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BTE 2440 (Intro. Micro.) Sem. I. 2011/12
Instructor
Prof. Dr. Mohamed Ismail Abdul Karim Tel: 603-6196-4573
E-mail: akismail @iiu.edu.my
Office hours
Rm. E5-212.7
Lecture period: Mon. 2.00 pm3.20 pmWed. 2.00 pm3.20 pm
Room: ENG-LRM (E2.3.8) Sem. I 2011/12.
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Welcome to BTE 2440
Introductory Microbiology: Types of
Microorganisms.
T4 phage
-Virus
Fungal wood degrader
Cyanobacteria:Partnership between
fungi and algae (has green
pigment/involve in phytosynthesis). E.g.Blue green algae and bacteria
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AlgaeCocconeis pediculus
Mushroom
ProtozoaEntamoeba histolytica
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Other Category of Microbes found:
Parasitic wormdivision of eucaryokes
Lichens/Fungi
Main Category of Microoganisms: Bacteria , Yeastsand Fungi found abundant in the environment.
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Parasitic worm e.g. tapeworms, nematodes
Parasitic worms or helminths are a division of eukaroyticparasitesl that liveinside their host. They are worm-like organismsthat live and feed off living hosts,
receiving nourishment and protection while disrupting their hosts' nutrientabsorption, causing weakness and disease. Those that live inside the digestive tractare called intestinal parasites. They can live inside humans as well as otheranimals. Helminthology is the study of parasitic worms and their effect on theirhosts. Diseases caused in humans by helminth infection include ascariasis,dracunculiasis, elephantiasis, hookworm, lymphatic filariasis, onchocerciasis,schistosomiasis, and trichuriasis.
Hookworms attached to the intestinal
mucosa
http://en.wikipedia.org/wiki/Parasiteshttp://en.wikipedia.org/wiki/Organismhttp://en.wikipedia.org/wiki/Host_%28biology%29http://en.wikipedia.org/wiki/Nourishmenthttp://en.wikipedia.org/wiki/Nutrienthttp://en.wikipedia.org/wiki/Diseasehttp://en.wikipedia.org/wiki/Digestive_tracthttp://en.wikipedia.org/wiki/Intestinal_parasitehttp://en.wikipedia.org/wiki/Helminthologyhttp://en.wikipedia.org/wiki/Host_%28biology%29http://en.wikipedia.org/wiki/Ascariasishttp://en.wikipedia.org/wiki/Dracunculiasishttp://en.wikipedia.org/wiki/Elephantiasishttp://en.wikipedia.org/wiki/Hookwormhttp://en.wikipedia.org/wiki/Lymphatic_filariasishttp://en.wikipedia.org/wiki/Onchocerciasishttp://en.wikipedia.org/wiki/Schistosomiasishttp://en.wikipedia.org/wiki/Trichuriasishttp://en.wikipedia.org/wiki/Hookwormhttp://en.wikipedia.org/wiki/Mucous_membranehttp://en.wikipedia.org/wiki/Mucous_membranehttp://en.wikipedia.org/wiki/Hookwormhttp://en.wikipedia.org/wiki/Trichuriasishttp://en.wikipedia.org/wiki/Schistosomiasishttp://en.wikipedia.org/wiki/Onchocerciasishttp://en.wikipedia.org/wiki/Lymphatic_filariasishttp://en.wikipedia.org/wiki/Hookwormhttp://en.wikipedia.org/wiki/Elephantiasishttp://en.wikipedia.org/wiki/Dracunculiasishttp://en.wikipedia.org/wiki/Ascariasishttp://en.wikipedia.org/wiki/Host_%28biology%29http://en.wikipedia.org/wiki/Helminthologyhttp://en.wikipedia.org/wiki/Intestinal_parasitehttp://en.wikipedia.org/wiki/Digestive_tracthttp://en.wikipedia.org/wiki/Diseasehttp://en.wikipedia.org/wiki/Nutrienthttp://en.wikipedia.org/wiki/Nourishmenthttp://en.wikipedia.org/wiki/Host_%28biology%29http://en.wikipedia.org/wiki/Organismhttp://en.wikipedia.org/wiki/Parasites -
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Lichens/Fungi A lichen is not a single organism, but the result of a partnership (mutualistic
symbiosis) between a fungus and an alga or cyanobacteria.The algal and/or
cyanobacterial partner(s) possess the green pigment chlorophyll, enabling them
to use sunlights energy to make their own food from water and carbon dioxide
through photosynthesis.
The thallus, or lichen body, comes in four shapes:Foliose: flat leaf-like lichens.Crustose: crust-like lichens that may be buried in tree bark, or even between the crystals ofrocks.
Fruticose: miniature shrub-like lichens.one lichen of this type is the famous "reindeer moss" of
Lapland.Squamulose: scaly lichens made of numerous small rounded lobes, intermediate betweenfoliose and crustose lichens.
Foliose Crustose Fruticose Squamulose
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Course Outline
Introduction to the biology of bacteria, eukarya
(big cell) and archaea (resistant to extremeconditions), and prokaryotes organisms (small
cell).
Topics includestress on:
Microbial history, classification, diversity,
systematics
Microbial nutrition, growth & control
Microbial metabolism & genetics Microbial ecology & symbiosis
Industrial and applied microbiology
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Course Objectives
Significant roles of microorganisms in nature and
industry
Basic knowledge of microbiology
- Biological Applications
- Industrial and Engineering applications
- Human diseases
Foundation for further courses and research anddevelopment in biological and biotechnology
engineering
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Biotechnology IndustryTraditional biotechnologystarted with the fermentation industry
many food products are made from microorganisms.
Some application are found in the agricultural and environmental
industrybio-control agent, increase soil fertility, nitrogen fixation,
carbon recycling, environmental pollution control.
Modern biotechnology discovery of DNA (Watson and Creek,
1953) and cloning of Dolly sheep DNA recombinant technology,
human genome project, etc . breakthrough in genetic engineering
revolutionize the biotechnology industry especially with use of
microorganisms for the production of goods and services becomes a
reality. Many biochemical and biotechnology products are producedthrough fermentation.
Recombinant Technology- become evident and play major role in
biotechnology, transfer of genes between cells become evident here.
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Biotechnology Engineering
Application of engineering principles, design
and application of bioreactor in scaling upoperation in biotechnology industry becomes
important in the new century globally.
Fermentation and bioprocess engineering in themanufacture of industrial and pharmaceutical
products are evident now.
Application in food, bioenvironmental andbiomolecular engineering becomes important too.
Upstream and Downstream processing.
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Evaluation method
Mid-term examination 40%
Materials week 1-7
Quizzes 15% (5/6 total)3% each quiz.
Final examination 45%
TOTAL 100%
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Texts
Required Prescott, L.M., Harley, J.P., and Klein, D.A.
2008. Microbiology (7th. Ed.). Mc Graw Hill.
Now 8th Edition available (2010).
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Recommended
1. Madigan, M.T., Martinko, J.M., and Parker, J. 2000.Brock Biology of Microorganism (9th. Ed.) Prentice Hall.
2. Talaro, K.P. and Talaro, A. 2002. Foundations inMicrobiology: Basic Principles (4th. ed.) Mc Graw Hill.
3. Tortora, C.J. 2000. Lab Experiments in Microbiology.Benjamin Cummings Pub.
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Biology?
Greek Bios = life + Logos = reckoning
What is Biology? Study of life
What is life for a biologist?
Life is a combination of all characteristicscommon to all living things and absent fromnon living things
Site where life exists is cell Cell is the simplest small functioning unit of
life
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Characteristics of living things
microbial cell.
Respiration-gaseous exchange, aerobic, anerobic.
Nutrition-inorganic and organic nutrients
Metabolism-anabolism, catabolism
Excretion-waste product transport
Sensitivity-stimulus, receptor, effectoraffected
by surrounding environment.
Locomotion-movement. Reproduction-sexual and asexual
Growth-development
Microbial metabolites
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Hallmarks of Cellular Life
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Microbes
Good guys vs. bad guys?
Bacillus anthracis Lactobacillus
Neiserria gonorhrrea Escherichia coli
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Microbiology?
Micro (Greek mikros) = small Organism = living body
Science or biology of microscopic
organisms (very small, unicellular,multicellular organisms) too small to be
seen with our naked eye.
The discipline is just over a century old(relatively new)
Foundation for Molecular biology and
Biotechnology
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Microbial HistoryMajor events and figures:
Antoni Van Leeuwenhoek layu-wen-hook(Dutch)-discovered first powerful microscopeobserved livingcells (living algae) difficult to be seen by our naked eye.
Louis PasteurDispelled Spontaneous generation
theory (Decayed matter could produce living matter).He disapprove this theory. Cell need nutrients to grow.Cannot grow automatically on decayed matter alone.
Robert Koch (German)Kochs postulate disease
caused by germs. Joseph Listerintroduce antiseptic agent. Sterilize
surface of humans with antiseptic agent can killmicrobes.
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Antoni Van Leeuwenhoek:(discover use of microscope to see
microorganisms/green algae)Prior, Robert Hooke (England)
described fruiting structure of molds
in 1664 utilizing compound
microscope. (Eukaryote-bigger size)
Size enlargement 20-30 times
Jan Swammerdam (Dutch) worked on
compound microscope.Various technical difficulties
Wrote illustrated bookMicrographia
which inspired Leeuwenhoek
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Compound light microscope
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Dutch amateur builder,
Leeuwenhoek- saw prokaryotes-
smaller size in 1684. Discovered
first bacteria (Green algae)
Made over 500 microscopes-
essentially magnifying glass
Excellent lenses grinding, acuteeyesight and lighting adjustment-
enlargement 200 times
Could only view microbes but notechniques available to study them
until later in 19th century.
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Spontaneous generation theory
Originated from Roman up to Middle Ages
Life form spontaneously arose from non-living
matter (decayed materials) e.g. microbial cell do
live on decayed organic/non organic matter but
will grow if expose to water/availability of
nutrients.
Eg. 1. Mixture of hay and water will produce
microbes after few days incubation.
Eg. 2. Dust carry microbes. Media in petri dish if
expose to air, can support growth of microbes.
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Louis Pasteur (French)Co-founder of modern bacteriology
Dispelled Spontaneous generation theory- doesnot grow automatically but cell need nutrientsand does not grow or remain dormant if withoutnutrients.
Pasteurs work with Pasteur flask
Sterilization technique Pasteurization
Heat liquid (wine) 55OC for few minutes, killspoilage microorganisms but not good microbes.
Attenuation (weakened virus) of virulent (active)
microbes
Vaccination development for anthrax, fowl cholera,rabbies
Discovered indirectly rabbies virus-agent so
small cannot be seen under microscope
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Copyright TheMcGraw-Hill
26
Industrial Microbiology and
Microbial Ecology Louis Pasteur
demonstrated that alcohol fermentations and
other fermentations were the result of microbialactivity. Yeasts is involved here.
developed the process of pasteurization to
preserve wine during storage
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Redis experiment
proved contamination cause
microbial growth.
1668 Francesco Redi-proposed
maggots develop from eggslaid by fliescontamination
must take place here.
Meat in jars-open, closed,
closed with gauze. Maggots
developed only in open flask.
Utilized control.
1.
2.
3.
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Needhams exp.
1745 John Needham conducted definitive exp.Boiled chicken broth in flask
Let it cool (being exposed before beingsealed)
Sealed flask.
Microbes grew
Concluded that exp. did not support (dispelled)spontaneous generation theoryshow presence of
nutrients support growth of microbial cells..
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Spallanzanis exp. proved besides
nutrients bacteria needs air too.
Lazzaro Spallanzani-suggested microbes
entered from air after boiling media butbefore sealing the flask.
Flask 1 was left open
Flask 2 was sealed
Flask 3 was boiled and then left open Flask 4 was boiled and then sealed
Place broth in flask, boiled, drew air out,
create vacuum, sealed, no microbesgrewIn case of flask 4.
Critics-Spallanzani only proved thatspontaneous generation could not occurwithout air. ( Need air besides nutrients)
1.
2.
3. 4.
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Pasteurs exp.
Louis Pasteur-boiled broth in flask,heated the neck of flask, and bend itinto swan shape (this draw oxygenout and create vacumn). Left flaskand no microbial growth found inbroth.
Air entered flask but microbes settledin neck of flask, could not entered
into broth, found no growth in broth. If allowed the broth to touch with the
dust in swans neck of flask,microbes are found to grow in the
media).
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PasteurizationOntario, Canada Pasteurization Regulations for Milk
63 C for not less than 30 min.,
72 C for not less than 16 sec., kill spoilage microbes.Can destroy spoilage microbes only. Continuous Pasteurizer
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Robert Koch (German)
Co-founder of modern bacteriology
Koch works on germ theory ofdisease.
Any disease has a causative agent.
- must be infected with thecausitive pathogn.
Discovered endospore in
Bacillus anthracis in sheep blood.
Able to be transferred
in blood stream
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Robert Koch-cont.Purification of mixed
bacterial populationmust
isolate the pure culture.
Pioneered usage of solid
nutrient media
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Staining techniques
with various dyes
Endospore stain - Schaeffer-
Fulton endospore stain method(all 100X oil immersion)
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Robert Koch-cont.
Steam sterilization technique Sterilization parameter:
Autoclave at 121O C at 1.05
kg/cm2 (15 psi) for 30minutes
Sterilization temp. is at
1210C/15psi/15min.- can
kill all microorganisms. Commonly use to sterilize
all microbial media.
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Kochs Postulates
Kochs postulate states:
1. Pathogen presents in all pathogenic infectedcases and absent in healthy organism.
2. Suspected pathogen grown in pure culture.
3. Suspected pathogen from pure cultureshould cause disease in healthy organism.
4. Pathogen should be re-isolated in infected
organism and be the same with the originalcausitive pathogen.
5. Disease is caused by pathogenic organisms
has to infect people/animal.
J h Li
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Joseph ListerSolved hospital disease (operative sepsis)-
open wounds caused by infection of
microorganisms.
Postulated that sepsis (wound) caused by
pollen like dust from the air (the dust carrymicrobes).
Clean and dress wound using carbolic acid
Clean wound with alcohol, can kill microbe
too.
Formulated antiseptic method for medical
operation
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Copyright TheMcGraw-Hill 38
Immunological Studies
Edward Jenner (ca. 1798)
used a vaccination procedure to protect
individuals from smallpox
NOTE: this preceded the work establishing the role of
microorganisms in disease.
- Smallpox vaccine evolved.
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Microbial studyneed to know:
Need to catogorize type of microbes:
Bacteriology, virology, mycology, viruses , etc.
Role of microbes: Microbial ecologyaffecting
growth. Its application in Medical, Industrial,
Environmental, Food and Agriculture sector. Techniques utilized:
characterization/Classification and application
using Molecular or microbial genetics is more
accurate compared to traditional methods.
Purpose of study: Need to understand basic and
applied microbiology and its application in
engineering.
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What are Microbes?Within 5 Kingdoms, Microbes are categorise into 1,2,3
1. Monera-Eubacteria and Archaebacteria
2. Protista
-animal like (protozoa)-Paramecium, Amoeba,
-plant like protists (euglenoids, diatoms)
3. Fungi: unicellular-yeast, multicellular-mushroom (spores spread by wind, etc.
4. Animalia-Coelenterates, Flatworms, Molluscs, Annelids, Arthropods,Echinoderms, Chordates
5. PlantaeBrown algae & red algae, green algae, mosses, liverworts, vascular plants.
Note: 1,2,3difficult to see with our naked eyes.
** Robert Whittakers five-kingdom scheme proposed based on physical structure & metabolic properties
(visual-phenotype) in 1959.
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What are Microbes?-cont.
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Universal tree
** Carl Woeses domains proposed based on genetic
material similarity representing evolutionary line in 1990.
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Phylogenic tree
Base on evolutionary development of microbes.
Determination of their 16s RNA and G+Ccontent of cellGenus and sp. relationship can
be determine (able to group them here).Grouping of their closeness and relationshipcan be drawn then.
Many new species can then be evolved if
mutation occurs and also if new discovery arefound.
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Domain-detail branches
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Prokaryotes are evolutionarily ancient, for billions of years the
only form of life.
Prokaryotes were the first type of cell to evolve, and unlike
eukaryotic cells, still lack a membrane bound nucleus. Their
genetic material is naked within the cytoplasm, ribosomes their
only type of organelle.
Prokaryotes are most always single-celled, except when they exist
in colonies. These ancestral cells, now represented by members of
the domains Archaea and Eubacteria, reproduce by means ofbinary fission, duplicating their genetic material and then
essentially splitting to form two daughter cells identical to the
parent.
http://microbiology.suite101.com/article.cfm/prokaryotic_and_eukaryotic_cellshttp://microbiology.suite101.com/article.cfm/prokaryotic_and_eukaryotic_cellshttp://microbiology.suite101.com/article.cfm/prokaryotic_and_eukaryotic_cellshttp://microbiology.suite101.com/article.cfm/prokaryotic_and_eukaryotic_cells -
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Ribosomesprotein synthesis.
Ribosomeinvolve in protein synthesis,
has mRNA (acting as blue print, transfer
genetic information) Procaryotic ribosomeshave sedimentation
value of 70S.
Eucaryotic ribosomeshave sedimentationvalue of 80S.
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Taxanomy-cont.SuperKingdoms:
1.Prokaryote (organisms without membrane boundnuclei)
- Monera only
2.Eukaryote (organisms with a separate membranebound nucleus)
- Protista, Fungi, Plantae, Animalia
3. Archaelive in extreme conditions (high saline,
temp., pressure, pH conditions)(cell wall having
long chains of hydrocarbons attached to glycerol
rather than fatty acids and connected by ester
links), also lack peptidoglycan
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Taxanomy-cont.
Yeast Human
Superkingdom Eukaryote Eukaryote
Kingdom Mycota Animalia
Phylum Ascomycota Chordata
Class Hemiascomyceti
dae
Mammalia
Order Endomycetales PrimateFamily Saccharomyces Hominidae
Genus Saccharomyces Homo
Species cerevisiae sapiens
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asexual
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Microbial Diversity Microbial Taxonomy & Phylogeny.
Summary- diversity of organisms-best to group similarorganisms together.
Procaryotic gps. (Archaea, Bacteria/Procaryote) first to be
developed, followed by eucaryotes. Found 5 Kingdomshave 3 Classes/Domain.-
Bacteria,Archae,Eucarya.
Classificationpossible evolutionary relationships(phenetic classification, taxanomy and physiologicalrelationship)resently phylogenetic classification becomeimportant- based on comparison of ribosomal RNAstructure and chromosome sequencefound treelikediagrams called dendrograms.
Cilli d Fl ll hi lik d i ll
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Cillia and Flagellawhip-like appendages in cell
that are associted motility of cell.
Cillia5 to 20 ug (microns) in length.
Flagella100200 ug in length.
Golgi apparatussac-like materials (stack of
cisternae) found in cell - helps in development of
cell membranes and packaging of cell products.
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Prokaryotes
Classification based on cell structure:
Small in size-1 to 5 um long
Lack of membrane enclosed nucleus
Lack of complex internal structures
Some differences in mechanisms of
replication, transcription, translation,
genetic transfer from eukaryotes
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Eukaryotes
Classification based on cell structure:
Bigger in size-More than 5 um long
Possesses membrane enclosed nucleus and
internal structures
Possesses complex internal structures
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There are big differences between eukaryotic and
prokaryotic cells, but they do have some things incommon:
Both have DNA as their genetic material.
Both are encased in cell membranes. The membranes
of Prokaryotic cells and of some eukaryotic cells are
surrounded by a strong cellwall.
Both have a similar basic metabolism (the word
metabolism refers to the formation and break down
of chemicals in the body).
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The major difference is that eukaryotes have a nucleus and
prokaryotes do not.
Also, eukaryotic cells contain a wide variety of organelles (tiny
"organs" or structures inside the cell) that perform various
functions. Some of the most important organelles are mitochondria,
chloroplasts, lysosomes and ribosomes
Eukaryotic cells are, on average, ten times as large as prokaryotic
cells. Their DNA is more complex and is formed into
chromosomes. And their organelles enable them to do more
complex jobs.
Mitosis and Meiosis
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Mitosis and Meiosis. MitosisMitosis (Asexual reproduction)is the process by which a eukaryotic
cell separates the chromosomes in its cell nucleus into two identical sets in twonuclei. Mitosis occurs exclusively in eukaryotic cells, but occurs in differentways in different species. For example, animals undergo an "open" mitosis,where the nuclear envelope breaks down before the chromosomes separate,while fungi such asAspergillus nidulans and Saccharomyces cerevisiae (yeast)undergo a "closed" mitosis, where chromosomes divide within an intact cellnucleus
Two diploid cells
.
Chromosomes is reduce by half (from diploid to haploid state, daughter cell
receiving one complete set of chromosomes). Haploid cell which act as gametesmay fuse with other cell to form diploid cell.
http://en.wikipedia.org/wiki/Eukaryotichttp://en.wikipedia.org/wiki/Chromosomehttp://en.wikipedia.org/wiki/Cell_nucleushttp://en.wikipedia.org/wiki/Eukaryotehttp://en.wikipedia.org/wiki/Animalhttp://en.wikipedia.org/wiki/Nuclear_envelopehttp://en.wikipedia.org/wiki/Fungihttp://en.wikipedia.org/wiki/Aspergillus_nidulanshttp://en.wikipedia.org/wiki/Saccharomyces_cerevisiaehttp://en.wikipedia.org/wiki/Yeasthttp://en.wikipedia.org/wiki/Cell_nucleushttp://en.wikipedia.org/wiki/Cell_nucleushttp://en.wikipedia.org/wiki/Cell_nucleushttp://en.wikipedia.org/wiki/Cell_nucleushttp://en.wikipedia.org/wiki/Yeasthttp://en.wikipedia.org/wiki/Saccharomyces_cerevisiaehttp://en.wikipedia.org/wiki/Aspergillus_nidulanshttp://en.wikipedia.org/wiki/Fungihttp://en.wikipedia.org/wiki/Nuclear_envelopehttp://en.wikipedia.org/wiki/Animalhttp://en.wikipedia.org/wiki/Eukaryotehttp://en.wikipedia.org/wiki/Cell_nucleushttp://en.wikipedia.org/wiki/Chromosomehttp://en.wikipedia.org/wiki/Eukaryotic -
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Meiosisis essential for sexual reproduction and therefore occurs in alleukaryotes (including single-celled organisms) that reproduce sexually. is
essential for sexual reproduction and therefore occurs in all eukaryotes
(including single-celled organisms) that reproduce sexually.
Homologous Meiosis I Meiosis II
Chromosomes Daughter I Daughter II
Prokaryotic cells, which lack a nucleus, divide by a process called binary
http://en.wikipedia.org/wiki/Sexual_reproductionhttp://en.wikipedia.org/wiki/Eukaryotehttp://en.wikipedia.org/wiki/Sexual_reproductionhttp://en.wikipedia.org/wiki/Eukaryotehttp://en.wikipedia.org/wiki/Eukaryotehttp://en.wikipedia.org/wiki/Sexual_reproductionhttp://en.wikipedia.org/wiki/Eukaryotehttp://en.wikipedia.org/wiki/Sexual_reproductionhttp://en.wikipedia.org/wiki/Prokaryotehttp://en.wikipedia.org/wiki/Binary_fissionhttp://en.wikipedia.org/wiki/Binary_fissionhttp://en.wikipedia.org/wiki/Prokaryote -
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y , , y p y
fission. Binary fission, or prokaryotic fission, is the form ofasexual
reproduction and cell division used by all prokaryotes, some protozoa, and
some organelles within eukaryotic organisms. This process results in the
reproduction of a living prokaryotic cell by division into two parts whicheach have the potential to grow to the size of the original cell.
http://en.wikipedia.org/wiki/Prokaryotehttp://en.wikipedia.org/wiki/Binary_fissionhttp://en.wikipedia.org/wiki/Binary_fissionhttp://en.wikipedia.org/wiki/Asexual_reproductionhttp://en.wikipedia.org/wiki/Asexual_reproductionhttp://en.wikipedia.org/wiki/Cell_divisionhttp://en.wikipedia.org/wiki/Prokaryoteshttp://en.wikipedia.org/wiki/Protozoahttp://en.wikipedia.org/wiki/Eukaryotichttp://en.wikipedia.org/wiki/Cell_%28biology%29http://en.wikipedia.org/wiki/File:Binary_fission.svghttp://en.wikipedia.org/wiki/Cell_%28biology%29http://en.wikipedia.org/wiki/Eukaryotichttp://en.wikipedia.org/wiki/Protozoahttp://en.wikipedia.org/wiki/Prokaryoteshttp://en.wikipedia.org/wiki/Cell_divisionhttp://en.wikipedia.org/wiki/Asexual_reproductionhttp://en.wikipedia.org/wiki/Asexual_reproductionhttp://en.wikipedia.org/wiki/Binary_fissionhttp://en.wikipedia.org/wiki/Binary_fissionhttp://en.wikipedia.org/wiki/Prokaryote -
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