Comparison Between Pro. and Eucr. (1)

8/6/2019 Comparison Between Pro. and Eucr. (1)

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Biological classification

Biological classification, or scientific classification in biology, is a method by

which biologists group and categorize organisms by biological type, such as

genus or species. Biological classification is a form of scientific taxonomy, but

should be distinguished from folk taxonomy, which lacks scientific basis.

Modern biological classification has its root in the work of Carolus Linnaeus,

who grouped species according to shared physical characteristics. These

groupings have since been revised to improve consistency with the Darwinian

principle of common descent. Molecular phylogenetics, which uses DNA

sequences as data, has driven many recent revisions and is likely to continue t o

do so. Biological classification belongs to the science of biological systematics.

Taxonomic ranks:

In biological classification, rank is the level (the relative position) in a hierarchy.

There are 7 main ranks defined by the international nomenclature codes:

Kingdom, phylum/division, class, order, family, genus, species. "Domain", a

level above kingdom, has become popular in recent years, but has not (yet)

been accepted into the codes.The most basic rank is that of species, the next

most important is genus, and then family. Sometimes (but only rarely) the term

"taxonomic category" is used instead of "rank".

The hierarchy of biological classification's eight major taxonomic ranks, which

is an example of definition by genus and differentia. Intermediate minor

rankings are not shown.


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Termi i mes

Taxaabove t e enus level areoften ivennamesbasedon t e t e enus,it a standard termination. The terminat ions used in forming these names

dependon the ingdom, andsometimes thephylumand lass, asset out in thetablebelow.

Rank Plants Al ae Fungi Animals acteria

Divisi n/Phylum -phyta -mycota

Subdivisi n/Subphylum -phytina -mycotina

Class -opsida -phyceae -mycetes -ia

Subclass -idae -phycidae -mycetidae -idae

Superorder -anae

Order -ales -ales

Suborder -ineae -ineae

Infraorder -aria

Superfamily -acea -oidea

Epifamily -oidae

Family -aceae -idae -aceae

Subfamily -oideae -inae -oideae

Infrafamily -odd[4]

Tribe -eae -ini -eae

Subtribe -inae -ina -inae

Infratribe -ad


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Tablenotes:

Inbotanyandmycologynamesat therankof familyandbelowarebasedon

thenameofagenus, sometimescalled the typegenusof that taxon, withastandardending. Forexample, therose family Rosaceae isnamedafterthe

genusRosa, with thestandardending -aceae" fora family. amesabove

the rankof familyare formed froma familyname, oraredescriptive like

GymnospermaeorFungi .

For animals, there are standard suffixes for taxa only up to the rank of

superfamily.

Forminganamebasedonagenericnamemaybenot straightforward. For

example, the atin "homo" has the genitive "homi

is", thus the genus

"Homo" human) is in the Hominidae, not "Homidae".

Kingdomsand domains:

From well before innaeus, plantsand animals was considered separate

Kingdoms. innaeusused thisas the top rank, dividing thephysical world

into the plant, animal and mineral kingdoms. As advances in microscopy

made classification of microorganisms possible, thenumber of kingdoms

increased, fiveandsix-kingdomsystemsbeing themost common.

omainsarearelativelynewgrouping. The three-domainsystemwas first

invented in 1990, but not gene rallyaccepteduntil later. ow, themajorityof

biologists accept the domain system, but a large minority use the

five-kingdommethod. Onemaincharacteristicof the three -domainmethod

is the separation ofArchaea and Bacteria, previously grouped into the

single kingdom Bacteria a kingdom also sometimes called onera).

onsequently, the three domains of life are conceptuali ed as Archaea,

Bacteria, and Eukaryota comprising the nuclei-bearing eukaryotes). A

small minority of scientists add Archaea as a sixth kingdom, but do not

accept thedomainmethod.


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Thomas avalier-Smith, whohaspublishedextensivelyon theclassification

ofprotists, hasrecentlyproposed that the eomura, theclade that groups

togethertheArchaeaandEukarya, wouldhaveevolved fromBacteria, more

precisely from Actinobacteria. His classification of 2004 treats the

archaebacteria aspart of asubkingdom of the Kingdom Bacteria, i.e. he

rejects the three-domainsystementirely.

Linnaeus1735

2 kingdoms

Haeckel1866

3kingdoms

Chatton1925

2 empires

Copeland1938

4kingdom

s

Whittaker1969

5kingdoms

Woeseetal.1977

6 kingdoms

Woeseetal.1990

3 domains

Cavalier-Smith2004

6 kingdoms

(not tr at d) Protista

Prokaryota onera oneraEubacteria Bacteria

BacteriaArchaebacteria Archaea

Eukaryota

ProtistaProtista Protista

Eukarya

Protozoa

hromista

Vegetabilia PlantaeFungi Fungi Fungi

Plantae Plantae Plantae Plantae

Animalia Animalia Animalia Animalia Animalia Animalia

TheChromistaareeukaryoticsupergroup, probably polyphyletic, whichmay

be treatedasaseparatekingdomorincludedamong theProtista. They include

all algaewhosechloroplastscontain chlorophyllsaandc, aswell asvarious

colorless forms that arecloselyrelated to them. Thesearesurroundedby four

membranes, andarebelieved tohavebeenacquired fromsome redalga.

THE THREE DOMAIN SYSTEM:

TheThree omain System, proposedby Woeseandothers, isanevolutionary

model of classification based on differences in the sequences of

nucleotides in the cell's ribosomal RNAs ( rRNA), as well as the cell's

membrane lipid structure anditssensitivity toantibiotics .

omparing rR A structure is especially useful. Because rRNA molecules

throughoutnaturecarry out thesame function, theirstructurechanges

very little over time. Therefore similarities and dissimilarities in rRNA

nucleotidesequenceareagood indicationof how related or unrelated

differentcellsand organismsare.


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Thissystemproposes that acommonancestorcell gaverise to threedifferent

cell types, each representingadomain. The threedomainsare the Archaea

archaebacteria), theBacteria eubacteria), and theEukar

a eukaryotes). The

Eukar

a are then divided into 4 kingdoms: Protists, Fungi, Anamalia, and

Plantae. A descriptionof the threedomains follows:

1. TheArchaea (archaebacteria)

TheArchaeapossess the followingcharacteristics:

y Archaeaareprokaryoticcells.

y Unlike the Bacteria and the Eukar

a, the Archaea have membranes

composedofbranched hydrocarbonchains attached toglycerol by

ether linkages Fig. 1).

y Thecell wallsofArchaeacontainno peptidoglycan.

y Archaeaarenot sensitive tosomeantibiotics that affect theBacteria, but

aresensitive tosomeantibiotics that affect theEukar

a.

y ArchaeacontainrRNA that is uniquetotheArchaeaas indicatedby

the presence molecular regions distin ctly different from the rR A of

BacteriaandEukar

a.

Archaea often live in extreme environments and include methanogens,

extreme halophiles, and hyperthermophiles. One reason for this is that the

ether-containing linkages in theArchaeamembranes ismorestabile than the

ester-containing linkages in the BacteriaandEukar

aandarebetterable to

withstandhighertemperaturesandstrongeracidconcentrations.

2. TheBacteria (eubacteria)

TheBacteriapossess the followingcharacteristics:

y Bacteriaareprokaryoticcells.

y ike the Eukar

a, they have membranes composed of unbranched

fatty acid chainsattached toglycerol by ester linkages Fig. 1).

y Thecell wallsofBacteria, unlike theArchaeaand the Eukarya, contain

peptidoglycan.


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y Bacteria are sensitive to traditional antibacterial antibiotics but are

resistant tomost antibiotics that affect Eukar

a.

y BacteriacontainrRNA that is uniquetotheBacteriaas indicatedby

the presence molecular regions distinctly different from the rR A of

ArchaeaandEukar

a.

y Bacteria include mycoplasmas, cyanobacteria, Gram-positive bacteria, and

Gram-negativebacteria.

3. TheEukarya (eukaryotes)

TheEukar

a alsospelledEucar

a)possess the followingcharacteristics:

y Eukar

ahaveeukaryoticcells.

y ike the Bacteria, they have membranes composed of unbranched

fatty acid chainsattached toglycerol by ester linkages Fig. 1).

y ot all Eukar

a possess cells with a cell wall, but for those Eukar

a

havingacell wall, that wall containsno peptidoglycan .

y Eukar

a are resistant to tradi tional antibacterial antibiotics but are

sensitive tomost antibiotics that affect eukaryoticcells.

y Eukar

acontainrRNA that is uniquetotheEukaryaas indicatedby

the presence molecular regions distinctly different from the rR A of

ArchaeaandBacteria.

Fig. 1:MembraneLipidsofArchaea,Bacteria,and Eukarya


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TheEukar

aaresubdivided into the followingkingdoms:

a. Protista Kingdom

Protistaaresimple, predominatelyunicellulareukaryoticorganisms. Examples

includesslimemolds, euglenoids, algae, andprotozoans.

b. Fungi Kingdom

Fungi areunicellularormulticellularorganismswitheukaryoticcell types. The

cellshavecell wallsbut arenot organized into tissues. Theydonot carryout

photosynthesisandobtainnutrients throughabsorptio n. Examples includesac

fungi, club fungi, yeasts, andmolds.

c. Plantae Kingdom

Plantsaremulticellularorganismscomposedofeukaryoticcells. Thecellsare

organized into tissues and have cell walls. They obtain nutrients by

photosynthesisandabsorpt ion. Examples includemosses, ferns, conifers, and

floweringplants.

d. Animalia Kingdom

Animalsaremulticellularorganismscomposedofeukaryoticcells. Thecellsare

organized into tissuesand lackcell walls. Theydonot carryout photosynthesis

andobtainnutrientsprimarilyby ingestion. Examples includesponges, worms,

insects, andvertebrates.


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Some features distinguishing prokaryotic and eukaryotic cells are

shown in Table 1:

Characters eukaryoticcell prokaryoticcell

1. nuclear

body

a. Thenuclearbody isboundedby

anuclearmembranehavingpores

connecting it with theendoplasmic

reticulum.

b. It containsoneormorepaired,

linear chromosomes composed

of deoxyribonucleic acid

A)

associatedwithhistoneproteins.

c. A nucleolus ispresent.

d. Thenuclearbody iscalleda

nucleus.

a. Thenuclearbody isnot boundedbya

nuclearmembrane.

b. It usually contains one circular

chromosome composed of

deoxyribonucleicacid

A)associated

withhistone-likeproteins.

c. There isnonucleolus.

d. Thenuclearbody iscalledanucleoid.

2. cell

division

a. Thenucleusdividesbymitosis.

b. Haploid1

)sexcells indiploidor 2

organisms are producedthroughmeiosis.

a. Thecell usuallydividesbybinaryfission. There isnomitosis.

b. Prokaryoticcellsarehaploid.

eiosisisnot needed.

3.cytoplasmic

membrane

(cell

membraneor

plasma

membrane)

a. Thecytoplasmicmembrane isa fluid phospholipid bilayercontainingsterols.

b. The membrane is capable ofendocytosis

phagocytosis and

pinocytosis)andexocytosis.

a. Thecytoplasmicmembrane isa fluidphospholipid bilayer usually lackingsterols

any bacteria do contain

sterol-likemoleculecalledhopanoids.

b. The membrane is incapable ofendocytosisandexocytosis.


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Cholesterol (A Sterol)Diploptene (A Hopanoid)

4.cytoplasmic

structures

a. Theribosomes arecomposedof a 60S and a 40S subunitformingan 80S ribosome.

b. Internal membrane-boundorganelles such as mitochondria,

endoplasmic reticulum, Golgiapparatus, vacuoles, andlysosomes arepresent.

c.!

hloroplasts serve asorganelles forphotosynthesis.

d. A mitotic spindle involved inmitosis is present during celldivision.

a. The ribosomes are composed of a50S anda 30S subunit formingan

"

0S

ribosome.

b. Internal membrane-boundorganellessuch as mitochondria, endoplasmic

reticulum, Golgi apparatus, vacuoles,and lysosomesareabsent.

c. There are no chloroplasts.Photosynthesis usually takes place ininfoldings or extensions derived fromthecytoplasmicmembrane.

d. There is no mitosis and no mitoticspindle.

5.respiratory

enzymesand

electron

transport

chains

- Theelectron transport system is

located in the innermembrane ofthemitochondria.

- The electron transport system is

located in thecytoplasmicmembrane.


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6. cell wall a. Plant cells, algae, and fungihavecell walls, usuallycomposedof cellulose or chitin. Eukaryoticcell walls are never composed ofpeptidoglycan.

b. Animal cells and protozoans

lackcell walls.

a.With fewexceptions, membersof thedomain Bacteria have cell wallscomposedofpeptidoglycan.

b.#

embersof thedomainArchaehavecell walls composed of protein, a

complex carbohydrate, or uniquemoleculesresemblingbut not thesameaspeptidoglycan.

7.locomotor

organelles

- Eukaryotic cells may haveflagella or cilia. Flagella and ciliaare organelles involved inlocomotionand ineukaryoticcellsconsist of a distinct arrangementofslidingmicrotubulessurroundedby a membrane. The microtubulearrangement is referred to as a2X9+2 arrangement.

StructureofEukaryotic

Flagellum

ElectronMicrograph ofMicrotubules

-$

anyprokaryoteshave flagella, eachcomposedofasingle, rotating fibril andusuallynot surroundedbyamembrane.

Therearenocilia.

Structure of a Bacterial Flagellum

8.representati

-ve

organisms

- The domain Eukar%

a: animals,plants, algae, protozoans, and

fungi.

- ThedomainBacteriaand thedomain

Archae.


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VIRUSES

General CharacteristicsofViruses

Viruses are infectious agents with both living and nonliving characteristics.Theycan infect animals, plants, andevenothermicroorganisms. Viruses that

infect onlybacteriaarecalledbacteriophagesand those that infect only fungi

are termedmycophages.

1. Livingcharacteristicsofviruses

a. Theyreproduceat a fantasticrate, but only in livinghost cells.

b. Theycanmutate.

2. Nonlivingcharacteristicsofviruses

a. Theyareacellular, that is, theycontainnocytoplasmorcellularorganelles.

b. Theycarry outno metabolism on theirownand mustreplicate using

the hostcell's metabolic machinery . Inotherwords, virusesdon't growand

divide. Instead, newviral componentsaresynthesizedandassembledwithin

the infectedhost cell.

c. Thevast majority ofviruses possesseitherDNA orRNA butnot both .

3. Criteria used to definea virus

a. Thevast majorityofvirusescontainonlyone typeofnucleicacid: A orR A, but not both.

b. They are totally dependent on a host cell for replicati on. They are strictintracellularparasites.)

c. Viral componentsmust assemble intocompleteviruses virions) togo fromonehost cell toanother.

4. Laboratory cultivationofviruses

Sinceviruses lackmetabolicmachineryof theirownandare totall ydependent

on their host cell for replication, they cannot be grown in synthetic culture

media. Animal virusesarenormallygrown inanimals, embryonatedeggs, orin


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cell cultureswhere inanimal host cellsaregrown inasyntheticmediumand

thevirusesare thengrown in thesecells.

Sizeand ShapesofViruses

1. Size( Fig. 2A,Fig. 2B,andFig. 2 ):

Fig.( 2A)


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(Figs. 2 B,2C)Virusesareusuallymuchsmallerthanbacteriaandaresubmicroscopic. ost

range in size from 5 to 300 nanometers (nm) .although some

Paramyxovirusescanbeup to 14,000nm long.

2. Shapes( Fig. 2A,Fig. 2B,andFig. 2 )

a. Helical viruses : consist ofnucleicacidsurroundedbyahollowprotein

cylinderorcapsidandpossessingahelical structure ( Fig.3 A).

Fig.3 A:Viral Structure (Helical Virus)


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b. Polyhedral viruses: consist of nucleic acid surrounded by a polyhedral

(many-sided)shell orcapsid, usually in the formofan icosahedron; ( Fig.3 B).

Fig. 3B:Viral Structure (Polyhedral Virus)

c. Enveloped viruses:consist ofnucleicacidsurroundedbyeitherahelical or

polyhedral coreandcoveredbyanenvelope ( Fig.3 andFig. 3 ).

Fig. 3C:Viral Structure (Enveloped Helical Virus)


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Fig. 3D:Viral Structure (Enveloped Polyhedral Virus)

d. Binal (complex) viruses: have neither helical nor polyhedral forms, are

pleomorphic(irregularshaped), orhavecomplexstructures (Fig. 3E).

Fig. 3E:Viral Structure (Binal)

A. Viral Structure:

Since viruses are not cells, they are structurally much more simple than

bacteria. An intact infectiousviral particle iscalleda virion andconsistsof:


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1. A genome:

Theviral genome isasingleorsegmented, circularor linearmoleculeof

nucleicacid functioningas thegeneticmaterial of thevirus. It canbe

single-strandedordouble-stranded A orR A (but neverboth), andcodesforthesynthesisofviral componentsandviral enzymes forreplication.

2. A capsid:

Thecapsidorcore, isaproteinshell surrounding thegenomeand isusually

composed of protein subunits called capsomeres . The capsid serves to

protect and introduce thegenome intohost cells. Somevirusesconsist ofno

more thanagenomesurroundedbyacapsidandarecalled nucleocapsid or

naked viruses ( Fig. 3AandFig.3 B). Attachment proteinsproject out from

thecapsidandbind the virustosusceptible hostcells .

3. Anenvelope:

Most animal virusesalsohaveanenvelopesurroundingapolyhedral orhelical

nucleocapsid, inwhichcase theyarecalled enveloped viruses( Fig. 3 ,Fig.

3 ).

The envelope is composed of phospholipids and glycoprote in and for most

viruses, isderived from host cell membranes by a process called

budding( Fig. 4). The envelope may come from the host cell's nuclear

membrane, vacuolarmembranes(packagedby the Golgi apparatus), orouter

cytoplasmicmembrane

.

Fig. 4:VirusObtainingIts Envelopefrom Host Cell Membrane by Budding


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Bacteriophages:areviruses that only infect bacteria. Some bacteriophages

are structurally much more complex than typical nucleocapsid or

enveloped virusesand may possessa uniquetail structure composedofa

baseplate, tail fibers, anda contractilesheath(Fig.3E). Otherbacteriophages,

however, aresimple icosahedralsorhelical (see Fig. 2B).

Life CycleofBacteriophages:

There are two primary types of bacteriophages: lytic bacteriophages and

temperate bacteriophages .

1. Bacteriophages that replicate through the lytic life cycle are called lytic

bacteriophages, andaresonamedbecause they lyse thehost bacteriumasa

normal part of theirlifecycle.

2. Bacteriophages capable of a lysogenic life cycle are termed temperate

phages. Whena temperatephage infectsabacterium, it caneither replicate

bymeansof the lytic lifecycleandcause lysisof thehost bacterium, or, it can

incorporate its A into the bacterium's A and become a noninfectious

prophage.

.

ElectronMicrograph ofColiphageT4

Afterinfectingbacteriawith lyticbacteriophages in the lab, plaquescanbeseen

on thepetri plates. Plaquesaresmall clearareason theagarsurface where the

host bacteriahavebeen lysedby lyticbacteriophages.


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Plaquesonanagarsurfaceafter infectingEscherichia coliwithColiphageT- 4

The lytic lifecycleconsistsof the followingsteps:

1. Adsorption:Attachmentsitesonthe phageadsorb toreceptorsiteson

the host bacterium( Fig.5). Most bacteriophagesadsorb to thebacterial cell

wall, although some are able to adsorb to flagella or pili. Speci fic strains of

bacteriophages can only adsorb to specific strain of host bacteria. This is

knownasviral specificity.

Fig.5: AdsorptionduringtheLyticLife CycleofaLyticBacteriophage

2. Penetration:In thecaseofphages that adsorb to thebacterial cell wall, a

phageenzyme "drills"ahole in thebacterial wall and the phage injects its

genome intothe bacterial cytoplasm ( Fig.6). Somephagesaccomplish this

by contracting a sheathwhich drives a hollow tube into thebacterium. Thisbegins theeclipseperiod. Thegenomeo fphageswhichadsorb to flagellaorpili

enter through theseholloworganelles. Ineithercase, only thephagegenome

enters thebacteriumso there isnouncoatingstage.


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Fig.6: Penetration duringtheLyticLife CycleofaLyticBacteriophage

3. Replication: Enzymes coded by the phage genome shut down the

bacterium's macromolecular (protein, R A, A) synthesis. The phage

replicates itsgenomeand uses the bacterium's metabolic machinery to

synthesize phageenzymesand phagestructural components (Fig. and

Fig.8).

Figs. 7&8: Early and lateReplication duringtheLyticLife CycleofaLyticBacteriophage

4. Maturation:Thephagepartsassemblearound thegenomes ( Fig.9).

Fig.9:Maturation duringtheLyticLife CycleofaLyticBacteriophage

5. Release: Usually, a phage-coded lysozyme breaks down the bacterial

peptidoglycan causing osmotic lysis and release of the intact

bacteriophages( Fig.10).


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Fig.10:Release duringtheLyticLife CycleofaLyticBacteriophage

6. Reinfection: From 50 to 200 phagesmaybeproducedperinfected

bacterium.

TheLysogenicLife CycleofTemperateBacteriophages:

Bacteriophages capable of a lysogenic life cycle are termed temperate

phages. Whena temperatephage infectsabacterium, it caneither replicate

by meansofthe lytic lifecycle andcause lysisof thehost bacterium, or, it

can incorporate its DNA into the bacterium's DNA and become a

noninfectiousprophage ( Fig.11).

Fig.11:LysogenicLife CycleofaTemperateBacteriophage


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induction occurs. The phage genes are activated and new phages are

produced by the lytic lifecycle.

ClassificationofViruses:

Virusescanstore theirgenetic information insixdifferent typesofnucleicacid

which are named based on how that nucleic acid eventually becomes

transcribed to theviral mR A capableof binding tohost cell ribosomesand

being translated intoviral proteins.

Only a (+) viral mRNA strand can betranslated into viral protein . These

six formsofviral nucleicacidare:

a. (+/-) double-stranded DNA.

b. (+) single-stranded DNA.

c. (+/-) double-stranded RNA.

d. (-) RNA

e. (+) RNA

f. (+) RNA Retroviruses Retroviruses, suchas HIV-1, HIV-2, and HTLV-1 are

examples.Viroidsand Prions:

Viroids: are even more simple than viruses. They are small, circular,

single-strandedmoleculesofinfectiousRNA lackingevenaproteincoat. They

are the cause of a few plant diseases such as potato spindle-tuber

disease,cucumber pale fruit, citrus exocortis disease, and cadang-cadang

(coconuts).

Prions:areinfectious protein particles thought toberesponsible foragroup

of transmissible and/or inherited neurodegenerative diseases . Most

evidence indicates that the infectious prion proteins are modified forms of

normal proteinscoded forbyahost gene in thebrain.


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Domain:Bacteria

Phylum: Cyanobacteria

Cyanobacteria(alsoknownasblue-greenalgae, blue-green bacteria, and

Cyanophyta) is a phylum of bacteria that obtain their energy through

photosynthesis. Thename"cyanobacteria"comes from thecolorof thebacteria

(Greek: (kyans) = blue).

Theabilityofcyanobacteria toperformoxygenicphotosynthesis is thought to

have converted the early reducing atmosphere into an oxidizing one, which

dramatically changed the composition of life forms on Earth by stimulating

biodiversityand leading to thenear-extinctionofoxygen-intolerant organisms.

According to endosymbiotic theory(Theendosymbiotic theoryconcerns theorigins ofmitochondriaandplastids(e.g. chloroplasts) ,which

areorganellesofeukaryoticcells. According to this theory, these organelles

originated as separateprokaryoticorganisms that were taken inside the cell

asendosymbionts. Mitochondria developed fromproteobacteria(in

particular, Rickettsialesor close relatives) and chloroplasts

fromcyanobacteria), chloroplasts inplantsandeukaryoticalgaehaveevolved

fromcyanobacteriaviaendosymbiosis.

Characteristics:

yanobacteria include unicellular and colonial species. olonies may form

filaments, sheets or even hollow balls. Some filamentous colonies show t he

ability to differentiate into several different cell types: vegetative cells, the

normal, photosynthetic cells that are formed under favorable growing

conditions; akinetes, the climate-resistant spores that may form when

environmental conditionsbecomeharsh;and thick-walledheterocysts, which

contain the enzyme nitrogenase, vital for nitrogen fixation. Heterocysts may

also formunder theappropriateenvironmental conditions(anoxic)when fixed

nitrogen is scarce. Heterocyst-forming species are specialized for nitrogen

fixationandareable to fixnitrogengas into ammonia(NH3), nitrites(NO2)or


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nitrates(NO3)whichcanbeabsorbedbyplantsandconverted toprotei nand

nucleicacids[atmosphericnitrogencannot beusedbyplantsdirectly].

Manycyanobacteriaalso formmotile filaments, called hormogonia, that travel

away from the mainbiomass to budand form new colonieselsewhere. Thecells inahormogoniumareoften thinner than in thevegetativestate, and the

cellsoneitherendof themotilechainmaybe tapered. Inorder tobreakaway

from theparent colony, ahormogoniumoftenmust tear apart aweakercell ina

filament, calledanecridium.

Each individual cell ofacyanobacterium typicallyhasa thick, gelatinous cell

wall.. They lack flagella, but hormogoniaandsomespeciesmaymoveabout by

gliding along surfaces. Many of the multi-cellular filamentous forms of

Oscillatoriaarecapableofawavingmotion.

Classification:

The cyanobacteria were traditionally classified by morphology into five

sections. The first three - hroococcales, Pleurocapsales, and Oscillatoriales -

arenot supportedbyphylogeneticstudies. However, the lattertwo -Nostocales

and Stigonematales - are monophyletic, and make up the heterocystous

cyanobacteria. The members of hroococales are unicellular and usually

aggregate in colonies. The classic t axonomic criterion has been the cell

morphologyand theplaneofcell division. In Pleurocapsales, thecellshave the

ability to form internal spores (baeocytes). The rest of the sections include

filamentousspecies. In Oscillatoriales, thecellsareunise riatelyarrangedand

do not form specialized cells (akinetes and heterocysts). InNostocales and

Stigonematales the cells have the ability to develop heterocysts in certain

conditions. Stigonematales, unlike Nostocales, includes species with truly

branched trichomes.


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Domain:Bacteria


Order: Nostocales

Genus: Nostoc

The Nostocales order contains

most of thespeciesofcyanobacteria. It

includes filamentous forms, bothsimple

or branched, and both those occurring as single strands or multiple strands

withinasheath. Somebut not all membersshowadecrease inwidth from thebase. Again, somebut not all have heterocysts

Oscillatoria isagenusof filamentouscyanobacteriawhich isnamed for the

oscillation in itsmovement. Filaments in thecoloniescanslidebackand forth

against eachotheruntil thewholemass is reoriented to its light source. It is

commonly found in watering-troughs waters, and is mainly blue-green or

brown-green. Oscillatoria is an organism that reproduces by fragmentation.

Oscillatoria forms long filamentsofce llswhichcanbreak into fragmentscalled

hormogonia. Thehormogoniacangrow intoanew, longer filament. Breaks in

the filament usuallyoccurwheredeadcells(necridia)arepresent. Oscillatoria

usesphotosynthesis tosurviveandreproduce.

Domain: Bacteria


Order: Oscillatoriales

Genus: Oscillatoria


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THE PROKARYOTIC CELL:BACTERIA

A. SIZES, SHAPES, AND ARRANGEMENTS OF BACTERIA

Bacteriaare:

a.prokaryotic.

b.single-celled, microscopicorganisms(Exceptionshavebeendiscovered that

can reach sizes just visible to the naked eye. They include Epulopiscium

fishelsoni, abacillus-shapedbacterium that is typically 80 micrometers(m) in

diameter and 200-600 m long, andThiomar&

aritanami' iensis, a spherical

bacteriumbetween 100 and 50 m indiameter.)

c.generallymuchsmaller thaneukaryoticcells.

d.verycomplexdespite theirsmall size.

Epulopiscium fishelsoni Thiomargarita namibiensis

Most bacteriacome inoneof three basicshapes: coccus, rodorbacillus, and

spiral.

1. Thecoccus:

The cocci are spherical or oval bacteria having one of several

distinct arrangementsbasedon theirplanesofdivision.


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ArrangementsofBacillia. bacillus: singlebacilli.

b. streptobacillus: bacilli arranged inchains.

c. acoccobacillus: oval andsimilartoacoccus.

Anaveragebacillus is 0.5-1.0 mwideby 1.0-4.0 m long.

3. Thespiral:

Spiralscome inoneof threeforms, avibrio, aspirillum, oraspirochete.

Spiral Forms A. Vibrio: acurvedorcomma-shapedrod.

B. Spirillum: a thick, rigidspiral.

. Spirochete: a thin, flexiblespiral.

Spiralsrange insize from 1 m toover100 m in length.


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4. Exceptionstotheaboveshapes

Trichome-forming, sheathed stalked, filamentous, square, star-shaped,

spindle-shaped, lobed, andpleomorphic.

B. CELL STRUCTURE OF THE DOMAIN BACTERIA: AnOverviewStructurally, a typical bacteriumusuallyconsistsof:

y acytoplasmicmembranesurroundedbyapeptidoglycancell wall and

maybeanoutermembrane;

y A fluidcytoplasmcontaininganuclearregion(nucleoid)andnumerous

ribosomes.

y Oftenvariousexternal structuressuchasaglycocalyx, flagella, andpili.

1. The CytoplasmicMembrane:

The cytoplasmic membrane, also called a cell membrane or plasma

membrane, isabout nanometers(nm; 1/1,000,000,000 m) thick. It lies internal

to thecell wall andencloses thecytoplasmof thebacterium (Fig. 1).


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Fig.2: Diagram ofa CytoplasmicMembrane

B. Functions:

The cytoplasmic membrane is aselectively permeable membrane that

determineswhatgoes inand outoftheorganism .

C. Functions of the cytoplasmic membrane other than selectivepermeability:

Functionsareassociatedwith thebacterial cytoplasmicmembrane include :

1. Energy production: The electron transport system for bacteria with

aerobic and anaerobic respiration, as well as photosynthesis for bacteria

converting light energy into chemical energy is located in the cytoplasmic

membrane.

2. Motility: Themotorthat drivesrotationofbacterial flagella is located in the

cytoplasmicmembrane.

3. Wasteremoval: Wastebyproductsofmetabolismwithin thebacteriummust

exit through thecytoplasmicmembrane.

4. Formationofendospores(discussed later;Fig.3).


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E. Gram-Positiveand Gram-NegativeBacteria:

Most bacteriacanbeplaced intooneof twogroupsbasedon theircolorafter

specificstainingproceduresareperformed: gram-positive, gram-negative, or

acid-fast.

y Gram-positive:retain the initial dyecrystal violet during the Gramstain

procedureandappear purplewhenobserved through themicroscope.

Common gram-positive bacteria of medical importance include

Streptococcuspyogenes,Streptococcuspneumoniae,Staphylococcus

aureus,Enterococcus faecalis,andClostridiumspecies.

y Gram-negative: decolorize during the Gram stain procedure, pick up

thecounterstainsafranin, andappear pinkwhenobserved through the

microscope. Common Gram-negative bacteria of medical importance

includeSalmonella species, Shigella species, Neisseriagonorrhoeae,

Neisseria meningitidis, Escherichia coli, Klebsiellapneumoniae, and

Pseudomonas aeruginosa. Also see gram stain of a mixture of

gram-positiveandgram-negativebacteria.(Fig.6)

Fig.6:A Gram StainofaMixtureofGram-Positiveand

Gram-NegativeBacteria


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Thegram staining procedure involvesfourbasicsteps:

1. The bacteria are first stained with the basic dye crystal violet. Both

gram-positiveandgram-negativebacteriabecomedirectlystainedandappear

purpleafterthisstep.

2. Thebacteriaare then treatedwith gram's iodinesolution. Thisallows the

stain toberetainedbetterby formingan insolublecrystal violet -iodinecomplex.

Bothgram-positiveandgram-negativebacteriaremainpurpleafterthisstep.

3. Gram's decolorizer, a mixture of ethyl alcohol and acetone , is then

added. This is the differential step. Gram-positive bacteria retain the crystal

violet-iodinecomplexwhilegram-negativearedecolorized.

4. Finally, the counterstain safranin (alsoa basicdye) is applied. Since the

gram-positivebacteriaarealreadystainedpurple, theyarenot affectedby the

counterstain. Gram-negative bacteria, which are now colorless, become

directly stained by the safranin. Thus, gram-positive appear purple, and

gram-negativeappearpink.

3. STRUCTURES LOCATED WITHINTHE CYTOPLASM

Wewill now lookat the followingstructures locatedwithin thecytoplasm.

a.Cytoplasm

b.Thenucleoid

c.Ribosomes

d.Endospores

e. Organelles forphotosynthesis


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Fig.7:Endospore Structure

Differentshapesofspores

C. FunctionofEndospores

Anendospore isnot areproductivestructurebut rathera resistant, dormant

survival form of the organism. Endospores are quite resistant to high

temperatures (including boiling), most disinfectants, low energy radiation,

drying, etc.

Bacterial endospores are resistant to antibiotics, most disinfectants, and

physical agentssuchasradiation, boiling, anddrying. The impermeabilityof the

spore coat is thought to be responsible for the endospore's resistance to

chemicals.


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4. STRUCTURES LOCATED OUTSIDE THE CELL WALL

a. glycocalyx(capsule)and S-layer

b. flagella

c. pili

The Glycocalyxand S-Layer

1. The Glycocalyx (Capsules and SlimeLayers)

All bacteria secrete some sort of glycocalyx, an outer viscous covering of

fibersextending from thebacterium(Fig. 1, Fig.23 , andFig. 24). If it appears

asanextensive, tightlyboundaccumulationofgelatinousmaterial adhering to

thecell wall, it iscalledacapsuleasshown in thephotomicrograph inFig. 23. If

theglycocalyxappearsunorganizedandmore looselyattached, it isreferred to

asaslime layer.

Fig.23:Capsule stain ofEnterobacteraerogenes

Fig.24: Encapsulated Brucella


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A. Structureand Composition

The glycocalyx is usually a viscous polysaccharide or polypeptide slime .

Actual productionofaglycocalyxoftendependsonenvironmental conditions.

B. Functionsand SignificancetoBacteria CausingInfections

Althoughanumberof functionshavebeenassociatedwith theglycocalyx, such

as protecting bacteria against drying, trap nutrients1, etc., for our purposes

thereare twovery important functions. Theglycocalyxenablescertainbacteria

to resist phagocytic engulfment 2 by white blood cells in the body or

protozoans in soil and water. The glycocalyxalsoenables some b acteria to

adhere toenvironmental surfaces3(rocks, root hairs, teeth, etc.), colonize, and

resist flushing.

2. The S-layer


Many gram-negative and gram-positive bacteria, as well a many Archaea

possess a regularly structured layer called an S-layer attached to the

outermost portion of their cell wall. It consists of a single molecular layer

composedof identical proteinsorglycoproteins.Although theyvarywith the

species, S-layersgenerallyhavea thicknessbetween 5 and 25 nm.

B. Functionsand SignificancetoBacteria CausingInfections

The S-layerhasbeenassociatedwithanumberofpossible functions. These

include the following:

a. The S-layermayprotect bacteriafrom harmful enzymes,from changes

in pH,from the predatory bacterium Bdellovibrio, aparasiticbacterium that

actuallyuses its motility topenetrateotherbacteriaandreplicatewithin their

cytoplasm, andfrom bacteriophages.


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Predatory bacterium Bdellovibrio

b. The S-layercanfunctionasanadhesin, enabling thebacterium toadhere

to hostcellsand environmental surfaces,colonize,and resistflushing .

c. The S-layer may contribute to virulence by protecting the bacterium

againstcomplementattackand phagocytosis .

Flagella


A bacterial flagellumhas 3 basicparts: a filament, ahook, andabasal body.

1)Thefilament is therigid, helical structure that extends from thecell surface.

It is composedof theprotein flagellin. With theexceptionof a fewbacteria,

such as Bdellovibrio and Vibrio cholerae, the flagellar filament is not

surroundedbyasheath( Fig.25).


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Fig.25: StructureofaBacterial Flagellum 2)Thehook isaflexiblecoupling betweenthefilamentand the basal body

( Fig.25).

3) The basal body consists of a rod and a series of rings that anchor the

flagellum to the cel l wall and the cytoplasmic membrane ( Fig.25). Unlike

eukaryotic flagella, thebacterial flagellumhasno internal fibrilsanddoesnot

flex. Instead, thebasal bodyactsasarotary molecularmotor,enablingthe

flagellum torotateandpropell thebacterium through thesurrounding fluid. In

fact, the flagellarmotorrotatesveryrapidly.

Bacteria flagella(Fig. 26andFig. 2 )are 10-20 m longandbetween 0.01 and

0.02 m indiameterandcome inanumberofdistinct arrangements.


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Fig. : Electron Microgra of Bacteria wit Flagella B. Flagellar rrangements( ig. )

. monotrichous: a single flagellum, usually at one pole

. amphitrichous: a single flagellum at both ends of the organism

. lophotrichous: two or more flagella at one or both poles

4. peritrichous: flagella over the entire surface

Fig. : Bacterial Flagellar rrangements 5. axial filaments: internal flagella found only in the spirochetes. Axial

filaments are composed of from two to over a hundred axial fibrils (or

endoflagella) that extend from both ends of the bacterium between the outer


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Fig33:Conjugation (Sex) PilusB. Functionsand SignificanceofPili toBacteria CausingInfections:

The short attachment pili or fimbriaeare organellesof adhesion allowing

bacteria tocolonizeenvironmental surfacesorcellsand resistflushing .

Somebacteriacanproduceaspecial piluscalledaconjugationorsex pilus

that enablesconjugation. Conjugation is the transferofDNA fromadonoror

malebacterium withasexpilus toa recipient or femalebacterium toenable

geneticrecombination. Scanningelectronmicrograph E. coli withaconjugation

pillus.


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C. ATYPICAL PATHOGENIC BACTERIA

These include themycoplasmas, therickettsias, and thechlamydias.

1. Mycoplasmas

a. Mycoplasmasaresmaller thanordinarybacteria, typicallybeing 0.15 - 0.30

micrometers (m) in size. They are the smallest microorganisms that can

independentlygrowonacell-freemedium.

b. Mycoplasmasare theonly prokaryotesthat lackacell wall andcontain

sterols in their cytoplasmic membrane. They are surrounded only by a

cytoplasmic membrane and are therefore highly pleomorphic, that is, their

shape varies. The sterols in the cytoplasmic membrane may provide added

strength. Inaddition, mycoplasmasareable tomaintainanearlyevenpressure

between the outer environment and the cytoplasm by actively pumping out

sodium ions.

Themost important mycoplasma in termsofhuman infections isMycoplasma

pneumoniae. This bacterium is a common cause of both upper an d lower

respiratory infections, including tracheobronchitis and primary atypical

pneumonia.

2. Rickettsias

a. Rickettsias are small and typically 0.3-1.0 m in size. They appear as

pleomorphicbacillaryorcoccobacillary forms.


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b. Most are obligate intracellular parasites. The infectious form or

elementary body utilizesadhesins toadhere to thesurfaceof thehost cell. It

thenusesinvasins toenterthecell.

c. Withrareexceptions, mammalsbecome infectedwithrickettsiaonly throughthebitesof infectedarthropods.

d. Theirstructureandreplicationaresimilartogram -negativebacteria.

3. Chlamydias

a. Chlamydiasarecoccoidbacteria that are alsoquite small, typicallybeing

0.2-0. m insize. Chlamydiasalso lack peptidoglycan in theircell wall.

b. Theyareclassified asatypeofrickettsia that donot requirearthropods for

transmission tohumans.

c. Chlamydiasareobligate intracellularparasites ofvertebrates.

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