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TAXONOMY

to put organisms into categories or taxa


to show degrees of similarities among
organisms
similarities are due to relatedness
Systematics, or phylogeny
study of the evolutionary history of
organisms
hierarchy of taxa reflects evolutionary,
or phylogenetic relationships.
SIMILARITIES OF ALL ORGANISMS:

all organisms are composed of cells


surrounded by a plasma membrane,
use ATP for energy,
store their genetic information in DNA.
Aristotle - organisms are classified either
plants or animals
Carolus Linnaeus (1735) - Swedish botanist
introduced a formal system of classification
dividing living organisms into two kingdoms-
Plantae and Animalia
Carl Von Nageli (1857 ) bacteria and fungi be
placed in the plant kingdom
Ernst Haeckel (1866) proposed the
Kingdom Protista to include bacteria,
protozoa, algae, and fungi
Because of disagreements over the definition
of protists, for the next 100 years biologists
continued to follow von Nageli's placement
of bacteria and fungi in the plant kingdom.
However, DNA sequencing places fungi
closer to animals than plants.
Fungi were placed in their own kingdom in
1959
The term prokaryote was introduced in
1937 by Edouard Chatton to distinguish
cells having no nucleus from the
nucleated cells of plants and animals.

In 1961, Roger Stanier provided the current


definition of prokaryotes: cells in which
the nuclear material (nucleoplasm) is not
surrounded by a nuclear membrane.
1968, Robert G.E. Murray proposed the
Kingdom Prokaryotae

1969, Robert H. Whittaker founded the five-


kingdom system in which prokaryotes
were placed in the Kingdom
Prokaryotae, or Monera, and eukaryotes
comprised the other four kingdoms.
The Kingdom Prokaryotae had been
based on microscopic observations.

Molecular biology revealed that there are


actually two types of prokaryotic cells
and one type of eukaryotic cell.
RIBOSOME
Basis of the discovery of the three cell types
Compared the sequences of nucleotides in the
rRNA showed that there are three distinct cell
groups : EUKARYOTES, BACTERIA,
ARCHAEA (PROKARYOTES)
1978 Carl Woese proposed the three domain
system
DIFFERENCES FOUND AMONG THE
ORGANISMS IN EACH DOMAIN

rRNA
Lipid structure
tRNA molecules
Sensitivity to antibiotics
ARCHAEA
3 MAJOR GROUPS:
The methanogens, strict anaerobes that
produce methane from carbon dioxide and
hydrogen .
Extreme halophiles, which require high
concentrations of salt for survival.
Hyperthermophiles, which normally grow in
extremely hot environments.
Taxonomic classification - Bergey's Manual of
Systematic Bacteriology
prokaryotes are divided into two domains:
Bacteria and Archaea
Each domain is divided into phyla.
Bacterial reproduction - Unlike reproduction in
eukaryotic organisms, cell division in bacteria is
not directly tied to sexual conjugation.

Definition: prokaryotic species - a population


of cells with similar characteristics.
---serovar/serotype - subdivision of a species or
subspecies distinguishable from other strains
therein on the basis of antigenic character.

Eukaryotic species - a group of closely related


organisms that can interbreed.
A pure culture is often a clone : a
population of cells derived from a single
parent cell; identical cells

In some cases pure cultures of the same


species are not identical in all ways
(group called strain)
Strains are identified by numbers, letters,
or names that follow the specific epithet.
e.g. - E. coli 0157: H7 pathogenic strain
Closely related to their host than to other
viruses
Host cell ecological niche
There are two hypotheses on the origin of viruses:
(I) they arose from independently replicating
strands of nucleic acids (such as plasmids),
(2) they developed from degenerative cells that,
through many generations, gradually lost the
ability to survive independently but could
survive when associated with another cell.
The International Committee on Taxonomy of
Viruses (ICTV) developed the current
classification system and put in place
guidelines that put a greater weighing on
certain virus properties to maintain family
uniformity.
A universal system for classifying viruses, and
a unified taxonomy, has been established since
1966.
In determining order, taxonomists
should consider
1. type of nucleic acid present - single-
or double-stranded,
2. presence or absence of an envelope
Aside from these properties, other
characteristics can be considered:
type of host,
capsid shape,
immunological properties
type of disease it causes
The system makes use of a series of
ranked taxons. The general
structure is as follows:
Order (-virales)
Family (-viridae)
Subfamily (-virinae)
Genus (-virus)
Species (-virus)
The Baltimore classification of viruses is
based on the mechanism of mRNA
production.

Viruses must generate positive strand


mRNAs from their genomes to produce
proteins and replicate themselves, but
different mechanisms are used to achieve
this in each virus family.
This classification places viruses into seven
groups:
I: Double-stranded DNA (e.g. Adenoviruses,
Herpesviruses, Poxviruses)
II: Single-stranded (+)sense DNA (e.g.
Parvoviruses)
III: Double-stranded RNA (e.g. Reoviruses)
IV: Single-stranded (+)sense RNA (e.g.
Picornaviruses, Togaviruses)
V: Single-stranded (-)sense RNA (e.g.
Orthomyxoviruses, Rhabdoviruses)
VI: Single-stranded (+)sense RNA with DNA
intermediate in life-cycle (e.g. Retroviruses)
VII: Double-stranded DNA with RNA
intermediate (e.g. Hepadnaviruses)
Kingdom Protista (1969)
-simple, eukaryotic, unicellular
-200,000 species ID
-nutritionally diverse photosynthetic to obligate
intracellular parasites
-rRNA sequencing divides protists into groups
based on their descent from common ancestor
-protists are divided into clades genetically
related groups
KINGDOM FUNGI
-unicellular yeasts, multicellular molds
and macroscopic species
mushroom

Hyphae thin tubes formed by joined


cells of a multicellular fungus; may
be divided by crosswalls that have
holes to allow the free flow of
cytoplasm
Genes that are highly conserved or rarely mutates
through time are now the basis in microbial
phylogenetics.

In bacteria and archaea 16S rRNA gene is now


used to classify them while LSU rRNA were
used for fungi and cyanobacteria

SSU rRNA for protists

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