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Bio 102 Syllabus
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:
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.
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.
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
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 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.
Classification
Upper case-V V-lower case
Homo sapien
italics
Manduca sexta
Genus species
Digression... What is a species?
From Campbell, (p. 446): 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 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."
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 27.6)
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. 505)
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.
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:
- 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
|
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)
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 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