IB Biology/Option F - Microbes and Biotechnology

Option F: Microbes and Biotechnology

Diversity of Microbes

F.1.1 Outline the classification of living organisms into three domains.

Three domains of living organisms

Archaea - very primitive; live in extreme habitats
Eubacteria - more advanced
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 complementary 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 (see F.1.3) 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 glyceral, 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 polyunstaturated, fluid, embeded 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, lipopoysaccharides outside of wall

Gram Positive

1 cell membrane, several layers 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

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.

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.

Capsid Proteins

Naked Capsid - no membrane/envelope outside protein coat
Enveloped Capsid - cell membrane from host surrounds protein coat

Genetic material

DNA (double or single stranded) or RNA (double or single stranded)

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	flagellae
Chlorella	autotroph	none	made of cellulose	present	absent

Sapratrophs are part of heterotroph.

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

examples: chlorella

Nitrogen fixers

Bacteria which remove nitrogen as from the atmosphere and fix it into nitrates which are usable by producers.

examples: rhizobium

Decomposers

Breakdown detritus (organic molecules) and release inorganic nutrients back into the ecosystem

examples: bacterial fungi

F.2.2 Draw and label a diagram of the nitrogen cycle http://www.edhsgreensea.net/Biology/taters/taters_images/nitrogen_cycle2.gif please see the link for the diagram

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 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(released from agriculture factories) => nitrification => eutrophication occurs due to high nutrient levels => algae proliferate => provided no algal bloom(abundance of algae) 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 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 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

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.

Defective gene in a somatic cell is corrected.

Affected individual is cured but he can still can pass the defective gene to his offspring.

Germ-line therapy: consists of treating the gametes

Defective gene in a germ cell(egg or sperm) is corrected.

Affected still has the disease but he can not pass on this to his offspring.

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(Adenosine Deaminase)

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

Sweet liquid wort is made from malt
Hops are added and liquid is boiled and cooled
Wetted barley allowed to germinate: amlyase is formed.
Amlyase 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 faeces 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

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 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 (e.g. Anabaena)
Photoheterotroph - Rhodospirillum; Rhodobacter
Chemoautotroph - Nitrobacter
Chemoheterotroph - Mycobacterium tuberculosis; Lactobacillus

F.5.3 Compare photoautotrophs with photoheterophs in terms of energy sources and carbon sources.

Both create ATP from light
Photoautotrophs use CO₂ as their carbon source
Photoheterotrophs use organic molecules as their carbon source

F.5.3 Compare chemoautotrophs with chemoheterotrophs in terms of energy sources and carbon sources.

Chemoautotrophs get their energy from chemicals and carbon from inorganic compounds
Chemoheterotrophs get their energy and carbon from organic compounds

F.5.4 Draw and label a diagram of a filamentous cyanobacterium.

Using Anabaena as an example, there are two types of cells:

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.5.5 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 oxidate hydrocarbons; takes a long time and some hydrocarbons are very difficult to oxidate.

Pesticide Pollution:

Microbes gradually break down pesticides

Selenium pollution:

Microbes absorb selenium ions and oxidate 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.

Food - ingestion of food with bacteria can cause food poisoning
Water - polluted or unclean water can cause disease
Air/Droplets - water droplets in the area can carry organisms
Animal vectors - insects and other animals can carry disease
Puncture wounds/Cuts - break the skin barrier and allow entry of bacteria or viruses.
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 (heat-stable) in the walls of Gram-negative bacteria that cause fever and aches.

Exotoxins

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.

Irradiation

Ionizing radiation

Some microbes are resistant (e.g. Clostridium botulinum)
Free radicals may alter the flavour
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 flavour 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 sterilisation; does not kill endospores, however.
Cannot be used on living tissue, nor through consumption.
Useful for sterilisation 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.

Antibiotics - antimicrobial agents produced by microbes which inhibit or kill other microbes
Cell wall synthesis inhibition (e.g. Penicillin)

Antibiotics inhibit 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)

Block some stage of protein synthesis by attacking the bacterial ribosomes.
Does not attack the ribosomes of human cells because bacterial ribosomes (70S) differ from those of humans (80S)
Nucleic acid inhibition (e.g. Rifampin)
Affect the synthesis of DNA/RNA or attach to DNA/RNA so that they cannot be read
Interferes with the growth of bacterial cells

F.6.6 Outline the lytic life cycle of the influenza virus

Virus attaches to cell surface by means of specific receptors (e.g. glycoproteins)
Virus is taken up in membrane-enclosed endosome during endocytosis
Uncoating occurs in endosome and viral RNA (genome) is released into the cytoplasm
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
Some RNA transported into cytoplasm and translated into viral proteins which are transported back into the nucleus to assemble the capsid
Viral envelope proteins assemble in cell membrane and the capsid buds off of these points, using the cell membrane as its envelope
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

Four species of the genus Plasmodium (falciparum, vivax, ovale, malariae)

Transmission

Transmitted from one person to the next by a female Anopheles mosquito which feeds on human blood (males only feed on plants)
Plasmodia reproduce in the gut of the female mosquito
Egg sac ruptures and releases cells called sporozoites which travel to the salivary glands
Sporozites enter bloodstream with mosquito bite and travel to the liver
Develop in liver cells, which change form, and then invade red blood cells
Another Anopheles female mosquito feeds on an infected individual, transferring Plasmodium falciparum into the gut of "Anopheles".

Symptoms/Effects

Presents as symptoms of anemia, bouts of fever chills, shivering, joint pain, and headache.
Cycle begins again when new mosquito bites a person infected with malaria.

F.6.10 Discuss the prion hypothesis for the cause of spongiform encephalopathies.

States that the causal agent for spongiform encephalopathies in humans has no nucleic acid and consists only of misfolded proteins (PrP^SC).
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 (PrP^C) 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.