Ib Option F - Microbes and Biotechnology

Option F: Microbes and Biotechnology

Diversity of Microbe
F.1.1
Outline the classification of living organisms into three domains.
Three domains of living organisms: 1. Archaea - very primitive; live in extreme habitats 2. Eubacteria - more advanced 3. Eukaryota - all life forms with eukaryotic cells (have a nucleus)
Use of ribosomal RNA sequences for classification rRNA is found in all cells rRNA is easy to isolate
Analyzed to determine the exact sequence of nucleotide bases
The bases are a complimentary copy of DNA
Can be compared by the use of computers and statistics
F.1.2
Explain the reasons for the reclassification of living organisms into three domains
There were found to be several differences between the domains now known as Archaea and Eubacteria. The major reason was due to differences in the genes that transcribe rRNA. Other reasons include cell wall differences, lipid bonding and rRNA sequences.
F.1.3
Distinguish between the characteristics of the three domains. Domain | Histones | Introns | Ribosome Size | Cell Wall made of peptidoglycan | Cell Membrane | Archaea | Proteins similar to histones | No | 70S | Not present | Ether-linked glycerides, chirality of glycerol, saturated, branched, L-form of glycerol | Eubacteria | No | No | 70S | Present | Ester-linked glycerides, unbranched, saturated or monounsaturated, D-form of glycerol | Eukaryota | Yes | Yes (most) | 80S | Cell wall not always present; not made of peptidoglycan | Ester-linked glycerides, unbranched polyunsaturated, fluid, embedded with proteins and glycoproteins, D-form of glycerol |
F.1.4
Outline the wide diversity of habitat in the Archaea as exemplified by methanogens, thermophiles and halophiles.
Methanogens:
* Obligate anaerobes (must be without oxygen) * Produce methane as waste product * Found in the guts of cows, termite guts, waste landfills and marshes
Thermophiles:
* Live at temperatures close to boiling * Tend to be extreme thermophiles (60°C to 100°C) * Found in deep sea vents and hot springs
Halophiles:
* Live in saline habitats with high salt concentrations * Tend to be extreme halophiles (very high concentrations) * Found in the Great Salt Lake, The Dead Sea, and on Saltines
F.1.5
Outline the diversity of Eubacteria, including shape and cell wall structure
Shapes of Eubacteria: * Coccus – round / spherical * Bacillus - rod-shaped * Spirilla - spiral * Vibrio - comma-shaped

Cell Wall Structure: * Gram Negative * 2 cell membranes * one single thin peptidoglycan * lipopolysaccharides outside of wall * Gram Positive * 1 cell membrane * several layers peptidoglycan
Peptidoglycan
Peptidoglycan
Protein
Protein

F.1.6
State, with one example, that some bacteria form aggregates that show characteristics not seen in individual bacteria
Some bacteria form aggregates that show characteristics not seen in individual bacteria
Vibrio fischeri: * Single individuals do not emit light unless they become part of a population with a high density * V. fischeri releases a regulatory substance into its surroundings * In dense populations, the concentration of the substance becomes high enough to trigger bioluminescence * Happens when V. fischeriare living in mucus matrix in a squid
Another example is Streptococcus mutans which forms biofilms on teeth, commonly known as plaque.
F.1.7
Compare the structure of the cell walls of Gram-positive and Gram-negative Eubacteria. Cell wall structure | Gram positive | Gram negative | Complexity | Simple | Complex | Amount of peptidoglycan | Large amount | Small amount | Peptidoglycan placement | In outer layer | Covered by outer membrane | Outer membrane | Absent | Present with lipopolysaccharide attached |
Gram-positive:
* Simple, one-cell membrane * Several layer of peptidoglycan * No outer membrane
Gram-negative:
* Complex cell wall * Small amount of peptidoglycan * Thin peptidoglycan layer * Inner and outer membrane with peptidoglycan in between
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.
Viruses are surrounded by Capsid Proteins * Naked Capsid - no membrane/envelope outside protein coat * Enveloped Capsid - cell membrane from host surrounds protein coat
Genetic material: * Class 1 – one molecule of double stranded DNA * Class 2 – one molecule of single stranded DNA * Class 3 – several molecules of doubles stranded RNA * Class 4 – one molecule of single stranded RNA
F.1.9
Outline the diversity of microscopic eukaryotes, as illustrated by Saccharomyces, Amoeba, Plasmodium, Paramecium, Euglena and Chlorella Organism | Nutrition | Locomotion | Cell Wall | Chloroplasts | Cilia or Flagella | Saccharomyces | heterotroph (extracellular digestion) | absent | made of chitin | absent | absent | Amoeba | heterotroph (intracellular digestion) | slides using pseudopodia (amoeboid movements) | absent | absent | absent | Plasmodium | heterotroph (intracellular digestion) | glides on substrate | absent | absent | absent | Paramecium | heterotroph (intracellular digestion) | swimming (cilia) | absent | absent | cilia | Euglena | autotroph and heterotroph | swimming (flagella) | absent | present | flagella | Chlorella | autotroph | none | made of cellulose | present | absent |
Microbes and the Environment
F.2.1
List the roles of microbes in ecosystems, including producers, nitrogen fixers and decomposers.
Producers:
* Microscopic algae and some bacteria use chlorophyll to trap sunlight * Chemosynthetic bacteria use chemical energy
Change inorganic molecules into organic molecules that can be used by other organisms for food
Nitrogen fixers: * Bacteria which remove nitrogen as from the atmosphere and fix it into nitrates which are usable by producers.
Decomposers:
* Breakdown detritus (organic molecules) and release inorganic nutrients back into the ecosystem
F.2.2
Draw and label a diagram of the nitrogen cycle

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F.2.3
State the roles of Rhizobium, Azotobacter, Nitrosomonas, Nitrobacter and Pseudomonas denitrificans in the nitrogen cycle.
Nitrogen Fixation: * Mutalistic: Rhizobium lives in symbiosis with legumes (its root nodules) and fixes nitrogen for them * Free-living: Azotobacter fixes nitrogen and lives freely in the soil without a host
Nitrification:
* Nitrosomonas converts ammonia (NH3) into nitrite (NO2-) * Nitrobacter changes nitrite into nitrate (NO3-) which is usable by plants
Denitrification:
* Conversion of nitrates to nitrogen gas * Pseudomonas denitrificans removes nitrates and nitrites and puts nitrogen gas back in atmosphere
F.2.4
Outline the conditions that favor Denitrification and nitrification.
Conditions favoring nitrification: * available oxygen/aerated soils * neutral pH * warm temperature
Conditions favoring Denitrification: * No available oxygen/anaerobic soils (flooding or compacted soil) * High nitrogen input
F.2.5
Explain the consequences of releasing raw sewage and nitrate fertilizer into rivers
Biochemical oxygen demand or BOD is a chemical procedure for determining the amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period
Raw Sewage =>
Raw sewage consists of organic matter and may contain pathogens, which are dangerous if drunk/bathed in 1. amount of saprotrophs increase to break down organic matter 2. a biochemical oxygen demand (BOD) occurs due to high levels of oxygen used 3. deoxygenation of water 4. oxygen-dependent organisms are forced to emigrate/die 5. death and decay 6. decomposition 7. ammonia, phosphorus and minerals released 8. nitrification 9. eutrophication occurs due to high nutrient levels 10. algae proliferate 11. provided no algal bloom occurs, the rivers recovers eventually
Nitrate Fertilizer => 1. Rivers leech off nitrate from soil 2. if application of nitrate fertilizer is great enough, eutrophication occurs 3. algae proliferate (increasing oxygen levels) 4. if nitrate levels in excess, algal bloom occurs 5. due to large amount of algae, some are deprived of sunlight and die 6. saprotrophs are needed to break down the organic matter 7. this creates a biochemical oxygen demand (BOD) 8. deoxygenation occurs 9. oxygen-dependent organisms are forced to emigrate/die 10. increase in ammonia and phosphorus levels 11. nitrification 12. eutrophication 13. algae proliferate 14. provided no new algal bloom occurs, river recovers eventually.
Simpler Module: 1. High and excess nitrates and phosphates fertilize the algae in water 2. Increased growth of algae (algal bloom) 3. Algae decomposed by aerobic bacteria which use up oxygen in water, resulting in deoxygenation 4. The high use of oxygen is called biochemical oxygen demand (BOD)
F.2.6
Outline the role of saprotrophic bacteria in the treatment of sewage using trickling filter beds and reed bed systems.
Primary treatment – is the removal of solid waste (plastic bags, wood and other inorganic material) and the killing of harmful bacteria. Fats and oil float to the top and solid material sinks to the bottom. Sludge decomposed by anaerobic bacteria and inorganic material is turned into methane. 30% is removed in this stage
Secondary treatment – uses aerobic bacteria to mix the air with the water. The bacteria feed on the inorganic matter. 60% is removed in this stage leaving 10%
Tertiary treatment – ponding occurs for ten days. Bacteria either starve to death or are killed by ultraviolet radiation
Trickling Filter System: * Bed of stones 1-2 meters wide * A biofilm of aerobic saprotrophs are on the rocks, which feed on organic matter, cling to the stones and act on the sewage trickled over (this is done to aerate the sewage), until it is broken down. * Cleaner water trickles out the bottom of the bed to another tank where the bacteria are removed and the water treated with chlorine to disinfect it

Reed Bed System: * Artificial wetland used to treat waste water * Waste water provides both the water and nutrients to the growing reeds * The reeds are harvested for compost and the organic waste is broken down by saprotrophic bacteria * Nitrification of ammonia to nitrite and nitrite to nitrate * Nitrates and phosphates released are used as fertilizer by the reeds * Remaining nitrates are denitrified
F.2.7
State that biomass can be used as raw material for the production of fuels such as methane and ethanol.
Biomass (organic matter) can be used as raw material for the production of fuels such as methane and ethanol. Examples include manure and cellulose.
F.2.8
Explain the principals involved in the generation of methane from biomass, including the conditions needed, organisms involved and the basic chemical reactions that occur.
One group of Eubacteria are needed to convert the organic matter into organic acids and alcohol
A second group of Eubacteria convert these into acetate, carbon dioxide and hydrogen
Methanogenic bacteria are needed to create the methane, by two chemical reactions:
Carbon dioxide + hydrogen -> methane + water
Acetate -> methane + carbon dioxide (breakdown of acetate)
Conditions required: * No free oxygen (anaerobic) * Constant temperature of about 35°C * pH not too acidic

Microbes and biotechnology

F.3.1
State that reverse transcriptase catalyzes the production of DNA from RNA.
Reverse transcriptase catalyzes the production of DNA from RNA and is used by retroviruses.

F.3.2
Explain how reverse transcriptase is used in molecular biology.
RNA and reverse transcriptase enter the host cell, injected by the virus. Reverse transcriptase makes a DNA copy of itself. DNA of virus injects into nucleus and integrates into the DNA of the host cell. It can be used to remove introns from DNA. Conversion of mRNA (made from DNA and with introns removed) to cDNA after extracted.

Life cycle of the HIV virus: 1. The HIV virus attaches to a host cell. 2. The RNA of the virus and the enzyme reverse transcriptase enter the host cell. 3. Within the cell, reverse transcriptase copies viral RNA into cDNA (complementary DNA). 4. Next, cDNA makes a second strand which is a complement to the first strand of DNA. Viral DNA is destroyed. 5. Finally, the new double-stranded viral DNA enters the nucleus of the host cell. 6. If the HIV virus is active, it will use this DNA to make more HIV viruses. They will then burst out of the cell and infect other cells.
F.3.3
Distinguish between somatic and germ line therapy.
Somatic: consists of replacing bodily cells. Somatic gene therapy cures the disease in the individual; however, it can still be passed to offspring.
Germ-line therapy: consists of treating the gametes. Germ-line therapy stops spread of genetic disease to offspring; however, individual remains afflicted.

F.3.4
Outline the use of viral vectors in gene therapy.
Viral vectors take out harmful genes and put the normal genes in the cells
Retroviral therapy has more permanent change and work better
SCIDS:
* First successful example of gene therapy * Replaced gene allows for the production of ADA
F.3.5
Discuss the risks of gene therapy. * Gene therapy is a very dangerous process; the viral vectors can trigger a cancer-causing gene. * Genes can be over-expressed and make too much protein. * Virus vector might place the new gene in the wrong location in the DNA molecule. * Might stimulate an immune reaction. * Virus vector might be transferred from person to person. * Does not always work, therefore raising the hopes of patients/families and then drop their hopes. * Potential Alternative: Adenoviruses do not incorporate themselves into the human genome

Microbes and Foods Production

F.4.1
Explain the use of Saccharomyces in the production of beer, wine and bread.
Beer:
1. Sweet liquid wort is made from malt 2. Hops are added and liquid is boiled and cooled 3. Wetted barley allowed to germinate: amylase is formed 4. Amylase catalysis starch into maltose 5. Fermentation by yeast produces beer containing ethanol and CO2

Wine: * Crushed grapes and yeast are put into a tank * Yeasts respite aerobically until oxygen is depleted * The yeasts then switch to fermentation (anaerobic) * Ethanol stays in the tank, while CO2 escapes * Process ends when ethanol concentration reaches ax. 15%, killing the yeast, or when substrates have been used up

F.4.2
Outline the production of soy sauce using Aspergillus oryzae. 1. Soak soy beans, boil and drain 2. Mix a mash of soy beans with toasted wheat 3. Add a culture Aspergillus oryzae 4. Incubate for 3 days at 30°C 5. Add salt and water and fermentation of starch and proteins to alcohol, organic acids, sugars and amino acids occurs for 3-6 months. 6. Filter and pasteurize; liquid produced is the soy sauce product.

F.4.3
Explain the use of acids and high salt or sugar concentrations in food preservation.
Food preservation with acid: * Microbes cannot live in low pH levels. Common examples include vinegar and production of yoghurt.
Food preservation with high sugar/salt concentrations: * High concentrations of either will kill any microbes in food samples, since the high concentration draws out water through osmosis. Common examples include honey, jam, and salted meat.

F.4.4
Outline the symptoms, method of transmissions and treatment of one named example of food poisoning.
Transmission of Salmonella food poisoning:
It lives in the intestinal tract and is transmitted after ineffective hand washing. It can be found in the feces of some pets and be transferred to food. It can also be transferred by eating contaminated foods which are not properly cooked. Uncooked meat cut on a cutting board which if not washed and raw eggs can also cause transfer of Salmonella
Treatment of Salmonella food poisoning: * Treat the dehydration by drinking lots of water * Serious dehydration is treated with intravenous * Antibiotics can be given if the infection is serious and has spread from intestine to the blood

Metabolism of Microbes (AHL)
F.5.1
Define the terms photoautotroph, photoheterotroph, chemoautotroph, and chemoheterotroph.
Photoautotroph:
* An organism that uses light energy to generate ATP and produce organic compounds from inorganic substances.
Photoheterotroph:
* An organism that uses light energy to generate ATP and obtains organic compounds from other organism.
Chemoautotroph:
* An organism that uses energy from chemical reactions to generate ATP and produces organic compounds from inorganic substances.
Chemoheterotroph:
* An organism that uses energy from chemical reactions to generate ATP and obtain organic compounds from other organisms.
F.5.2
State one example of a photoautotroph, photoheterotroph, chemoautotroph and chemoheterotroph.
Photoautotroph - Cyanobacteria (e.g. Anabaena)
Photoheterotroph – Rhodobacter sphaeroides
Chemoautotroph – Nitrosomonas (a nitrogen-fixing bacteria in the soil)
Chemoheterotroph - Saccharomyces
F.5.3
Compare photoautotrophs with photoheterophs in terms of energy sources and carbon sources.
Both create ATP from light | Photoautotrophs | Chemoheterotrophs | Energy source | Light | Light and organic compounds | Carbon source | Carbon dioxide | Organic compounds |
F.5.4
Compare chemoautotrophs with chemoheterotrophs in terms of energy sources and carbon sources. | Chemoautotrophs | Chemoheterotrophs | Energy source | Inorganic compounds | Organic compounds | Carbon source | Carbon dioxide | Organic compounds |
F.5.5
Draw and label a diagram of a filamentous cyanobacterium.

* Photosynthetic cells contain genetic material, cell walls and photosynthetic membranes. * Heterocysts act as nitrogen-fixers; are much larger and fewer than the photosynthetic cells.

F.5.6
Explain the use of bacteria in the bioremediation of soil and water.
Bioremediation
* Use of microbes, fungi, plants or enzymes to remove environmental contaminants from water and soil. * The bacteria break down the chemicals or convert them so that they can be filtered out
Oil Spills: * Microbes oxidize hydrocarbons; takes a long time and some hydrocarbons are very difficult to oxidize.
Pesticide Pollution: * Microbes gradually break down pesticides
Selenium pollution: * Microbes absorb selenium ions and oxidize them into metallic selenium, which is far less toxic.
Solvent pollution: * Microbes dechlorinate these solvents in anaerobic conditions, releasing far less toxic substances.
Examples:
* Pseudomonas using oil for energy * Dehalococcoides ethenogenes breaking down chlorinated solvents in soil

Microbes and Disease (AHL)
F.6.1
List six methods by which pathogens are transmitted and gain entry to the body. 1. Food - ingestion of food with bacteria can cause food poisoning 2. Water - polluted or unclean water can cause disease 3. Air/Droplets - water droplets in the area can carry organisms 4. Animal vectors - insects and other animals can carry disease 5. Puncture wounds/Cuts - break the skin barrier and allow entry of bacteria or viruses. 6. Sexual contact - with an infected person can transmit disease
F.6.2
Distinguish between intracellular and extracellular bacterial infection using Chlamydia and Streptococcus as examples.
Intracellular Bacterium – Chlamydia: * Rely on host's metabolism for certain of metabolic processes. * Live within the epithelial cells of that line the genital tract * Does not produce toxins nor directly damage cells, but can cause long-term problems (such as pelvic inflammatory disease or infertility) * Is not targeted by the immune system due to its hidden nature
Extracellular Bacterium – Streptococcus: * Lives inside the host, but in the intercellular spaces and use the nutrients available there. * Produces toxins and damage cells. * Streptococcus produces toxins that kill host cells and molecules called invasins which split open and dissolve host cells * Is targeted immediately by the immune system and antibodies are made to fight the infection
F.6.3
Distinguish between endotoxins and exotoxins.
Endotoxins:
Lipopolysaccharides less toxic but are heat-stable and are located in the walls of Gram-negative bacteria that cause fever and aches.
Composed of primary lipids
Exert effect only when bacteria die
Dose required to produce symptoms is relatively high
Exotoxins:
Specific proteins secreted by bacteria that cause symptoms such as muscle spasms (tetanus) and diarrhea
Are located in gram-positive bacteria
Released as part of normal
F.6.4
Evaluate methods of controlling microbial growth by irradiation, pasteurization, antiseptics and disinfectants.
Irradiation:
* Ionizing radiation * Some microbes are resistant (e.g. Clostridium botulinum) * Free radicals may alter the flavor * Some consumers are afraid to use products of 'radiation'
Pasteurization:
* Application of high temperature, which is very quickly cooled down and repeated. * Very effective, can kill all pathogens if done at high enough temperatures at long enough periods * Usually, however, this is not done as it alters the flavor of e.g. milk
Antiseptics:
* Kill/prevent microbial growth; prevent infection * Mild chemicals that are less effective than disinfectants but not damaging to skin and mucous membranes * Too toxic to be taken through consumption
Disinfectants:
* Extremely effective sterilization; does not kill endospores, however. * Cannot be used on living tissue, or through consumption. * Useful for sterilization of medical tools, floors, furniture, etc.

F.6.5
Outline the mechanism of the action of antibiotics, including the inhibition of synthesis of cell walls, proteins and nucleic acids.
An Antibiotic is a substance produced by one microorganism that is capable of destroying or inhibiting the growth of another microorganism. Antibiotics are regarded as secondary metabolites because they are not essential for the growth or reproduction of the organism that produces them. * Antibiotics that destroy – biocidal * Antibiotics that inhibit growth – biostatic
Cell wall synthesis inhibition (e.g. Penicillin): * Antibiotics inhibit the synthesis of peptide links interrupting the production of peptidoglycan for the cell walls of bacteria – Without cell walls, the new bacteria cannot survive
Protein synthesis inhibition (e.g. Erythromycin, Streptomycin): * Either inhibit protein synthesis or promote the synthesis of abnormal proteins in bacteria cells – the bacteria bind to the ribosomes (the sites of protein synthesis) * Does not attack the ribosomes of human cells because bacterial ribosomes (70S) differ from those of humans (80S)
Nucleic acid inhibition (e.g. Anthracyclines, Rifampin): * Disrupt the synthesis of nucleic acids. * Anthracyclines inhibit DNA replication * Rifampin prevents transcription – DNA to mRNA

F.6.6
Outline the lytic life cycle of the influenza virus 1. Virus attaches to cell surface by means of specific receptors (e.g. glycoproteins) 2. Virus is taken up in membrane-enclosed endosome during endocytosis 3. Uncoating occurs in endosome and viral RNA (genome) is released into the cytoplasm 4. RNA of viral genome transported into the nucleus, where it is copied and replicated by the viral enzyme into RNA, acting as template for more RNA and a messenger 5. Some RNA transported into cytoplasm and translated into viral proteins which are transported back into the nucleus to assemble the capsid 6. Viral envelope proteins assemble in cell membrane and the capsid buds off of these points, using the cell membrane as its envelope 7. Lysis, or the bursting of the cell, occurs and releases new virus particles to attack other cells.

F.6.7
Define epidemiology.
Epidemiology is the study of the occurrence, distribution and control of disease.
F.6.8
Discuss the origin and epidemiology of one example of a pandemic.
Spanish Flu of 1918 * Killed 40-50 million people * Origin believed to be in China * Travel of soldiers for WWI aided spread of flu * Hang washing encouraged, public gathering banned
F.6.9
Describe the cause, transmission and effects of malaria, as an example of disease caused by a protozoan.
Cause:
* Malaria is caused by parasites that live in red blood cells and cells of the liver. The parasites are transmitted from person to person by the female mosquito
Transmission:
* Uninfected female Anopheles mosquito bites an infected person * The mosquito takes up parasites in her meal of blood * Once they are safely inside the mosquito, some of these parasites reproduce sexually in the mosquito’s gut * The parasites then travel to the salivary glands of the mosquito where they mature into sporozoites * At the next meal, the mosquito injects a small amount of saliva into her victim to stop the blood clotting, the sporozoites are then passed into a new host * The sporozoites are carried along in the blood of the new host until they reach the liver
Symptoms/Effects:
* Presents as symptoms of anemia, bouts of fever chills, shivering, joint pain, and headache
F.6.10
Discuss the prion hypothesis for the cause of spongiform encephalopathy’s.
States that the causal agent for spongiform encephalopathy’s in humans has no nucleic acid and consists only of misfolded proteins (PrPSC).
The infecting agent is a prion and the abnormal protein alone causes the disease.
Scientists have not found any nucleic acids in prion particles.
Abnormally shaped prions that can cause normal proteins (PrPC) to change to an abnormal shape, resulting in cell death.
Chronic, degenerative diseases of the nervous system that form holes in brain tissue (hence the name), causing symptoms such as memory loss, personality changes, speech lapses and ultimately death. * Examples include scrapies in sheep, BSE in cattle and CJD in humans.