Types of Microorganisms

• Bacteria
– Gram positive & gram negative
• Viruses
– RNA & DNA
• Fungi
– Yeasts & molds
• Protozoa
 History
Anton van Leeuwenhoek
– Made lenses or simple microscopes
• Magnification about 300x
– Discovered protozoa in drop of water
– Bacteria in plaque of teeth
– Father of Bacteriology & Protozoology
 Spontaneous Generation
• Abiogenesis-living matter arising from
nonliving matter
• Redi –maggots & meat
• Pasteur disproved abiogenesis
– Fermentation
• Yeast ferment grape juice –alcohol
• Bacteria ferment grape juice-acids
• Pasteurization
 Germ Theory of Disease
• Koch
– Proved microbes caused disease
– Koch’s postulates
– Developed pure culture techniques
• Gelatin to broth
 Epidemiology
• Study of source, cause, mode of
transmission of diseases
• Semmelweis
– Puerperal fever related to lack of hand
cleansing
• John Snow
– Cholera outbreak traced to sewage
contaminated street pump
 Immunology/Chemotherapy
• Jenner and smallpox vaccine
– Used cowpox virus
• Fleming & penicillin
 Binominal Nomenclature
• Genus - collection of species
– Members have common characteristics
– species can be subdivided into strains
• Strains have small genetic differences
– Nutrition
– Antibiotic resistance
– Toxins
 Classification
• Both genus & species underlined or
italicized
• Strain-subdivision of species
– ID by name, number or letter
– Example- Escherichia coli- E. coli K12
• Plasmids
• E. coli 0157:H7
 Early Classification
5 kingdoms
– Plants- photosynthetic, multicellular
– Animals-engulf & digest food, multicellular
– Fungi- non photosynthetic, enzymes for
absorption, unicellular & multicellular
– Protista- unicellular with nucleus
– Monera or Prokaryote- unicellular with no
nucleus
 Prokaryotes

They’re almost everywhere!!

 Prokaryotic Phylogeny
• Groups reflect derivation from common
ancestors
– Molecular data
– Sequence of RNA, DNA, proteins
• Evolutionary relatedness
– Reflects actual evolution & biology of
organisms
Diverse Adaptations of Form
and Function
Prokaryotes - single celled organisms, although some
occur as aggregates, colonies, or simple multi-cellular
forms.
three most common shapes are spherical (cocci) , rod
shaped (bacilli), and helical forms
Nearly all have external cell walls - protect and shape
the cell and prevent osmotic bursting
-Cell walls of eubacteria typically contain the
polymer peptidoglycan
Gram-positive and gram-negative
bacteria differ in the structure of their walls and other
surface layers.
 Classification into Domains
• Carl Woese-1980s
• Based upon modern techniques
– Sequence of rRNA in ribosomes
– tRNA - differentiate the Proteobacteria into 5
divisions (alpha, gamma, beta, delta, epsilon)
– Plasma membrane lipid structure
– Sensitivity to antibiotics
– High and low GC base pairs
 Prokaryotic DNA
• The prokaryotic genome consists of a
single circular DNA molecule in a
nucleoid region unbounded by a
membrane.
• Many species also possess smaller
separate rings of DNA called plasmids,
which code for special metabolic
pathways and resistance to antibiotics.
 Prokaryote ADAPTATIONS
• Many species secrete sticky substances that form capsules.

• Some have surface appendages called pili outside the cell wall.

• Both structures help the cells adhere to one another, and some
pili are specialized for conjugation (bacteria sex!)
 Prokaryote Adaptations

• Motile bacteria propel themselves by flagella,

• or use flagella-like filaments positioned inside
the cell wall (spirochetes) or glide on slime
secretions.
 Prokaryote Adaptations

• Prokaryotic cells are not

compartmentalized by endomembranes.
-- invaginations of the plasma
membrane provide internal membrane
surface for specialized functions (such as
cell respiration)
• Endospores –

– Allows bacteria to persist until favorable

conditions
– Oldest endospore found to be 250 myo
 REPRODUCTION
• Bacteria reproduce asexually.
• The type of cell division by which these
prokaryotes reproduce is called binary
fission.
• During binary fission, each dividing
daughter cell receives a copy of the
single parental chromosome.
 Prokaryotic reproduction

• Asexual reproduction
via binary fission
– Exponential growth
 Bacterial genetics
• Nucleoid:
region in bacterium
densely packed with
DNA (no membrane)
• Plasmids:
small circles of DNA
• Reproduction:
binary fission (asexual)
 Bacterial DNA-transfer
processes
• Transformation: genotype alteration by
the uptake of naked, foreign DNA from
the environment (Griffith expt.)
• Transduction: phages that carry
bacterial genes from 1 host cell to
another •generalized~ random
transfer of host cell chromosome
•specialized~
incorporation of prophage DNA into host
chromosome
• Conjugation: direct transfer of genetic
material; cytoplasmic bridges; pili;
sexual
 Bacterial Plasmids
• Small, circular, self-replicating DNA separate from the bacterial
chromosome
• F (fertility) Plasmid: codes for the production of sex pili (F+ or F-)
• R (resistance) Plasmid: codes for antibiotic drug resistance
• Transposons: transposable genetic element; piece of DNA that can
move from location to another in a cell’s genome (chromosome to
plasmid, plasmid to plasmid, etc.); “jumping genes”
 OPERONS
a group of key nucleotide sequences
includes:
- operator - enables transcription
- promoter- regulates activity of
structural genes
-one or more structural genes that are
controlled as a unit to produce
messenger RNA (mRNA).
 Def: Unit of genetic function – i.e., clusters of
Operons genes with related functions (transcription unit)

• Repressible (trp operon):

• tryptophan (a.a.) synthesis
• promoter: RNA polymerase binding
site; begins transcription
• operator: controls access of RNA
polymerase to genes (tryptophan
not present)
• repressor: protein that binds to
operator and prevents attachment of
RNA polymerase ~ coded from a
regulatory gene (tryptophan present
~ acts as a corepressor)
• transcription is repressed when
tryptophan binds to a
regulatory protein
 VARIATION
• Genetic variation occurs in prokaryotes
through mutation and gene transfer --
“conjugation”
• All major types of nutrition and
metabolism evolved among
prokaryotes.
• The evolution of prokaryotic
metabolism was both cause and effect
of changing environments on Earth.
 Metabolism and energy
( anaerobic or aerobic respiration )

• Autotroph; An organism able to use CO2 as sole source of carbon

• Chemoorganotroph; An organism obtaining its energy from the

oxidation of organic compounds

• Chemolitotroph; An organism obtaining its energy from the

oxidation of inorganic compounds
 Metabolism
• The following use oxygen or sulfur as electron acceptor:
• Iron bacteria - oxidize ferrous iron (Fe2+) into ferric iron (Fe3+)
• Nitrifying bacteria - oxidize ammonia (NH3) into nitrite (NO−2)
or, alternatively, nitrite (NO−2) into nitrate (NO−3).
• Purple sulfur bacteria and some chemolithotrophs oxidize
sulfide (S2−) into sulfur (S0) (oxygen is the electron acceptor).
• Sulfur bacteria use oxidized sulfur compounds to produce
sulfide. They also can grow on a number of oxidized or partly
oxidized sulfur compounds (sulfur is the electron acceptor)
• Hydrogen bacteria oxidize hydrogen to water.
• Carboxydotrophic bacteria oxidize carbon monoxide to carbon
dioxide.
 Metabolism
• The following use compounds other than oxygen as an
electron acceptor:
• Methanogens (Archae) capable of oxidising hydrogen,
reducing carbon dioxide to methane.
• Thiobacillus denitrificans - a sulfur bacteria, oxidizes
reduced sulfur compounds with nitrate instead of
oxygen.
• The recently discovered Anammox bacteria oxidize
ammonia with nitrite as electron acceptor to produce
nitrogen gas.
• Phosphite bacteria oxidize phosphite into phosphate.
use sulfate as electron acceptor, and reduce it into sulfide.
 Growth conditions
• Oxygen
– Strict aerobes
• Require oxygen
– Strict anaerobes
• Oxygen is toxic
– Facultative anaerobes
• Use oxygen when available
• Can grow without oxygen
– Aerotolerant anaerobes
• Can’t use oxygen but not toxic
– Microaerophilic
• Need low concentrations of oxygen
Three Domains of Life
 Three Domains
• Domains are above Kingdom level
– Plants, animals, fungi, protists, bacteria
• I) Bacteria or Eubacteriae
– Prokaryotes with peptidoglycan in cell wall
– Divide by binary fission
– Motile by flagella or cilia
– Sensitive to antibiotics
II) Archaeabacteriae
• Ancient prokaryotes
– Cell wall present, not peptidoglycan
– Live in extreme environments
– Have unusual metabolic processes
– Not sensitive to antibiotics
• Include:
– Methanogens -strict anaerobes
• Produce methane from CO2 + H2
• Live in anaerobic mud lakes
• Intestine of cows
 Archaea
• Include:
Halophiles
• Require high concentration of salt
– Maintain cell wall
• Spoilage of food-salted fish
• Salt lakes
Thermophiles
Live in hot sulfurous waters or acidic water
• Nucleic acids/proteins do not function at low temperatures
• Volcanic vents in ocean
 archae and microbial evolution

• Archea: adaptation to environmental extremes which probably

existed on early Earth
• Many Archea (especially hyperthermophiles) evolved at slower rate
than Bacteria
• Slow evolution rate in hyperthermophillic Bacteria: Thermotoga and
Aquifex
• Extreme environments => Strong evolution pressure => slow
evolutionary clocks
III) Eukarya
• All eukaryotes
• Cell wall varies in composition
• Not sensitive to antibiotics
• Fungi-yeasts and molds
• Protists-slime molds, protozoa, & algae
• Plants & animals
 Endosymbiotic Theory
• Eukaryotes evolved from prokaryotes
• 1.4 billion years ago
• Supported by similarities between
prokaryotes & organelles in eukaryotes
• Mitochondria & chloroplasts same size as
prokaryote cell
– Contain DNA, 70S ribosomes
• Endosymbiont-organism that lives within
another
 Support for Theory
» Prokarya Eukarya Mitoch & Chloro

• DNA circular linear circular

• Histones No Yes No
• Ribosomes 70S 80S 70S
• Growth binary mitosis binary
• Cyanophora
 Viruses
• Obligate intracellular parasites
• Not “cells”, so non-living agent
• No ribosomes
• Classification is different
 Viral structure
• Virus: “poison”
(Latin); infectious
particles consisting
of a nucleic acid in a
protein coat
• Capsid; (viral
envelopes); DNA or
RNA
• Bacteriophages
(phages)
 Structure of viruses
-Proteinous coat either in the form of a
capsid or capsomere
-Genetic element – RNA or DNA
-Single stranded OR Double Stranded
-ssRNA, dsRNA, ssDNA, dsDNA
-Viral envelope – a membrane in some
viruses
-Glycoproteins for recognition
 Viral reproduction: Lytic Cycle
• Host range: infection of a
limited range of host cells
(receptor molecules on the
surface of cells)
• The lytic cycle:
1- attachment
2- injection
3- hydrolyzation
4- assembly
5- release
• Results in death of host cell
• Virulent virus (phage
reproduction only by the lytic
cycle)
 Viral reproduction: Lysogenic Cycle
• Genome replicated w/o
destroying the host cell
• Genetic material of
virus becomes
incorporated into the
host cell DNA
(prophage DNA)
• Temperate virus
(phages capable of
using the lytic and
lysogenic cycles)
• May give rise to lytic
cycle
Lysogenic Cycle
 RNA viruses
• Retroviruses: transcribe
DNA from an RNA
template (RNA--->DNA)
• Reverse transcriptase
(catalyzing enzyme)
• HIV--->AIDS
Retrovirus (HIV)
HIV cycle
 Viroids & Prions
• Viroids
– Single short piece of RNA
– Cause disease in plants
– ? In humans
• Prions
– “naked” Protein
– Cause neurodegenerate diseases
– Humans & animals
– mad cow
 Viroids and prions
• Viroids: tiny, naked
circular RNA that infect
plants; do not code for
proteins, but use
cellular enzymes to
reproduce; stunt plant
growth
• Prions: “infectious
proteins”; “mad cow
disease”; trigger chain
reaction conversions; a
transmissible protein
 New Challenges
• Antibiotic resistance
• Emerging diseases
– SARS & Avian Influenza
• Bioterrorism
– Anthrax, smallpox, plague, botulism