1. Taxonomy, Classification, and Characterization of Prokaryotes, Viruses, and Prions
“Nature makes no jumps. All taxa show relationships on all sides like the countries on a map of the world.” – Carl Linnaeus

2. (REVIEW) A Quick Note on Taxonomy
Carl Linnaeus ( )
Swedish botanist, physician, and zoologist
The Father of Modern Taxonomy
Established the binomial system for scientific nomenclature: Genus + species
Genus – italicized and capitalized
Species – italicized and lowercase
e.g. Entamoeba histolytica (protozoa)
e.g. Bacillus anthrasis (bacteria)
e.g. Saccharomyces cerevisiae (fungi)
e.g. Homo sapiens (animalia)
Regardless of domain, kingdom, or phylum, the binomial nomenclature system prevails

3. (REVIEW) Classification of Microbes: Overview
Living
Domain Eukarya – Eukaryotic Cells
Kingdom Animalia
Kingdom Plantae
Kingdom Fungi
Kingdom Protista (technically obsolete, classifications are ever changing)
Domain Archaea
Domain Bacteria
Nonliving
Viruses
Prions
Prokaryotic Cells

4. evolutionary history of organisms (i.e. tracing common ancestors)
Taxonomy
Taxo- arrangement
-nomy
custom
Allows for a way of classifying, identifying, and naming
A way of organizing large amounts of information about organisms
Allows for predictions to be made based on knowledge of similar organisms
Modern taxonomy focuses on similar genetic patterns to work in step with phylogeny
evolutionary history of organisms (i.e. tracing common ancestors)
Linnaeus’ Binomial System: Genus + species
What exactly defines a species?
Phylo- tribe
-geny origin

5. DOMAIN KINGDOM PHYLUM CLASS ORDER FAMILY GENUS SPECIES
Microbiology with Diseases by Body System, 4th Ed., Pearson Education, 2015; Figure 4.22 Levels in a Linnaean taxonomic scheme.
SPECIES

6. Concept Check: Why Aren’t There Domains for Viruses and Prions?

7. Identification by Dichotomous Keys
Series of paired statements where only one of two "either/or" choices applies to any particular organism
Key directs user to another pair of statements until the name of the organism is reached
Statements include but are not limited to: Gram-staining, tolerating oxygen, fermentation reactions, utilization of citric acid, and gas production
Microbiology with Diseases by Body System, 4th Ed., Pearson Education, 2015; Figure 4.27 Use of a dichotomous taxonomic key.

8. Overview: Methods of Identifying Microorganisms (Besides Microscopy)
________________________________
(FYI) Biochemical tests
(FYI) Analysis of nucleic acids

9. Classification by Physical Characteristics
Eukaryotes (protozoa, fungi, algae, and helminths) can often be identified based only on their morphology or anatomy
e.g. Cestodes (tapeworms) have no body cavity or digestive tube while Trematodes (flukes) have no body cavity but have a digestive tube
“Some bacterial colonies have distinct appearance used for identification”
Grammar aside, the publisher thought this was a worthwhile sentence, without giving examples—academia at its finest

10. Prokaryotic Classification by Morphology
Pleo- many
And Pleomorphic – able to alter its shape

11. Prokaryotic Classification by Morphology: Cocci
Plane of Division
Cocci Type
Plane of division
Diplococci
Streptococci
Tetrads
Sarcinae
Staphylococci
Microbiology with Diseases by Body System, 4th Ed., Pearson Education, 2015; Figure 11.8 Arrangements of cocci

12. What Are These?

13. What Are These?

14. Prokaryotic Classification by Morphology: Bacilli What Do You Think?
Looking at the figure, how many planes of division are associated with
A single bacillus _____
Diplobacilli _____
Streptobacilli _____
Palisade bacilli _____
V-shaped bacilli _____
Single bacillus
Diplobacilli
Streptobacilli
Palisade
V-shape
Microbiology with Diseases by Body System, 4th Ed., Pearson Education, 2015; Figure 11.9 Arrangements of bacilli

15. Latin and Greek of Bacterial Morphology
Coccus – Gk. kókkos = seed Bacillus – L. bacillum = small staff Strepto – Gk. streptós = twisted chain Sarcinae – L. sarcina = package Staphylo – Gk. staphulḗ = bunch of grapes

16. Prokaryotic Colony Classification by Morphology
SHAPE OF COLONY
EDGE
ELEVATION

17. (FYI) Classification by Biochemical Reactions: Gas Detection
Microbiology with Diseases by Body System, 4th Ed., Pearson Education, 2015; Figure 4.23 Two biochemical tests used for identifying bacteria.
Gas bubble
Inverted tubes to trap gas G A S IS U L Y
CO2
No hydrogen sulfide
produced
Hydrogen sulfide produced
Acid formed with gas
Inert; no acid and no gas formed
Acid formed with no gas

18. Bacteria is grown on culture and transferred into liquid suspension
(FYI) Classification by Biochemical Reactions: Automated Identification Systems
Bacteria is grown on culture and transferred into liquid suspension
Suspension is poured into a cassette and is then transferred into an ID card with wells; each well houses a different biochemical reaction (e.g. resistance to certain antimicrobials, catabolizing glucose, etc.)
ID card is placed into an incubator for several hours, and results are read through a computer program

19. (FYI) Classification by Biochemical Reactions: Automated Identification Systems
Microbiology with Diseases by Body System, 4th Ed., Pearson Education, 2015; Figure 4.24 One tool for rapid identification of bacteria, the automated MicroScan system;

20. Classification by Serological Tests
Serology – study of serum
Blood – clotting factors = serum
Major source of _____________which bind to ________________________________
Serological tests make use of serum antibodies to see if they bind to any specific antigens of a sample
EPITOPES
© 2013 Pearson Education Inc.

21. What Do You Think?
Can an antibody have more than one type of binding site?
Can an antigen have more than one type of epitope?

22. Classification by Serological Tests
Microbiology with Diseases by Body System, 4th Ed., Pearson Education, 2015; Figure 4.25 An agglutination test, one type of serological test.

23. Classification by Phage Typing
Phage = shorthand for bacteriophage
A virus that solely infects bacteria
Phages don’t just infect any ole bacteria, they’re picky and will only infect specific types

24. Classification by Phage Typing
_____________________ – dense growth of bacteria on a Petri dish
___________________– clear or discolored area that represents bacterial death
Microbiology with Diseases by Body System, 4th Ed., Pearson Education, 2015; Figure 4.26 Phage typing.

25. (FYI) Classification by Analysis of Nucleic Acids
Sequencing a microorganism’s genetic code
Utilizes a lot of different methods: UV spectrophotometry, gel electrophoresis, fluorometry, southern blotting, Sanger sequencing, DNA microarray, various types of polymerase chain reactions
…I’ll leave that for when you take genetics, microbiology, and human biochemistry in college

26. Characteristics of Prokaryotes
Most numerous and diverse of all living microbes
Bacteria have been shown to be human pathogens, _________________________
(REVIEW) 70S (30S + 50S) ribosomes, circular DNA in the nucleoid, no nuclei, no membrane-bound organelles, reproduce by binary fission
Archaea – no peptidoglycan in cell wall, histone-wrapped DNA
Bacteria – peptidoglycan cell wall
Can be classified as Gram-positive and Gram-negative

27. Prokaryotes Classified as Endospore-Forming
(REVIEW) Vegetative cells transform into hardened endospores to survive harsh environmental changes
Bacteria
Gram-positive
RODS ONLY! Genus: Bacillus, Clostridium
Putting it all together: ________________________________________________________________________
Microbiology with Diseases by Body System, 4th Ed., Pearson Education, 2015; Figure 11.2 Locations of endospores.
Endospore
Vegetative
cell

28. Prokaryotes Classified by Reproduction Methods
But Mr. Fenlon, you said that prokaryotes replicate by binary fission
I lied; that is the rule for almost all prokaryotes but there are but a few exceptions but ALL PROKARYOTIC REPRODUCTION METHODS ARE ___________________
Other methods
(FYI) Snapping division (type of binary fission by which a palisade arrangement arises from incomplete separation of the daughter cell; innermost portion of cell wall is deposited across the newly forming cell, and as it thickens/matures the old portion of the cell wall, that is still attached to the original cell, snaps from the increased tension; e.g. Genus: Corynebacterium)
(FYI) Reproductive spores (Fungus-like family: Actinomycetaceae)
(FYI) Budding (DNA is replicated and buds off into a smaller daughter cell)
Viviparity …

29. Viviparous Reproduction
Vivi- life
-parous pertaining to child birth
Live child birth
Genus: _________________
1-12live, grown/growing offspring lyse from the mother cell, killing her in the process
Microbiology with Diseases by Body System, 4th Ed., Pearson Education, 2015; Figure 11.7 Viviparity in Epulopiscium.

30. (FYI) Phototrophic Prokaryotes Classification
Adapted from Pearson Education Inc. Animation, B.J. Cummings, 2007

31. Gram-Positive Bacteria with Low Guanine + Cytosine Content
(FYI) Genera: Bacillus, Clostridium, Streptococcus, Enterococcus, Staphylococcus
Genus: Listeria
Namesake: Joseph Lister
Contaminates milk and meat products; capable of reproducing under refrigeration
Survives inside phagocytic white blood cells
In pregnant women, can kill the fetus if crosses the placenta; rarely causes disease in adults
Genus: Lactobacillus
Grows in the human mouth, stomach, intestinal tract, and vagina
Rarely causes disease
Inhibits the growth of pathogens within the body (the good bacteria in ________________)

32. Gram-Positive Bacteria with Low Guanine + Cytosine Content
Genus: Mycoplasmas
The only bacteria that lack cell walls
Smallest free-living cells
Microbiology with Diseases by Body System, 4th Ed., Pearson Education, 2015; Figure The distinctive “fried egg” appearance of Mycoplasma colonies.

33. So, the 3 Gram-Positive Low G+C Content Bacteria You Need to Know Are…
Lactobacillus, Listeria, and Mycoplasmas
Lact lister Myc
“______________________________”

34. Gram-Negative Proteobacteria
Five Classes
Alphaproteobacteria
Nitrogen fixing bacteria (e.g. Genera Azospirillum, Rhizobium, Nitrobacter, and Rhodopseudomonas palustris)
Genus: Rickettsia – arthropod-transmitted, causes typhus, DO NOT CAUSE RICKETS (VitD deficiency)
Betaproteobacteria
Bordetella pertussis – causes “whopping cough”/pertussis
Gammaproteobacteria
Deltaproteobacteria
Epsilonproteobacteria
Genera Helicobacter and Campylobacter (cause GI inflammation, and if untreated, can lead to cancer)

35. Misc. Gram-Negative Bacteria
Genus Chlamydia – causes Chlamydia
Most common sexually transmitted bacteria in the United States
Spirochetes – spiral-shaped, move in a corkscrew-like motion due to the movement of their axial filaments composed of endoflagella
Causes ___________________

36. A Closer Look at Chlamydias & Rickettsias
Both are Gram-negative
Both reproduce by means of binary fission
Both are obligate intracellular parasites
Chlamydias and Rickettsias are black swans: they’re obligate intracellular parasites but have ribosomes of their own
Chlamydias – don’t have an ATP synthase (i.e. can’t produce ATP); require host cell cytoplasm
Rickettsias – have a REALLY permeable membrane that leaks out cofactors necessary for metabolism; balanced out by a nutrient-rich host cell cytoplasm

37. Archaeal Extremophiles
Thermophiles
Will not function below a certain temperature (100+°F)
Two representative genera
Geogemma
Pyrodictium
Human biotechnological use: using enzymes in recombinant DNA technology and laundry detergent
Halophiles
Depend on at least a 9% NaCl environment
For comparison, the human body is less than half-a-percent NaCl
e.g. Halobacterium salinarium
(REVIEW) Methanogens- produce methane gas in marshes, swamps, sewage plants, and human and animal digestive tracts
(REVIEW) Acidothermophiles – reside in hot and acidic environments (e.g. acidic hot springs)
(REVIEW) Cold-dwelling – reside in cold environments (e.g. Antarctic)

38. Viral Taxonomy
Domain
Kingdom
Phylum
Class
Order
Family
Genus
Species

39. Characteristics of Viruses
Obligate intracellular parasites
________________________
________________________________________________
Do not contain a plasma membrane, cytosol, or organelles
Contain either DNA or RNA (NEVER both)
dsDNA, ssDNA, dsRNA, +/-ssRNA
Linear or circular

40. Viruses Classified by the Hosts They Infect
________________________= infects bacteria
_______________= infects plants
_______________= infects fungi
Viruses that infect Kingdom Animalia do not have a specific name

41. Viruses are T I N Y Poliovirus Spacing outlined in red ≈0.5 mm
Viruses are T I N Y
Poliovirus
Spacing outlined in red ≈0.5 mm
How many Poliovirus structures could fit into the red box?

42. 2 Viral States Extracellular = _______
Protein coat (________) surrounding nucleic acid
Nucleic acid + capsid = ____________________
Some have phospholipid envelope (thus, viruses are classified as enveloped or non-enveloped)
Intracellular = ___________________

43. Capsid Morphology Icosahedral – twenty-sided polyhedron
Filamentous/Helical – cylindrical capsid that usually contains nucleic acid in a helix
Complex – not a distinct, classifiable, or symmetrical shape; mixture of many shapes
Head-tail – a type of complex virus; what comes to mind when we think of a virus; head-tail viruses are bacteriophages
3D solid with flat polygonal surfaces
Gk. eíkosi - twenty

44. Viral Envelopes
Icosahedral, filamentous/helical, and complex viruses can all be enveloped as well
The envelope can provide additional protection; contains glycoproteins, some called viral spikes, that attach to receptors on its host cell

45. Identify These Viruses’ Morphology and Either Enveloped or Naked

46. Bacteriophage Replication
Lytic Cycle
Lysogenic Cycle

47. 3. Prophage: phage DNA integrated in chromosome 1. Attachment 2. Entry
Microbiology with Diseases by Body System, 4th Ed., Pearson Education, 2015; Figure The lysogenic replication cycle in bacteriophages.
3. Prophage: phage DNA integrated
in chromosome
1. Attachment 1 3 2
2. Entry
Phage
Lytic
cycle
Lysogenic
Cycle
7. Synthesis: viral DNA is transcribed and translated into viral proteins
9. Release
4. Replication of
chromosome
and virus;
cell division
8. Assembly: viral proteins are assembled into phages
6. Induction: a genetic “switch” is flipped that excises the prophage DNA
5. Further replications and cell divisions

48. Entry of Animal Viruses
Viral genome
inside capsid 2 3
Capsid attaches to receptors
Capsid 2 3
Cytoplasmic membrane
of host engulfs virus
(endocytosis) 4
Receptors on
cytoplasmic membrane
Viral genome 6 5
Direct penetration of the viral genome 3
Viral
glycoproteins 4
Viral
genome
Viral membrane is FUSED with host membrane
Envelope
Uncoating
capsid
Endocytosis of the whole enveloped virus
Receptors on
cytoplasmic
membrane
of host
Microbiology with Diseases by Body System, 4th Ed., Pearson Education, 2015; Figure Three mechanisms of entry of animal viruses.
Viral genome
Uncoating
capsid
Membrane fusion

49. Central Dogma of Biochemistry/Molecular Biology
This applies to prokaryotes and eukaryotes, with the eukaryotic process being much more complex
DNA mRNA PROTEIN

50. Viral Replication (Applies to All Types of Viruses)
(REVIEW): Viruses can have dsDNA, ssDNA, dsRNA, or +/-ssRNA, but DO NOT have DNA and RNA
The process of viral replication changes depending on what type of nucleic acid is present
dsDNA – feeds directly into the central dogma procedure: viral dsDNA is transcribed to mRNA by host cell enzymes, and is translated into viral proteins by host cell ribosomes
ssDNA – host cell enzymes turn it into dsDNA, where it is transcribed into mRNA, and translated by host cell ribosomes into viral proteins

51. (Cont.) Viral Replication (Applies to All Types of Viruses)
dsRNA – unwound and transcribed by a viral RNA-dependent RNA polymerase; the +ssRNA is directly translated by host cell ribosomes into viral proteins; the -ssRNA reanneals with +ssRNA to be exported as a dsRNA virus out of the cell
+ssRNA = ________; essentially bypassed a step in the central dogma procedure; +ssRNA is directly translated by host cell ribosomes into viral proteins
-ssRNA – it’s reading the wrong way so it needs to be transcribed into +ssRNA (mRNA) by a viral RNA-dependent RNA polymerase, from there it can be translated by host cell ribosomes into viral proteins

52. Overview: Exit of Animal Viruses
Overview: Exit of Animal Viruses
NOTE: lysis can occur with enveloped viruses as well

53. Lytic Exit of Naked Animal Virus

54. Budding Exit of Enveloped Animal Virus

55. Lytic Exit of Enveloped Animal Virus
3. Viral nucleic acid replicates using host (or viral) cellular machinery, depending on the type of virus, but will always use host cell ribosomes.

56. Viroids _____________________________________ ____________________

57. Prions Disease-causing misfolded _______________ Cellular Prion (PrPC)
Made by all mammals
Normal, functional structure has α-helices
Disease-Causing Prion (PrPSC)
Disease-causing form has β-sheets
PrPSC causes PrPC to refold into prion PrPSC

58. Prion Secondary Protein Structure
α-helices
β-pleated sheet
Microbiology with Diseases by Body System, 4th Ed., Pearson Education, 2015; Figure The two stable, three-dimensional forms of prion protein (PrP)
PrPC
PrPSC

59. PrPC  PrPSC  Disease
β-sheets aggregate into amyloid fibrils, which then aggregate into amyloid deposits/plaques in the brain, which cause neuronal cell death
PrPC  PrPSC  amyloid fibrils  amyloid deposits  neuronal cell death

60. PrPSC
History
18th century farmers in the UK began to note their sheep were exhibiting strange behavior and developing skin lesions  Scrapie
20th century farmers in the UK let their cattle graze on cow meat, including their brains
Cattle began to grow sick, exhibiting strange behavior  Bovine Spongiform Encephalopathy = ____________________
Humans eat beef from mad cows  Creutzfeldt-Jakob Disease
Can also be inherited or spontaneous
1950s: Transmission of PrPSC in humans
Fore Tribe in Papua New Guinea  ______