Microbes and
biotechnology
Option F.1
Assessment statements
F.1.1 Outline the classification of living organisms into three domains.
F.1.2 Explain the reasons for the reclassification of living organisms into three
domains.
F.1.3 Distinguish between the characteristics of the three domains.
F.1.4 Outline the wide diversity of habitat in the Archae, as exemplified by
methanogens, thermophiles and halophiles.
F.1.5 Outline the diversity of Eubacteria, including shape and cell wall structure.
F.1.6 State, with one example, that some bacteria form aggregates that show
characteristics not seen in individual bacteria.
F.1.7 Compare the structure of the cell walls of Gram-positive and Gram-negative
Eubacteria.
F.1.8 Outline the diversity of structure in viruses including: naked capsid versus
enveloped capsid; DNA versus RNA; and single stranded versus double
stranded DNA or RNA.
F.1.9 Outline the diversity of microscopic eukaryotes, as illustrated by
Saccharomyces, Amoeba, Plasmodium, Paramecium, Euglena and Chlorella.
The five kingdoms
• Established in 1959 by Robert Whittaker
• Bacteria: single-celled organisms with no organized
nucleus and no membrane-bound organelles
• Protista: single-celled organisms with an organized
nucleus and organelles each surround by a membrane
• Fungi: multicellular organisms which obtain their food
using extracellular digestion and have cell walls of chitin
• Plants: multicellular organisms which obtain their food
by photosynthesis and have cell walls of cellulose
• Animals: multicellular organisms which obtain their food
by feeding on other organisms and have no cell wall
Five kingdoms grouped into two
categories
• Prokaryotes: bacteria
which have no
organized nucleus and
no membrane-bound
organelles
• Eukaryotes: all of the
other kingdoms which
have an organized
nucleus
The three domains
• Attempt by Carl Woese to improve
the accuracy of the classification
system based on studies of rRNA
Eubacteria: ‘true’ bacteria,
prokaryotes with no organized
nucleus and no membrane-bound
organelles.
• Archaea: archaebacteria or ‘ancient’
bacteria are also prokaryotes; most
live in extreme environments
• Eukarya: single-celled and
multicellular organisms which all
have their DNA contained in a
nucleus; plants, animals, protists,
and fungi
Reasons for reclassification into
three domains
• rRNA is a molecule
common to all
organisms
• Performs same
function in all
organisms
• Coded for by DNA
• By looking at variation
in the sequence of
rRNA, evolutionary
relationships became
apparent
• Eubacteria and
Archaea have different
molecules making up
their cell walls
• E and A have different
molecular structure of
their cell membranes
• E and A have different
sequences of
nucleotides in their
rRNA
Characteristics of the three
domains
Histones
Introns
Size of
Ribosomes
Cell
membrane
lipids
Peptidoglycan
in cell walls
Organelles
Eukarya
Present
Present
Large
subunits
(80S)
Unbranched
hydrocarbons
Absent
Present
Archaea
Histonelike
proteins
Present
in some
Small
subunits
(70S)
Some
branched
hydrocarbons
Absent
Absent
Eubacteria
Absent
Absent
Small
subunits
(70S)
Unbranched
hydrocarbons
Present
Absent
Homework
• What is the RNA world hypothesis?
• Give supporting and refuting details for the
hypothesis.
• NO OPINIONS!!!
Diversity of habitat of
Archaebacteria
• Methanogens – use carbon dioxide to make
methane; strict anaerobes; live in guts of
termites and cattle, Siberian tundra, swamps
rice fields, and in large intestines of dogs,
pigs, and humans
• Thermophiles – live in sulfur hot springs
where the pH is very acidic and temperatures
are up to 90°C; some live in hydrothermal
vents up to 105°C
• Halophiles – live in the Dead Sea, the Great
Salt lake, and evaporated salt water ponds
Diversity of Eubacteria
•
Three main shapes
• Spheres (cocci)
• Rods (bacilli)
• Helices (spirilla)
•
•
•
Varieties of shape
• Chain (strepto)
• Cluster (staphylo)
• Pair (diplo)
Aggregation
• Vibrio fischeri emit light when in large
groups, but not alone
• Bioluminescence caused by turning on of
gene by increased amount of signal
molecule
• Exist in light organs of squid
• Bacteria senses high density based upon
amt. of signal present called quorum
sensing
Variety of cell wall
• Gram +
• Stain purple
• Gram –
• Stain pink
Comparison of gram + and gram bacteria
Cell wall structure
Gram + bacteria
(stain purple)
Gram – bacteria
(stain pink)
Complexity
Simple
Complex
Amount of
peptidoglycan
(protective sugar
network)
Large amount
Small amount
Peptidoglycan
placement
In outer layer of bacteria Covered by outer
membrane (protects
from antibiotics)
Outer membrane
Absent
Present with
lipopolysaccharides
(toxic to host) attached
Diversity of structure of viruses
•
•
•
•
Are viruses alive?
Not cellular
Cannot reproduce without a host
Basic structure
• Nucleic acid
• DNA (double- or singlestranded)
• RNA (double- or singlestranded)
• Several enzymes
• Protein coat (capsid)
• Naked
• Enveloped by membrane
Homework:
Fill in chart
Organism
Saccharomyces
Amoeba
Plasmodium
Paramecium
Euglena
Chlorella
Nutrition Locomotion Cell wall Chloroplasts
Cilia or
flagella
Saccharomyces (yeast)
• Ferments
carbohydrates in flour
or malt and gain
energy from this
digestion
• Carbon dioxide gas (in
bread) and ethanol (in
beer) are by-produces
• Fungi
• Secrete enzymes
outside their cells and
absorb the produces
of digestion back into
the cell
• Have chitin in cell wall
Amoeba
• Fluid state of
cytoplasm enables it
to change its shape
easily
• Pseudopodia wrap
around a prey in order
to trap it in a food
vacuole for
intracellular digestion
Plasmodium
• Parasitic heterotroph
• Mosquitoes carry and
infect humans causing
malaria
Paramecium
• Ciliated heterotroph
• Intracellular digestion
• Food taken into oral
groove and passes to
gullet
Euglena
• Both autotrophic and
heterotrophic
• Contains chlorophyll
• Has eyespot which
facilitates movement
towards light
• Can absorb food from
outside the cell
• Has flagellum
Chlorella
• Single-celled green
algae
• Non-motile
• Cell wall of cellulose
Microbes and
biotechnology
Option F.2
Assessment Statements
• F.2.1 List the roles of microbes in ecosystems, including producers,
nitrogen fixers and decomposers.
• F.2.2 Draw and label a diagram of the nitrogen cycle.
• F.2.3 State the roles of Rhizobium, Azotobacter, Nitrosomonas, Nitrobacter
and Pseudomonas denitrificans in the nitrogen cycle.
• F.2.4 Outline the conditions that favour denitrification and nitrification.
• F.2.5 Explain the consequences of releasing raw sewage and nitrate
fertilizer into rivers.
• F.2.6 Outline the role of saprotrophic bacteria in the treatment of sewage
using trickling filter beds and reed bed systems.
• F.2.7 State that biomass can be used as raw material for the production of
fuels such as methane and ethanol.
• F.2.8 Explain the principles involved in the generation of methane from
biomass, including the conditions needed, organisms involved and the
basic chemical reactions that occur.
Role of microbes in ecosystems
•
•
•
Producers
• Change inorganic
molecules into organic
molecules
• Algae and some
bacteria use chlorophyll
to trap sunlight
• Chemosynthetic
bacteria use chemical
energy
Nitrogen fixers
• Bacteria remove
nitrogen gas from the
atmosphere and fix it
into nitrates which are
useable by producers
Decomposers
• Breakdown detritus and
release inorganic
nutrients back into the
ecosystems
The nitrogen cycle
•
•
•
•
•
Mutualistic nitrogen fixation:
bacteria forms symbiotic
relationship with a host plant
and fix nitrogen for it
(Ex.Rhizobium)
Free-living nitrogen fixation:
live in soil (Ex. Azotobacter)
Industrial nitrogen fixation:
burning of fossil fuels to
produce fertilizer
Nitrification: ammonia turned
into nitrites by bacteria (Ex.
Nitrosomonas) and to turn
nitrites into nitrates (Ex.
Nitrobacter)
Active transport of nitrates:
nitrates taken in by roots
•
•
•
•
Plants and animals: plants use nitrates
to make their own proteins; animals feed
on plants, digest and rearrange proteins to
make their own proteins
Death and excretion: products of
digestion and dead bodies contain
molecules which contain nitrogen
Putrefaction: decomposers break down
complex proteins and release nitrogen
gas into the atmosphere
Denitrification: bacteria remove nitrates
and nitrites and put nitrogen gas back into
the atmosphere (Ex. Pseudomonas
denitrificans)
Conditions which favor
nitrification and denitrification
• Nitrification
• Carried out by
Nitrosomonas
(ammonia into
nitrate)
• Carried out by
Nitrabacter (nitrite
into nitrate)
• Available oxygen
• Neutral pH
• Warm temperature
• Denitrification
• Carried out by
Pseudomonas
denitrificans
(nitrates into
nitrogen gas)
• No available
oxygen
• High nitrogen input
Consequences of releasing raw
sewage and nitrate fertilizer into rivers
• High nitrates and phosphates
fertilize the algae present in
water
• Increased growth of algae
• Algae are decomposed by
aerobic bacteria which use up
the oxygen in the water
(biochemical oxygen demand
– BOD)
• Water becomes low in oxygen
and fish and other organisms
which need oxygen die
Sewage treatment by
saprotrophic bacteria
• Stages of sewage treatment:
• Inorganic materials are removed and
organic matter is left
• 90% of the organic matter is removed
by saprotrophic bacteria
Trickling filter system
• Bed of stones 3-6 feet wide
• Saprotrophic bacteria adhere to the
stones and act on the sewage trickled
over them until it is broken down
• Cleaner water trickles out of the bottom
of the bed
• This flows to another tank where the
bacteria are removed
• The water is further treated with
chlorine to finish the disinfectant
process
Reed bed
• Waste water provides water and the nutrients to the
growing reeds
• Reeds are then harvested for compost
• Breakdown of organic waste is again accomplished
by saprotrophic bacteria
• Nitrate and phosphates released as a result of
bacterial action are used as fertilizer by the reeds
• Can only handle small sewage flow
Water Alert!
Homework
• Fill in the blank: The three wastewater
treatment plants in Mobile have a total
design flow of _____ million gallons per
day.
• Read the following article:
• http://www.usaid.gov/our_work/environ
ment/water/us_japan_init.html
• What has been done in the countries
aided by this project?
Sewage treatment video
Biomass can be used as raw material
for the production of fuels such as
methane and ethanol
• To make biogas, manure and
cellulose are put into a digester
without oxygen
• Anaerobic decomposition is
performed by bacteria which occur
naturally in the manure
• Manure and cellulose are broken
down into organic acids and
alcohol
• Organic acids and alcohol are
broken down into carbon dioxide,
hydrogen, and acetate
• Finally two type of bacteria work
on these to produce methane
which can be used to run
electrical machinery
• Ammonia and phosphate are
byproducts and can be used as
fertilizer
• Conditions to be kept constant in
digester
• No free oxygen
• Constant temperature of 95
degrees F
• pH (not too acidic)
• Bacteria required for
methanogenesis
• Acidogenic bacteria convert
organic matter to organic
acids and alcohol
• Acetogenic bacteria make
acetate
• Methanogenic bacteria
create the methane
Topic F.3
Assessment Statements
F.3.1 State that reverse transcriptase
catalyses the production of DNA from
RNA.
F.3.2 Explain how reverse transcriptase is
used in molecular biology.
F.3.3 Distinguish between somatic and germ
line therapy.
F.3.4 Outline the use of viral vectors in gene
therapy.
F.3.5 Discuss the risks of gene therapy.
Background information
• Genetic material of virus can be RNA or
DNA
• An RNA virus is called a retrovirus
• Flow of genetic information in a retrovirus
is from RNA back to DNA
• The enzyme which enables backwards
transcription is reverse transcriptase
HIV life cycle
1. HIV attaches to a host cell
2. RNA of the virus and the enzyme reverse
transcriptase enter the host cell
3. Reverse transcriptase copies viral RNA
into cDNA (complementary DNA)
4. cDNA makes a second strand which is a
complement to the first strand of DNA;
viral RNA is destroyed
5. New double-stranded viral DNA enters
the nucleus of the host cell
6. If HIV is active, it will use this DNA to
make more HIV viruses; they will then
burst out of the cell and infect other cells
How reverse transcriptase is used
in molecular biology
•
1.
2.
3.
4.
5.
6.
7.
8.
To make therapeutic proteins such as insulin and
somatostatin
Human DNA molecule is taken from a pancreas cell
mRNA copies the DNA without the introns
Reverse transcriptase produces a new single strand
of DNA called cDNA
The single strand replicates to make doublestranded DNA using DNA polymerase
Inserted into plasmid
Bacteria cell is stimulated to take up plasmid
Bacteria multiply and produce insulin
Insulin is harvested and used by diabetics
somatic and germ line therapy
• Gene therapy aims to replace defective
genes with effective ones which give the
message to make the correct protein
• Genes are delivered by vectors which are
viruses that have been genetically
engineered to infect certain cells in the
patient
• Somatic therapy – affects only the patient
involved; may be possible to cure singlegene defects such as cystic fibrosis and
hemophilia
• Germ line therapy – changes gamete
DNA, which would be passed to offspring
use of viral vectors in gene
therapy
• Treatment of a disease called severe combined
immune deficiency disease (SCID)
• Children do not produce enzyme ADA and thus
have no immune system
• In 1998 stem cells were withdrawn from kids with
SCID
• Cells mixed with a virus carrying normal form of
gene that produces ADA
• Virus transferred normal copy of gene into stem
cells
• Stem cells then infused back into bone marrow
• Immune systems were restored
risks of gene therapy
• Virus vector may enter another cell by
mistake
• Virus vector might put gene in wrong place
and cause mutation
• Genes could be over-expressed and too
much protein produced
• Virus vector might stimulate immune
reaction
• Virus vector might be transferred from
person to person
• Children might be more sensitive
Benefits of gene therapy
• Possibility of curing a disease caused by a
single-gene or multiple genes
F.4
Microbes and food
production
Assessment Statements
F.4.1 Explain the use of Saccharomyces in
the production of beer, wine and bread.
F.4.2 Outline the production of soy sauce
using Aspergillus oryzae.
F.4.3 Explain the use of acids and high salt
or sugar concentrations in food
preservation.
F.4.4 Outline the symptoms, method of
transmission and treatment of one named
example of food poisoning.
The successful making of bread,
beer, and wine
• Yeast was discovered as the fungus
responsible for products
• Saccharomyces cerevisae
• Yeast uses sugars for energy and
reproduces quickly by ‘budding’
• Bud breaks off and forms a new yeast cell
• Turns glucose into two molecules of
ethanol and two molecules of carbon
dioxide gas as waste product
Beer
• Source of glucose:
grain
• Sweet liquid wort is
made from malt
• Hops are added and
liquid is boiled and
cooled
• Fermentation by yeast
produces beer
containing ethanol and
carbon dioxide
Wine
• Crushed grapes and
yeast are put into a
tank
• Ethanol stays in the
tank, while carbon
dioxide escapes
Bread
• Fermentation of
sugars in the dough
by yeast
• Carbon dioxide makes
the dough rise
• Baking in the oven
kills the yeast, stops
fermentation and
evaporates the
ethanol
Production of soy sauce
• Soak soy beans, boil
and drain
• Mix a mash of soy
beans with toasted
wheat
• Add a culture of
Aspergillus oryzae
• Incubate for 3 days at
85°F
• Add salt and water
and ferment for 3-6
months
• Filter and pasteurize
Food preservation with sugar
•
1.
2.
3.
4.
Increasing sugar
content of food
preserves it because
it is a dehydrating
environment for
bacteria, yeast, and
mold
Boil fruit with sugar to
kill microorganisms
and dissolve sugar
Add some pectin so it
will gel
Seal in hot sterile jars
No need to
refrigerate
Food preservation with acid
• Leave vegetables in a
salt solution, then
strain and rinse
• Place raw vegetables
in sterile jars
• Pour hot vinegar and
spices over the
vegetables creating an
acid environment
• Put on lids and
process in a hot
water-bath to give a
tight seal by creating a
vacuum so that no
mold can grow
Salmonella poisoning
• Symptoms occur 12-72 hrs after infection and last 4-7
days
• Diarrhea
• Fever
• Abdominal cramps
• Small # develop Reiter’s syndrome
• Transmission
• Improper hand washing after going #2
• Improper cooking of food
• Improper hand washing after touching feces of pets
• Improper hand washing after handling reptiles
• Raw meat cut on cutting board transferred to other
food
• Irrigation with contaminated water
• Raw eggs
• Unpasteurized milk or dairy products
• Treatment
• Treat dehydration by drinking lots of water,
preferably with sugar and salt
• Intravenous fluid
• Antibiotics if passed to blood
• What food product was there a recent recall of due
to food poisoning?
• What should be done to keep another such
outbreak from causing sickness and death?
• http://www.washingtonpost.com/wpdyn/content/article/2009/05/03/AR2009050301828.
html
F.5
Metabolism of microbes
Assessment Statements
F.5.1 Define the terms photoautotroph,
photoheterotroph, chemoautotroph and
chemoheterotroph.
F.5.2 State one example of a photoautotroph,
photoheterotroph, chemoautotroph and
chemoheterotroph.
F.5.3 Compare photoautotrophs with
photoheterotrophs in terms of energy sources and
carbon sources.
F.5.4 Compare chemoautotrophs with
chemoheterotrophs in terms of energy sources and
carbon sources.
F.5.5 Draw and label a diagram of a filamentous
cyanobacterium.
F.5.6 Explain the use of bacteria in the bioremediation
of soil and water.
Definitions
• Photoautotroph – an organism that uses
light energy to generate ATP and
produces organic compounds from
inorganic substances (Anabaena)
• Photoheterotroph – an organism which
uses light energy to generate ATP and
obtains organic compounds from other
organisms (Rhodobacter sphaeroides)
• Chemoautotroph – an organism that
uses energy from chemical reactions to
generate ATP and produces organic
compunds from inorganic substances
(Nitrosomonas)
• Chemoheterotroph – an organism that
uses energy from chemical reactions to
generate ATP and obtains organic
compounds from other organisms
(Saccharomyces)
Photoautotroph
Photoheterotroph
Energy source
Light
Light and organic
compounds
Carbon source
Carbon dioxide
Organic
compounds
Chemoautotroph
Chemoheterotroph
Energy source
Inorganic
compounds
Organic compounds
Carbon source
Carbon dioxide
Organic compounds
Anabaena
• Filamentous cyanobacterium
• Lives on grass and in freshwater ponds
• Two distinct and interdependent cell types
• Heterocysts
• Photosynthetic cells
• Heterocysts fix nitrogen from dinitrogen in
the air into nitrogen compounds such as
ammonia which is used to make proteins
• Photosynthetic cells produce
carbohydrates
• Akinete - spore-like cell capable of
withstanding certain environmental
extremes and of germination
Bioremediation
• Use of bacteria and fungi to treat
environments such as soil or water
contaminated with polluting agents such
as pesticides, oil and industrial solvents
• The microorganisms derive energy for
their own growth and reproduction
F.6
Microbes and disease
Assessment Statements
F.6.1 List six methods by which pathogens are transmitted
and gain entry to the body.
F.6.2 Distinguish between intracellular and extracellular
bacterial infection using Chlamydia and Streptococcus as
examples.
F.6.3 Distinguish between endotoxins and exotoxins.
F.6.4 Evaluate methods of controlling microbial growth by
irradiation, pasteurization, antiseptics and disinfectants.
F.6.5 Outline the mechanism of the action of antibiotics,
including inhibition of synthesis of cell walls, proteins and
nucleic acids.
F.6.6 Outline the lytic life cycle of the influenza virus.
F.6.7 Define epidemiology.
F.6.8 Discuss the origin and epidemiology of one example of
a pandemic.
F.6.9 Describe the cause, transmission and effects of
malaria, as an example of disease caused by a
protozoan.
F.6.10 Discuss the prion hypothesis for the cause of
spongiform encephalopathies.
Methods of transmission of
pathogens
1.
2.
3.
4.
5.
6.
Food
Water
Aerial (water droplets in air)
Anima vectors
Puncture wounds
Sexual contacts
Intracellular infections
• Example: Chlamydia
• Live inside a cell of the host (epithelial
cells which line genital tract)
• When cells reproduce, bacterium splits out
and moves into genital tract
• Does not produce toxins (some people are
asymptomatic)
• Does not directly damage cells (may
cause PID or infertility)
• Not targeted by immune system
Extracellular infections
•
•
•
•
Example: Streptococcus
Lives in the host but outside a host cell
Produces toxins
Damages cells (produces invasins which
split open and dissolve host cells)
• Is targeted immediately by the immune
system
Endotoxins and exotoxins
• Endotoxins
• Lipopolysaccharides in walls of Grambacterium that causes fever and aches
• Ex. Salmonella
• Exotoxins
• Specific proteins secreted by bacteria
that causes symptoms such as muscle
spasms and diarrhea
• Ex. Clostridium tetani and Vibrio
cholerae
Methods to control bacterial
growth
•
•
•
•
Irradiation
• Gamma radiation kills all microbes
• Microwaves kill all microbes
• UV radiation is weakest; kills all bacteria but
leaves endospores
Disinfectants
• Kills bacteria but not endospores
• Damaging to mucous membranes and skin
Antiseptics
• Less effective, but safe for skin
Pasteurization
• Kills pathogens, but is bacteriostatic for
nonpathogenic bacteria
Antibiotics
• Antimicrobial agents produces by
microbes which inhibit or kill other
microbes
• Cell wall synthesis inhibition – inhibit
production of peptidoglycan (ex. penicillin)
• Protein synthsis inhibition – attack the
bacterial ribosome (ex. streptomycin)
• Nucleic acid inhibition – affect synthesis
of DNA and RNA or attach to DNA or RNA
so message can’t be read (ex. rifampicin)
Epidemiology
• Study of the occurrence, distribution, and
control of disease in a population
• Occurrence - # of people with disease
• Distribution – regions of the country/world
where it is occurring
• Control – best strategies to prevent its
spread
Pandemic
• Worldwide infections
• Spanish flu (1918)
• Asian flu (1957)
• Hong Kong flu (1968)
Spanish Flu
• Occurrence
• Killed 40-50 million people
• Distribution
• Across the globe
• Control
• gauze masks were issued and directed to be
worn in public
• Public gatherings banned
• Public institutions closed
• Quarantine of patients with flu
• Public education about hygiene
• Use of disinfectants and sterilization methods
• Development of vaccines
Lytic life cycle of influenza virus
1. Virus attaches to receptors on cell
2. Virus is taken into an endosome by endocytosis into
the cytoplasm
3. Coat of virus is removed and viral RNA enters the
cytoplasm
4. Viral RNA enters nucleus and makes mRNA
5. Some mRNA is transported to the cytoplasm where
it makes viral proteins (translation)
6. Viral proteins are transported back to the nucleus to
form a capsid around viral RNA
7. ER of the cell synthesizes viral envelope proteins
8. Viral envelope proteins are packaged at the Golgi
apparatus and transported to the cell membrane
9. Viral nucleocapsid recognizes proteins on the
membrane and buds off surround by the viral
envelope proteins
Malaria
• Causes
• Plasmodium falciparum
• Plasmodium vivax
• Plasmodium ovale
• Plasmodium malariae
• Transmission
• By female Anopheles mosquito
• Plasmodia reproduce in gut of mosquito
• Egg sac ruptures and releases cells
called sporozoites which travel to
salivary glands
• When mosquito bites human,
sporozoites enter bloodstream and travel
to liver
• Develop further and burst out of the liver
to invade red blood cells
• Symptoms
• Anemia
• Bouts of fever chills
• Shivering
• Pain in the joints
• headache
Spongiform encephalopathies
• Holes form in brain tissue
• Similar to scrapie which is common in
sheep
• It jumped species barrier and was
transmitted to cattle in their feed
• Humans then contracted disease by eating
contaminated meat
• Variant Creutzfeldt-Jakob disease
Prion hypothesis
• The casual agent for vCJD is caused by a
virus with a nucleic acid core and a protein
coat protecting and hiding the nucleic acid
• Protein causes disease
• Nucleic acids have not been found
• Have witnessed proteins causing normal
proteins to change shape which argues
against model that only nucleic acids can
code for the shape of proteins