Microbiology: A Microbiology: A Systems Approach, 2Systems Approach, 2ndnd

ed.ed.Chapter 4: Prokaryotic Profiles- Chapter 4: Prokaryotic Profiles-

the Bacteria and Archaeathe Bacteria and Archaea

How are Prokaryotes Different from How are Prokaryotes Different from Eukaryotes?Eukaryotes?

The way their DNA is packagedThe way their DNA is packaged No nucleusNo nucleus Not wrapped around Not wrapped around histoneshistones

The makeup of their cell wallThe makeup of their cell wall Bacteria- peptidoglycanBacteria- peptidoglycan Archae- tough and made of other chemicals, Archae- tough and made of other chemicals,

distinct to themdistinct to them Their internal structuresTheir internal structures

No complex, membrane-bound organellesNo complex, membrane-bound organelles

4.1 Prokaryotic Form and Function4.1 Prokaryotic Form and Function

Structures common to all bacterial cellsStructures common to all bacterial cells

Cell membraneCell membrane CytoplasmCytoplasm RibosomesRibosomes One (or a few) chromosomesOne (or a few) chromosomes

Structures found in most bacterial cellsStructures found in most bacterial cells

Cell wallCell wall Surface coating or glycocalyxSurface coating or glycocalyx

Structures found in some bacterial cellsStructures found in some bacterial cells

FlagellaFlagella PiliPili FimbriaeFimbriae CapsulesCapsules Slime layersSlime layers InclusionsInclusions Actin cytoskeletonActin cytoskeleton EndosporesEndospores

Figure 4.1

4.2 External Structures4.2 External Structures

AppendagesAppendages: Cell extensions: Cell extensions Common but not present on all speciesCommon but not present on all species Can provide Can provide motility motility ((flagellaflagella and axial and axial

filaments)filaments) Can be used for attachment and mating (Can be used for attachment and mating (pilipili

and and fimbriaefimbriae))

FlagellaFlagella

Three parts: Three parts: FilamentFilament, hook (sheath), and , hook (sheath), and basal bodybasal body

Vary in both number and arrangementVary in both number and arrangement Polar arrangement: flagella attached at one Polar arrangement: flagella attached at one

or both ends of the cellor both ends of the cell• MonotrichousMonotrichous- single flagellum- single flagellum• LophotrichousLophotrichous- small bunches or tufts of flagella - small bunches or tufts of flagella

emerging from the same siteemerging from the same site• PeritrichousPeritrichous- dispersed randomly over the - dispersed randomly over the

structure of the cellstructure of the cell

Figure 4.2

Figure 4.3

Flagellar FunctionFlagellar Function

ChemotaxisChemotaxis- positive and negative- positive and negative PhototaxisPhototaxis Move by runs and tumblesMove by runs and tumbles

Figure 4.4

Figure 4.5

Axial FilamentsAxial Filaments

AKA periplasmic flagellaAKA periplasmic flagella In spirochetesIn spirochetes A type of internal flagellum that is A type of internal flagellum that is

enclosed in the space between the cell enclosed in the space between the cell wall and the cell membranewall and the cell membrane

Figure 4.6

PiliPili

Elongate, rigid tubular structuresElongate, rigid tubular structures Made of the protein pilinMade of the protein pilin Found on gram-negative bacteriaFound on gram-negative bacteria Used in Used in conjugationconjugation

Figure 4.8

FimbriaeFimbriae

Small, bristlelike fibersSmall, bristlelike fibers Most contain proteinMost contain protein Tend to stick to each other and to surfacesTend to stick to each other and to surfaces

Figure 4.7

The The GlycocalyxGlycocalyx

Develops as a coating of repeating Develops as a coating of repeating polysaccharide units, protein, or bothpolysaccharide units, protein, or both

Protects the cellProtects the cell Sometimes helps the cell adhere to the Sometimes helps the cell adhere to the

environmentenvironment Differ among bacteria in thickness, Differ among bacteria in thickness,

organization, and chemical compositionorganization, and chemical composition Slime layerSlime layer- a loose shield that protects some - a loose shield that protects some

bacteria from loss of water and nutrientsbacteria from loss of water and nutrients CapsuleCapsule- when the glycocalyx is bound more when the glycocalyx is bound more

tightly to the cell and is denser and thickertightly to the cell and is denser and thicker

Figure 4.9

Functions of the GlycocalyxFunctions of the Glycocalyx

Many pathogenic bacteria have Many pathogenic bacteria have glycocalyces glycocalyces

Protect the bacteria against phagocytesProtect the bacteria against phagocytes Important in formation of biofilmsImportant in formation of biofilms

4.3 The Cell Envelope: The Boundary 4.3 The Cell Envelope: The Boundary layer of Bacterialayer of Bacteria

Majority of bacteria have a cell envelopeMajority of bacteria have a cell envelope Lies outside of the cytoplasmLies outside of the cytoplasm Composed of two or three basic layersComposed of two or three basic layers

Cell membraneCell membrane Cell wallCell wall In some bacteria, the outer membraneIn some bacteria, the outer membrane

Differences in Cell Envelope StructureDifferences in Cell Envelope Structure

The differences between The differences between gram-positivegram-positive and and gram-negativegram-negative bacteria lie in the cell bacteria lie in the cell envelopeenvelope

Gram-positiveGram-positive Two layersTwo layers Cell wall and cytoplasmic membraneCell wall and cytoplasmic membrane

Gram-negativeGram-negative Three layersThree layers Outer membrane, cell wall, and cytoplasmic Outer membrane, cell wall, and cytoplasmic

membranemembrane

Figure 4.12

Structure of the Structure of the Cell WallCell Wall

Helps determine the shape of a bacteriumHelps determine the shape of a bacterium Provides strong structural supportProvides strong structural support Most are rigid because of peptidoglycan Most are rigid because of peptidoglycan

contentcontent

Figure 4.13

Structure of the Cell Wall, cont.Structure of the Cell Wall, cont.

Keeps cells from rupturing because of Keeps cells from rupturing because of changes in pressure due to osmosischanges in pressure due to osmosis

Target of many antibiotics- disrupt the cell Target of many antibiotics- disrupt the cell wall, and cells have little protection from wall, and cells have little protection from lysislysis

Gram-positive cell wallGram-positive cell wall A thick (20 to 80 nm), homogeneous sheath of A thick (20 to 80 nm), homogeneous sheath of

petidoglycan petidoglycan Contains tightly bound acidic polysaccharidesContains tightly bound acidic polysaccharides

Gram-Negative Cell WallGram-Negative Cell Wall Single, thin (1 to 3 nm) sheet of peptidoglycanSingle, thin (1 to 3 nm) sheet of peptidoglycan Periplasmic space surrounds the peptidoglycanPeriplasmic space surrounds the peptidoglycan

Figure 4.14

Nontypical Cell WallsNontypical Cell Walls

Some aren’t characterized as either gram-Some aren’t characterized as either gram-positive or gram-negativepositive or gram-negative

For example, For example, Mycobacterium Mycobacterium and and NocardiaNocardia- unique types of lipids (acid-fast)- unique types of lipids (acid-fast)

Archaea - unusual and chemically distinct Archaea - unusual and chemically distinct cell wallscell walls

Some don’t have a cell wall at allSome don’t have a cell wall at all MycoplasmasMycoplasmas- lack cell wall entirely- lack cell wall entirely

Mycoplasmas and Other Cell-Wall-Mycoplasmas and Other Cell-Wall-Deficient BacteriaDeficient Bacteria

Mycoplasma cell membrane is stabilized Mycoplasma cell membrane is stabilized by sterols and is resistant to lysisby sterols and is resistant to lysis Very small bacteria (0.1 to 0.5 µm)Very small bacteria (0.1 to 0.5 µm) Range in shape from filamentous to coccusRange in shape from filamentous to coccus Not obligate parasitesNot obligate parasites Can be grown on artificial mediaCan be grown on artificial media Found in many habitatsFound in many habitats Important medical species: Important medical species: Mycoplasma Mycoplasma

pneumoniaepneumoniae

Some bacteria lose their cell wall during Some bacteria lose their cell wall during part of their life cyclepart of their life cycle L-formsL-forms Arise naturally from a mutation in the wall-Arise naturally from a mutation in the wall-

forming genesforming genes Can be induced artificially by treatment with a Can be induced artificially by treatment with a

chemical that disrupts the cell wallchemical that disrupts the cell wall• When this occurs with gram-positive cells, the cell When this occurs with gram-positive cells, the cell

becomes a becomes a protoplastprotoplast• With gram-negative cells, the cell becomes a With gram-negative cells, the cell becomes a

spheroplastspheroplast

Figure 4.16

The Gram-Negative The Gram-Negative Outer MembraneOuter Membrane

Similar to the cell membrane, except it contains Similar to the cell membrane, except it contains specialized polysaccharides and proteinsspecialized polysaccharides and proteins

Outermost layer- contains lipopolysaccharideOutermost layer- contains lipopolysaccharide Innermost layer- phospholipid layer anchored by Innermost layer- phospholipid layer anchored by

lipoproteins to the peptidoglycan layer belowlipoproteins to the peptidoglycan layer below Outer membrane serves as a partial chemical Outer membrane serves as a partial chemical

sievesieve Only relatively small molecules can penetrateOnly relatively small molecules can penetrate Access provided by special membrane channels Access provided by special membrane channels

formed by porin proteinsformed by porin proteins

Cell Membrane Cell Membrane StructureStructure

Also known as the Also known as the cytoplasmic membranecytoplasmic membrane Very thin (5-10 nm)Very thin (5-10 nm) Contain primarily phospholipids and proteinsContain primarily phospholipids and proteins The exceptions: mycoplasmas and archaeaThe exceptions: mycoplasmas and archaea FunctionsFunctions

Provides a site for functions such as energy Provides a site for functions such as energy reactions, nutrient processing, and synthesisreactions, nutrient processing, and synthesis

Regulates transport (selectively permeable Regulates transport (selectively permeable membrane)membrane)

SecretionSecretion

Practical Considerations of Differences Practical Considerations of Differences in Cell Envelope Structurein Cell Envelope Structure

Outer membrane- an extra barrier in gram-Outer membrane- an extra barrier in gram-negative bacterianegative bacteria Makes them impervious to some antrimicrobial Makes them impervious to some antrimicrobial

chemicalschemicals Generally more difficult to inhibit or kill than gram-Generally more difficult to inhibit or kill than gram-

positive bacteriapositive bacteria Cell envelope can interact with human Cell envelope can interact with human

tissues and cause diseasetissues and cause disease Corynebacterium diphtheriaeCorynebacterium diphtheriae Streptococcus pyogenesStreptococcus pyogenes

4.4 Bacterial Internal Structure4.4 Bacterial Internal Structure

Contents of the Cell Contents of the Cell CytoplasmCytoplasm Gelatinous solutionGelatinous solution Site for many biochemical and synthetic Site for many biochemical and synthetic

activitiesactivities 70%-80% water70%-80% water Also contains larger, discrete cell masses Also contains larger, discrete cell masses

(chromatin body, ribosomes, granules, and (chromatin body, ribosomes, granules, and actin strands)actin strands)

Bacterial ChromosomeBacterial Chromosome

Single circular strand of DNASingle circular strand of DNA Aggregated in a dense area of Aggregated in a dense area of

the cell- the the cell- the nucleoidnucleoid

Figure 4.17

PlasmidsPlasmids

Nonessential, double-stranded circles of Nonessential, double-stranded circles of DNADNA

Present in cytoplasm but may become Present in cytoplasm but may become incorporated into the chromosomal DNAincorporated into the chromosomal DNA

Often confer protective traits such as drug Often confer protective traits such as drug resistance or the production of toxins and resistance or the production of toxins and enzymesenzymes

RibosomesRibosomes

Made of RNA and Made of RNA and proteinprotein

Special type of RNA- Special type of RNA- ribosomal RNA ribosomal RNA (rRNA)(rRNA)

Characterized by S Characterized by S (for Svedberg) units- (for Svedberg) units- the prokaryotic the prokaryotic ribosome is 70Sribosome is 70S

Figure 4.18

InclusionsInclusions Inclusions- also known as Inclusions- also known as inclusion bodiesinclusion bodies

Some bacteria lay down nutrients in these Some bacteria lay down nutrients in these inclusions during periods of nutrient abundanceinclusions during periods of nutrient abundance

Serve as a storehouse when nutrients become Serve as a storehouse when nutrients become depleteddepleted

Some enclose condensed, energy-rich organic Some enclose condensed, energy-rich organic substancessubstances

Some aquatic bacterial inclusions include gas Some aquatic bacterial inclusions include gas vesicles to provide buoyancy and flotationvesicles to provide buoyancy and flotation

GranulesGranules A type of inclusion bodyA type of inclusion body Contain crystals of inorganic compoundsContain crystals of inorganic compounds Are not enclosed by membranesAre not enclosed by membranes Example- sulfur granules of photosynthetic Example- sulfur granules of photosynthetic

bacteriabacteria Polyphosphate granules of Polyphosphate granules of CorynebacteriumCorynebacterium and and

MycobacteriumMycobacterium are called are called metachromatic metachromatic granulesgranules because they stain a contrasting color in because they stain a contrasting color in methylene bluemethylene blue

Magnetotactic bacteria contain granules with iron Magnetotactic bacteria contain granules with iron oxide- give magnetic properties to the celloxide- give magnetic properties to the cell

Figure 4.19

The Actin CytoskeletonThe Actin Cytoskeleton

Long polymers of Long polymers of actinactin Arranged in helical ribbons around the cell Arranged in helical ribbons around the cell

just under the cell membranejust under the cell membrane Contribute to cell shapeContribute to cell shape

Figure 4.20

Bacterial Bacterial EndosporesEndospores: An Extremely : An Extremely Resistant StageResistant Stage

Dormant bodies Dormant bodies produced by produced by Bacillus, Bacillus, Clostridium, Clostridium, and and SporosarcinaSporosarcina

Figure 4.21

Endospore-Forming BacteriaEndospore-Forming Bacteria

These bacteria have a two-phase life cycleThese bacteria have a two-phase life cycle Phase One- Vegetative cellPhase One- Vegetative cell

• Metabolically active and growingMetabolically active and growing• Can be induced by the environment to undergo Can be induced by the environment to undergo

spore formation (spore formation (sporulationsporulation))

Phase Two: EndosporePhase Two: Endospore

Stimulus for sporulation- the depletion of nutrientsStimulus for sporulation- the depletion of nutrients Vegetative cell undergoes a conversion to a Vegetative cell undergoes a conversion to a

sporangiumsporangium Sporangium transforms in to an endosporeSporangium transforms in to an endospore Hardiest of all life formsHardiest of all life forms

Withstand extremes in heat, drying, freezing, Withstand extremes in heat, drying, freezing, radiation, and chemicalsradiation, and chemicals

Heat resistance- high content of calcium and Heat resistance- high content of calcium and dipicolinic aciddipicolinic acid

Some viable endospores have been found that were Some viable endospores have been found that were more than 250 million years oldmore than 250 million years old

GerminationGermination Breaking of dormancyBreaking of dormancy In the presence of water and a specific In the presence of water and a specific

germination agentgermination agent Quite rapid (1 ½ hours)Quite rapid (1 ½ hours) The agent stimulates the formation of hydrolytic The agent stimulates the formation of hydrolytic

enzymes, digest the cortex and expose the core enzymes, digest the cortex and expose the core to waterto water

Medical SignificanceMedical Significance Several bacterial pathogensSeveral bacterial pathogens

• Bacillus anthracisBacillus anthracis• Clostridium tetaniClostridium tetani• Clostridium perfingensClostridium perfingens• Clostridium botulinumClostridium botulinum

Resist ordinary cleaning methodsResist ordinary cleaning methods

4.5 Bacterial Shapes, Arrangements, 4.5 Bacterial Shapes, Arrangements, and Sizesand Sizes

Three general shapesThree general shapes CoccusCoccus- roughly spherical- roughly spherical BacillusBacillus- rod-shaped- rod-shaped

• CoccobacillusCoccobacillus- short and plump- short and plump• VibrioVibrio- gently curved- gently curved

SpirillumSpirillum- curviform or spiral-shaped- curviform or spiral-shaped PleomorphismPleomorphism- when cells of a single - when cells of a single

species vary to some extent in shape and sizespecies vary to some extent in shape and size

Figure 4.22

Figure 4.23

Figure 4.24

Arrangement, or GroupingArrangement, or Grouping Cocci- greatest variety in arrangementCocci- greatest variety in arrangement

SingleSingle Pairs (diplococci)Pairs (diplococci) TetradsTetrads Irregular clusters (staphylococci and micrococci)Irregular clusters (staphylococci and micrococci) Chains (streptococci)Chains (streptococci) Cubical packet (Cubical packet (sarcinasarcina))

Bacilli- less variedBacilli- less varied SingleSingle Pairs (diplobacilli)Pairs (diplobacilli) Chain (streptobacilli)Chain (streptobacilli) Row of cells oriented side by side (Row of cells oriented side by side (palisadespalisades))

SpirillaSpirilla Occasionally found in short chainsOccasionally found in short chains

Figure 4.25

4.6 Classification Systems in the 4.6 Classification Systems in the Kingdom ProkaryotaeKingdom Prokaryotae

One of the original classification systems- shape, One of the original classification systems- shape, variations in arrangement, growth characteristics, variations in arrangement, growth characteristics, and habitatand habitat

Currently by comparing sequence of nitrogen Currently by comparing sequence of nitrogen bases in rRNAbases in rRNA

Definitive published source for bacterial Definitive published source for bacterial classificationclassification Bergey’s ManualBergey’s Manual Since 1923Since 1923 Early classification- the Early classification- the phenotypicphenotypic traits of bacteria traits of bacteria Current version- combines phenotypic information Current version- combines phenotypic information

with rRNA sequencingwith rRNA sequencing

Taxonomic SchemeTaxonomic Scheme

Kingdom Prokaryotae- 4 divisions based Kingdom Prokaryotae- 4 divisions based upon the nature of the cell wallupon the nature of the cell wall GracilicutesGracilicutes- gram-negative- gram-negative FirmicutesFirmicutes- gram-positive- gram-positive TenericutesTenericutes- lack cell wall- lack cell wall MendosicutesMendosicutes- the archae- the archae

Diagnostic SchemeDiagnostic Scheme

Many medical microbiologists preferMany medical microbiologists prefer Informal working systemInformal working system See Table 4.2See Table 4.2

Species and SubspeciesSpecies and Subspecies Common definition of species used for animals (can Common definition of species used for animals (can

produce viable offspring only when it mates with produce viable offspring only when it mates with others of its own kind) does not work for bacteriaothers of its own kind) does not work for bacteria

Bacteria do not exhibit a typical mode of sexual Bacteria do not exhibit a typical mode of sexual reproductionreproduction

For bacteria- a species is a collection of bacterial cells, For bacteria- a species is a collection of bacterial cells, all of which share an overall similar pattern of traitsall of which share an overall similar pattern of traits

Individual members of a bacterial species can show Individual members of a bacterial species can show variationsvariations Subspecies, strain, or type- bacteria of the same species Subspecies, strain, or type- bacteria of the same species

that have differing characteristicsthat have differing characteristics Serotype- representatives of a species that stimulate a Serotype- representatives of a species that stimulate a

distinct pattern of antibody responses in their hostsdistinct pattern of antibody responses in their hosts

Obligate Intracellular Obligate Intracellular ParasitesParasites

RickettsiasRickettsias Very tinyVery tiny Gram-negativeGram-negative Atypical in lifestyle and other adaptationsAtypical in lifestyle and other adaptations

• Most-pathogens that alternate between a mammalian Most-pathogens that alternate between a mammalian host and blood-sucking arthorpodshost and blood-sucking arthorpods

• Cannot survive or multiply outside a host cellCannot survive or multiply outside a host cell• Cannot carry out metabolism completely on their ownCannot carry out metabolism completely on their own

Human diseasesHuman diseases• Rocky Mountain Spotted Fever by Rocky Mountain Spotted Fever by Rickettsia rickettsiiRickettsia rickettsii• Endemic typhus by Endemic typhus by Rickettsia typhiRickettsia typhi

ChlamydiasChlamydias Genera Genera Chalmydia Chalmydia and and ChalmydophilaChalmydophila Require host cells for growth and metabolismRequire host cells for growth and metabolism Not closely relatedNot closely related Not transmitted by arthropodsNot transmitted by arthropods Human diseasesHuman diseases

• Chlamydia trachomatisChlamydia trachomatis- causes a severe eye - causes a severe eye infection (trachoma) and the chlamidial STDinfection (trachoma) and the chlamidial STD

• Chlamydophila pneumoniaChlamydophila pneumonia- causes lung infections- causes lung infections

Free-Living Nonpathogenic BacteriaFree-Living Nonpathogenic Bacteria

Photosynthetic BacteriaPhotosynthetic Bacteria Produce oxygen during photosynthesisProduce oxygen during photosynthesis Some produce other substances during Some produce other substances during

photosynthesis, such as sulfur granules or photosynthesis, such as sulfur granules or sulfatessulfates

Cyanobacteria: the Blue-Green BacteriaCyanobacteria: the Blue-Green Bacteria For many years, called Blue-Green AlgaeFor many years, called Blue-Green Algae Gram-negative cell wallGram-negative cell wall General prokaryotic structureGeneral prokaryotic structure Can be unicellular or can occur in colonial or Can be unicellular or can occur in colonial or

filamentous groupingsfilamentous groupings Specialized adaptation- Specialized adaptation- thylakoids thylakoids

• Chlorophyll aChlorophyll a• Other photosynthetic pigmentsOther photosynthetic pigments

Gas inclusionsGas inclusions Widely distributed in natureWidely distributed in nature

Figure 4.27

Green and Purple Sulfur Green and Purple Sulfur BacteriaBacteria

Green and Purple Sulfur BacteriaGreen and Purple Sulfur Bacteria PhotosyntheticPhotosynthetic Contain pigmentsContain pigments Different chlorophyll than cyanobacteria- Different chlorophyll than cyanobacteria-

bacteriochlorophyllbacteriochlorophyll Do not give off oxygenDo not give off oxygen Live in areas deep enough for anaerobic Live in areas deep enough for anaerobic

conditions but yet where their pigments can conditions but yet where their pigments can absorb lightabsorb light

• Sulfur springsSulfur springs• Freshwater lakesFreshwater lakes• SwampsSwamps

Archae: The Other ProkaryotesArchae: The Other Prokaryotes

Domain ArchaeaDomain Archaea Prokaryotic in general structureProkaryotic in general structure Share many bacterial characteristicsShare many bacterial characteristics Evidence may be pointing to them being Evidence may be pointing to them being

more closely related to Domain Eukarya more closely related to Domain Eukarya than to bacteriathan to bacteria

How they differ from other cell typesHow they differ from other cell types Certain genetic sequences are found only in their Certain genetic sequences are found only in their

rRNArRNA Unique membrane lipids and cell wall Unique membrane lipids and cell wall

constructionconstruction The most primitive of all life formsThe most primitive of all life forms Most closely related to the first cells that Most closely related to the first cells that

originated on earthoriginated on earth Modern archaea live in habitats that share Modern archaea live in habitats that share

conditions with the ancient earthconditions with the ancient earth Methane producersMethane producers HyperthermophilesHyperthermophiles Extreme halophilesExtreme halophiles Sulfur reducersSulfur reducers