Todays Plan: 4/20/16

Bellwork: Check plates, do

Transduction questions (30 mins)
Finish Prokaryotes activities (40
mins)
Finish Paper Plasmid discussion
questions first
Classification notes (the rest of class)
Todays Plan: 4/21/16
Bellwork: Check plates and bacterial
respiration activity(20 mins)
Protist activities (40 mins)
Finish Bacteria notes and start Protist
Notes (the rest of class)
Todays Plan: 4/14/15
Bellwork: Go over test (30 mins)
Continue activities (30 mins)
Prokaryotes notes (the rest of class)
Todays Plan: 4/15/15
Bellwork: Finish prokaryotes notes
(20 mins)
Try to finish prokaryotes and protists
activities today (40 mins)
Virus notes (the rest of class)
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 youre handwriting a scientific name, you underline it in
stead of using italics
Phylogeny vs. Cladistics
Phylogeny is the study of an
organisms 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 arent always
accurate with respect to time, but
you can get a sequence from the
tree
Its sometimes difficult to tell the
evolutionary relationships
between certain taxa (like
families) on phylogenetic trees
We cant 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, its 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, its called a
shared derived character
Figure 27-1

This is a monophyletic group This is a monophyletic group

that shares a derived trait that shares a derived trait
(the C in the third position) (the G in the fifth position)

1 2 3 4

B C

AAC GCT ACT AAA GGT ACT

Trait (in this case,

A
a DNA sequence)
AAA GCT ACT in the ancestral
population
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
Homoplasy: Traits are similar but were not inherited from a common ancestor.

Common dolphin Ichthyosaur

es

rs
au
ns d
ls
m

rs
ds

s
ts

hi n
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re

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ur
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os
lp s a
ts
an
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ot

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at

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on

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im
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no
ep

od

ht
rd
er
ar

za
h
M
Sy

Pr

Ic
Pt

Bi
M

El

Di

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R

W
The dolphin and ichthyosaur The members of lineages
lineages are far apart on the between the dolphins and
evolutionary tree, suggesting ichthyosaurs do not have
that they are not closely adaptations such as:
related streamlined bodies
long jaws filled with teeth
fins and flippers

Homology: Similarities are inherited from a common ancestor.

Fruit-fly Hox complex

Human Hox complex

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an er

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cr ect od

he or

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sq ils s
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The genes in the Hox

(s ino
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w

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complexes of fruit flies

at

h
o
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h
An

Ec
Ar
Fl

C
and humans have similar
sequences and are in the
same order on their
chromosomes

Annelids, mollusks, and

echinoderms also have
Hox genes

Infer that common

ancestor had 8
Hox genes
The difficult nature of classification
As youve done your lab work, youve no doubt
noticed that theres a certain arbitrary nature to this
work, and that the graphics used are often unable to
depict something important about an organisms
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 (Occams 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 bodys
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 have flagella to help them move directionally
(the flagellum isnt 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 Decomposition
from soil

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 skins 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 were 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 dont 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 youre most familiar with
and are also extraordinarily diverse
 Bacteria
Figure 28-12

Archaea

Fi
rm
i
Sp cut
Eukarya

iro es
Ac cha
tin el
e
C ob s
hl a
am cte
C r
ya ydi ia
no ale
ba s
- ct
Pr er
ia
Bacteria

- ote
Pr o
- ote bac
Pr o te
- ote bac ria
Pr o te
- ote bac ria
Pr o te
ot ba ri
eo ct a
Proteobacteria

ba e r
ct ia
er
ia

Su
lf
A olo
er b
Th opy us
e ru
Crenarchaeota

A rm m
rc op
M hae las
Archaea

et o m
Py han glo a
ro oc bu
co o s
cc cc
Euryarchaeota

us us
Eu
ka
ry
a
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 m in diameter, while Thiomargarita
namibiensis cells (right) are about 150 m 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.