Today’s Plan: 4/24/18

 Bellwork: Look at quests (20 mins)

 Classification notes (20 mins)
 Work on poster (the rest of class)
 Background with:
 bacterial structure and a picture
 description of what it means when bacteria
are “competent” and how to make them
competent
 When are bacteria used in biotech and
when are they not, why not?
 Data pictures/descriptions
 Conclusion questions
Today’s Plan: 11/26/18
 Bellwork: Transpiration Bellwork (10
mins)
 Set up transpiration lab (20 mins)
 BLAST Lab (the rest of class)
 Turn in BLAST Lab today!
 Look at last quest when you get a
chance.
Today’s Plan: 11/27/18
 Bellwork: Mass Plants! And finish
BLAST (30 mins)
 Classification notes (20 mins)
 Begin Immune System POGIL (the
rest of class)
Today’s Plan: 11/28/18
 Bellwork: Mass Plants and record data
(10 mins)
 Viral cycle notes (20 mins)
 Finish POGIL (the rest of class)
Today’s Plan: 11/30/18
 Bellwork: Plants!(10 mins)
 Finish d and e (15 mins)
 Bacteria notes (30 mins)
 Transpiration Lab report (the rest of
class)
Today’s Plan: 12/3/18
 Bellwork: Go over equipment and use
(10 mins)
 Transformation lab (the rest of class)
 During incubation/down times, work
on the bacteria culture assignment
Classification
 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.
 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
 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
 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
 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
According to morphological
similarities, prokaryotes should
be closely related

Bacteria 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
Peptidoglycan

Plasma
Protein
membrane
Figure 28-14c

Cell walls in Gram-negative bacteria have some

peptidoglycan and an outer membrane.
Gram-negative
cell wall
Polysaccharides

Cell Outer
wall 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
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
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
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

Denitrification Fixation by
by bacteria bacteria and archaea
and archaea

Organic compounds Decomposition

with amino (–NH2) by bacteria,
groups archaea, fungi

Uptake Decomposition
from soil
Uptake
from soil
NO3– NH3
Plants
(nitrate) (ammonia)
Uptake
from soil Decomposition

Nitrification Nitrification
by bacteria by bacteria
NO2–
(nitrite)
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 gram-
negative 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 Large Compare relative sizes

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.