Download Classification and Bacteria Notes

Today’s Plan: 3/22/10
 Bellwork:
Announcements/Housekeeping (5
mins)
 Endosymbiant Article and questions
(20 mins)
 Classification Activities (30 mins)
 Notes on Classification (25 mins)
 Pack/Wrap-up (last few mins of class)
Today’s Plan: 3/23/10
 Bellwork: Graphic for Classification
lab (15 mins)
 Bacteria essential questions/activities
(45 mins)
 Finish Bacteria Notes (the rest of
class)
Today’s Plan: 3/24/10
 Bellwork: Finish Prokaryote Notes (15
mins)
 Prokaryote and Protist Activities (45
mins)
 Protist notes (the rest of class)
Classification
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Recall that in Biology, you learned the 7-step hierarchical
classification scheme: KPCOFGS
Some scientists have proposed a less-hierarchical, more
descriptive PhyloCode for classification, which would include
more info about evolutionary history, but this is still
controversial
Modern scientists have added a step to the front of this
scheme: Domain.
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3 domains
Archea: contains only the archaebacteria
Bacteria: contains only the eubacteria
Eukarya: contains the other 4 kingdoms; Protista, Fungi,
Plantae, and Animalia (all are eukaryotic)
Also recall that this is simply a modernization of Linnaeus’
scheme. We still use his Binomial Nomenclature for
scientific names
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Remember that this is correctly written as Genus species or G.
species, and that scientific names are in Latin
If you’re handwriting a scientific name, you underline it in
stead of using italics
Phylogeny vs. Cladistics
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Phylogeny is the study of an
organism’s evolutionary history
This is traced on phylogenetic
trees, which are based on all
known data for classification and
branch according to the
hierarchical system of
classification
Branch points aren’t always
accurate with respect to time, but
you can get a sequence from the
tree
It’s sometimes difficult to tell the
evolutionary relationships
between certain taxa (like
families) on phylogenetic trees
We can’t necessarily infer that an
organism directly evolved from
the taxon next to it on the tree
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Cladistics is a slightly different
approach that uses common
ancestry as the primary criterion
for classifying organisms.
This is used to construct
Cladograms, graphic
representations of the
relationships between Clades (a
group containing the ancestral
species and all of its
descendants)
Cladograms are constructed
using Derived Characters, which
are new characteristics that
appear with each branch on a
cladogram.
If all organisms have a trait, and
that trait is used to determine
common ancestry, it’s called the
shared ancestral character
If all organisms have a trait, and
the trait is not used as the
primary trait for determining
common ancestry, it’s called a
shared derived character
Figure 27-1
Distinguishing between Homology
and Analogy
 Homology=traits that are similar due
to shared ancestry
 Analogy=traits that are similar due to
convergent evolution (also called
homoplasies)
 In general, to distinguish between
these, Molecular data, as well as
complete anatomical/physiological
data is necessary
Figure 27-2
The difficult nature of classification
 As you’ve done your lab work, you’ve no doubt
noticed that there’s a certain arbitrary nature to this
work, and that the graphics used are often unable to
depict something important about an organism’s
lineage
 We should always remember that all phylogenetic
trees are hypothetical!
 Scientists use several things to try to be as accurate
as possible (achieve maximum parsimony)
 Some phylogenetic trees use proportional branch
lengths to demonstrate the degree of genetic change
since divergance
 Scientists try to use the simplest explanation
consistent with the facts (Occam’s razor)
 Some scientists use the principle of maximum
likelihood-given certain rules about how DNA changes
over time, a tree can be constructed that reflects the
most likely sequence of genetic change
Figure 28-11
Bacteria
According to morphological
similarities, prokaryotes should
be closely related
Archaea
Eukarya
Prokaryotes
 Mostly single-cellular, but sometimes form colonies
 Have cell walls that contain peptidoglycan (hybrid
sugar-protein molecules) as opposed to chitin or
cellulose of eukaryotic cells
 React to Gram staining differently
 Gram positive have simpler cell walls and retain the
stain
 Gram negative have less peptidoglycan in their cells
walls, are more complex and retain less stain
 This is important b/c it has treatment implications for
patients with bacterial infections, since gram negative
bacteria tend to be more resistant to the body’s
defenses and to antibiotics
Figure 28-14a
Gram-positive cells retain Gram stain more
than Gram-negative cells do.
Gram-positive
cells
Gram-negative
cells
Figure 28-14b
Cell walls in Gram-positive bacteria have extensive
peptidoglycan.
Gram-positive
cell wall
Polysaccharides
Cell
wall
Plasma
membrane
Peptidoglycan
Protein
Figure 28-14c
Cell walls in Gram-negative bacteria have some
peptidoglycan and an outer membrane.
Gram-negative
cell wall
Polysaccharides
Cell
wall
Outer
membrane
Peptidoglycan
Plasma
membrane
Protein
Prokaryotes, cont.
 Many have a capsule, which is sticky (made of
polysaccharides or proteins) and allows the bacteria
to stick to a substrate or to other bacteria to form a
colony
 Some have fimbriae, which are long, hair-like
projections that allow them to fasten to the mucous
membranes of their hosts
 Many also have sex pili for conjugation (passing
pieces of DNA back and forth for sexual reproduction)
 About ½ have flagella to help them move directionally
(the flagellum isn’t as thick as a eukaryotic flagellum
and is not covered by an extension of the plasma
membrane)
 Come in 3 main shapes, bacillus, coccus, and spiral
Figure 28-10
Escherichia coli, strain K-12
Growth in liquid medium
Growth on solid medium
Reproduction and Adaptation
 Recall that prokaryotes have a single chromosome but
also may contain small plasmids that occurs in the
nucleoid region of the cell
 Prokaryotes can reproduce asexually by binary fission
(see the cell division notes) or can reproduce sexually
using conjugation and binary fission
 Under ideal conditions, bacteria can divide every 20
minutes (in reality, they divide every 12-24 hours)
 Certain bacteria can produce an endospore when
conditions are lacking
 The bacteria produces a copy of its chromosome
(internally), and surrounds it with a tough wall.
 The rest of the cell dehydrates and dies
 When conditions are better, the endospore resumes
its metabolism
 Endospores can be hard to kill (can survive heat up
to 121 C
The success of Prokaryotes
 Rapid reproduction, genetic recombination, and
mutation provides diversity
 Prokaryotes are therefore highly evolved
 Genetic recombination happens b/c of
 Transformation-this can happen spontaneously in
nature if bacteria come into contact with other strains
that have died
 Transduction-bacteriophages carry genes from one
host to the other. This is accidental as it provides no
advantage for the virus
 Conjugation-through the sex pilus b/c of the F factor
(25 genes) that are required for production of the sex
pilus (can be on a plasmid or in the chromosome)
 R plasmids (resistance to antibiotics) can be transferred
by conjugation too
Prokaryote Metabolism
 Like Eukaryotes, some Prokaryotes are
autotrophic, while others are heterotrophic
 There are 4 main Nutritional Modes:
 Autotrophs
 Photoautotrophs-Do photosynthesis
 Chemoautotrophs-Do chemosynthesis using
Hydrogen sulfide in stead of light
 Heterotrophs
 Photoheterotrophs-Can harness light energy but
need to get Carbon in an organic form
 Chemoheterotrophs-Must consume organic
molecules to get energy and carbon
More Metabolism
 Role of oxygen
 Some are obligate aerobes, some are obligate
anaerobes
 Anaerobes can do fermentation, while others just do
anaerobic respiration in which nitrates or sulfates act
as electron acceptors in stead of Oxygen
 Facultative anaerobes can use oxygen if present, but
can also carry out anaerobic respiration in the
absence of oxygen
 Metabolic cooperation
 Bacteria in colonies can become specialized to carry
out just 1 metabolic function (ex: just nitrogen
fixation, or photosynthesis)
 Such bacteria form Biofilms with channels that allow
nutrient transport. The cells in a biofilm chemically
signal one another
Figure 28-00
Ecological Importance of
Prokaryotes
 Nitrogen fixation-Eukaryotes can only
accept Nitrogen in certain forms,
prokaryotes can accept it in virtually any
form, which allows them to pull
atmospheric nitrogen and convert it to
ammonia and other nitrogen-containing
compounds
 Root nodules of plants contain bacteria that
release usable nitrogen to plants
Figure 28-16
N2
in atmosphere
Fixation by
bacteria and archaea
Denitrification
by bacteria
and archaea
Organic compounds
with amino (–NH2)
groups
Uptake
from soil
Decomposition
by bacteria,
archaea, fungi
Decomposition
Uptake
from soil
NO3–
(nitrate)
Plants
Uptake
from soil
Nitrification
by bacteria
NH3
(ammonia)
Decomposition
NO2–
(nitrite)
Nitrification
by bacteria
Figure 28-6
Root nodules
Other Interactions of bacteria
 Mutualistic relationships Gut bacteria that help you digest food
 Root nodule bacteria
 Decomposing bacteria in the soil
 Commensal relationships Bacteria that live on your skin’s surface
 Parasitic relationships Disease-causing bacteria produce poisons that cause
illness
 Exotoxins-proteins secreted by bacteria (Ex: Cholera,
botulinum)
 Endotoxins-lipopolysaccharide components of gramnegative bacteria which are only released when the
bacteria die (Ex: Salmonella, typhoid fever)
Figure 28-2-Table 28-2
Non-symbiotic uses of Prokaryotes
 Food Production
 Biomedical Research
 Biormediation-using bacteria to
remove pollutants from soil, air, or
water
But we’re still dealing with 2
Domains, right?
 Archaea
 Known as the extremophiles
 3 main types:
 Extreme halophiles-”love salt” like in the Great Salt
Lake or the Dead Sea. Their cell walls are adapted to
such conditions
 Extreme thermophiles-”love heat” like in volcanic
springs. Their DNA and proteins are adapted so that
they don’t denature in high heat
 Methanogens-Anaerobic bacteria that relase methane as
their waste product. Found in marshes or under ice in
Greenland
 Bacteria
 These are the bacteria that you’re most familiar with
and are also extraordinarily diverse
Figure 28-12
Bacteria
Archaea
Eukarya
Bacteria
Archaea
Proteobacteria
Crenarchaeota
Euryarchaeota
Figure 28-1-Table 28-1
Figure 28-13
Small
Size varies
The sizes of bacteria and archaea vary. Mycoplasma
cells (left) are about 0.5 µm in diameter, while Thiomargarita
namibiensis cells (right) are about 150 µm in diameter.
Shape varies
The shapes of bacteria and archaea vary from
rods such as Bacillus anthracis (left) and spheres
to filaments or spirals such as Rhodospirillum.
In some species, such as Streptococcus faecalis
(right), cells attach to one another and form chains.
Mobility varies
A wide variety of bacteria and archaea use flagella (left)
to power swimming movements. These cyanobacterial
cells (right) move by gliding across a substrate.
Large
Compare relative sizes