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The First Organisms
What is the meaning of the word "prokaryote"? pro = karyon =
What is the meaning of the word "eukaryote"? eu = karyon =
At one time, all prokaryotes were lumped into "Kingdom Monera."
We now know that there are two distinct lineages of prokaryotic organisms:
Domain Archaea (archaeans)
Domain Bacteria (bacteria)
This tree is based upon shared and derived rRNA sequences.
Note the recency of common descent. Not what one might expect. (Recall that the diagram
can be swiveled at any node, and it would be
just as correct to have Archaea and Eukarya on the left side of the phylogenetic tree).
The earliest known fossil organisms are nearly indistinguishable from archaebacteria. It is currently thought that Archaean-like prokaryotes were the first inhabitants of earth,
and spent their first 2 billion years alone (taxonomically).
Both Archaea and Bacteria are considered to be pre-nuclear (from the Greek pro, meaning "before" and karyon, meaning "nut").
They lack membrane bounded organelles or nuclei, though many do have
internal membrane systems.
NOTE: The term "prokaryote" descriptive, not phylogenetic: the lack of
a characteristic (in this case, a membrane-bounded nucleus) usually is not a very
good basis for classification.
The divergence of prokaryotic lineages happened so long
ago that it may not be possible to determine exact evolutionary relationships.
Domain Archaea: Nature's Extremophiles
This Domain includes organisms that can withstand the most extreme environments of any living thing known. They are not classified on the basis of common descent (as far as we know), but rather are placed into form taxa that reflect their metabolic strategies (which do not necessarily represent physiological homologies).
methanogens - methane-generating archaeans
thermophiles - archaeans living in extremely hot environments such as
DNA is a single, circular chromosome with a single copy of every gene (archaeans are haploid)
genome size ranges from just under 500,000 base pairs (537 protein-coding genes in Nanoarchaeum equitans) to nearly 6 million base pairs in Methanosarcina acetivorans.
some shapes are similar to those of Bacteria (spherical, rod-shaped)
cell wall is made of material unique to Archaeans
flagella are composed of multiple proteins (flagellins)--encoded by several genes--unique to Archaeans
Archaeans have tRNAs that are unique to them, different from all other tRNAs.
Archaean ribosomes are more similar to those of eukaryotes than to those of Bacteria.
cell membrane structure and composition is unique to Archaeans
Domain Bacteria: They're Everywhere
The beta taxonomy (The level of taxonomy concerned with arranging species into higher (and sometimes lower) taxa) of these organisms isn't complete, and their true evolutionary relationships may never be known. Modern classification changes as new data become available.
Bacterial Structure and Function
Bacteria may be unicellular, aggregate or colonial.
More derived species may form colonies with a division of
labor among cells.
The genome is contained in a single, circular chromosome with one copy of each gene (like archaeans, bacteria are haploid)
The average bacterial genome has about 1000 genes.
Bacteria may be categorized (but not classified) on the basis of shape:
A clustering bacteria may be given the prefix staphyl (Greek for "a cluster" or "bunch of grapes") (as in
A link-forming bacteria may be given the prefix "strept-" (Greek for "bent; pliable) (as in
Bacterial shapes do not necessarily reflect phylogenetic relationships. There may be
convergence (e.g., spirillum & spirochete)
a diversity of shapes in closely related bacteria (e.g. spirillum & vibrio)
Still, shape is useful for grouping and identifying on a visual basis.
External to the cell wall, some species have a gel capsule that is
often protective against predators (or a host's immune system).
Bacteria range in size from 1-5 micrometers--much smaller than most
eukaryotic cells (100-1000 micrometers).
The circular chromosome of double-stranded DNA is organized in the
nucleoid region of the cell.
The average bacterium has about 1000 genes.
some bacteria contain plasmids small, circular pieces of autonomously replicating DNA. A plasmid usually contains only
a few genes, and is not considered part of
the bacterium's genome. However, it may confer phenotypic traits (e.g., antibiotic resistance or the ability to produce toxins) on the host bacterium.
(Note: In some eukaryotic organisms, such as plants and fungi, plasmids can cause disease.)
Many species have fimbriae (singular = fimbria extending from the cell surface that allow them to attach to substrates or to other bacteria.
A pilus (plural = pili) is type of fimbria used in exchange of genetic material during conjugation.
Most bacteria are motile (they can move); the means of locomotion is another way to identify them.
means "movement. Bacteria exhibit various forms of
positive or negative taxis, depending on species and specific
environmental conditions (e.g. phototaxis, chemotaxis, etc.). Bacteria may move by means of
gliding (on a secreted slime trail)
flagellum (composed of a single flagellin, unique to Bacteria)
Note the difference between the prokaryotic and eukaryotic flagella:
Another diagnostic character is the nature of the cell
wall, which is present in most bacteria.
(Exception: mycoplasmas, all of
which are intracellular parasites; they are not classified via Gram Staining, as they have no cell wall.)
Two main types of cell wall can be
distinguished with Gram Staining.
The major difference is the amount and location of a
mucopolysaccharide known as peptidoglycan.
Peptidoglycan forms a thick,
rigid layer in both Gram positive (G+) and Gram negative (G-) cells.
It composed of an
overlapping lattice of two sugars (N-acetyl glucosamine (NAG)
and N-acetyl muramic acid (NAM, which is unique to bacterial cell walls and found nowhere else.))crosslinked by amino acids.
The exact molecular composition of peptidoglycan layers is species specific.
Gram Positive (G+): stain dark with Gram method, due to thick peptidoglycan layer
Gram Negative (G-): do not stain with Gram method (appear pink from
safranin counterstain), as they have a relatively thin layer of peptidoglycan sandwiched between inner and outer plasma membranes.
Gram staining properties are linked to pathogenicity:
G- are often
often being more dangerous than G+ because the peptidoglycan layer of G- is protected by a gel or slime layer it is less susceptible to attack by the host's immune system or antibiotics that
interfere with the formation of peptidoglycan amino acid bonds (e.g., penicillins)
Bacterial cells can be grown in culture on appropriate nutrient media
(e.g., agar with broth). A bacterial colony on an agar plate is
called a lawn, and various species have characteristic lawn phenotypes, which make them useful in the study of bacterial genetics.
transformation (genetic recombination via uptake of bacterial genes from environment)
transduction (genetic recombination via transfer of bacterial genes by virus)
Endospore: Dormant Phase
Some species can form a tough, environment-resistant structure called an
endospore that can survive extremes of temperature and drought.
An endospore is little more than the DNA surrounded by a thick
wall. It's nearly impossible to kill an endospore, so pathogens that can
form them (e.g. Clostridium tetani, the cause of tetanus) can be particularly pernicious.
Metabolic Diversity of Prokaryotes
Three basic types of organisms re: oxygen tolerance/metabolism
obligate anaerobe - can do only fermentation; killed by oxygen
obligate aerobe - operates primarily on aerobic metabolism;
cannot survive long without oxygen.
facultative anaerobe - can do either aerobic
respiration or fermentation, depending on environmental conditions.
In the Krebs Cycle, the terminal electron acceptor can be
oxygen (in aerobes)
nitrate or nitrite (in denitrifying bacteria, which
return nitrogen gas to the atmosphere)
Four Main Categories of Prokaryotic Energy Transduction
use CO2 as carbon source
use light as Energy source
cyanobacteria are the most common in this group
use CO2 as carbon source
use inorganic compound oxidation as Energy source (e.g.,
H2, ammonia or iron ions)
many archaebacteria fall into this category
use organic molecules as a carbon source
use light as energy source
relatively few bacteria in this group
obtain energy from organic compounds
vast majority of bacteria are in this category, along with most
protists, animals, fungi and some plants.
a saprobe is a chemoheterotroph that breaks down decaying organic matter for energy.
a parasite is a chemoheterotroph that uses the organic
molecules of living tissue for energy
How did it all begin?
Early hypotheses about the origin of bacterial metabolism suggested that the earliest cells used ATP from the "primordial soup".
Problem: it's not likely there was enough ATP out there to fuel those newly made cells. ATP is highly
unstable, and won't remain in solution for long.
More plausible is the idea that CO2 was the first Carbon
source, and that early cells had plasma-membrane anchored enzymes that
could oxidize inorganic compounds to make the energy needed to drive
synthesis of carbon compounds.
Ecological Importance of Prokaryotes
Along with fungi, they are the biosphere's main decomposers.
Pseudomonas spp. - converts
nitrite or nitrate into N2 (denitrification)
Although Pseudomonas bacteria are ubiquitous in the environment, they usually do not cause disease.
However, in an immunocompromised animal, they can proliferate and cause infection. Hence, they are considered opportunistic pathogens.
Prokaryotes as Pathogens
A pathogen is a disease-causing agent.
The vast majority of bacteria are non-pathogenic, or even beneficial. However, a number of bacteria can cause disease in plants and animals.
In order for a microorganism to be declared the cause of a particular
disease it must meet four criteria (Koch's Postulates):
it must be isolated from a diseased individual
it must be grown in pure culture from that sample
it must cause the disease in a healthy individual when introduced
from that culture
it must be isolated from the newly infected individual
Some pathogens don't meet the postulates, so clinicians must be a
little bit flexible when trying to determine how to treat difficult-to-culture pathogens.
How do bacteria cause diseases?
Invasion of tissues (again, some pathogens are merely opportunistic)
exotoxins (secreted into the medium in which the bacterium lives)
Clostridium spp.,such as C. tetani, C. botulinum and other Clostridium species.
Their toxins block inhibitory neurotransmitters at the neuromuscular junction, causing constant stimulation of muscle contraction.
endotoxins (part of plasma membrane (primarily in G- bacteria)
Vocabulary Word of the Day: An iatrogenic infection
- one that is caused by the place of healing or the healer (iatros is Greek for "healer").
Antibiotics: Fighting Back
Competition exists at even the microscopic level. Antibiotics are
substances that inhibit the growth of prokaryotic cells. They are
manufactured not only by plants and fungi, but also by some bacteria.
Humans can use and modify naturally produced antibiotics for their own use and protection against bacteria.
Antibiotics are not effective against viruses, and generally not against most eukaryotes. Their are primarily effective against bacteria, though they can have side effects in eukaryotes.
A bacteriostatic substance inhibits the growth
of bacterial culture.
A bacteriocidal substance kills bacteria outright.
Different antibiotics attack different aspects of the bacterial life cycle, and most fall into one of four main categories, in terms of their mechanism of action:
inhibition of enzymes involved in cell wall biosynthesis (e.g., penicillins)
interference with normal nucleic acid (DNA, RNA) function and repair (e.g., fluoroquinolones)
interference with protein synthesis/ribosome function (e.g., chloramphenicol)
disruption of the cell membrane
Bacteria can be our competitors, our enemies, or our allies, but they form vital, ubiquitous threads in the Web of Life.