Tree of life

Common ancestor
to all life

• Phylogeny is the evolutionary history of a species or group

of related species.
– provides important information about similar characteristics
in closely related species
– classifies organisms and determines their evolutionary
relationships.
– Phylogenetic trees: show patterns of descent
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 Classification of living things
• Scientists have a system for naming all the living organisms on
earth.
• The system was created by a Swedish scientist named Carl
Linnaeus
• He gave each organism a two-word Latin name (Binomial
Nomenclature)
Linneaus’ System of Scientific Names

• Each species of a living thing is given a DOUBLE NAME

• First Name (Genus)

• tells which group of similar species the living thing belongs to

• Second Name (Species)

• tells the name of the one particular species in that genus
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 3 Domains

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 Cell size

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 Overview of prokaryotes

• Prokaryotes exist in all of the habitats on Earth

• Domain Archaea
• Archaea-thrive mostly in extreme environments
– Extreme cold, Extreme heat,
– Low O2
– Extreme pressure
– High salt (halophiles)
• exits in environments that are too extreme or inhospitable for
eukaryotic cells – extremophiles!!
• Living life on the edge

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 Oxygen Requirements

•Prokaryotic metabolism varies with respect to O2

• Obligate aerobes require O2 for cellular respiration

• Obligate anaerobes are poisoned by O2 and use

fermentation or anaerobic respiration

• Facultative anaerobes can survive with or without O2

• Aerotolerant anaerobes don’t use O2.for growth but

tolerate its presence

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 Prokaryotic cell structure

Bacteria and Archaea have molecular differences such as

composition of their cell wall
• Main component of bacterial cell wall is peptidoglycan
layer
• peptidoglycan layer is the target for antibiotics (damage
bacterial cell wall resulting in cell lysis)
• However, Archea has no cell wall (S-layers instead)

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 Bacterial cell wall

• The bacterial cell wall comprise mostly of peptidoglycan - a

network of sugar polymers cross-linked by polypeptides

• The amount of peptidoglycan within the cell wall can differ

between bacteria

Gram negative Gram positive

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 Bacterial cell wall
• Gram staining technique is used to divide bacteria into 2
groups; Gram-positive and Gram-negative.
• This depends on the thickness of peptidoglycan layer
– Gram-positive bacteria stains purple: more peptidoglycan
which traps crystal violet during Gram staining e.g.
Staphlyloccoccus aureas.
– Gram-negative bacteria stains pink: less peptidoglycan crystal
violet easily rinsed away e.g. Escherichia coli

Gram-positive bacteria have a thicker Gram-negative bacteria have a thin

peptidoglycan layer and stain purple.
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layer of peptidoglycan and stain red.
 Archaea cell wall
Pseudomurein is one of the many different cell wall polymers present in Archaea,
being found only in Methanobacteriales and the genus Methanopyrus.
Pseudomurein has a similar overall 3-dimensional structure to murein, the
predominant component of bacterial cell walls.

The main chemical

differences in the
methanogen
pseudomurein cell
walls result in the
pseudomurein-
containing
methanogens being
resistant to lysozyme
and other bacterial cell
wall hydrolases.

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 S-Layer
• In both Bacteria and Archaea, S-layers are composed of only one or, in a few
cases, two different (glyco) proteins. These are produced in large amounts
within the cell and self-assemble into a paracrystalline surface layer
• Depending on the organism, the S-layer lattice symmetry can consist of one
(p1), two (p2), three (p3), four (p4), or six (p6) protein units, which results in
regularly spaced pores
• As S-layers are monomolecular arrays of identical subunits, pores are identical
in shape and size
• Although the function of S-layers was initially not understood, they are now
recognized to function as protective coats, molecular sieves, molecule and ion
traps, as well as perform roles in surface recognition and cell shape
maintenance

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Domain Archaea

• Four phyla
• Euryarchaeota and Crenachaeota (two mostly studied)
• Korarchaeota and Nanoarchaeota (less studied)

Although both Archaea and bacteria are simple life-forms and belong
to prokaryotes, Archaea are very different from bacteria.

• Don’t need oxygen like bacteria.

• Absorb CO2, N2, or H2S and give off methane gas as a waste
product.

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Importance in Biotechnology

• Archaea can be useful for many processes that we depend on

– Sewage treatment; different types of bacteria are needed to
decompose organic waste
– Bioremediation; some special bacteria are used to degrade toxic
compounds in to less toxic residues
– Biogas is produced from the decomposition of organic matter
under anaerobic conditions by a group of archaea called
methanogens
• They don’t need oxygen
• Use CO2, N2, or H2S as alternative electron acceptor and give
off methane gas (biogas) as a waste product

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 Euryarchaeota

• Extremely halophilic Archaea

• Require high salt concentration
– > 1.5 M (~9%) NaCl
• Highly diverse metabolism, reflecting the diversity in salt
composition of saline environments
• Thermoplasmatales highly acidophilic and thermophilic;
Thermoplasma and Ferroplasma lack cell walls
• Archeoglobus and Ferroglobus early H2S reducers and
Fe2+ oxidizers, repectively

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 Euryarchaeota

 Methane gas: discovered in the

late 1770 by Alessandro Volta
“combustible gas”)
 Use CO2 as a terminal electron
acceptor and produce
(methane), CH4
 The terminal oxidation step in
many anaerobic environment
(marshes, the GI tract,
geothermal sources, sludge
digesters)
 Methane gas used to produce
electricity, heat, fuel
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 Crenarchaeota

• Live at temperature extremes

• (>100 oC - < - 10oC)
• Thermophile/acidophilic
• Metabolism associated with sulfur or sulfide as
substrates for reduction and oxidation.
• Isolated from geothermally heated
environments (solfarata, heated industrial
effluents, deep sea hydrothermal vents)

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 Importance of archaea

• Methanogens (produce methane gas)

– Grow in anaerobic conditions e.g. Bottom of lakes (swap
bubbling), sewage treatment, landfills, digestive tract of
animals.
• Thermophilic bacterium Thermus aquaticus produce special enzyme
Taq polymerase

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 Nutrition

• Phototrophs obtain energy from light.

• Chemotrophs obtain energy from chemicals.
• Autotrophs require CO2 as a carbon source.
• Heterotrophs require an organic nutrient to make organic
compounds.

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 Nutritional modes

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 What are viruses?

• Edward Jenner (1798), introduced the term virus in

microbiology.
• Virus in Greek means poison
• Ultramicroscopic size cannot be seen by light microscope
BUT by electron microscope only
• Inactive outside the host cell and active only inside host
cells
• Lack machinery for synthesizing proteins and metabolic
enzymes’

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 Where do viruses come from?

• The evolutionary history of viruses represents a

fascinating, albeit murky, topic for virologists
and cell biologists. Because of the great diversity among
viruses, biologists have struggled with how to classify
these entities and how to relate them to the conventional
tree of life.
– They may represent genetic elements that gained the
ability to move between cells.
– They may represent previously free-living organisms that
became parasites.
– They may be the precursors of life as we know it.

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 • The progressive, or escape, hypothesis states
that viruses arose from genetic elements that
gained the ability to move between cells;
• The regressive, or reduction, hypothesis
asserts that viruses are remnants of cellular
organisms
• The virus-first hypothesis states that viruses
predated or coevolved with their current cellular
hosts.

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 Basics of Viruses

• Viruses can be classified on the basis of the hosts they infect

• Bacterial viruses (bacteriophages)
• Archaeal viruses
• Animal viruses (including humans)
• Plant viruses
• Other viruses
We know that viruses are quite diverse. Unlike all other biological
entities, some viruses, like poliovirus, have RNA genomes and some,
like herpesvirus, have DNA genomes. Further, some viruses (like
influenza virus) have single-stranded genomes, while others (like
smallpox) have double-stranded genomes. Their structures
and replication strategies are equally diverse. Viruses, do, however,
share a few features:
• First, they generally are quite small, with a diameter of less than
200 nanometers (nm).
• Second, they can replicate only within a host cell.
• Third, no known virus contains ribosomes, a necessary component
of a cell's protein-making translational machinery.

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 Overview of microbial eukaryotes

Two microbial kingdoms:

1. Fungi

2. Protista (2 Subkingdoms)
• a. Algae (plant-like)
• b. Protozoa (animal-like)

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