years 500 million years 500 million years 425-450 million years 365 million years 300 million years 220 million years 1-2 million years 100,000 years fig. 30.32 fig. 30.32 "naked seeds", conifers, etc. "contained seeds", flowering plants jawless, fishlike Hox gene duplications

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:
1. Prokaryotic cell organization: membrane, DNA, protein synthesis, metabolic activities 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. 2. Eukaryotic cell organization: nucleus, organelles (endosymbionts) ....DNA sequences of mitochondria and chloroplasts are more similar to bacterial homologoues than to nuclear homologues - more latter) 3. Multicellularity, specialization.

Summary: Differences between the three domains

From Campbell, p. 509: CHARACTERISTIC Nuclear envelop Membrane-enclosed organelles Peptidoglycan in cell wall Membrane lipids RNA polymerase Bacteria (Prokaryote) no no yes unbranched hydrocarbons one gene Archaea (Prokaryote) no no no some branched hydrocarbons several genes Eukarya (Eukaryote) yes yes no unbranchced hydrocarbons several genes

Start amino acid Introns Sensitivity to antibiotics streptomycin and chloramphenicol

formyl-Met no yes

Met some species no

Met yes no

Prokaryotic Biodiversity?
Numerous Major groups (sub-domains / Kingdoms, sub-kingdoms, etc.) 4000 named species estimates from 400,000 - 4 million species (or higher?) (from Campbell) 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

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.

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)

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 grampositive bacteria represent a fairly small proportion the 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. 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). Other 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
Upper case-V V-lower case Homo sapien Manduca sexta Genus species

species
italics

Digression... What is a species?

From Campbell, (p. 437-438): 4 different ways of putting it... "...a species [is] a population or group of populations whose members have the potential to interbreed with one another in nature to produce biable, fertile offspring, but who cannot successfully interbreed with members of other species." "...a species is the largest unit of population in which genetic exchange is possible, and that is genetically isolated from other such populations." "...each species is circumscribed by reporductive barriers that preserve its integrity as a species by blocking genetic mixing with other species." "Members of a species, said to be conspecific, are united by being reproductively compatible, at least potentially." From Freeman & Herron (1998) Evolutionary Analysis, Prentice Hall, Upper Saddle River. p. 314. 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.

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 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

Cell Membrane - phospholipid bilayer - "Plasma membrane" 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 25.5) Cytoplasm - all the stuff inside the membrane - the inside of the cell water, ions (Na+, K+, Cl-, Ca++, Mg++), amino acids & proteins, nucleotides and nucleic acids (DNA, RNA), sugars, lipids, etc. Cell Wall: Peptidoglycan (see Campbell, p. 501) 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. 501) "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. Cell surface: attachment 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. 505... Mode of Nutrition Autotroph ....Photoautotroph ....Chemoautotroph Heterotroph ....Photoheterotroph ....Chemoheterotrophic Energy Source Carbon Source CO2 CO2

Light Inorganic Chemicals Light Organic Compounds

Organic Compounds Organic Compounds

Nitrogen Metabolism (refer to fig. 49.11): 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. 9-14) ATP can be produced less effeciently, in glycolysis, without using O2 (p. 166-7) 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) 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:

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 25.4) 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