Viruses, Bacteria, Protists and Fungi

Module Two: Life at a Molecular, Cellular and Tissue Level

Paper One

Overview• Owing to evolution, we have a large diversity of life on planet

Earth. The earliest organisms that were thought to have developed were viruses, protists, bacteria and fungi. These are the organisms we will be focussing on. They:– Are an extremely diverse group found in virtually all of the planet’s

environments.– Occur in vast numbers.– Vary in size. Some are micro-organisms (microbes) while others are

macro-organisms (e.g. fungi and some algae).– Can be acellular (fungi) or cellular (bacteria, protists, fungi)– Cellular forms can be prokaryotes (bacteria) or eukaryotes (protists and

fungi)– Unicellular, or form colonies of similar cells, or are made of primitive

tissue.

• Micro-organisms can be useful.• Pathogenic/non-pathogenic:

– Pathogenic (disease-causing), i.e. germs– Non-pathogenic (harmless to plants and animals).

Viruses• Viruses can infect animals, plants and even bacteria.• Viruses are not included in the major plant kingdoms.• Viruses were discovered after bacteria, as they are smaller

and can only be seen by an electron microscope. • In 1900, a Dutch scientist became the first to discover and

investigate viruses. He did experiments on tobacco plants suffering from mosaic disease.

• The word ‘virus’ is Latin, meaning ‘poison’.• In 1940, more experiments could be carried out due to the

development of the electron microscope.

Viruses: Characteristics

• Exist in two distinct states: a virus (when active) and a virion (when dormant and not in contact with a host cell).

• Can also remain dormant within an organism (latency).• A viriod (NOT VIRION) is an infectious RNA particle that

resembles a virus – but is smaller.• Are not really living: they don’t respire, eat, excrete, grow or

move on their own.• Viruses are obligate intracellular parasites and can only survive

inside the cells.• Can only reproduce within a living cell, or when the viral nucleic

acids use the host cell material to replicate.• Associated with disease. After the virus leaves the host cell, the

host cell is destroyed.

Viruses: Structure• A virus is acellular, i.e. it is NOT a cell

as it has no nucleus, cytoplasm or organelles.

• Viruses have a simple structure consisting of a core of DNA or RNA, but not both. The DNA/RNA is not contained in a nuclear membrane.

• The nucleic acid is surrounded by a protein coat or capsid,

• In some viruses, the capsid is covered by an envelope of a lipid bilayer.

envelope

DNA/RNA

Capsid

Viruses: Structure• Viruses can have different shapes:

– Polyhedral cubical e.g. adenovirus

– Helical spiral cylinder e.g. tobacco virus

– Complex tadpole-like e.g. bacteriophage

Viruses: Life Cycle1) AdsorptionVirus approaches a cell.

2) PenetrationVirus attaches to the cell, injecting nucleic acid into the cell. Capsid left outside cell.

3) Latent phaseVirus multiplies its nucleic acid using materials from the host cell.

4) LysisProtein coats form around strands of nucleic acid. The cell releases viruses.

Viruses: Effects on Body

• Host cells are affected in three ways:– The host cells may be destroyed. They may swell and burst, as with

nerve cells infected with the rabies virus.– The host cells may not be able to function correctly, e.g. ciliated

epithelial cells infected with the influenza virus.– The virus can interact with the host cell’s chromosomes causing a

mutation, e.g. warts and cancer cells.

• The immune system becomes activated in order to fight the infection. This may lead to fever, tiredness or an opportunistic disease.

HIV, a Viral Disease• HIV/Aids is the most serious disease facing the world today.

South Africa has the highest prevalence of HIV in the world; 18% of the adult population is infected with HIV.

• Human Immunodeficiency Virus (HIV) affects the immune system because it is specialised to infect CD4 cells (helper T lymphocytes ), which play a significant role in immunity.

• As it effects the immune system, the infected individual is prone to many new ‘opportunistic diseases’, which the immune system is too weak to fight off. This can kill the individual if certain procedures aren’t adhered to.

Effects of HIVPhysical effects:• Weakened immune system, resulting in fatigue, weight loss,

frequent fevers and sweats, fungal infections, shingles (nerve disease), skin rashes and flaky skin, diarrhoea, spots or blemishes on tongue, in mouth or throat.

• When the CD4 count is less than 200 cells/ml blood (normal is 600-1200), it is said that the illness has progressed to full-blown AIDS (Acquired Immune Deficiency Syndrome).

• At this point, many viruses, bacteria, fungi and protozoa are able to invade the body. Other infections could include drug resistant TB, cancer and pneumonia as well as memory loss, depression and other neurological disorders.

Effects of HIV• Economic Effects

– The affected family will lose money as the ill person may be unable to work, for the travel costs to clinics and dispensaries and burial costs.

– The country loses money as many productive people are sick and unable to work. The government has to spend money on medication as well as maintaining health facilities and staff.

– In countries which are badly affected by HIV/AIDS, such as ours, such costs can slow down economic growth.

• Emotional Effects– Feelings of depression, loneliness and ostracism as there is often a

stigma attached to HIV/AIDS.– Families are being destroyed. Orphaned children may become heads

of houses or would have to live with other family.

Management of HIV• Awareness of one’s HIV status is the first step.• Treatment with a combination of anti-retrovirals (ARV’s).This

doesn’t cure HIV but slows down viral replication, allowing the immune system to recover and helping the individual to feel healthy again.

• Monitoring the viral load (amount of HIV in one’s blood) enables medical staff to adjust the combination of ARV’s.

• Treat opportunistic infections immediately.• Boost the immune system.• Care for the mental and emotional health of sufferers.• Sensible financial planning.• Giving ARV’s to pregnant women to reduce the chance of infecting

the baby.

Drug-resistant HIV• Drug-resistance is the ability of disease-causing viruses to

continue multiplying, despite the presence of drugs which usually kill them.

• ARV’s consist of a ‘cocktail’ of various classes of drugs, specific to the stage of the disease, to attack the viruses at different stages of it’s replication.

• If the virus is allowed to multiply it would do so rapidly, blocking the working of the ARV’s, and becoming drug resistant.

• This is caused by not taking the drugs exactly as prescribed, poor absorption of the ARV’s or unsafe sex with a drug-resistant HIV positive person.

“Life-Cycle” of HIV1. HIV locater spikes attach to

receptor proteins of CD4 cell2. HIV cell RNA penetrates CD4 cell,

shedding protein coat. 3. RNA enters cell. Reverse

transcriptase enzyme uses a single strand of RNA to create a double strand of DNA, destroying RNA.

4. Viral DNA enters nucleus, joining with cell. It reprograms the cell DNA to form viral RNA.

5. Cell stops normal functions, and instead becomes a factory, sending out replicas of the virus.

Bacteria• Ancestors of current bacteria were unicellular micro-organisms

which were the first forms of life to develop on earth, 4 billion years ago. They belong to the kingdom Monera.

• The idea of micro-organisms and pathogens which cannot be seen with the naked eye, dates back to 400AD Rome.

• Bacteria was only officially discovered in the 17th century, after the invention of a microscope.

• Bacteria are the most diverse and abundant group of organisms on Earth. They inhabit practically all environments on earth. Some, extremophiles, thrive in climatic or environmental extremes, e.g. intense heat or intense cold.

• Bacteria are mostly useful, but some cause disease.

Bacteria: Characteristics• Bacteria are unicellular and are among the smallest organisms. • In favourable conditions, bacteria will reproduce rapidly by binary

fission, an asexual process whereby one bacteria can split into two every 10-15 minutes.

• In unfavourable conditions, bacteria may survive by becoming dormant. They form spores with a thick, protective coat around them, which will split open in favourable conditions.

• Endospores are spores created by a small group of bacteria. They are specialized to withstand unfavourable conditions. They can survive for thousands of years and can cause diseases such as tetanus and anthrax.

Bacteria: Characteristics

• Bacteria vary in shape and can be classified accordingly:– Spherical bacteria are called cocci– Rod-shaped bacteria are called bacilli– Spiral shaped bacteria are called spirilla– Comma-shaped bacteria are called

vibrios.

• Can occur singly, in chains (streptococcus) or in clumps (staphylococcus).

Bacteria: Structure• Bacteria are unicellular and are made up of simple cells, but can

carry out all the functions of living organisms. • Have a rigid cell wall which consists of large peptidoglycan*

molecules. • They have a plasma membrane, which serves as a mitochondrion,

endoplasmic reticulum and sometimes a chloroplast. Also controls exit and entry of materials.

• As prokaryotes, they do not have a true nucleus. This is because they do not have a true nuclear membrane and the DNA isn’t combined with the protein found in eukaryotes.

• Single chromosome of DNA – closed loop.• Pathogenic bacteria have a waxy capsule.• Some bacteria have flagella to enable them to move around.

Bacteria: Effects on BodyPathogenic bacteria infect our bodies in order to get food. They may:• Destroy body cells which are then used as a source of food.• Absorb material directly from body fluids such as blood.• Release harmful substances, called toxins. Toxins may:

– Cause symptoms like a rash or a high temperature. – Block metabolic pathways in the host cells which can have a

devastating effect on the body.

Tuberculosis• TB is a chronic infection caused by myocardium tuberculosis, aka

the TB bacillus. It is covered in a waxy layer which protects it from drying out, heat, and being destroyed by the immune system.

• It affects all organs, including the brain and bones, but especially the lungs. This is called pulmonary tuberculosis.

• It is highly contagious and is spread by moisture droplets.• After infection one of the following might occur:

– If the person has a strong immune system, the infection would be contained. It will be walled off and can lie dormant for years. The person will display little/no symptoms of TB.

– If the person has a weak immune system, the bacilli will multiply further and within four to six weeks, the individual will be ill with pulmonary TB.

Effects of Tuberculosis• The sufferer feels tired and weak. They may cough up blood,

lose weight rapidly, and have fevers and night sweats.• The patient could lose earnings while ill and unable to work.• The government has to cover the cost of medication, clinics

and medical staff.• There is a stigma attached to this disease. Thus, an infected

person could feel ostracized and lonely.• If left untreated, a person could infect on average between

10-15 people each year.

Treatment of TB• TB can be cured by an anti-biotic which is free and easily

available. The treatment is a six-month regime, known as DOTS (Directly Observed Therapy, Short Course).

• The patients are carefully monitored to ensure they take the full course of antibiotics. Within days of starting the treatment, the patient will be unable to infect others.

• Many patients stop taking medication when they start to feel better. As a result:– illness is prolonged– the patient becomes infectious again– they can develop multi-drug-resistant TB, which is difficult to treat and can

be fatal.

Management of TB• Areas most affected by TB are poverty stricken and overcrowded.

Malnutrition and bad sanitation exacerbate the situation.• To prevent the spread of TB:

– screen those at risk – treat the infected ASAP– reduce overcrowding, bad sanitation and malnutrition

• Quality education and information about TB must be given out via schools, clinics, pamphlets, posters etc.

• Health care workers must be passionate, trained and well-equipped.

• People should be immunised against TB with the BCG vaccine.

Uses of Bacteria*Bacteria can be used to:• Replace pesticides• Degrade herbicides• Eat or neutralize toxic waste• Synthesise riboflavin• Decompose sewage waste• Produce food by fermentation processes• Make probiotics • Separate the fibres of jute, hemp and flax in preparation for

making sacks and ropes.

ProtistaThe Protista do not form part of any other kingdom. They share the following characteristics:

– All are eukaryotic (have a true nucleus)– All live in moist environments as they have no means of preventing

themselves from drying out.

However, there is a lot of variety in this group. The following characteristics are variable:

– Can be unicellular or multicellular– Can be microscopic or over 100 metres long– Can be heterotrophs or autotrophs.

The Protista Kingdom is grouped into the following subcategories:– Plant-like protista– Animal-like protista

Plant-like ProtistaPlant-like Protista are known as algae.• Algae are simple, aquatic eukaryotes (have true nuclei)• Contain chlorophyll. They photosynthesis, thus they are

autotrophic.• Release large chains of oxygen during photosynthesis.• Mostly free-floating but some, e.g. kelp, are attached.• Can be unicellular: e.g. diatoms, or multicellular: e.g. seaweeds.• Usually reproduce asexually.• Grouped into: green algae, brown algae, red algae, diatoms and

dinoflagellates.

Plant-like ProtistaAlgae can be divided into the following groups:• Green algae

– e.g. spirogyra (slime found in fresh water) and green seaweeds (found in shallow water – for photosynthesis)

• Brown algae, – e.g. kelp (found in deep water)

• Red algae, – e.g. red seaweeds (found in deep water)

• Diatoms – microscopic, unicellular algae whose cell walls contain silica.

• Dinoflagellates – microscopic, unicellular algae with flagella. Found in surface waters.

Animal-like ProtistaAll animal-like protista, or protozoa, are:• Unicellular.• Heterotrophs.

– They cannot make their own food. Some kinds engulf their food, e.g. Amoeba, while others absorb it directly through their cell membranes, e.g. plasmodium.

• Swim around actively looking for food.• Groups consist of: amoeboids, cilliates, flagellates, parasitic.

Malaria• Malaria is a chronic, life-threatening parasitic disease

transmitted through a bite of a female Anopheles mosquito. The mosquito acts as a vector.

• It affects mainly poor countries as the mosquitoes thrive in tropical environments.

• In 1880, scientists discovered it originates from a unicellular protozoan called Plasmodium.

• Plasmodium is carried in the salivary glands of the mosquito.

Effects of Malaria• Physical effects:

– Flu-like. Fever, chills, headache, muscle ache, vomiting, tiredness, anaemia, brain disease, kidney failure.

• Can result in the destruction of red blood cells (anaemia) or clogging of capillaries surrounding the brain (cerebral malaria), which results in death.

• Can be costly to individuals and government, impeding economic growth.

Treatment of Malaria• Treat the illness:

– with a multi-drug called Coartem. – It contains sweet wormwood which is an important natural herb.– It is unfortunately quite expensive.– It is a 3 day course.

• Kill the mosquitoes:– insecticide-treated mosquito nets act as a physical barrier and actively

kill the mosquitoes.– Spraying with DDT, a repellent. This is, however, harmful to the

environment.

Economic Uses for Algae*

Extracts from algae can be used as the following:• Plant growth regulators.• Phycocolloids are used:

– As gelling agents– As thickening and stabilizing agents– To make agar plates

• Natural pigments, used as an alternative to chemical dyes.• Nutrient extracts.• Iodine from kelp is used in mineral salt tablets.• Used in food, e.g. in sushi and in Eastern soups.• Kelp feeds harvested abalone.

Fungi • Fungi were put into a single kingdom because of their:– Similar ecological roles – i.e. they’re decomposers of

organic matter.– Similar anatomical and biochemical features.

• The kingdom contains about 1 million species.

Characteristics of Fungi• Fungi are found everywhere, usually invisible to the naked eye.• They are mostly free-living, living in the soil, air and dead matter.• They are heterotrophs; they obtain food from other organisms.

– Most feed on dead organisms, i.e. are saprotrophic.– Some are parasitic and cause ill health – e.g. thrush and athlete’s foot in

humans, and rust in plants.

• Some live in symbiotic relationships with plants and animals, e.g. lichen (a combination of fungi and algae), and mycorrhizae.

• Most are useful• Reproduce:

– Asexually by means of reproductive spores – Sexually, when in unfavourable conditions, by resistant zyrospores.– By budding or binary fission (e.g. yeast)

Structure of Fungi• Mostly multicellular• Multicellular fungi consist of a mass of branched filaments

(hyphae), enclosed by a rigid cell wall of chitin and glucan.• The hypha is a multi-branched tubular cell that could be

separated or continuous.• When the fungi produce asexually they form spore-

producing bodies, e.g. mushrooms or sporangia.

Candidiasis Thrush• Caused by Candida albicans, a yeast or fungus.• Affects the mucous membranes in the mouth (babies) or vagina

(adult females)• Makes one more vulnerable to HIV, as it affects mucous

membranes.• Can occur harmlessly in the intestine.• The immune system usually keeps this in check, but in certain

cases overgrowth may occur:– Excessive taking of antibiotics– Weak immune system due to AIDS, stress, lack of sleep, poor diet or

illness.– Warmth and moisture from tight underwear and being obese.

75% of women at child-bearing age would have suffered from this condition at least once. • Oral thrush is treated with an antifungal mouth wash.• Vaginal yeast infections can be treated with a topical

medication.

Treatment of Thrush

Athlete’s Foot• Caused by a fungus called Tinea which grows in damp areas.• It is quite common. It usually affects the skin between the

toes and makes the skin crack and flake.• It feeds on keratin, found in skin cells.• Treated with dryness and an antifungal powder.

Uses of Fungi• As a food source, i.e. mushrooms.• Produce biological compounds, e.g. alcohol, plant growth

regulators and enzymes.• Produce anti-biotics, e.g. penicillin.• Control haemorrhage after birth.• Control cholesterol levels• For fermentation processes, e.g. yeast.

Uses of Micro-organisms

Most micro-organisms are extremely useful. They can be:• Plant-degraders. Cellulose-degrading fungi and bacteria clean

up dead plant matter.• Micro-regulators of nutrients. They further break down the

nutrients left behind by scavengers.• Algae such as cyanobacteria and phytoplankton regenerate

oxygen in the atmosphere.• Transform nitrogen.• Biological control agents – they control pests, pathogens and

weeds.

• Escherichia coli and humans – this is found in the colon and is part of the normal gut flora.– Bacteria benefit by obtaining glucose and other nutrients from

undigested food remains in the colon.– Humans gain vitamin K2, which helps blood clotting. We are also

protected from pathogenic bacteria within the gut.

• Nitrogen-fixing bacteria and plants – bacteria converts nitrogen into useful forms for living organisms. Lives

in root nodules of legumes.– Rhizobium benefits by gaining glucose and other nutrients as well as a

favourable habitat.– Plant gains ammonia – forms amino acids, which form protein.

Symbiotic Relationships

• Mycorrhizal fungi and plant roots– The fungus gets glucose.– The plant has an increased surface area, improving nutrient uptake, as

well as protection against pets and diseases.

Symbiotic Relationships

Plants have an innate immune system. The infected cells will:• Produce salicylic acid• Activate resistance genes – e.g. to resist viral replication.• Self-destruct so that the disease cannot spread.• The SA moves around the plant to activate the immune

system, making the cells become resistant to the pathogen.The closing of stomata can play an active role in limiting bacterial infection.

Immune response by Plants

• First line of defence is the skin. Prevents entry of pathogen.• The second like of defence involves two responses. – The primary response is to prevent pathogens from

spreading, by:• Inducing inflammation (if it is a local infection) • Inducing fever (raised body temperature.)

– The secondary response is to activate the immune system.

Immune Response by Animals

Essentially involves:• The destruction of the invading germs• Holding a memory of this response.The immune processes involve two groups of WBC:• Lymphocytes • Phagocytes

Immune System

B-lymphocytes destroy germs by:• Reading the antigen on the pathogen, which tells it that it is

dangerous. There are many B-lymphocytes, all specific to their own antigen.

• If a B-lymphocyte recognizes its pathogen, it replicates itself many times.

• They are then stimulated to produce antibodies which are secreted into the plasma.

• The antibodies combine with antigens on the germ’s surface, thus neutralizing or destroying the pathogen. Some cause the cell to burst, others label the germs for phagocytosis, others clump the germs together, thus weakening them.

Lymphocytes

• Some of the B-lymphocytes stay on in the lymph glands as memory cells. If the antigen is encountered again, the immune response will be faster. This is the basis of immunity.

• Natural immunity occurs when an attack of a disease is prevented by antibodies and memory cells

Lymphocytes