Lecture 1: Microbial World and Procaryotic Cell Anatomy

Microbes/Microorganisms?

• Too small to see with the “naked” eye• Beneficial

– Ecological: Recycle nutrients• Bioremediation

– Industrial: Food, chemicals, drugs• Fermented Foods• Antibiotics• Ethanol and other chemicals• Enzymes – Cellulase, Peroxidase

• Destructive/Pathogenic– FEW

Nomenclature

• Scientific Nomenclature– System devised by Linnaeus

• Genus and species– Both italicized or underlined– Genus name Upper-case; species lower-case

– Name describes the organism• Ex. Staphylococcus aureus

– Staphylococcus: cluster of spheres– aureus: golden aura of colonies

– Name honors the scientist• Ex. Escherichia coli

– Escherich: honors the discoverer, Theodor Escherich– coli- describes the habitat – the colon or the small intestine

Three Domains of Life– Archaea

• prokaryotes• Primarily extremophiles• Not disease-causing

– Bacteria• prokaryotes

– Eukarya• Nucleated organisms• Uni- or multi-cellular• Fungi• Protista• Plants• Animals

Classification of Microbes

• Archaea• Bacteria• Fungi• Algae• Protozoa• Multicellular Animal Parasites• Viruses

Classification of Microbes

BacteriaSporangia

Prey

Pseudopods

CD4+ T cell HIVs

Archaea

• Prokaryotes• No peptidoglycan in cell wall• Habitat

– Extreme environments• Methanogens (methane)• Halophiles (salt)• Thermophiles (heat)

• Not known to cause disease in humans

Bacteria

• Prokaryotes• Cell structure

– Bacillus, Coccus, Spiral• Cell wall

– Peptidoglycan• Cell Division

– Binary Fission• Metabolism: Energy source

– Inorganic/ organic chemicals– Photosynthesis

Fungi

• Eukaryotes• Chitin cell walls• Energy Source:

– Organic matter • Multicellular

– Molds and mushrooms • Unicellular

– Yeasts

Protozoa• Eukaryotes• Unicellular• Motile

– Pseudopodia– Cilia– Flagella

• Shape– Variety of shapes

• Habitat– free entities or parasites

• Energy source– organic compounds

Algae

• Eukaryotes• Cellulose cell walls• Energy source

– Photosynthesis• Produce molecular oxygen and organic

compounds

Viruses

• Neither eukaryote or prokaryote• Acellular• Obligate Intracellular Parasites

– Only replicate when present in living host cell• Genetic Material

– Either DNA or RNA• Structure

– Nucleocapsid• Nucleic acid core• Protein coat surrounds core

– Lipid Envelope• Not always present

Multicellular Animal Parasites

• Eukaryotes• Multicellular• Parasitic flatworms and roundworms.

Conditions Results

Nutrient broth placed in flask, heated, NOT sealed

Microbial growth

Nutrient broth placed in flask, heated, then sealed

No microbial growth

Louis Pasteur• 1861: Louis Pasteur demonstrated that

microorganisms are present in the air

Important Events in Microbiology

• Germ Theory of Disease– Germs present in the air cause disease, spoil food

• Louis Pasteur’s work

– Cleaning with disinfectants decreases infection• Joseph Lister’s work

• Vaccination– Jenner – Pasteur (small pox)

• Discovery of Antibiotics and Synthetic Drugs– Fleming – Penicillin– Sulfa drugs

The Birth of Modern Chemotherapy

• Chemotherapy– Treatment with chemicals

• Treatment of infections– Antibiotics

• Naturally synthesized• bacteria and fungi

– Synthetic Drugs• Artificially synthesized• First Drugs: Sulfa drugs

A Fortunate Accident—Antibiotics

• 1928: Alexander Fleming discovered the first antibiotic

• Fleming observed that Penicillium fungus made an antibiotic, penicillin, that killed S. aureus

• 1940s: Penicillin was tested clinically and mass produced

Normalbacterialcolony

Area of inhibition of bacterial growth

Penicilliumcolony

Figure 1.5 The discovery of penicillin.

Microbes in Human Welfare

• Microbial ecology: – Bacteria recycle inorganic material

• carbon, sulfur, phosphorus • Used by plants and animals

– Turns N to Nitrates and Nitrites so plants can use it

• Bioremediation: – Bacteria degrade organic matter

• Sewage treatment• Detoxify pollutants

– Oil and mercury spills

• Biotechnology

Biotechnology

• Recombinant DNA technology – Taking parts of DNA and recombining it back into the DNA (E. coli produces purple because

it was engineered then recombined into the DNA to make it happen)

– Engineer viruses, bacteria and fungi• Produce proteins

– Vaccines, enzymes, hormones

– Gene therapy• Replace missing or defective genes in human cells

– Hemophilia– Blindness

– Agriculture• Genetically modified bacteria

– Protect crops from insects and freezing

Normal Microbiota/ Normal Flora

• Nomenclature– Old: Normal Flora

• Because bacteria initially classified as plants

– New: Normal microbiota• Microbes present on or in the human body

– prevent growth of pathogens– produce growth factors, such as folic acid and

vitamin K

Biofilms Complex aggregation of microbes Microbes attach to solid surfaces and grow into

masses grow on rocks, pipes, teeth, and medical implants Difficult to treat with antibiotics

Infectious Diseases

When a pathogen overcomes the host’s resistance, disease results

Emerging infectious diseases (EIDs): New diseases and diseases increasing in incidence

1. Evolutionary2. Increased human exposure in undergoing

ecological changes3. Antimicrobial resistance

MRSA

• Methicillin-resistant Staphylococcus aureus• 1950s: Penicillin resistance developed• 1980s: Methicillin resistance• 1990s: MRSA resistance to vancomycin

reported– VISA: Vancomycin-intermediate-resistant S. aureus – VRSA: Vancomycin-resistant S. aureus

Figure 25.12

Escherichia coli O157:H7• Toxin-producing

strain of E. coli• First seen in 1982• Leading cause of

diarrhea worldwide

Figure 23.21

Ebola Hemorrhagic Fever

• Ebola virus• Causes fever, hemorrhaging, and blood

clotting• First identified near Ebola River, Congo• Outbreaks every few years

Prokaryotic Anatomy

Average size: 0.2–1.0 µm in diameter 2–8 µm in length (10^-6 meters)

Most bacteria are monomorphic (single shape)

What can alter shape? Cell wall (membrane or wall)

Prokaryotic Cells: Shapes

Figure 4.2b-c Bacilli.

Streptobacilli

Diplobacilli

Figure 4.1ad Arrangements of cocci.

Plane of division

Diplococci

Streptococci

Staphylococci

Arrangements

• Pairs: diplococci, diplobacilli

• Clusters: staphylococci or staphylobacilli• More than one plane of division

• Chains: streptococci, streptobacilli• One plane of division• Grows in strands

Vibrio

Spirochete

Spirillum

Figure 4.4 Spiral bacteria.

Star-shaped bacteria

Figure 4.5a Star-shaped and rectangular prokaryotes.

Rectangular bacteria

Figure 4.5b Star-shaped and rectangular prokaryotes.

Figure 4.6 The Structure of a Prokaryotic Cell.

Capsule

Cell wall

Plasmamembrane

Fimbriae

Cytoplasm

Pilus

70S Ribosomes

Plasma membrane

Inclusions

Nucleoid containing DNA

Plasmid

Flagella

CapsuleCell wall

.

Not all bacteria have all the structures shown; only structures labeled in red are found in all bacteria.

Although the nucleoid appears split in the photomicrograph, the thinness of the “slice” does not convey the object’s depth.

© 2013 Pearson Education, Inc.

Bacterial Cell: Specific Roles

• Capsule: bacterial virulence• Cell Wall or Flagella: bacterial identification• Cell Wall: target for antimicrobial agents• Plasmids: encode genes for production of

toxins– Circular DNA that is independent to all the rest of

the chromosomal DNA. They are not needed for the survival unless an it contains genetics that help it in it’s outside living conditions

Glycocalyx

Outside cell wall Usually sticky, “sugar coating” (glue) Capsule: neatly organized Slime layer: unorganized and loose (EPS) Extracellular polysaccharide (glycocalyx in

general) allows cell to attach, chemical composition varies by species

Capsules (negative stain [will not stain]) prevent phagocytosis

Example: Streptococcus pneumoniae

Figure 24.12 Streptococcus pneumoniae, the cause of pneumococcal pneumonia.

Flagella• Motility

– Propel bacteria (word to move is taxis [move to light=phototaxis])

• Long filamentous appendages– Three basic parts

• Filament (outermost region): globular protein• Hook: different protein• Basal body

• Anchored to cell wall and membrane by the basal body

• Distribution– No Flagella: ATRICHOUS– Evenly distributed: PERITRICHOUS– Polar: at one or both poles/ends

Figure 4.7 Arrangements of bacterial flagella.

Peritrichous Monotrichous and polar

Lophotrichous and polar Amphitrichous and polar

Basal body

Peptidoglycan

Hook

Cell wall

Gram-positive

Filament

Flagellum

Plasmamembrane

Cytoplasm

Parts and attachment of a flagellum of a gram-positive bacterium

Figure 4.8b The structure of a prokaryotic flagellum.

Plasmamembrane

Cell wallBasal body

Gram-negative

Peptidoglycan

Outermembrane

Hook

Filament

Cytoplasm

Flagellum

Parts and attachment of a flagellum of a gram-negative bacterium

Figure 4.8a The structure of a prokaryotic flagellum.

Motility

• The ability of an organism to move by itself toward a favorable environment (taxis)

• Chemotaxis signals: oxygen, ribose and galactose receptors

• Flagella proteins are H antigens (e.g., E. coli O157:H7)

Axial Filaments

• Also called endoflagella• In spirochetes• Anchored at one end of a cell• Rotation causes cell to move• Treponema pallidum: syphilis

Figure 4.10a Axial filaments.

A photomicrograph of the spirochete Leptospira, showing an axial filament

• Thinner than flagellum• Attachment and DNA transfer • Fimbriae allow attachment: involved in

forming biofilms• What happens if fimbriae are absent (genetic

mutation)?– Becomes less virilant, disallows attachment

Fimbriae and Pili

Figure 4.11 Fimbriae.

Fimbriae

Fimbriae and Pili

• Pili – Usually longer than fimbriae – Gliding motility– Twitching motility (like a worm)

The Cell Wall

• Major function: prevents osmotic lysis• Maintains shape and point of anchorage for

basal bodies• Made of peptidoglycan (in bacteria)• Gram positive and Gram negative

Peptidoglycan

• Major component of cell wall in bacteria• Polymer of sugars and amino acids

– Form a mesh-like layer – Each strand two sugars linked alternatively

• N-acetylglucosamine• N-acetylmuramic acid

– peptide chain of three to five amino acids. – peptide chain of one strand cross-linked to the peptide chain

of another strand forming the 3D mesh-like layer.

L-Ala, d-Glu-NH2 etc. are amino acids

This is the cell wall, the more ladders,the thicker the wall is

• Thick peptidoglycan• Teichoic acids

– makes the wall like crosshairs + where – is peptidoglycan and | is teichoic acids

Gram-PositiveCell Wall

Thin peptidoglycan Outer membrane

Gram-NegativeCell Wall

Plasmamembrane

Cell wallLipoteichoicacid

PeptidoglycanWall teichoic acid

Protein

Gram-negative cell wall

Lipopolysaccharide

Outer membrane

PeptidoglycanPlasmamembrane

Cell wall

Lipid A Porin protein

Phospholipid

Lipoprotein

Periplasm Protein

Lipid A

Core polysaccharide

O polysaccharide

Parts of the LPS

Core polysaccharide

O polysaccharide

Gram-positive cell wall

Figure 4.13b-c Bacterial cell walls.

• Many layers (thick) of peptidoglycan • Teichoic acids

– Alcohol and phosphate; negative charge • May regulate movement of cations: cell

growth, preventing extensive wall break down and possible cell lysis

• Polysaccharides provide antigenic variation = identification

Gram-Positive Cell Walls

• Thin layer of peptidoglycan and an outer membrane

• Lipopolysaccharides (LPS) (outer)• LPS: evade phagocytosis and actions of

immunity, provide barrier to certain antibiotics and enzymes

• Porins: proteins that form channels, selective permeability

Gram-Negative Cell Wall

Gram-Negative Outer Membrane

LPS Composition: Lipid A – functions as an endotoxin ,

responsible for symptoms associated with gram - infections

Core Polysaccharide – attached to Lipid A, provides stability

O Polysaccharide – functions as an antigen, useful in identification

The Gram Stain Mechanism

• Crystal violet-iodine crystals form in cell• Gram-positive: Purple

– Alcohol dehydrates peptidoglycan– CV-I crystals do not leave

• Gram-negative: Red– Alcohol dissolves outer membrane and leaves

holes in peptidoglycan– CV-I washes out

• 2-ring basal body– In the membrane

• Thick Peptidoglycan• Purple Gram Stain• Disrupted by

lysozyme (breaks the bonds between NAM’s and NAG’s

• Penicillin sensitive• Exotoxins

Gram-PositiveCell Wall

4-ring basal body 1 outer 1 wall 2 inner

Thin Peptidoglycan Red Gram Stain Outer Membrane Tetracycline sensitive Exo and Endotoxins

Gram-NegativeCell Wall

Damage to the Cell Wall

• Exposure to digestive enzyme lysozyme, destroys peptidoglycan (gram positive)

• Penicillin inhibits peptide bridges in peptidoglycan (prevents formation of functioning cell wall)

The Plasma Membrane

• Contains enzymes for metabolic reactions • Most lack sterols, Mycoplasma is exception• Disruption: membrane’s phospholipids =

antibiotics: polymyxins

Cytoplasm

• Contains nucleoid, ribosomes and inclusions• 80% water and contains primarily proteins

(enzymes), carbs, lipids, inorganic ions and many lower molecular weight compounds

The Nucleoid

• Bacterial chromosome: cell’s genetic information• Not surround by a nuclear envelope • Plasmids: not connected to main bacterial

chromosome but have very important functionsAntibiotic resistanceTolerance to toxic metalsProduction of toxins Can be transferred from one bacterium to another

The Prokaryotic Ribosome

Protein synthesis Consist of two subunits: protein and type of RNA (rRNA) Prokaryotic: 70S ribosomes

50S(subunit = protein plus two molecules of rRNA) + 30S subunits (subunit = protein plus one molecule rRNA)

Antibiotics: inhibit protein synthesis. Examples: gentamicin and streptomycin attach to 30S subunit and interfere with protein synthesis

Erythromycin and chloramphenicol interfere with 50SWhy can these antibiotic drugs work without affecting host cells? Host cells are made up of 80S ribosomes

Inclusions

• Located within cytoplasm• Reserve deposits: environment is deficient • Some are common to a wide variety of

bacteria• May serve as a basis for identification • Example: C. diphtheriae

Endospores

• Resting cells: when essential nutrients are depleted

• Resistant to desiccation, heat, chemicals• Bacillus, Clostridium; Gram positive • Sporulation: endospore formation• Germination: return to vegetative state

– Germination <-> Sporulation