Option F: Microbes and Biotechnology


F1 Diversity of Microbes

F.1.1. Outline the classification of living organisms into three domains
There are three domains into which all living things are classified into. The three domains are: Archaea, Eukarya, and Eubacteria. Eukarya is the only domain with eukaryotes. Archaea and Eubacteria are both prokaryotes. Archaea is a domain with organisms that are very primitive and live in extreme environments. An example would be thermophiles. Eubacteria is basically the bacteria domain and they are more advanced versions of organisms in the Archaea domain. An example is E. coli. Finally Eukarya is the domain with all eukaryotic organisms. An example would be animals, humans, plants, etc. rRNA is used to help with the classification of organisms because it is easy to locate and found in all cells. The use the sequences help to define the organism’s domain.

F.1.2. Explain the reasons for the reclassification of living organisms into three domains.
This reclassification is different from the original. This one is based on the rRNA sequences, the differences in cell walls, etc. It is broader than the binomial nomenclature. The differences in the genes that transcribe rRNA are a major reason for reclassification too.

F.1.3. Distinguish between the characteristics of the three domains.
Eukarya
Eubacteria
Archaea
Eukaryotic cells
Histones
Most organisms in this domain contain introns
Size of ribosome: 80S
Cell wall not always present; Not made of peptidoglycan
Cell wall with ester links, D-form glycerol, polyunsaturated, fluid with many proteins
Prokaryotic cells
No histones
No introns
Size of ribosome: 70S
Cell wall of peptidoglycan
Cell membrane with ester links, D-form glycerol, unsaturated/monounsaturated
Prokaryotic cells
Contains proteins similar to histones
No introns
Size of ribosome: 70S
Cell wall of protein but lack peptidoglycan
Cell membrane of phospholipids, contain ether lipids, saturated, L-form of glycerol


F.1.4. Outline the wide diversity of habitat in the Archaea as exemplified by methanogens, thermophiles, and halophiles.
Methanogens must be without oxygen and produces methane as a waste product. It can be found anywhere from the guts of cows to marshes. Thermophiles match the name “thermo” because it can survive at temperatures close to boiling. They can be found in hot springs. Halophiles live in high salt concentrated environments. They can be found in the Great Salt Lake. This shows how different and unique Archaea can be. They are very diverse and have a high range of habitats from volcanoes to guts.

F.1.5. Outline the diversity of Eubacteria, including shape and cell wall structure.
Eubacteria is a diverse domain and has a high range. The basic shapes of Eubacteria are coccus, bacillus, spirilla, and vibrio. These are basically round, rod-shaped, spiral, and comma-shaped. There are two different cell wall structures specific to the Eubacteria domain. The first is 2 cell membranes, one thin layer of peptidoglycan with polysaccharides out of the wall. The second type is one with multiple layers of peptidoglycan.

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. An example of this is Vibrio fisheri. It is a bacteria found in seawater with the ability to emit light. As an individual bacterium it cannot but as they become part of a population with high density they are able to. V.fisheri releases regulatory substances into the environment and when a group comes together the concentration can become high enough to trigger bioluminescence. An example of when it happens is when V.fisheri is living in a group in a mucus matrix in the light organs of a squid.

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F.1.7. Compare the structure of the cell walls of Gram-positive and Gram-negative Eubacteria.

Gram-Positive
Gram-Negative
Simple
One-cell membrane
Multiple layers of peptidoglycan
No outer membrane
Complex cell wall
Only a thin layer of peptidoglycan
Inner and outer membrane with peptidoglycan in between
Small amount of peptidoglycan



cellwall.gif


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.
In a naked capsid virus there is no membrane outside protein coat. In an enveloped capsid virus the cell membrane from host cell surrounds protein coat. DNA is double stranded while RNA is single stranded. RNA viruses are more prone to mutations because RNA polymerase lacks the proofreading ability of DNA polymerase.

F.1.9. Outline the diversity of microscopic eukaryotes, as illustrated by Saccharomyces, Amoeba, Plasmodium, Paramecium, Euglena and Chlorella.

Cell Wall
Chloroplasts
Cilia/Flagella
Mode of Locomotion
Mode of Nutrition
Saccharomyces
Present
Absent
Absent
Absent
Heterotrophic
Amoeba
Absent
Absent
Absent
Slides using pseudopodia
Heterotrophic
Plasmodium
Absent
Absent
Absent
Glides on substrate
Heterotrophic
Paramecium
Absent
Absent
Cilia
Swimming with Cilia
Heterotrophic
Euglena
Absent
Present
Flagella
Swimming with Flagella
Heterotrophic and Autotrophic
Chlorella
Present
Present
Absent
None
Autotrophic

F2 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.
http://latewire.com/images/fekken_random/nitrogen-cycle-diagram.gif
http://latewire.com/images/fekken_random/nitrogen-cycle-diagram.gif


F.2.3.

  • 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 favour denitrification and nitrification.
  • Conditions favouring nitrification
  • available oxygen/aerated soils
  • neutral pH
  • warm temperature
  • Conditions favouring 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
  • Raw Sewage
  • Raw sewage consists of organic matter and may contain pathogens, which are dangerous if drunk/bathed in => amount of saprotrophs increase to break down organic matter => a biochemical oxygen demand (BOD) occurs due to high levels of oxygen used =>deoxygenation of water => oxygen-dependent organisms are forced to emigrate/die => death and decay => decomposition => ammonia, phosphorus and minerals released => nitrification => eutrophication occurs due to high nutrient levels => algae proliferate => provided no algal bloom occurs, the rivers recovers eventually
  • Nitrate Fertilizer
  • Rivers leech off nitrate from soil => if application of nitrate fertilizer is great enough, eutrophication occurs => algae proliferate (increasing oxygen levels) => if nitrate levels in excess, algal bloom occurs => due to large amount of algae, some are deprived of sunlight and die => saprotrophs are needed to break down the organic matter => this creates a biochemical oxygen demand (BOD) => deoxygenation occurs => oxygen-dependent organisms are forced to emigrate/die=> increase in ammonia and phosphorus levels => nitrification => eutrophication => algae proliferate => provided no new algal bloon occurs, river recovers eventually.
  • Simpler Module:
  • High and excess nitrates and phosphates fertilize the algae in water
  • Increased growth of algae (algal bloom)
  • Algae decomposed by aerobic bacteria which use up oxygen in water, resulting in deoxygenation
  • 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.

Trickling Filter System
  • Bed of stones 1-2 meters wide
  • A biofilm of aerobic saprotrophs are on the rocks, which feed on organic mater, 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 hte water treated with chlorine to disinfect
Red Beed System
  • 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 principles 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 mater 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


F3 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
  • Can be used to remove introns from DNA
  • Conversion of mRNA (made from DNA and with introns removed) to cDNA after extracted

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.
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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
  • 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

F4 Microbes and Foods Production


F.4.1 Explain the use of Saccharomyces in the production of beer, wine and bread.
  • Beer
  • Sweet liquid wort is made from malt
  • Hops are added and liquid is boiled and cooled
  • Wetted barley allowed to germinate: amlyase is formed.
  • Amylase catalyses starch into maltose.
  • Fermentation by yeast produces beer containing ethanol and CO2
  • Wine
  • Crushed grapes and yeast are put into a tank
  • Yeasts respirate 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.
  • Bread
  • Fermentation of sugars in the dough by yeast
  • CO2 makes the dough rise
  • Baking in the oven kills the yeast, stops fermentation and evaporates the ethanol


F.4.2 Outline the production of soy sauce using Aspergillus oryzae.
  • Soak soy beans, boil and drain
  • Mix a mash of soy beans with toasted wheat
  • Add a culture Aspergillus oryzae
  • Incubate for 3 days at 30°C
  • Add salt and water and fermentation of starch and proteins to alcohol, organic acids, sugars and amino acids occurs for 3-6 months.
  • 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, 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
  • Lives in the intestinal tract and is transmitted after ineffective hand washing
  • Can be found in the feces of some pets and be transferred to food
  • Eating contaminated foods not properly cooked
  • Uncooked meat cut on a cutting board which if not washed can cause transfer of Salmonella
  • Raw eggs
  • 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



  • F5 Metabolism of Microbes


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 organisms.
  • Chemoautotroph: An organism that uses energy from chemical reactions to generate ATP and produce 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 Photoheterotroph: Rhodospirillum; Rhodobacter
Chemoautotroph: Nitrobacter Chemoheterotroph: Mycobacterium tuberculosis; Lactobacillus

F.5.3. Compare photoautotrophs with photoheterotrophs in terms of energy sources and carbon sources.
Photoautotrophs and photoheterotrophs both create energy with the use of light. Photoautotrophs use CO₂ as their carbon source whereas photoheterotrophs use organic molecules as their carbon source.

F.5.4. Compare chemoautotrophs with chemoheterotrophs in terms of energy sources and carbon sources.
Chemoautotrophs get energy from chemicals. Their carbon source is organic compounds. While chemoheterotrophs get both their energy and carbon sources from organic compounds. They both share the same carbon source but their energy source differs.

F.5.5. Draw and label a diagram of a filamentous cyanobacterium.
I will use Anabaena as an example and label the photosynthetic cell (have genetic material, cell walls and photosynthetic membranes) and the heterocysts (nitrogen-fixing cells).
Heterocysts-2-LMagLab.jpganabaena.gif



















F.5.6. Explain the use of bacteria in the bioremediation of soil and water.
Bioremediation is a process that uses microorganisms, fungi, green plants and their enzymes to return the natural environment altered by contaminants to its original state. The enzymes in the bacteria are used to break down the contaminants so they can be filtered out. An example of bioremediation is selenium pollution. Microbes are used to absorb selenium ions and oxidize them into metallic selenium which is less toxic. Another example is solvent pollution in which microbes de-chlorinate solvents in anaerobic conditions producing less toxic wastes. The bacteria Dehalococcoides ethenogenes breaks down chlorinated solvents in soil.




F6 Microbes and Disease

F.6.1. List six methods by which pathogens are transmitted and gain entry to the body.
  1. Ingestion through food
  2. Breathing in airborne pathogens
  3. A cut, wounds, scrapes, etc.
  4. Polluted water
  5. “Vectors” such as mosquitoes, fleas, etc.
  6. Sexual contact

F.6.2. Distinguish between intracellular and extracellular bacterial infection using Chlamydia and Streptococcus as examples.
Chlamydia (intracellular)
Streptococcus (extracellular)
Relies on host for certain metabolic processes
Live in epithelial cells that line genital area
Do not produce toxins
Long-term damage
Is not detected by immune system as a threat
Lives in host in intercellular area where it gets it nutrients
Produces toxins to damage cells
Is detected by immune system which produces antibodies to fight it off immediately
Streptococcus produces toxins which kill host cells and molecules which do so too

F.6.3. Distinguish between endotoxins and exotoxins.
Endotoxins are the lipopolysaccharides in the walls of Gram-negative bacteria that cause fever and aches. Exotoxins are specific proteins secreted by bacteria that cause symptoms such as muscle spasms (tetanus) and diarrhea.

F.6.4. Evaluate methods of controlling microbial growth by irradiation, pasteurization, antiseptics, and disinfectants.
There are many methods in controlling microbial growth. In the chart below some of the methods are evaluated:
Irradiation
Pasteurization
Antiseptics
Disinfectants
Some microbes are resistant
Consumers are afraid to use “radiation” as it can cause cancer
Some microbes are resistant to high temperatures
Slows growth
Takes a long period of time
Can be very effective if done long enough and at a high enough temp.
Some can only prevent growth or inhibit
Too toxic to consume
Mild chemicals are less effective than disinfectants but less damaging
Potentially harmful/toxic
Does not kill endospores
Extremely effective
Cannot be used on living tissue or used for consumption

F.6.5. Outline the mechanism of the action of antibiotics, including inhibition of synthesis of cell walls, proteins and nucleic acids.
Antibiotics work by releasing antimicrobial agents produced by microbes which inhibit or kill other microbes. They inhibit the synthesis of cell walls by inhibiting the production of peptidoglycan found in bacteria cell walls. Without cell walls they will be unprotected and new bacteria cannot survive. They also inhibit synthesis of proteins by attacking the ribosomes of bacterial cells. They don’t attack human cells because of the size difference. With nucleic acid inhibition they affect the DNA/RNA synthesis or attach to them so they can’t be read. All of these interfere with the growth of bacterial cells.

F.6.6. Outline the lytic life cycle of the influenza virus.
- Virus attaches to cell surface
- Virus is taken in during the process of endocytosis
- Uncoating takes place and virus (RNA) is released
- RNA is taken into the nucleus where it is copied and replicated
- Some RNA is transported into cytoplasm and translated into viral proteins then back to the nucleus for assembling of capsid (shell of protein to protect nucleic acid)
- These enveloped proteins assemble in cell membrane and the capsid buds off
- The cell bursts and new viral particles are released

F.6.7. Define epidemiology.
Epidemiology is the study of the occurrence, distribution, and control of diseases.

F.6.8. Discuss the origin and epidemiology of one example of a pandemic.
A pandemic is a very widespread epidemic that affects a large geographic area, such as a continent. The example I will be using is the Bubonic plague a.k.a. The Black Death. It was a widespread bacterial infection in Europe. It is said to be originated in the Gobi Desert. It was carried by fleas on rats. The trade routes ships had carried these rats all around the world but it particularly occurred in Europe in which a claimed 200 million people died. The fleas use rodents as a host and leave them when they die. The bacterium aggregates in the guts of the fleas which regurgitates infected blood into the bite of rats/humans. The bacterium quickly multiplies and spreads. Quarantining was attempted but the disease was spreading rapidly. They did not have the knowledge of antibiotics or cures back then.

F.6.9. Describe the cause, transmission, and effects of malaria, as an example of disease caused by a protozoan.
Cause
Transmission
Effects
It is caused by an infection with a parasite called Plasmodium.
Plasmodium falciparum -causes malignant malaria. It causes the most severe symptoms and results in the most fatalities.
Plasmodium vivax - causes benign malaria with less severe symptoms than P. falciparum. P. vivax can stay in your liver for up to three years and can lead to a relapse.
Plasmodium ovale - causes benign malaria and can stay in your blood and liver for many years without causing symptoms.
Plasmodium malariae - causes benign malaria and is relatively rare.
A “vector” in this case a female mosquito Anopheles bites you after biting someone with malaria.
Plasmodia forms in the gut of the mosquito and the egg sac ruptures releasing sporozoites and travel to salivary glands.
These cells enter the bloodstream with mosquito bite and travel to liver.
There they develop, change form and invade red blood cells.
Then the process occurs again once a mosquito bites you.
It is an on-going cycle.
Some symptoms are rise of temperature, a fever, chills, loss of appetite, weakness, vomiting, headache, muscle pains, etc.
There are antibiotics to treat malaria.
Complications can occur if it is a serious case of malaria.
Many deaths are caused by malaria.

F.6.10. Discuss the prion hypothesis for the cause of spongiform encephalopathies.
A prion is an infectious agent mostly composed of protein. Spongiform encephalopathy is a disease more commonly known as mad cow disease. The prion hypothesis is a hypothesis proposed by Stanley Prusiner, in which he stated that denatured or malformed prions, proteins, are causing a disease. They change from the alpha helix form into the beta pleated. The validity of the hypothesis is still pondered. It can be genetic or formed by contact with an infected organism. Scientists have not found any nucleic acids in prion particles which causes the disease alone by infecting other cells causing the death of the cell. This in turn causes the death of the organism by destroying all the cells or making holes in the tissues of the brain/spinal cord.