CHAPTER 3:

MICROBES AND BIOTECHNOLOGY

3: MICROBES AND BIOTECHNOLOGY

Traditional classification systems have recognized 2 categories of organismsm based on cell types:

- EUKARYOTES- PROKARYOTES

Domains of life:based on ribosomal RNA (rRNA)

BACTERIA ARCHAEA EUKARYOTA

HISTONES ASSPCIATED WITH DNA

Absent Proteins similar to histones bond to DNA

Present

PRESENCE OF INTRONS

Rare or absent Present in some genes

Frequent

STRUCTURE OF CELL WALLS

Made of chemical called petidoglycan

Not made of peptidoglycan

Not made of peptidoglycan; not always present

CELL MEMBRANE DIFFERENCES

Glycerol-ester lipids; unbranched side-chains, d-form glycerol

Glycerol-ether lipids; unbranched side-chains, I-form of glycerol

Glycerol-ester lipids; unbranched side chains: d-form of glycerol

ARCHAEA

• Found in a broad range of habitats:- Ocean surface- Deep ocean sediments- Oil deposists They are always found in very extreme conditios.

Example:1) Halophiles water with high salt concentrations2) Thermophiles Close to boiling water Tº3) Methanogens anaerobes, give off methane in

cattle’s intestine

Diversity of EUBACTERIA

1) Coccus: spherical bacteria2) Baccilus: rod-shaped bacteria3) Vibrio: comma shaped rods4) Spirilli: twisted bacteria

Some bacteria can group together to form AGGREGATES:

Prefix “strepto-” form filamentsPrefix “ staphylo-” form clustersEx: Staphylococcus form spherical clusters.

Biofilms

Biofilm a surface – coating colony of organisms.

Pseudomonas aeruginosa produces biofilms in burned patients and in patiens with cystic fibrosis. Its is easuer this way for bacteria to acquire resistance to antibiotics because they can cooperate and interact in different ways

Autoinducers

Autoinducers: help coordinate the action of a group of bacteria.

Vibrio fischeri is a bacterium found in sea water that is able to bioluminiscence emit light. Individuals do not emit light unless they become part of a population of certain density. V. Fischeri releases an autoinducer into its surroundings. In a dense population, the concentration of the inducer becomes high enough to trigger bioluminiescence.

Gram cell wall

Gram cell wall

A traditional test used to classify bacteria is wether they are Gram-negative or Gram-positive, based on how they react to Gram-staining.

The cell wall of Gram-positive bacteria consists of many layers of peptidoglycan ( a polymer consisting of amino acids and sugars). These layers are connected by amino acid bridges.

The cell wall of Gram-negative bacteria is much thinner (only about 20% peptidoglycan). Gram-negative have 2 unique regions that surround the outer plasma membrane ( the periplasmic space and the lipopolysaccharide layer). The periplasmic space separates the outer plasma membrane from the peptidoglycan layer.

VIRAL DIVERSITY

A VIRUS is a biological structure that is organized but non- cellular. It can reproduce only within a host cell.Viruses consist of NUCLEIC ACID covered by a protein coat called CAPSID.Some capsids are covered in a membranous bilayer derived from the membrane of the host cell that they infect.The nucleic acid can be: RNA or DNA; single stranded or double stranded.

VIRAL STRUCTURE

Herpesviridae

1) Herpes zoster: Chicken pox

2) There are two main strains of the Herpes virus: HSV-1 and HSV-2. Either of these strains can cause genital herpes

3) VHH-4: Epstein-Barr: the “kiss infection”

HerpesviridaeDNA double stranded- dsDNA

Retroviridae

- HIV AIDS- Single stranded RNA- Retrovirus: Reverse

transcriptase. Its ARN can be turned into DNA when it inffects a cell.

RETROVIRIDAE- HIV-AIDS

Genus Saccha-romyces

Amoeba Plasmo-dium

Parame-cium

Euglena Chlorella

Nutrition Heterotrophic: feed on glucose and other organic compounds absorbed from their surroundings

Heterotrophic: feed on smaller organisms and detritus by endocytosis

Heterotrophic: feed parasitically on red blood cells by digesting the hemoglobin

Heterotrophic: feed on smaller organisms and detritus by endocytosis

Heterotrophic and autotrophic: they possess chloroplasts and take organic matter by endocytosis

Autotrophic: they possess chloroplasts and synthesize organic compounds by photosynthesis

Locomotion

Non- motile

Move by a flow of cytoplasm to form outgrowths

Some stages in the life cycle can glide over surfaces

Move by beating their cilia rhytmically

Move by beating their flagellum

Non-motile

Cell wall Made of chitin

absent absent absent absent Made of cellulose

The Nitrogen cycle

• Microbes occupy a number of niches in ecosystems: as saprotrophs (decomposers) they release nutrients trapped in detritus and make it available to ecosystems. Cyanobacteria (blue-green algae) and protocists such as algae Euglena are photosynthetic and act as producers

• The bacteria Rhizobium and Azotobacter can fix nitrogen and convert it to a form that living things can use.

• Bacteria such as Nitrobacter and Nitrosomonas can use inorganic chemicals as energy sources. They are known as chemoautotrophs.

• Nitrogen would quickly become a limiting factor for ecosystems if it were not for the bacteria involved in the nitrogen cycle.

• In agriculture, soil nitrogen is often supplemented with fertilizer. Fertilizer can be industrially produced through the Haber process, which produces ammonia from atmospheric nitrogen. Alternatively, other sources such as manure from livestock production can be used.

NITROGEN CYCLE: showing the roles of Rhizobium, Azotobacter, Nitrosomas, Nitrobacter and Pseudomonas

Sewage and sewage treatment

• The consequence of not treating sewage and allowing it to flow in to watercourses would be nutrient enrichment, or eutrophication.

• This favours algal blooms. When the mats of algae die, it leads to a loss o oxygen, because of bacterial activity on the dead organic matter. This is called biological oxygen demand

*Sewage: water-carried wastes Eutrophication: is the addition of artificial or natural substances, such as

nitrates or phosphates, through fertilizers or sewage to an aquatic environment.

• Many sewage treatment plants make use of biofilms. A trickling filter system has a rock bed that can be up to 2 metres deep. The rocks are colonized by a biofilm of aerobic bacteria. Sewage water is sprayed onto rocks. The process of spraying adds oxygen to the sewage, which is necessary for the aerobic bacteria to digest the sewage content.

• Reed-bed systems make use of a range of ecological community members to treat sweage. Artificial oxygenation supports aerobic bacteria in lowering the biological oxygen demand (BOD) of the sewage. Plants such as reeds extract nitrogen from the water, small animals such as rotifers and other filter-feeding vertebrates extract particles

Sewage

Sewage treatment plant

Methane generation• Three different communities of anaerobic microbes are

required.1) The first group converts the raw organic waste into a mixture

of organic acids: alcohol, hydrogen and carbon dioxide.2) The second group uses the organic acids and alcohol from

the first stage to produce acetate, carbon dioxide and hydrogen.

These first two communities are Eubacteria3) The last group are Archea called methanogens. They produce

methane by one of these reactions:CO2 + 4H2 CH4 + 2H2O (reduction)

CH3COOH CH4 + CO2 (splitting acetate)

Methane generator

Gene therapy

• Some inherited diseases are caused by a defective gene, that results in the lack of particular enzyme or protein. Cystic fibrosis is one such disease. It is caused by th lack of cystic fibrosis transmembrane protein (CFTP). This protein normally transports chloride ions out of cells and into mucus. The chloride ins draws water out of the cells and make mucus watery. Cystic fibrosis patients suffer fro thick mucus, which builds up in the airways.

• Gene therqapy may offer a cure for inherited diseases like cystic fibrosis. In gene therapy, working copies of the defective gene are inserted into a person’s genome. To do this, a gene delivery system or vector is needed.

• It’s very normal to use viruses as vectors.• The viral genome is altered so that the

particles are not virulent. The therapeutic gene is then inserted into the virus. The viral DNA is then inserted into the genome.

• However therapeutic genes are not passed from one generation to the other, so treatment has to be repeated.

• A challenge of using viruses as vectors is that the host may develop immunity to teh virus.

• The treatments may be of two types:a) Using somatic cells (body cells)b) Using egg cells. Injection of therapeutic genes into

egg cells. The missing gene would be expressed in all cells of the organism. It is called Germ line therapy

Using Saccharomyces in food production

• Saccharomyces cerevisiae is a fungus that is widely used in biotechnology. Alcoholic fermentation produces alcohol and CO2.Its fermentation reactions are used in the production of beer, wine and bread.

1) In wine production, Saccharomyces occurs naturally on the surface of grapes. Crushed grapes are allowed to ferment in the presence of the yeast. If the grape skins are left within the fermentation vessel during this time, the alcohol that develops will be a red wine.

2) In beer production, barely grains are allowed to germinate so taht some starch is converted to maltose. The grains are then heated to denature the amylase and further processed so that the sugars are washed out of the,. The resulting solution has Saccharomyces added and is allowed to ferment.

3) In bread productionm Saccharomyces is added as an ibgredient to the dough. The dough is left to rise, which means the yeast is allowed to operate on the sugars in the flour or on added sugars.

The CO2 produced as a result of fermentation caused the bread to rise.

To make soy sauce a salted mixture of crushed soybeans and wheat is treated with the fungus Aspergillus, which breaks down the starch in the substrate of glucose. This is the fermented in the presence of salt, by other microbes to produce soy sauce

Saccharomyces

Food preservation and food poisoning

• Food preservation involves controlling the growth of microorganisms. High salt or high sucrose concentrations provide osmotic inhibition.

• Pickling is a process that often involves storing food in stalt or vinegar solution and allowing anaerobic respiration to occur. The inorganic acids produced, such as lactic acid, inhibit growth of other kinds of microbes.

• Food poisoning is an illnes caused by eating foods containing toxins produced by pathogens. Poor preparation of foods such as poultry or other meat products is often the source of pathogens.

EXAMPLES:

1) Clostridium botulinum is a rod-shaped bacterium that produces neurotixins known as botulinum neurotoxins that cause muscular paralysis.

Botulism poisoning can occur due to improperly preserved or home-canned, low-acid food that was not processed using correct preservation times and/or pressure.

Clostridium botulinum

2) Certain strains of Staphylococcus aureus can produce food poisoning. If food is contaminated with these bacteria and stored at temperatures above 4ºC, they multiply and produce harmful toxins (enterotoxins). Many foods can be contaminated, including poultry, meat, eggs, salads and a wide variety of processed foods.

The symptoms caused by the toxins are nausea, vomiting and diarrhoea and these develop within a few hours.

Treatment does not involve killing the bacteria, but instead replacing substances lost in diarrhoea.

Oral rehydratation fluids are usually given.

Staphylococcus aureus

Bioremediation *

• Bioremediation is the use of microbes, fungi, plants or enzymes to remove environmental contaminants from water or soil.

1 )The bacterium Dehalococcoides ethenogenes has been used to break down chlorinated solvents in soil.

2) The bacterium Geobacter sulfurreducens uses uranium as an electron acceptor converting it from soluble to insoluble form, which allows the uranium to settle out and be collected.

3) Some members of the genus Pseudomonas can use crude oil for energy. They also require substances such as potassium and urea as nutrients. These are often sprayed on to an spill to aid the bacteria in their work.

Bacteria are very useful in bioremediation because they can multiply very quickly by binary fission and they are very varied in their metabolism. Bacteria carry out a wider range of chemical reactions, especially inorganic reactions, than any other group of organisms. There is often a species of bacterium that will perform the necessary reaction in a bioremediation process.

Controlling Microbial growth

Because microbes can cause disease and food spoilage, a number of methods have been devised to control their growth.

1) EXPOSITION TO GAMMA RADIATION: This method has the advantage of destroying nearly all microbes as well as insects and other pests. It is sometimes used with fruit; but some consumers are reluctant to consume radiated food.

2) PASTERIZATION:Is a method of treating food by heating it to certain temperature to kill pathogenic organisms but not to harm the flavour or quality of the food.-Milk 60°C / 30’-Flash pasteurization 70°C/ 15´´, coolong -10°C and storage at lower temperatures.- Used in beer, wine, fruit juces, cheese and egg

products.- Its main disadvantage is that it does not kill

all microbes.

3) ANTISEPTICSAre chemical substances that kill or prevent the growth of microbes on living surfaces such as the skin and wounds.Most common:- Iodine- Hydrogen peroxyde- Isopropyl alcohol.

They may be toxic when being ingested, that’s why they are not used in foods.

4) DESINFECTANTS:Are chemical substances taht kill or prevent the growth of microbes on non-living surfaces.- Used on food preparation surfaces and

medical equipment.- They are too toxic to be used on living surfaces

or in foods

5) ANTIBIOTICS:

PANDEMICS

An EPIDEMIC is a widespread outbreak of an infectious disease, in which many people are infected at the same time.

A PANDEMIC is a very widespread epidemic that affects a large geographic area and crosses international boundaries.

1) A recent pandemic began in 2009, whrn a new strain of influenza virus appeared, called H1N1, but commonly referred to as swine flu. • It probably appeared in Asia and affected pigs

only, but then it got to mexico and infected humans.

• It spread throughout the world by human-to-human transmission.

2) MalariaIs caused by the transmissiom of an unicellular eukaryote. In humans:Plasmodium falciparumPlasmodium vivaxPlasmodium ovalePlasmodium malariaeThey affect red blodd cells and are transmited by a vector: the mosquito from the gender Anopheles.

P. Malariae cycle

Metabolism of microbes *

• Microbes can be classified by their mode of nutrition, including their sources of energy and of carbon.

1) Photoautotrophs: obtain energy from light, source of carbon it’s inorganic. Ex: Cyanobacteria

2) Chemoautotroph: source of energy, inorganic chemicals (H2S), source of carbon inoganic. Ex: Nitrobacter

3) Photoheterotroph: source of energy is light, source of carbon is organic. Ex: Rhodobacter.

4) Chemoheterotroph: Source of energy, organic compounds; source of carbon, organic compounds. Ex: Mycobacterium tuberculosis.

Microbes and disease

• Pathogenic microbes obtain nutrients through parasitism. To do this they need to gain entry to their hosts. Pathogens are transmitted in a number of ways:

1) Direct contact between the infected and uninfected person of between a surface and the new host. Example: Norwalk virus

2) Cuts: Clastridium tetani

3) Droplets: coming in contact with droplets from an infected person such as through a cough or sneezing. Ex: Influenza virus

4) Ingesting contaminated food or water. Ex: Salmonella enterica.

5) Insects acting as vectors. Ex: West Nile virus6) Sexually transmitted diseases. Ex: Chlamydia. After a pathogen enters the body, a disease can be caused if the microbe colonizes a tissue. Bacteria such as Streptococi release digestive enzymes that allow them to invade tissues.

Most bacterial infections are found around cells, but some actually infect cells intracellularly, such as Rickettsia and Clamydia.

Influenza

• Flu is caused by a virus.• The virus is spread in droplets, such as those

released by an infected person when they cough or sneeze.

• When the viruses are inhaled, they bind to the surface of the epithelial cells in the respiratory system. They are brought inside through the cell’s own endocytosis mechanism.

Influenza life cycle

• Influenza is a single stranded enveloped RNA virus.• Once inside the cell, the genetic material and

accesory proteins are uncoated and the viral molecules enter the nucleus.

• The viral enzyme RNA- dependent RNA transcriptase begins making complementary copies of the viral RNA.

• The viral RNA is either exported into the cytoplams and translated, or it remains in the nucleus.

• Some newly synthesized viral proteins are inserted in the cell membrane and some are transported back into the nucleus to assemble the new viral proteins.