Microbiology Notes Chapters 4 – 6
Cell structure and function of prokaryotes – prokaryotes are generally smaller and more simple than
eukaryotes
Cytoplasm – internal fluid enclosed by the cell membrane
Flagellum – provide motility to the cell; in general, all spirilla, about 50% of bacilli and a small percent of
cocci have flagellum – at least 1, but sometimes multiple. Prokaryotes (bacteria) with flagella are able to
move and respond to the chemistry of their environment – this is termed chemotaxis. Positive
chemotaxis – cell moves towards a favorable stimulus, negative (harmful) stimuli repel the cell.
Spirochetes – bacteria with a corkscrew shape, use a periplasmic (internal, enclosed) flagella to contract
and expand, moving like a coil. Thought to be the origin of flagella in other prokaryotes by
endosymbiosis.
Fimbria – bacterial surface appendage involved in interactions with other cells (not involved in
locomotion). Fimbriae are small, hair-like fibers on the surface of many cells. Help in clinging and
formation of biofilms. Pilus – rigid tubular protein structure found only on gram negative bacteria and
used primarily in conjugation – the transfer of bacterial DNA between cells. See figure 4.8.
Glycocalyx – a surface coating of macromolecules that protects the cell and is involved in formation of
biofilms. Slime layer – a loose, thin type of glycocalyx. Capsule – a think, stronger glycocalyx layer. See
figure 4.9. Bacteria with capsules tend to exhibit greater pathogenicity because they tend to be
protected from white blood cells.
Basic Types of Cell Envelopes – cell envelope may include cell membrane, cell wall. The Gram stain is a
technique to differentiate 2 general types of bacteria based on morphology of the cell envelope. Gram
positive bacteria – 2 layers – thick cell wall, cell membrane; Gram negative bacteria – 3 layers – outer
membrane, thin peptidoglycan layer, cell membrane. See figure 4.12. Peptidoglycan is a support layer
that prevents cells from internal rupture due to absorption of excess water by osmosis. Some antibiotics target peptidoglycan to lead to cellular lysis. Some bacteria have no cell wall (mycoplasms), but
all have cell membrane.
Figure 4.14 – comparison of structures composing cell envelopes.
Bacterial chromosome – usually a single circular strand of DNA, sometimes bacteria have multiple
chromosomes, but never a true nucleus – the DNA is not enclosed by a nuclear membrane, just
aggregated into the nucleoid region. Many bacteria contain plasmids – nonessential pieces of DNA that
may express traits such as resistance to antibiotics or may produce enzymes or toxins.
Ribosomes – made of RNA and protein, involved in the synthesis of protein.
Inclusions – used by the bacterial cell to store nutrients. Granules – type of inorganic inclusion with no
membrane.
Bacterial cytoskeleton – actin filaments are protein structures that give support and shape to the cell
Endospore – certain environmental signals may lead to the formation of protective coats (endospores).
A vegetative cell is one that is growing and replicating, when threatened the endospore may form and
the cell becomes dormant until positive conditions return. Figure 4.22. Bacterial endospores are
extremely long lasting and difficult to destroy. Germination occurs when conditions are favorable for
vegetative growth. Most endospore-forming bacteria are harmless to human; anthrax, tetanus, and
botulism are caused by bacteria that form endospores.
Bacterial shapes and arrangements – bacteria are usually independent single-cells or unicellular
organisms. Coccus – sphere or oval shaped bacteria, bacillus – rod shaped, vibrio - gentle curved rod,
spirilla - spiral shaped rods, spirochete – spring-like rods. Bacterial cells may cluster into groups.
Common traits to distinguish and identify bacteria include: cell morphology, Gram stain, presence of
specialized structures, macroscopic appearance, biochemistry, unique composition of DNA and rRNA.
Although the majority of bacteria are heterotrophic (obtain nutrients from other organisms), some
photosynthetic bacteria use special light-trapping pigments for energy in the synthesis of nutrients from
inorganic compounds. Cyanobacteria – also known as blue green bacteria, previously classified as algae,
among the oldest of all bacteria on earth. Cyanobacteria contain chlorophyll and gas inclusions allowing
them to float on the surface of water to absorb light. Types of cyanobacteria grow in freshwater or sea
water. Green and purple sulfur bacteria – contain bacteriochlorophyll – photosynthetic but do not give
off oxygen. Tend to live in sulfur springs and deep in anaerobic swamps and metabolize sulfur.
Although most bacteria are free living (do not require a host) or occasionally parasitic, some require host
cells to live: obligate intracellular parasites such as Rickettsias – live off blood cells of mammals and are
responsible for Rocky Mountain spotted fever and endemic typhus - and Chlamydias – require host cell
but not a vector; cause eye infections, STDs, and lung infections.
Archaea – simple, single celled organisms with no nucleus or organelles that tend to inhabit extreme
environments in terms of temperature, pH, high pressure, salt concentration, etc. Archaea have unique
rRNA sequences, unique membrane lipids and cell walls. Archaea reproduce asexually by budding,
binary fusion, or fragmentation. Examples of Archaea – methanogens convert CO2 and H2 into CH4
(methane). Halophiles – require salt and can tolerate high salt concentrations – inland seas, salt lakes,
salt mines. Hyperthermophiles – grow best at high temperatures between 80C and 121 C, but cannot
grow below 50 C. Psychrophiles – survive in very low temperatures.
Chapter 5
Eukaryotes – appear in the fossil record around 1.8 to 2 billion years ago, thought to have evolved by
endosymbiosis – the merging of multiple prokaryotic cells to form beneficial, stable partnerships. See
figure 5.2 for eukayotic cell structure and function. Cillia – small hairs used for locomotion found only in
protozoans and animal cells. Many other eukaryotes have flagella for locomotion. Most eukaryotes
have glycocalyx similar to the slime layers and capsules of eukaryotes. Some eukaryotes have thick cell
walls, some have only a cell membrane for protection.
Nucleus – separated from the cytoplasm by the nuclear envelope – a porous membrane. The condensed
mass of the nucleus is called the nucleolus and is the site of rRNA synthesis and collection of ribosomal
subunits. The nucleolus contains chromatin – the condensed form of eukaryotic chromosomes. These
chromosomes contain the genetic information of the cell.
Endoplasmic reticulum (ER) – series of membrane-like tubes involved in cellular transport and synthesis.
Rough ER – has ribosomes (protein synthesis), smooth ER – used for detoxification of metabolites,
storage, synthesis, and transport.
Golgi apparatus – organelle where proteins are collected and packaged for their final destinations,
closely associated with the ER in location and function. The ER releases membrane-bound transport
vesicles that contain proteins and the Golgi modifies these to produce condensing vesicles which will
serve different purposes. See figures 5.7 – 5.9.
Mitochondria – responsible for the generation of ATP in the cell; ATP is used for energy release.
Chloroplasts – responsible for generation of ATP in plant, algae, and other photosynthesizing cells.
Ribosomes – sites of protein synthesis, may be attached to Rough ER or free floating in the cytoplasm.
Cytoskeleton – flexible support framework composed of microfilaments and microtubules. See figure
5.13.
Fungi – around 100,000 known species, originally classified with photosynthetic plants; have survived for
more than 650 million years. Fungi may be microscopic or macroscopic, either unicellular or
multicellular. Fungi have special cell walls made of chitin. Hyphae – long, threadlike cells that compose
filamentous fungi – woven mass of hyphae make up the mycelium; yeast – round, oval shaped cells. All
fungi are heterotrophic – obtain nutrients from other organic sources (substrates). Fungi tend to be
decomposers, though some cause fungal infections – mycoses. Most fungi grow by fragmentation or
spore formation (sexual or asexual). See figures 5.19 and 5.20. Mycoses – fungal infections; often effect
immune-compromised individuals. A variety of fungal infections harm plants and agricultural crops.
Fungi play a crucial beneficial role in the cycling of nutrients – they make associations with root
structures (microrrhizae) and help the plant breakdown/absorb complex nutrients. Yeasts provide
alcohol through fermentation, some fungi produce antibiotics.
Chytrid fungi – primitive fungi that may be unicellular or form colonies, have flagellated spores, may be
decomposers or parasites. Chytrid fungi are currently decimating the global amphibian population.
Algae – are photosynthetic protists, they may be unicellular, colonial, or filamentous in form. Algae are
essential in marine and aquatic food chains. Algae are rarely infectious, though some produce
potentially harmful toxins.
Protozoans – about 65,000 species have been identified, single-celled, often responsible for parasitic
infections. Protozoans are heterotrophic, move by pseudopods, flagella or cilia. Many types are able to
form cysts – dormant, protective stages of the life cycle. Trypanosomes are a type of flagellated,
pathogenic protozoan responsible for Chagas disease.
Helminths –includes tapeworms, flukes, roundworms – begin as multicellular worms under 1mm in
length. Adults are usually macroscopic. Not all helminthes are parasitic, some are free-living in soil and
water. About 50 species are known to parasitize humans. See figure 5.34.
Viruses – types of intracellular obligate parasites – they require host cells for replication. They can infect
every type of cell – bacterial, algal, protozoan, plants, fungi, and animals. The small size of viruses
delayed their discovery until about 1890. Viruses are thought to have originated billions of years ago,
but evidence is difficult to analyze due to their small size. Thought to have evolved as loose strands that
developed protective coating or as regression from bacterial cells. Viruses are the most abundant
microbes on earth, out numbering bacteria 10 to 1.
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Fungi
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Eukaryotes – uni or multicellular
Most are composed of filamentous (tube-like strands called hypha (singular) or hyphae
(plural)
• mycelium = aggregate of hyphae
• multicellular, such as mycelial cords, rhizomorphs, and fruit bodies (mushrooms)
Humans and Fungi
Beneficial Effects of Fungi
• Decomposition - nutrient and carbon recycling
• Biosynthetic factories. Can be used to produce drugs, antibiotics, alcohol, acids, food
(e.g., fermented products, mushrooms)
• Model organisms for biochemical and genetic studies
• Food
• Long historical use of psychoactive fungi for spiritual purposes; modern use as
entheogens and treatment of psychiatric disorders and addiction
• Harmful Effects of Fungi
• Destruction of food, lumber, paper, and cloth
• Animal and human diseases/infections, allergies
• Toxins produced by poisonous mushrooms and within food (e.g., grain, cheese, etc.)
• Plant diseases
Fungal Characteristics
Cell wall composed of cellulose and/or chitin
Food storage - generally in the form of lipids and glycogen
Eukaryotes - true nucleus and other organelles present
All fungi require water and oxygen (no obligate anaerobes).
Fungi grow in almost every habitat imaginable, as long as there is some type of organic matter
present
Number of described species - between 69,000 to 100,000 (estimated 1.5 million species total)
Fungal Infections
Mycoses – fungal infections
Chytrid fungus – Chytridomycota = fungal group of unusual, very primitive fungi that may grow
as single cells or colonies of cells
Most Chytrids do not form hyphae or yeast-like cells; often have flagellated spores called
“zoospores”
Typically free-living saprobes found in soil, water, decaying organic material
Some are parasites of plants, animals, and other microbes
Not known to cause human infections, but responsible to wiping out huge populations of
amphibians around the world
Ringworm – dermatophytosis – human skin fungal infection
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Some human fungal diseases may be systemic – histoplasmosis
Fungal lifestyles
Heterotrophy - 'other food'
• Saprophytes or saprobes - feed on dead tissues or organic waste (decomposers)
• Symbionts - mutually beneficial relationships between a fungus and another organism
• Parasites - feeding on living tissue of a host.
• Parasites that cause disease are called pathogens.
Fungal interactions
Fungal decomposition
Fungi get carbon from organic sources
Hyphal tips release enzymes
Enzymatic breakdown of substrate
Products diffuse back into hyphae
Hyphae: tubular, hard cell wall of chitin
Multinucleate
Grow at tips
Hyphal growth from spore
Mycorrhizae
“Fungus roots”
Mutualism between:
• Fungus (nutrient & water uptake for plant)
• Plant (carbohydrate for fungus)
Several kinds
• Zygomycota – hyphae invade root cells
• Ascomycota & Basidiomycota hyphae invade root but don’t penetrate cells
• Extremely important ecological role of fungi!
Lichen
Mutualism between
• Fungus – structure and
• Alga or cyanobacterium – provides food
• Three main types of lichens:
• Crustose lichens form flat crusty plates
• Foliose lichens are leafy in appearance, although
lobed or branched structures are not true leaves
• Fruticose lichens are even more finely branched,
may hang down from branches or
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grow up from ground
Lichens - nature’s biological monitors of pollution and air quality
• Some species more sensitive to pollution
• Which species are present can indicate air quality
• Most resistant species can also be analyzed for pollutants, including bioaccumulation of
heavy metals and radioactive isotopes
Fungi applications
http://www.ted.com/talks/paul_stamets_on_6_ways_mushrooms_can_save_the_world.html
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Helminths
Multicellular invertebrate worms; typically macroscopic as adults; may be parasitic/infectious or
neutral heterotrophs found in soil and water of virtually all environments
Contaminate food, water, air, feces, pets, wild animals, and various surfaces
Prevention:
• Frequent hand washing
• Frequent cleaning of bathrooms and kitchens
• Thorough cooking of beef, pork, sausage, and game meat
Common helminths
Roundworms aka Nematodes
• Parasitic nematodes - hatch/live in intestines
• Symptoms
• fatigue
• Weight loss
• Irritability
• Poor appetite
• Abdominal pain
• Diarrhea
• Untreated
• Anemia
• malnutrition
- about 1 million species
Common helminths in meat
Trichina spiralis (trichinosis)
• Ingested via undercooked pork, sausage, or game meat – especially bear meat
(responsible for 1/3 of the 100,000 cases of trichinosis in the US per year)
• Spread throughout bloodstream and lymphatic system
• Symptoms of infection
• First stage – Vomiting, diarrhea, muscle cramps, fever, sweating
• Untreated – Second stage
• Penetration of muscles, heart, and brain – intense muscle and joint pain,
shortness of breath
• Symptoms usually subside, but there is no cure for the infection once the larvae
are encysted in muscles and may lead to death
Common helminths
Tapeworms (cestodes)
• Ingested via undercooked beef or sometimes raw pork
• Live in intestines – up to 25 M long – absorbs nutrients through its body
• Symptoms
• Usually absent
• May include abdominal pain, fatigue, weight loss, diarrhea
Pinworms
AKA: seatworms or threadworms
Most common worm infection in the US
• Ingested in contaminated food or drink, or by hand – self inoculation is common
• Embryonated eggs are on clothes, bedding, bathroom fixtures or dust
• 42 million people infected globally
• Mostly children aged 5-14 years
• Commonly institutional settings such as child care facilities, hospitals, or family
members
Only helminthic infection with approved OTC treatment
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Symptoms – itching, sleep disruption, sometimes nausea, abdominal pain and diarrhea