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REPLACEMENT
Date : 11 February 2011
Time : 10 am 12 noon
Venue : BioTech 2.1
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EXAM 1Date : 17 February 2011Time : 8 - 10 am
Venue : BioTech 2.2
REPLACEMENT (with Dr. Wan Zuhainis)
Date : 18 February 2011
Time : 8 10 am
Venue : BioTech 2.2
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HOW TO
PASS A TEST
WITH DIGNITY
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Kingdom ofProcaryotae:Eubacteria and Archaeabacteria
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Tree of Life
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11
PROKARYOTESPROKARYOTES
BACTERIABACTERIA ARCHAEAARCHAEA
EUKARYOTESEUKARYOTES
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Learning objectives
1. To describe different categories of
prokaryotes
2. To compare and differentiate the features
of eubacteria and archaebacteria
3. To discuss the features and importance of
some members of kingdom prokaryote
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The Archaea
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Mount St. Helen (erupting in July 1980)
home to Archaea
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Yellowstone
NationalPark
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Geysers
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Antarctics
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Polymerase chain reaction
DNA polymerase from Thermus aquaticus,
an archaeon
Not denatured at 94oC
For PCR (denaturation at
94oC, priming at 65oC andextension at 72oC)
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Characteristics:
As diverse as eubacteria- Gram +/-
- Shape
- Size: 0.1-15 um; 200 Qm (filaments)- Multiplication: binary fission, budding,
fragmentation
- Respiration: aerobic, anaerobic(facultative / obligate)
- Nutrition: chemolithoautotrophs /
organotrophs
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Habitat:
mesophiles
hyperthermophiles ( >100o
C )
cold environments
hypersaline
anaerobic environment
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Unique feature: Cell Wall
Gram Positive Archaea Gram Positive Bacteria
Single thick
homogenous layer
Single thick
homogenous layer
- Different chemistry
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Cell Wall of Gram +ve Archaea
- Pseudomurein
N-acetyltalosaminuronic acid (not N-
acetylmuramic acid as inpeptidoglycan)
F(13) glycosidic bond (not F(14)
glycosidic bond)
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N-
acetyltalosaminuronic
acid
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Unique feature: Cell Wall
Archaea (+/-) Bacteria (+/-)
Susceptible tolysozyme and F-
lactam antibiotics
F(13) glycosidic
bond
Resistant tolysozyme and F-
lactam antibiotics
F(14)
glycosidic bond
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Comparison of Gram -ve cell wall
Archaea
Layer of protein or
glycoprotein
Bacteria
Peptidoglycan network
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Unique feature: Membrane lipids
- Differ from bacteria and eucaryotes
Archaea Bacteria/Eucaryote
HC-HC-HC
Glycerol
Ether
linkHC-HC-HC
Fatty
acid
Ester
link
Branched
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MembraneLipids
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Membrane
Lipid
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Unique feature: Genetics
Archae Bacteria
Single closed DNA
circle
Single closed DNA
circle
Genome size: smaller
(~0.5-5.8 Mbp)
Genome size: bigger
(~0.6 10 Mbp)
Great variations in GCcontent (21-68%)
Lower variations inGC content
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Unique feature: Start codon
- AUG start codon
Archaea: methionine (as in eukaryotes)
Bacteria: N-formylmethionine
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Archaeal Taxonomy
- 1st edition Bergeys Manual (based onphysiological and morphological
differences)
a. Methanogenic archaeab. Archaea sulfate reducers
c. Extremely halophilic archaea
d. Cell wall-less archaeae. Extremely thermophilic sulfur
metabolizers
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Archaeal Taxonomy
- 2nd edition Bergeys Manual
(based on rRNA)
a. Phylum Euryarchaeota
b. Phylum Crenarchaeota
Discussion based on 2ndedition of Bergeys Manual
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Phylum Crenarchaeota
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Geogemma
- Currently the record holder for
surviving high temperatures 130oC
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Phylum Euryarchaeota
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Phylum Euryarchaeota
Based on physiology and ecology, thedominant groups are:
a. Methanogens
b. Halobacteria
c. Thermoplasms
d. Extremely Thermophilic S0-Metabolizers
e. Sulfate-reducing Archaea
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The Methanogens
- Largest group of archaea
- Morphology:
long rods (filamentous) / spirilla
straight or curved rods
irregular cocci
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The Methanogens
- Cell wall composition: pseudomurein or
heteropolysaccharides or
proteins
- Gram reaction: +/-/variable
- Motility: +/-
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The Methanogens
- Strict anaerobe
- Convert CO2, H2, formate, methanol,
acetate methane (end product)
Energy obtained
C source
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Where to find them?
- Marine/fresh water sediments
- Deep soils
- Intestinal tract (ruminant)
belch 200-400 L of CH4
a day
- Sewage treatment facilities
Anoxic environments rich in organic
matters:
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In sewage treatment plants:
Sludge (organic matters)
H2 + CO2 + acetate
Methanogens
CH4
Hydrogenotrophic methanogenesis
Acetoclastic
methanogenesis
CO2 + CH4
1 kg organic matter 600 liter methane
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The Methanogens
Beneficial:
Methane clean burning fuel energyfor heat and electricity
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The Methanogens
Harmful:
Methane absorbs infrared
radiation global warming
25x more potent than CO2
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Phylum EuryarchaeotaHalobacteria or extreme halophiles
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The Halobacteria
- Aerobic
- Motile or non-motile
- High concentration of 3 - 4 M NaCl
- Habitat: salt lakes, salted fish spoilage -
Red-yellow pigmentation
li h bi
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Hypersaline habitats:
Great Salt Lake, Utah (left)
San Francisco Bay, California (right)
EVAPORATING POND
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The Halobacteria- e.g. Halobacterium salinarium
- Photosynthesis with bacteriochlorophylls
Purple pigment (light-
harvesting pigment =
bacteriorhodopsin)
Pigment absorbs light energy form proton gradient on
membrane synthesis of ATP
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HOW TO
PASS A TEST
WITH DIGNITY
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The Eubacteria( True bacteria )
Discussion based on Bergeys Manual ofDeterminative
Bacteriology (9th edition, 1994)
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Importance of Bacteria
Life is microbial ! Micro-organisms colonise
every environment on earth
>80% of lifes history was
bacterial You have more bacterial
cells than human cells
Pathogenic microbes
globally are the most
important cause of human
disease and death
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Microbes in the News
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Microbes in the News
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Bacterial cell
iff b i l
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Differences between Bacterial
and Human Cells
Bacterial cells
No nucleus
No intracellularorganelles
(but ribosomes)
No introns Plasmids,
bacteriophage
Human cells
Nucleus
Intracellularorganelles
Introns
Viruses
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Size matters
Animal cell
1 micron
10 microns
Bacterial cells
Diff b t
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Differences between
Bacteria and Viruses
Viruses
Obligate intracellular
parasites
No ribosomes
DNA or RNA, not
both
seen by EM
10-100s of genes
Bacteria
Usually free-living,
but can be parasites
Ribosomes
DNA and RNA
Seen by LM 100s-1000s of genes
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Kingdom Procaryotae
4 categories:
a. Gram-ve eubacteria with
cell walls
b. Gram+ve eubacteria with
cell walls
c. Eubacteria lacking cellwalls
d. The archaeabacteria
Based on
nature of
bacterial
cell wall
Categories (a) and (b):
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Categories (a) and (b):
Thin layer of peptidoglycan in
between cytoplasmic membrane
and outer membrane (*)
Peptidoglycan
Cytoplasmic
membrane
*Outer membrane
(lipopolysaccharide & protein)
Gram ve cell wall Gram +ve cell wall
Thicker layer of
peptidoglycan
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Developed and published in 1884 by theDanish physician Hans Christian Gram
An important tool in bacterial taxonomy,
distinguishing so-called Gram-positivebacteria, which remain coloured after the
staining procedure, from Gram-negative
bacteria, which do not retain dye and need
to be counter-stained.
Staphylococcus aureus (Gram-positive cocci)
Escherichia coli (Gram-negative rods)
The Gram Stain
The Gram stain procedure
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Crystal violet
(primary stain)
Gram's iodine
(trapping agent)
Decolorise with
acetone or alcohol
Counterstain with
safranin
Gram-positives
appear purple
Gram-negatives
appear pink
The Gram stain procedure
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Gram-positive rods
Gram-negative rods
Gram-positive cocci
Gram-negative cocci
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Cell morphology
Important features:
- Gram stain reaction
- Shape
- Size
- Endospore presence
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Endospore-forming Bacteria
- Shape, position and size of endospore useto identify species
Oval, terminal
C. barkeri
Spherical, terminal
C. tetani
Oval, between
center and end
C. botulinum
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Metabolism
Processes to obtain energy + convertenergy into usable form
Important features:
- Enzymes
- Metabolized sugars
- Metabolized amino acids
- Photosynthesis??
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How to use metabolic diversity in
classifying bacteria?
Bacterium NO
Bacterium YA
Substrate A
B C D E
W X Y Z
Intermediates in differentmetabolic pathways
EndProduct
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Reproductive traits
Important features:
- Influence by light ??
- Influence by oxygen??
- Colony morphology
G N i R d
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Gram-Negative Rods
Enteric BacteriaEscherichia coli
Salmonella
ShigellaYersinia
Pseudomonas
ProteusVibrio cholerae
Klebsiella pneumoniae
G N i R d
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Gram-Negative Rods Fastidious GNRs
Bordetella pertussis
Haemophilus influenzae
Campylobacter jejuni
Helicobacter pylori
Legionella pneumophila
Anaerobic GNRs
Bacteroides fragilis
Fusobacterium
G N ti C i
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Gram-Negative Cocci
Neisseria gonorrhoeae causes gonorrhea
Neisseria meningitidis causes meningitis
Both Gram-negativeintracellular diplococci
G P iti C i
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Gram-Positive Cocci
Staphylococci catalase-positive
cocci in clusters
Staphylococcus aureus
coagulase positive
Staphylococcus epidermidis
coagulase negative
G P iti C i
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Gram-Positive Cocci
Streptococci catalase negative
cocci in chains or pairs
Streptococcus pyogenes
Streptococcus pneumoniae
E nterococcus faecalis
G P iti R d
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Gram-Positive Rods Clostridia
Anaerobes
C. perfringens
C. tetani
C. botulinum
Bacillus cereus
Aerobe
Listeria monocytogenes
Faculative anaerobe
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Non-Gram-stainable bacteria
Unusual gram-positives
Spirochaetes
Obligate intra-cellular bacteria
Unusual Gram-positives
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Category (c) : Eubacteria lackingcell walls
- Bacteria without cell wall
- No definite shape
- E.g. mycoplasmas
Unusual Gram positives
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M l
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Mycoplasmas
- No peptidoglycan and stained pink (Gram -)
- DNA sequences similarity to Gram positive- Irregular shape/pleomorphic
- = protoplast but resistant to osmotic lysis
- Strong plasma membrane presence ofsterols and lipoglycan
- Smallest free-living cell
- Require organic growth factors e.g. cholesterol,fatty acids, vitamins, amino acids and
nucleotides or growth.
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Mycobacteria
Acid-fast bacilli stained by Ziehl-Neelsen stain
M. tuberculosis
M. leprae
M. avium
S i h t
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Spirochaetes Thin spiral bacteria
Viewable by phase-contrast
microscopy
Treponema pallidum
Borrelia burgdorferi
Leptospira
Obligate intracellular
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g
bacteria
Rickettsia
ChlamydiasC. trachomatis
C. pneumoniae
C. psittaci
Rickettsias growing within the host cells