Bacteria and Archaea

Naming microorganisms

• Uses a binomial system: Genus species

• Genus is always capitalized, species is always lowercased

• both names should be italicized in print or underlined when written

• the genus name can be shortened if it has already been stated

Bacterial are all alive

• bacteria cells are capable of carrying out all necessary life activities

• - Reproduction, metabolism, nutrient processing

• Bacteria can also act as a group

• - biofilms, quoroms sensing

Bacteria arrangement and sizing

• variety in shape and size and colonial arrangement

• Average size: 1 micrometer

• Coccus: round or circular

• Rod/bacillus

• Vibrio: bent rod

• Spirillum

• Spirochete

• Branching filaments

• pleomorphism - variation in size and shape among cells of a single species

- Arrangements and groupings of cocci

• Diplo: pairs

• Tetrads: Groups of four

• Sarcina: cubical packet of 8, 16, or more

• Staphylococci: irregular clusters

• Streptococci: chains of a few to hundreds of cells

- Arrangements and groupings of bacilli

• Diplobaccilli: pairs of cells with their ends attached

• Streptobaccilli: chains of cells

• Palisades: cells of a chain remain partially attached and fold back, creating a side by side row of cells

- Spirilla are occassionally found in short chains

- Spriochetes rarely remain attached after cell division

Structure of the Cell Wall

Peptidoglycan

• found in cell walls of most bacteria

• Glycan chains cross-linked with short peptides

• provides a strong but flexible support framework

• offers protection from environment

Lipopolysaccharide

• found in Gram negative bacteria

• outer leaflet of the outer membrane

• highly immunogenic

• in bloodstream leads to septic shock

The Gram Stain

1. bacteria fixed to slide

2. crystal-violet stain attracted to peptidoglycan, both Gram + and Gram - look purple

3. Add iodine to complex w/ Crystal Violet, makes harder to wash out of peptidoglycan

4. Decolorize with alcohol, Thin peptidoglycan layers in Gram- cell walls loose all Crystal Violet. Gram+ walls thick enough that some, but not all, Crystal Violet lost

5. Counterstain both cell types with Safranin. Safranin lighter than Crystal Violet; will only be visible on unstained cells- only Gram- cells show pink/red coloration

​Non-typical Cell Walls

Mycoplasmas

• naturally lack a cell wall

• membrane is stabilized by sterols and resistant to lysis

• Pleomorphic shape, range from 0.1 – 0.5 μm, ranging from filamentous to coccus or doughnut shaped​

• Example: Mycoplasma pneumoniae​

Mycolic Acid or cord factor

• Found in the cell walls of Mycobacterium and Nocardia​

• Very long-chain fatty acid

• Contributes to pathogenicity of these organisms

• Acid-fast stain used to diagnose tuberculosis and leprosy

Acid-fast stain

• Gram stain technique does not work on acid-fast organisms

  • Mycolic acids are impervious to crystal violet (waxy coating)​

  • Mycolic acid does not bind to dye​

• Acid-fast stain uses carbol fuchsin (ring structure can slip through mycolic acids) and phenol (fat/non-polar soluble) to help carbol fuchsin get in

  • ​Carbol fuchsin is insoluble in PG layer​

Functions of the Cell Membrane

Selective permeability:

• water and small uncharged molecules diffuse freely

• Special carrier mechanisms exist for passage of most molecule

  • ion pumps

  • sugar transporters

• Discharge of metabolic products into the extracellular environment​

  • example: collegenase secretion

Membrane Transport - a comparison

Prokaryotic Transport:

• Substrate pumps

  • sodium-potassium pump

  • glucose pump

• Both are membrane spanning, control at level of transcription – no signaling control​

Eukaryotic Transport

• substrate pumps

  • sodium-potassium pump, glucose pump

• endocytosis initiated by specific receptors

  • Clathrin coated pits

  • Pinocytosis

• Similar pumps as prokaryotes, plus higher order transport that requires extensive intracellular signaling​

Functions of the Cell Membrane

Porin Proteins:

• completely span the outer membrane

• Only allow relatively small molecules to penetrate

• size can be altered to block the entrance from harmful chemicals

  • Act as a defense against antibiotics

Capsule Stain

• capsule does not absorb stain

• capsule stain uses two different kinds of stain

  • Regular simple stain

    • Safranin, which stains cell

    • Negative stain, repelled by cell

      • Congo red, which stains background

    • Capsule is the unstained part

What is a Biofilm?

• Group of bacteria that enhance each others’ survival​

  • Often multiple bacterial species​

  • Bacteria cooperate together​

• Bacteria secrete a slime ​

• Can only be disrupted with detergents or mechanical disruption​

• Biofilms can be one species or a mixture of many

Making a Biofilm

1. Attachment: Bacteria attach to a surface such as a rock, pipe, medical devise such as a catheter, or even human tissue using flagella, fimbrae, and/or pili.​

2. Bacteria begin secreting slime layer

3. Expansion/Maturation: Other bacteria join the growing biofilm, contribute to the slime layer and welfare of other bacteria within biofilm​

4. Dispersal: Once the biofilm grows large enough, small chunks can break off and colonize a new surface​

*The slime layer can protect against harmful substances like antibiotics

Exotoxins

• target a specific structure or function in host cell

• secreted under specific conditions

Endotoxins

• part of Gram - membrane

• Do not target host cells

• Recognized by immune cells

Gram + Extoxins:

• Streptolysin O

• Staphylococcal enterotoxin

• Tetanus toxin

• Botulinum toxin

• Anthrax toxins

Gram - Exotoxins:

• Cholera toxins

• Shiga toxins

External Structures:

• Three major groups of appendages:

  • flagella and axial filaments: provide movement

  • fimbriae and pili: provide attachment points or channels

  • Secretion systems

    • Transport of DNA and proteins

Flagellar Structure

• Flagella can be present in both Gram + and - bacteria

• Motors are anchored to the cytoplasmic membrane

• Gram - bacteria have more rings in the outer membrane

• Both bacterial classes have a hook structure and a filament outside the cell

Flagellar Arrangement

• Polar: Flagellar attached to one or both ends of the cell

Flagellar Function

• Chemotaxis: movement in response to chemical signals

  • positive chemotaxis

  • negative chemotaxis

Periplasmic Flagella

Axial Filament:

• two or more long coiled threads found in spirochetes

• Internal flagellum enclosed between the cell wall and cell membrane​

• Impart a twisting or flexing motion to the cell- think corkscrew​

• Not same as types of flagella discussed in previous slides​

​Cilia and Flagella in Eukaryotes

• Eukaryotic (vs. bacterial) flagella:

  • 10x thicker

  • Structurally more complex

  • Covered by an extension of the cell membrane

  • Long sheathed, cylinder containing regularly spaced hollow microtubules

    • 9+2 arrangement

• Cilia:

  • Similar in overall structure to flagella

  • shorter and more numerous

  • Found only in a single group of protozoa and certain animal cells

Bacterial Secretion Systems

• Used to actively transport cytsolic contents outside the cell, or into a target cell

Using secretion to interact with other cells

• Type III Secretion System

• structurally similar to a flagellar apparatus

• Translocates protein “affectors” into a host target

  • Plants, mammals, insects

• Effectors reprogram target cells

  • turn off immune functions

  • induce cells to perform things they don’t normally do

  • Common virulence factor in Gram - pathogens

  • E. coli, salmonella

• Type IV Secretion Systems (T4SS)

• Can translocate proteins or DNA into a host cell

• Used by pathogens to control target cells

• Helicobacter pylori, Brucella abortis, Legionella pneumophila, Bartonella​

• Used by plant pathogens ​

  T6S bolt is tipped and filled with effectors

• ​Shaft can be filled with effectors​

• VgrG warhead is decorated with effectors​

• Bolt complex falls apart upon impacting target​

• Released effectors then act upon molecular targets​

• Usually PG layer, cell membranes​

  Appendages for ​
  Attachment and Mating

• ​Attachment can enhance pathogenicity in some bacteria.​

  • Pilus (plural: pili)​

  • Fimbria (plural: fimbriae)​

• Both provide adhesion but (usually) not locomotion

  Fimbriae

• ​Small, bristle-like fibers sprouting off the surface of certain species of bacteria​

• Composition varies, but most contain protein​

• Have the inherent tendency to stick to each other and to surfaces​

• Contribute to the initiation of biofilm formation​

  ​Pili

• Also known as a sex pilus​

• Long, rigid tubular structure made of pilin protein​

• Can be lengthened or shortened​

• Only found in gram-negative bacteria​

• Used in conjugation, the transfer of DNA from one cell to another​

• Can be used for crawling locomotion

  Genome

• Chromosome​

  • Encodes essential functions for growth​

  • Usually 1, but occasionally more​

  • Circular​

  • In cytoplasm ​

  • No nucleus​

  • Nucleoid​

• Plasmids​

• None, some, or many

• One copy to thousands per cell

  What is a Plasmid?

• ​Non-essential pieces of DNA​

• Separate from chromosome​

• Double stranded, usually circular​

• Duplicated and passed onto offspring during replication​

• Confer protective traits​

• Important in genetic engineering​

  Central Dogma

• ​Central Dogma states that DNA is transcribed to RNA and RNA is translated to protein​

• DNA is the master blueprint for all aspects of an organism​

• Messenger RNA (mRNA) carries the message of what protein is going to be made​

• Ribosomes read the mRNA message and manufacture the protein which goes off to perform a function​

  Ribosomes

• Made of RNA and protein.​

• Dispersed throughout the cytoplasm, often found in chains.​

• Svedberg (S) units:​

  • Measurement of the relative size of cell parts through sedimentation during centrifugation​

  • Bacterial ribosomes:​

    • 70S = 50S larger subunit+ 30S smaller subunit​

  • Eukaryotic ribosomes:​

    • 80S = 60S larger subunit+ 40S smaller subunit​

• Often attached to the ER​

• Ribosomal rRNA often sequenced in order to categorize unknown bacteria

  DNA to RNA to proteins

• ​​Bacterial ribosomes have direct access to the genome, they can begin translating mRNA to protein as soon as it is made.​

  Bacterial Endospores

• ​Endospores:​

  • Withstand hostile conditions and facilitate survival​

  • Spore forming bacteria have a two-phase life cycle:​

    • Vegetative cell: metabolically active​

    • Endospore: inert, resting condition, metabolically inactive​

• Sporulation: act of spore formation, induced by unfavorable environmental conditions

  The Archaea

• Distinct from other cell types:​

  • Prokaryotic​

  • Certain genetic sequences are only found in their rRNA​

  • Ribosome structure similar to eukaryotes​

  • One to a few circular chromosomes​

  • Unique and chemically distinct cell walls​

• The most primitive of all life forms.​

  • Live in habitats that are similar to ancient extreme environments​

    • heat, salt, pH, pressure​

• Sulfur reducers and methane producers

• ​Methanogens:​

  • Convert CO2 and H2 into methane gas (CH4)​

  • Common inhabitants of anaerobic swamp mud, bottom sediments of lakes and oceans, and the digestive systems of animals​

  • Gas produced in swamps may become a source of fuel​

  • May contribute to greenhouse gases and global warming​

• Methane has ~25x the greenhouse capacity of CO2

• Extreme halophiles:​

  • Require salt to grow​

  • Can multiply in 36% NaCl that would destroy most cells​

  • Exist in inland seas, salt lakes, salt mines, and in salted fish​

• Use a red pigment to synthesize ATP in the presence of light​

• ​Psychrophiles: adapted to grow at very low temperatures.​

• Hyperthermophiles:​

  • Flourish at temperatures between 80° and 113°C and cannot grow below 50°C​

  • Live in volcanic waters and soils and submarine vents​

  • Often salt and acid tolerant as well as heat tolerant​​​

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