Bacteria & Archaea: Cell Organization & Internal Structures

Bacterial Cells
Morphologies:
y Coccus: spherical y Bacillus: straight rods y Vibrio: gently curved rods,

Arrangements:
y Individual cells y Diplo- pairs y Strepto- chains y Staphylo- clusters y Tetrads- squares of 4 cells y y Sarcina- cubical packets of 8

comma-shaped helical rods

y Spirillum or Spirochete: y Pleomorphic y Appendaged: have tubes or

cells

stalks

Bacterial Morphology & Arrangements

Bacterial Cell Sizes

y Escherichia coli: 1.0 m by 2.0 to 6.0 m long,

average bacterium size, vertebrate intestines uncultured

y Nanobacteria: approx 0.2 m diameter, most are y Giant bacteria:

y Epulopiscium fisheloni: 80 m x 600 m long,

surgeonfish intestines
y Thiomargarita namibiensis: 100 to 750m diameter,

ocean sediments

Prokaryotic Cell Organization

y Internal Structures
y Cytoplasm y Cytoskeletons y Intracytoplasmic Membranes y Nucleoid & Plasmids y Ribosomes y Inclusions y Endospores

y Cell Envelope
y Cytoplasmic membrane y Periplasmic Space y Cell Wall
y

Exception: Mycoplasma (bacterium) and some Archaea

y Glycocalyx y S-layers

y External Structures
y Flagella y Fimbriae and Pili

Prokaryotic Cell Organization

Bacterial* Cell Organization

* Archaea cells have similar organization but capsules are rare

Cytoplasm
y

Cell pool for all biosynthetic functions

y Mixture of sugars, amino acids & salts y 70-80% water y Enzymes

http://www.emc.maricopa.edu/faculty/farabee/biobk/ fig2_2.jpg

Cytoskelton
Proteins in Eukarya:
y

Homologs in Bacteria:
y FtsZ
y Helps septum formation in cell

Microtubules
y Tubulin in Eukarya)

division

y Microfilaments
y Actins in Eukarya

y MreB and Mbl

y Maintains shape in rod-shapes y Localizes proteins/cell machinery y Aids chromosome segregation

y Intermediate filaments
y Lamin & keratin in Eukarya

y CreS
y Induces curvature in rods

Cytoskelton
Proteins in Eukarya:
y

Homologs in Bacteria:
y FtsZ
y Helps septum formation in cell

Microtubules
y Tubulins & spindle fibers

division

y Microfilaments
y Actins maintain cell shapes as a

y MreB and Mbl

y Maintains shape in rod-shapes y Localizes proteins/cell machinery

network of fibers within the cell

y Actins are important in amoeboid

& contractile movement

y Aids chromosome segregation

y Intermediate filaments
y Lamin & keratin

y CreS
y Induces curvature in rods

Intracytoplasmic Membranes
y
y y

Observed in some Bacteria

Photosynthetic bacteria Nitrifying bacteria

y y
y y

Derived from invaginations of the plasma membrane Part of more complex organelle structures in Eukarya
Mitochondria Chloroplasts

Nucleoid (Chromosomal dsDNA)

y Usually a single circular chromosome
y

Exceptions!
y y

Vibrio cholerae > 1 chromosome Borrelia burgdorferi has linear chromosome

y Usually not bound by a membrane

defines prokaryote or

eukaryote ?
y

Exception!
Some Planctomycetes bacteria have membrane around DNA

y 0.6-10 million base pairs in length, 1000X longer than cell if stretched out
y y

Must unwind for replication & expression Packaging around histone-like proteins

y Contains genes which are essential for survival

Plasmids (Extrachromosomal dsDNA)

y Contain genes that enhance survivability y Replicate independently of chromosome
y Can also integrate within bacterial chromosome (genetic

recombination) = episome

y Circular, like chromosome y Plasmid types:

y Conjugative

horizontal gene transfer, includes F factor and R plasmids (carry antibiotic resistance genes) carry virulence genes carry genes for alternative metabolic substrates

y Virulence y Metabolic y Col

carry genes for colicin production

Inclusions
y
y y

Granules in the cytoplasm and/or gas vacuoles

Composed of organic or inorganic materials Membranes are may be phospholipid bilayers (see intracytoplasmic membranes) or proteins Some are common to many bacteria, some are more rare

y y

Often visible with light microscope Formed for storage purposes primarily each inclusion body stores different substances

Example Inclusions
1. Poly--hydroxybutyric acid (PHB)
y Lipid-like, carbon & energy source y Found in purple photosynthetic bacteria y Surrounded by a single layer of protein & phospholipids

2. Glycogen
y Starch-like, carbon & energy source y Found in many bacteria

3. Volutin
y Polyphosphate reservoirs (metachromatic granules); energy y Found in many bacteria

Example Inclusions (cont.)

4. Sulfur granules/globules y Elemental sulfur and H2S for example, energy & electron source y Found in purple photosynthetic bacteria 5. Cyanophycin granules
y Polymer of aspartic acid and arginine (amino acids), stored

nitrogen source

y Found in cyanobacteria

6. Carboxysomes (microcompartments)
y Contain ribulose-1,5-bisphosphate (Rubisco) and CO2 for carbon

fixation reactions

y Surrounded by a protein coat y Found in cyanobacteria, thiobacilli and nitrifying bacteria

Example Inclusions (cont.)

6.
y

Magnetosomes
Not a storage product, allows orientation for navigation toward nutrients Found in magnetic bacteria

7.
y y y

Gas vacuoles aggregates of many gas vesicles

Each vesicle is composed of repeating units of a single protein Impermeable to water but permeable to gases Provides buoyancy for aquatic bacteria
y

Aquatic organisms can alter depths in water to obtain proper light intensity, oxygen levels, or nutrients

Inclusion Bodies

Example Inclusions (cont.)

8. Ribosomes
y Site of translation (protein

synthesis)
y Each ribosome made of two

separate subunits
y Bacteria and Archaea:

30S + 50S subunits = 70S total

y y

30S : 16S rRNA plus 21 proteins 50S: 5S rRNA, 23S rRNA, & 34 proteins

y
y y

Eukarya: 40S + 60 S subunit = 80S total

40S: 18S rRNA plus 33 proteins 60S: 5S rRNA, 28S rRNA,5.8SrRNA, &
48 proteins

Endospores
y Develop within vegetative cells during unfavorable

growth conditions = sporulation

y For surviving environmental extremes

y Heat, drying, radiation, pH extremes y Common isolates of soil and rock environments, aquatic

sediments, mud, deserts

y Most species with spores are Gram+

y Clostridium
y

Medical importance: tetanus, botulism, gangrene

y Bacillus
y

Medical importance: anthrax, food poisoning

Endospores (cont.)
y Spores have a VERY low water content
y Metabolically inactive

y Sterilization must eliminate spores

y Some can survive an hour s boiling

y Recovered from both ancient mud (>7500 years

old) and fossilized amber

viable cells

y Found that spores could still germinate to produce

Endospores (cont.)
y Contain dipicolinic acid (15%)
y Previously thought responsible for heat-resistance y Dipicolinic acid mutants have been isolated and still

form resistant spores

y Calcium-dipicolinate thought to help stabilize DNA

y Contain some DNA repair enzymes & DNA

binding proteins

Endospores (cont.)
y Sporulation process: seven stages
I: DNA condenses & forespore is produced II: Cell membrane folds inward
= form a septum between forespore & rest of cell

III: Forespore engulfed by rest of former cell

= double layer membrane = protection

IV: Cortex forms around forespore V: Spore coat synthesis begins VI: Spore coat is complete
= true endospore; resistance!

VII: Lysis
= endospore released/ free from vegetative cell

Endospores (cont.)
y
y y

Dormant spores transform to vegetative cells in three stages

Activation: usually by heat Germination: spore swells and spore coat ruptures; loses resistance Outgrowth: spore protoplast synthesizes new components and returns to vegetative cell state

Endospore Images

Bacteria & Archaea: Cell Envelope

Prokaryotic Cell Organization

y Internal Structures
y Cytoplasm y Cytoskeletons y Intracytoplasmic Membranes y Nucleoid & Plasmids y Ribosomes y Inclusions y Endospores

y Cell Envelope
y Cytoplasmic membrane y Periplasmic Space y Cell Wall
y

Exception: Mycoplasma (bacterium) and some Archaea

y Glycocalyx y S-layers

y External Structures
y Flagella y Fimbriae and Pili

Cytoplasmic Membrane Bacteria

y y
y

Boundary between a cell and environment Dynamic interface

Changes with temperature, age, environment

y
y

Flexible, phospholipid bilayer sheet

Hydrophobic tails & hydrophilic heads

y
y

Often contain hopanoids to stabilize structure

Steroid-like, analogous to cholesterol & ergosterol in Eukarya

Cytoplasmic Membrane Bacteria

y

Membrane Proteins:
y

Peripheral:
y

Loosely connected to the cytoplasmic membrane Hydrophilic nature

Integral:
y

Amphipathic- have both hydrophilic and hydrophobic portions Extend from within the cytoplasm into the exterior environment

Cytoplasmic Membrane Bacteria

Cytoplasmic Membrane Bacteria

y
y

Functions: analogous to Eukarya

Regulates transport of sugars, salts, other metabolites into cell & export of proteins Acts as a site for enzyme interactions Houses components of electron transport chain

y y

Cell Wall - Bacteria

y
y

Withstands osmotic pressure to prevent cell from lysis and confers cell shape
Approx. 75 psi- constantly in aqueous environment with low [solute]

y
y

About 100 different types known but two major groups are Gram + & Gram
Both contain peptidoglycan (murein):
y y

Gram + have thick layer = primary structural component Gram have thin layer = secondary structural component

Gram + vs. Gram - Cell Walls

PM = Plasma membrane, OM = Outer membrane, W = Gram + wall, M = Peptidoglycan (murein), P = Periplasmic space

Cell Wall Bacteria (cont.)

y

Peptidoglycan backbone is composed of alternating 2 amino sugars

y y

N-acetylmuramic acid (NAM) N-acetylglucosamine (NAG)

Analogy : a chain of metal links

Cell Wall Bacteria (cont.)

y

Peptidoglycan strength & rigidity increased via cross-linked tetrapeptide chains between layers of the NAM-NAG backbone Analogy: Chain link fence

Tetrapeptide chain

*The 5 Gly bridge is most typical. However, variation of this linkage does occur widely

Cell Wall Bacteria (cont.)

y Peptidoglycan differences
y Gram s: (top) y Diaminopimelic acid (DAP) links to D-alanine directly y DAP is unique to Bacteria y Gram + s: (bottom) y Interpeptide bridges (5 glycines) form between D-alanine and Llysine between opposing tetrapeptide chains
y

Remember, interbridges can vary greatly depending on species

Gram + Cell Walls

y Very thick peptidoglycan & thin

periplasmic space
y Teichoic acids aid stability
y Unique to Gram + bacteria y Polymers of ribitol-PO4 or glycerol-

PO4
y Connect peptidoglycan layers
y
y

via covalent bonds with NAM

Analogy: Fenceposts

y Lipoteichoic acids connect

peptidoglycan to cytoplasmic membrane lipids

Gram + Cell Walls

What s wrong here?

Gram - Cell Walls

y Peptidoglycan is much thinner than Gram + s y Major cell wall component = outer membrane
y Outermost edge consists = lipopolysaccharides (LPS)

y Braun s lipoproteins anchor outer membrane to

peptidoglycan layer

y Contains porins: provide channels for smaller

molecules to pass through

y Larger periplasmic space than Gram + s

y Between outer membrane & cytoplasmic membrane y Contains thin peptidoglycan layer

no fenceposts here!

Gram - Cell Walls

What s wrong here?

Gram - Cell Walls: LPS

y Lipid portion (Lipid A) y Anchors molecule to outer membrane y Fatty acids attached to a disaccharide y Causes endotoxic shock y Sugar portion y Core polysaccharide y O-polysaccharide varies within strains

Preventing Cell Growth & Causing Cell Lysis

y Preventing synthesis of peptidoglycan is an effective

way to control new microbial growth

cells via binary fission

y No new peptidoglycan = no new cell wall = no new

y If peptidoglycan strength is compromised, cells cannot

prevent osmotic pressure from bursting cells open

existing cells

y Existing cells are lysed, preventing microbial growth of

Antibiotics & Peptidoglycan

y Penicillin

prevents new cell wall formation

y Binds to transpeptidases to prevent crosslinking of

glycan chains
y More effective on Gram + s than Gram
y

Lesser peptidoglycan in Gram cell walls

y

Peptidoglycan compromised but outer membrane layer still provides major structural support

Porins in outer membrane of Gram s act to selectively exclude penicillin and other chemicals

Lysozyme & Peptidoglycan

y Lysozyme weakens existing peptidoglycan
y Natural antimicrobial found in tears and saliva y Breaks the glycosidic bonds between NAM & NAG y Decreases rigidity of the cell wall as peptidoglycan

backbone is cut

y Forms protoplast (Gram +) or a spheroplast (Gram -) y More effective on Gram + s than Gram
y

Spheroplasts still have outer membrane for osmotic stability

Cell Wall & Gram Stain Chemistry

y LPS is dissolved by alcohol decolorization in Gram negatives, leaving peptidoglycan layer intact y Alcohol dehydrates the peptidoglycan- makes pores smaller
y Depth of peptidoglycan on Gram + bacteria acts as extreme

barrier so purple dye complex stays inside

y Thinness of peptidoglycan in Gram

bacteria allows easier

loss of dye from within cells

y Differences in the cross-linking of glycan chains may cause different pore sizes in the bacterial cell wall
y Less stereochemistry in Gram

bacteria may allow crystals to

be washed free

Glycocalyx
y Exopolysaccharide (EPS) in most cases y Not made by all bacteria y Synthesis is usually regulated y Serves as a energy storage molecule and/or protection y Capsules & slime layers are specific types of a glycocalyx

Glycocalyx
Slime layer Capsule

Loose & soluble Protects against drying Involved in biofilm formation

Thick & tightly bound Antiphagocytic Protect against dessication Aids in attachment to surfaces Most often polysaccharide, but
can be made of protein

S-Layers
y Found on some Gram + and Gram - bacteria; common in Archaea
y In Gram

s, adheres to outer membrane with the peptidoglycan

y In Gram + s, directly associated

y In Archaea, may be only cell

wall component present

S-Layers
y Are regularly structured layers of

protein or glycoprotein patterned like floor tiles

y Protects against:
y pH fluctuation y Osmotic stress y Hydrolytic enzymes & predatory

bacteria:
y

Vampirococcus, Bdellovibrio, and Daptobacter (top to bottom)

http://www.globalcommunity.org/wtt/ walk_photos/print_pages/2800.htm

Bacteria & Archaea: External Cell Structures

Prokaryotic Cell Organization

y Internal Structures
y Cytoplasm y Cytoskeletons y Intracytoplasmic Membranes y Nucleoid & Plasmids y Ribosomes y Inclusions y Endospores

y Cell Envelope
y Cytoplasmic membrane y Periplasmic Space y Cell Wall
y

Exception: Mycoplasma (bacterium) and some Archaea

y Glycocalyx y S-layers

y External Structures
y Flagella y Fimbriae and Pili

Bacterial Flagella
y Confer swimming motility in liquids y E. coli = 270 rps y Vibrio alginolyticus = 1100 rps

y May also aid in attachment and virulence

y Slender, rigid, threadlike propellers
y

20 nm diameter x 15-20 um length

y Complex protein structure made of flagellin

y

Different than flagella found in Eukarya

Bacterial Flagella (cont.)

y Axial filaments are

specialized flagella
y Winds around cell within

the periplasmic space

y Mechanism not

completely understood
y Found in spirochetes:
y

Treponema pallidum (syphillus) Borrelia burgdorferi (Lyme disease)

Bacterial Flagella Structure

y Filament (thread)
y y y

Hollow, rigid, helical cylinder Growth occurs at distal end Subunits move down hollow core; assemble spontaneously in a helical fashion

y Hook
y y

Anchored to cell wall Filament extends from this structure into the environment

y Basal Body
y

Motor for rotation

y

Some parts spin (rotor) and some parts remain stationary (stator)

Embedded in plasma membrane

Bacterial Flagellar Structure

Bacterial Flagellar Movement

y
y y

Bacteria swim through the rotation of flagella in a run and tumble pattern
Counterclockwise rotation produces a run Bacteria stops and switches to clockwise rotation to produce a tumble and direction change

y
y

Movement not driven by ATP synthesis like for eukaryotic flagellar rotation
Proton motive force (PMF) via Na+ or H+ gradients are thought to provide energy

Flagella Motors
y Rotor
y Turns in a cylindrical ring of

electromagnets
y Made of MS and C rings

y Stator
y Elecromagnetic ring made

of MotA and MotB

y Forms a fixed channel in

plasma membrane
y MotB anchors MotA to

L & P Rings
found in outer membranes only act as a bearing for the flagellum

peptidoglycan

Fimbriae & Pili

y y
y

Formerly interchangeable terms now more discretely separated based on function Short hairlike external appendages
Thinner than flagella, not usually as long

Functions:
y

Fimbriae attach bacteria to solid surfaces

y

Dental plaques

Pilus (pili) involved in bacterial conjugation or transport of molecules in/out of cells

y

Allow transfer of plasmids from one bacterial cell to another

Pili and Fimbriae

with fimbrae fimbrae

Pili and Fimbriae