1. Lecture 1: Microbial World and
Procaryotic Cell Anatomy

2. 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

3. 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

4. Three Domains of Life
– Archaea
• prokaryotes
• Primarily extremophiles
• Not disease-causing
– Bacteria
• prokaryotes
– Eukarya
• Nucleated organisms
• Uni- or multi-cellular
• Fungi
• Protista
• Plants
• Animals

5. Classification of Microbes
• Archaea
• Bacteria
• Fungi
• Algae
• Protozoa
• Multicellular Animal Parasites
• Viruses

6. Classification of Microbes
Bacteria
Sporangia
Prey
Pseudopods
CD4+ T cell HIVs

7. Archaea
• Prokaryotes
• No peptidoglycan in cell wall
• Habitat
– Extreme environments
• Methanogens (methane)
• Halophiles (salt)
• Thermophiles (heat)
• Not known to cause disease in humans

8. Bacteria
• Prokaryotes
• Cell structure
– Bacillus, Coccus, Spiral
• Cell wall
– Peptidoglycan
• Cell Division
– Binary Fission
• Metabolism: Energy source
– Inorganic/ organic chemicals
– Photosynthesis

9. Fungi
• Eukaryotes
• Chitin cell walls
• Energy Source:
– Organic matter
• Multicellular
– Molds and mushrooms
• Unicellular
– Yeasts

10. Protozoa
• Eukaryotes
• Unicellular
• Motile
– Pseudopodia
– Cilia
– Flagella
• Shape
– Variety of shapes
• Habitat
– free entities or parasites
• Energy source
– organic compounds

11. Algae
• Eukaryotes
• Cellulose cell walls
• Energy source
– Photosynthesis
• Produce molecular oxygen and organic
compounds

12. 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

13. Multicellular Animal Parasites
• Eukaryotes
• Multicellular
• Parasitic flatworms and roundworms.

14. 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

15. 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

16. 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

17. 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

18. Normal
bacterial
colony
Area of
inhibition of
bacterial
growth
Penicillium
colony
Figure 1.5 The discovery of penicillin.

19. 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

20. 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

21. 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

22. 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

23. Infectious Diseases
 When a pathogen overcomes the host’s
resistance, disease results
 Emerging infectious diseases (EIDs): New
diseases and diseases increasing in incidence
1. Evolutionary
2. Increased human exposure in undergoing
ecological changes
3. Antimicrobial resistance

24. 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

25. Figure 25.12
Escherichia coli O157:H7
• Toxin-producing
strain of E. coli
• First seen in 1982
• Leading cause of
diarrhea
worldwide

26. Figure 23.21
Ebola Hemorrhagic Fever
• Ebola virus
• Causes fever, hemorrhaging, and blood
clotting
• First identified near Ebola River, Congo
• Outbreaks every few years

27. Prokaryotic Anatomy

28.  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

29. Figure 4.2b-c Bacilli.
Streptobacilli
Diplobacilli

30. Figure 4.1ad Arrangements of cocci.
Plane of
division
Diplococci
Streptococci
Staphylococci

31. Arrangements
• Pairs: diplococci, diplobacilli
• Clusters: staphylococci or staphylobacilli
• More than one plane of division
• Chains: streptococci, streptobacilli
• One plane of division
• Grows in strands

32. Vibrio
Spirochete
Spirillum
Figure 4.4 Spiral bacteria.

33. Star-shaped bacteria
Figure 4.5a Star-shaped and rectangular prokaryotes.

34. Rectangular bacteria
Figure 4.5b Star-shaped and rectangular prokaryotes.

35. Figure 4.6 The Structure of a Prokaryotic Cell.
Capsule
Cell wall
Plasma
membrane
Fimbriae
Cytoplasm
Pilus
70S Ribosomes
Plasma membrane
Inclusions
Nucleoid containing DNA
Plasmid
Flagella
Capsule
Cell 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.

36. 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

37. 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

38. Figure 24.12 Streptococcus pneumoniae, the cause of pneumococcal pneumonia.

39. 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

40. Figure 4.7 Arrangements of bacterial flagella.
Peritrichous Monotrichous and polar
Lophotrichous and polar Amphitrichous and polar

41. Basal body
Peptidoglycan
Hook
Cell wall
Gram-
positive
Filament
Flagellum
Plasma
membrane
Cytoplasm
Parts and attachment of a flagellum of a
gram-positive bacterium
Figure 4.8b The structure of a prokaryotic flagellum.

42. Plasma
membrane
Cell wall
Basal body
Gram-
negative
Peptidoglycan
Outer
membrane
Hook
Filament
Cytoplasm
Flagellum
Parts and attachment of a flagellum of a
gram-negative bacterium
Figure 4.8a The structure of a prokaryotic flagellum.

43. 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)

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

45. Figure 4.10a Axial filaments.
A photomicrograph of the spirochete
Leptospira, showing an axial filament

46. • 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

47. Figure 4.11 Fimbriae.
Fimbriae

48. Fimbriae and Pili
• Pili
– Usually longer than fimbriae
– Gliding motility
– Twitching motility (like a worm)

49. 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

50. 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.

51. L-Ala, d-Glu-NH2 etc. are amino acids
This is the cell wall, the more ladders,
the thicker the wall is

52. • Thick peptidoglycan
• Teichoic acids
– makes the wall like
crosshairs + where – is
peptidoglycan and
| is teichoic acids
Gram-Positive
Cell Wall
 Thin peptidoglycan
 Outer membrane
Gram-Negative
Cell Wall

53. Plasma
membrane
Cell wall
Lipoteichoic
acid
Peptidoglycan
Wall teichoic acid
Protein
Gram-negative cell wall
Lipopolysaccharide
Outer membrane
Peptidoglycan
Plasma
membrane
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.

54. • 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

55. • 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

56. 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

57. 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

58. • 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-Positive
Cell Wall
 4-ring basal body
 1 outer
 1 wall
 2 inner
 Thin Peptidoglycan
 Red Gram Stain
 Outer Membrane
 Tetracycline sensitive
 Exo and Endotoxins
Gram-Negative
Cell Wall

59. 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)

60. The Plasma Membrane
• Contains enzymes for metabolic reactions
• Most lack sterols, Mycoplasma is exception
• Disruption: membrane’s phospholipids =
antibiotics: polymyxins

61. Cytoplasm
• Contains nucleoid, ribosomes and inclusions
• 80% water and contains primarily proteins
(enzymes), carbs, lipids, inorganic ions and
many lower molecular weight compounds

62. 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 functions
Antibiotic resistance
Tolerance to toxic metals
Production of toxins
Can be transferred from one bacterium to another

63. 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 50S
Why can these antibiotic drugs work without affecting host
cells? Host cells are made up of 80S ribosomes

64. 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

65. 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