From the molecules of life, to the
simpler organisms
Part
I
Paula B. Matheus Carnevali
Outline
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The first organisms
Classification systems
The major divisions of life
Phylogeny of bacteria
Prokaryotic cell structure and function
Gram negative vs. Gram positive
Cartoon of the tree of life
Figure 1. Last Universal Common Ancestor
The first cellular
life whose
descendants
ultimately
survived, appeared
at least 2 billion
years ago and
Figure 2. Fossilized bacteria. a) Archean Apex, 3.5 probably much
billion yrs old, b) Gloeodiniopsis, 1.5 billion yrs old,
c) Palaeolyngbya, 950 million yrs old.
earlier
From Prescott et al., 2005
Which of its two most vital substances
did life acquire first, proteins or DNA?
Ribozymes
Figure 3. The mechanism of action of the ribozymes.
From Essential cell biology, 2/e, 2004, Garland Science
Characteristics of the first
organisms
• Self-replicating systems
• Use of DNA to store heritable information
• Use of proteins to express information
• Cellular forms
• Cellular membranes
Classification of organisms
• Taxonomy is the science of biological classification.
• Classification is the arrangement of organisms into groups or
taxa (s. taxon) based on mutual similarity or evolutionary
relatedness.
• Nomenclature is the branch of taxonomy concerned with the
assignment of names to taxonomic groups in agreement with
published rules.
• Identification
is the process of determining that a particular
isolate belongs to a recognized taxon.
• Systematics is the scientific study of organisms with the ultimate
object of characterizing and arranging them in an orderly manner.
Some remarkable discoveries
in microbiology
• Aristotle first classified living things in
Plants and Animals
• Bacteria were first observed by Anton van Leeuwenhoek in 1676
using a single-lens microscope of his own design.
• The invention of the Electron Microscope allowed for the
distinction between Prokaryotic and Eukaryotic cells
• In the 1960s Robert Whittaker presented the five kingdoms
system of classification including Fungi
• Based on 16S rDNA Carl Woese and his collaborators suggested
that prokaryotes were divided into two distinct groups very early
on, and presented the Three domain system including Archaea
Prokaryotes vs. Eukaryotes
Table 1. Comparison of Prokaryotic and Eukaryotic cells
From Prescott et al., 2005
Prokaryotes vs. Eukaryotes
Figure 4. Comparison of Prokaryotic and Eukaryotic cell structure. (a) The
prokaryote Bacillus megaterium, (b) The eukaryotic alga Chlamydomonas
reinhardtii, a deflagellated cell. From Prescott et al., 2005
Whittaker’s 5-Kingdom system
It lacks distinction
between Archaea
and bacteria. The
kingdom Protista
also may be too
diverse to be
taxonomically
useful. The
boundaries
between kingdoms
are ill-defined
Figure 5. The five kingdom system proposed by
Whittaker. From Prescott et al., 2005
Major characteristics used in
taxonomy
1. Classical Characteristics:
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Morphological characteristics
Physiological and metabolic characteristics
Ecological characteristics
Genetic analysis
2. Molecular characteristics:
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Comparison of proteins
Nucleic acid base composition
Nucleic acid hybridization
Nucleic acid sequencing
Phylogeny of bacteria
Figure 6 . Hierarchical arrangement in taxonomy. From Prescott et al. , 2005
•A prokaryotic species is a collection of strains that share many stable
properties and differ significantly from other groups or strains.
•A species (genomospecies) is a collection of strains that have a similar
G+C composition and 70% or greater similarity as judged by DNA
hybridization experiments.
Woese’s
three
domain
system
Figure 7. Tree of life by the three domain system
Bacteria, Archaea and Eucarya
Table 2. Comparison of Bacteria, Archaea, and Eucarya
From Prescott et al., 2005
Figure 8a.
Prokaryotic cell
Figure 8b.
Eukaryotic cell
Table 2 cont. Comparison of Bacteria, Archaea, and Eucarya
Eukaryotic cells arouse form
prokaryotic cells
Figure 9. A schematic representation of the process of endosymbiosis
Endosymbiotic hypothesis
Figure 10. A schematic representation of the process of endosymbiosis
Phylogeny of bacteria
Figure 11. Phylogeny of Bacteria. The tree is based on 16S rRNA comparisons.
From Prescott et al., 2005.
Purpose of the Gram Stain
To separate bacteria based upon their cell wall
structure and to determine their morphology
and possible cellular arrangement
Gram-positive cocci in chains
Gram-negative rod
Figure 12. The Gram-Positive and Gram-Negative envelopes.From Prescott et al., 2005
Gram negative vs Gram positive
Table 3. Comparison between Gram-positive and Gram-negative bacteria
Modified from Prescott et al., 2005
Prokaryotic cell organization
Figure 13. A prokaryotic cell
Size, shape and arrangement
Figure 14. Examples of bacterial shapes. From Prescott et al., 2005
Size, shape and arrangement
Figure 15. Comparison between the size of a human
cell, bacteria and viruses. From Prescott et al., 2005
Table 4. Prokaryotic structures
From Prescott et al., 2005
Plasma membrane
Figure 16 . Plasma membrane structure. From Prescott et al., 2005
Cell wall
Figure 17. The cell wall. The Gram+ envelope is from Bacillus licheniformis, and the
Gram- micrograph is of Aquaspirillum serpens. M=peptidoglycan or murein layer,
OM=outer membrane, PM=plasma membrane, P=periplasmic space, W=Gram+
peptidoglycan wall. From Prescott et al., 2005
Gram positive cell walls
Figure 18. The Gram-Positive envelope. From Prescott et al., 2005
Gram negative cell walls
Figure 19. The Gram-Negative envelope. From Prescott et al., 2005
Bacterial nucleoid
Figure 20. Some bacterial nucleoids.
From Prescott et al., 2005
E. coli chromosome growing
Flagella and motility
Figure 21. The ultrastructure of bacterial flagella. Flagellar basal
bodies and hooks in (a) gram-negative and (b) gram-positive bacteria.
From Prescott et al., 2005
Flagella and motility
Figure 22. The long flagella and the numerous shorter
fimbriae on Proteous vulgaris. (a) Monotrichous polar,
(b) Lophotricous, (c) Peritrichous.
From Prescott et al., 2005