Micro-Organisms

1.3 Aspects of BiologyGaze

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Key ConceptsStructure and function of parts of bacteria, fungi and viruses

Extra-cellular digestion by bacteria and fungi

Aerobic and anaerobic respiration

Bacterial reproduction by binary fission

Viral reproduction

Excretion of toxins

Other life processes for bacteria, fungi and viruses

Culturing micro-organisms

Conditions for growth of micro-organisms – temperature, food, moisture, pH, oxygen.

Disinfectants, antiseptics and antibiotics

Disease

Nutrient cycles – carbon and nitrogen

Food production Gaze

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Living, Non-living or Dead?

• Biology is the study of living things• A living object is an object that

caries out life functions• A non-living object is an object that

has not been alive• A dead object is an object that was

once alive

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Revision

Functions of Living organismsBiologists have decided that an object is living if it carries out the following 8 functions:

Movement: all or part of the living object can move

Respiration: living things obtain energy from food during respiration

Sense the environment: living things respond to changes in their environment

Circulation: living things circulate gases and other chemicals

Growth: living things grow

Reproduction: living things produce new offspring

Excretion: living things are able to get rid of waste products from their bodies

Nutrition: living things can make their own food or obtain it by eating other living or once-living (dead) things.

Mrs C. Gren.Gaze

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Revision

fire fish virus algae

jellyfish coral mould bacteria

amoeba crystals yeast fungus

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Living or Non-Living?

The three domains of LifeAll living organisms are divided into three domains based on their similarity.

The Archaea were the first type of living organism found on Earth. They are all unicellular, (single cell) prokaryote (simple cells without a nucleus) organisms.

The Bacteria are also unicellular and prokaryote.

The Eukaryotes are both unicellular and multicellular. Their cells contain a nucleus plus mitochondria. This domain contains fungi, protisa, plants and animals.

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The Five Kingdoms of Life

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The traditional division of living organisms.

There is much more variety between the Monera Kingdom (divided into the Bacteria and Archaea Domains) than there is between the remaining 4 kingdoms that make up the Eukaryote Domain.

Plant Classification

Scientists universally use a classification system developed from Linnaeus (1753) to catergorise every species of living organism so far discovered.

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Animal Classification

Current classification systems have developed from Linnaeus' original work. However, modern classification systems are much more complicated having many levels of hierarchical organization. These systems are also taxonomic (structural and physiological connections between organisms), phylogenic (classification based on genetic connections between organisms), and are structurally based on Darwin's theory of evolution.

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Micro-organismsLiving Non-living

Viruses

Fungi - Eukaryote

Bacteria - Prokaryote Gaze

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“Animal” “Plant” “Bacteria” “Virus”

enclosed by a plasma membrane and containing a membrane-bound nucleus and organelles.

>small vacuoles, no chloroplasts, no cell wall.

similar to the animal cell, but >does not have centrioles, lysosomes, cilia, or flagella (except some photosynthetic protists).

>It does have a rigid cell wall, central vacuole, plasmodesmata, and chloroplasts.

Does not have nucleus or organelles (except ribosomes).

Not considered living or consisting of cells but contains genetic material (RNA/DNA) similar to all other living things.

Cell Types

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Cell Structure - Prokaryotes

Absence of nucleus

No organelles in cytoplasm (except ribosomes)

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Prokaryotes and EukaryotesProkaryotes Eukaryotes

>lack cell nucleus>DNA/RNA material stored in a single loop in an area called the nucleoid >have no membrane bound organelles.>reproduce asexually by binary fission

>have membrane bound nucleus containing genetic material>DNA stored on Chromosomes >has membrane bound organelles (mitrochondria – respiration, Chloroplasts – photosynthesis)>usually reproduce sexually by meiosis

Unicellular and MulticellularUnicellular Multicellular>fully functioning (MRS C GREN) independent cell unit>can be grouped into colonies (eg algae) but are still able to separate and survive>most kingdoms have examples of unicellular organism

>cells within an organism are specialised to perform a life function (or part of one)>single cells cannot live independently>all cells co-ordinate into one organism to collectively perform all the functions of life.>generally Plant and Animal kingdoms are multicellularParamecium - Protist

Human - Animal

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Micro-organismsMicro-organisms (or microbes) are very small organisms, which are usually only visible with the aid of a microscope. Sometimes a colony of micro-organisms can be seen with the naked eye.

Micro-organisms which have single cells are unicellular. Those made of many cells are multicellular. Some have no cells at all – viruses.

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Relative size of Micro-organisms

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Scale of size

10mm1mm

100µm10µm

1µm100nm

10nm1nm0.1nm

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Microscopes

Most cells are to small to be clearly seen by eye and require a microscope to view.

Magnification: the number of times the image is enlarged

Resolution: the clarity and ability to see detail in the image

The branch of biology relating to preparation and viewing tissue under a microscope is known as Histology.

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Microscopesarm - this attaches the eyepiece and body tube to the base.base - this supports the microscope.body tube - the tube that supports the eyepiece.coarse focus adjustment - a knob that makes large adjustments to the focus.diaphragm - an adjustable opening under the stage, allowing different amounts of light onto the stage.eyepiece - where you place your eye.fine focus adjustment - a knob that makes small adjustments to the focus (it is often smaller than the coarse focus knob).high-power objective - a large lens with high magnifying power.inclination joint - an adjustable joint that lets the arm tilt at various angles.low-power objective - a small lens with low magnifying power.mirror (or light source) - this directs light upwards onto the slide.revolving nosepiece - the rotating device that holds the objectives (lenses).stage - the platform on which a slide is placed.stage clips - metal clips that hold a slide securely onto the stage.

1. Use unlined paper. 2. Draw in pencil. 3. Always print. 4. Leave at least a 5mm margin on all four sides of the paper. 5. Center the title and print it in capital letters. 6. Center the drawing on the page. 7. Never cross lines. 8. Never use the plural form of a work when pointing to a single

object or part. 9. Do little or no erasing. 10. When using the scientific name of an organism in places other

than the title, remember that the genus or first part of a scientific name is always capitalized. The species or second part of a scientific name is not.  

FOR EXAMPLE:      Canis familiaris is the genus and species name for a dog. In a

title it would be CANIS FAMILIARIS  

11. Print your name and other information as specified by your teacher.

RULES FOR A Biological drawing

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VirusViruses are not plants, animals, or bacteria. Viruses are not living organisms because they are unable to carry out all of the characteristics of living organisms without invading a living cell and ‘hijacking’ it’s processes. Viruses do not posses cells or cell components of their own.

They cannot synthesise proteins, because they lack ribosomes. Viruses cannot generate or store energy.

Because viruses can not survive without cells, scientists predict that they originated from rogue pieces of DNA/RNA strand.

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Examples of viruses

Rabies virus

Bacteriophage virus

Influenza virus

Viruses can take numerous forms Gaz

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Virus Structure

Protein Coat

RNA/DNA strands

Example – HIV Virus

Spikes

Lipid layer

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Virus StructureAll viruses contain:

>Nucleic acid, either DNA or RNA (but not both),

>a protein coat (capsid), which encases the nucleic acid.

Some viruses are also enclosed by an envelope of fat and protein molecules.

Protein Coat

RNA/DNA strands

Example – HIV Virus

Spikes

Lipid layer

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Function of Virus ComponentsCapsid - The capsid is the

protein shell that encloses the nucleic acid; The capsid has three functions:

1)it protects the nucleic acid from digestion by enzymes,

2) contains special sites on its surface that allow the virus to attach to a host cell, and

3) provides proteins that enable the virus to penetrate the host cell membrane and, in some cases, to inject the infectious nucleic acid into the cell's cytoplasm.

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Function of Virus Components

Nucleic Acid - Just as in cells, the nucleic acid (DNA or RNA) of each virus encodes the genetic information for the synthesis (creation) of all proteins. While the double-stranded DNA is responsible for this in prokaryotic and eukaryotic cells, only a few groups of viruses use DNA. Most viruses have single-stranded RNA. The genetic material can only make protein when it is slotted into the DNA of a host cell.

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Culturing VirusViruses will not grow on agar (jelly made from seaweed with nutrients) because they cannot feed.

They need living cells to reproduce in and are often grown in fertile hen’s eggs.

The introduction of micro-organisms onto agar or into living cells is known as inoculation.

It is to dangerous to grow viruses in the school laboratory as all viruses are Pathogens (harmful to living organisms).

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Reproduction of viruses

Absorption

Viruses can enter an organism through any cavity or broken surface of an organism. Once inside, they find a host cell to infect.

Entry

The Virus attaches to a specific cell type and ‘injects’ its genetic material.

Replication

The viruses genetic material joins into the cell DNA and viral protein is made.

Assembly

Various pieces of viral protein are constructed into individual viral particles (or virions).

Release

The newly created virions break through the cell wall (killing it) and proceed to infect other cells.

Lysogenic Cycle

Once inside the host cell, some viruses, such as herpes and HIV, do not reproduce right away. Instead, they mix their genetic instructions into the host cell's genetic instructions. When the host cell reproduces, the viral genetic instructions get copied into the host cell's offspring. The host cells may undergo many rounds of reproduction, and then some environmental or predetermined genetic signal will stir the "sleeping" viral instructions. The viral genetic instructions will then take over the host's machinery and make new viruses as described above. This cycle, called the lysogenic cycle, is shown in the figure above.

Extra

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Targeted cells

There are three requirements that must be met to ensure successful infection of a virus:

1. sufficient virus must be present2. the cells must be susceptible and

permissive (matching) to the virus, 3. and local defenses (immune system)

must be absent.

The virus attaches to the target cell, usually through specific protein-protein interactions between capsid and cell surface receptors. Only then can the genetic material be taken into the host cell.

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Fungi

FUNGI ARE:

• Made of tangled threads called HYPHAE

• Parasites or decomposers

• Spread by spores

• Fuzzy- looking!

FungiFungi can either be multicellular such as mushrooms and mould or unicellular such as yeast.

The Fungi have their own Kingdom but share similarties with both plants – do not move around, and animals – can not make their own food.

Fungi are either parasitic – feeding off live hosts or saprophytic – feeding off dead organisms.

Fungi make up an important part of the food chain as decomposers – breaking down dead organic mater and returning the nutrients so they are availible to other organisms. Gaz

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Fungi Structure

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Spores

Sporangium

Stalk

hyphae

Fungi Structure (Multicellular)>Spores, haploid (only

half the chromosomes) used for reproduction – both asexual (growing into an exact copy) or sexual (when combining with a spore from another fungus)

>Sporangium or fruiting body. The visible part of the fungi that produces and distributes the spores.

> Hyphae, the feeding threads. A mat of hyphae is called a mycelium. The hyphae can also be involved in sexual reproduction when they come in contact with hyphae from another fungus.

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Spores

Sporangium

Stalk

hyphae

Fungus Reproduction

• Can be ASEXUAL – by spreading spores• Can be SEXUAL – where two hyphae touch

Fungi Reproduction

Fungi Asexual Reproduction1.Special spore capsules or cases called sporangia develop and

produce the spores. These spores are haploid – they have only half the number of chromosomes. They can be either + or – strains. (rather than male or female).

2. Millions of spores are released to float in the air

3. When spores land on tissue they germinate, sending out hyphae that rapidly branch and invade the new host.

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Fungi Sexual Reproduction1. Fungi form a gamete producing area called a Gametangia.

2. Gametangia from a + strain and a – strain join – but still from the same species of fungi.

3. The 2 gametes (haploid) fuse to form a diploid zygote with a full set of chromosomes.

4. The zygote grows to produce spores (haploid)

5. This process allows the fungi to produce variation amongst the offspring

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Fungi Nutrition

Multicellular fungi are made up of a mass of very fine threads called hyphae, which invade the tissue of the host organism or dead matter.

Fungi feed like bacteria by releasing digestive enzymes onto food, then reabsorbing the nutrients. This is called extra-cellular digestion.

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Fungi Extra-cellular Digestion

Steps to feeding;

1. Enzymes are released from the hyphae.

2. The food material outside the hyphae is digested.

3. The food molecules are small enough to diffuse into the hyphae.

Fungal hypha

Large food particle

Enzymes secreted to break up large particles

Smaller food particles absorbed

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Sugar alcohol + carbon dioxide

C6H12O6 CH3CH2-OH

+ 2CO2 (+ 2ATP)

This can be aerobic (with oxygen) or anaerobic (without oxygen). Bread and wine yeasts respire anaerobically, producing carbon dioxide and alcohol. This is important in wine making, brewing of beer and rising of bread. The process is called fermentation.

Fungi Respiration

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Fungi Excretion

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Carbon dioxide and alcohol (ethanol) are waste products of yeasts. Other fungi may produce different waste products including toxins.

Toxins excreted by fungi that kill or stop the growth of bacteria are known as antibiotics.

Humans have made use of the antibiotics produced by fungi to fight harmful bacteria in their bodies. The most commonly used antibiotic is produced by the penicillin sp. of fungi.

Helpful vs. Unhelpful FungiUNHELPFUL:

• Mould is a fungus that is unhelpful when it gets on food like bread and spoils it

• Yeast is a fungus that is unhelpful to humans when it causes infections like “Thrush”

• Penicillin is a fungus that looks really bad for you

HELPFUL:

• However, humans eat some moulds like the “blue” in blue cheese!

• However, yeast is useful in fermentation to make beer, wine and ginger beer and for making bread rise

• However, Penicillin is an important antibiotic medicine

HOW TO MAKE A CULTURE…

• Collect a “swab” and petri dish

• Wash your hands - to avoid contamination of plate

• Swab area you have been asked to investigate

• Lift up side of petri dish lid without taking it off - to avoid contamination

• Swab agar hard enough to leave microbes on - take care not to tear agar

• Close lid and tape sides of the petri dish - so you can still see your cultures

• Write your name and place you swabbed in small writing on bottom of dish - so you can still see your cultures

IDENTIFYING MICROBES• Name: M. luteus (type of

bacteria)• How you identify it: bright yellow,

shiny, & smooth

• Name: Staphylococcus aureus (type of bacteria)

• How you identify it: large & cream-colored

• Name: Streptococcus pyogenes (type of bacteria)

• How you identify it: smaller than staphylococcus & white

• Name: Corynebacteria (type of bacteria)

• How you can identify it: dry and crinkly

• Name: Fungi• How you can identify it: fuzzy

Bacteria

BACTERIA:

• Are microscopic

• Are made up of one cell

• Are round, long & thin, or spiral shaped

• Need food and warmth to grow

• Use enzymes to digest food

Unique features of BacteriaBacteria are sufficiently different to be classified within their own domain, separate from the plants, fungi, protists and animals. Bacteria have a vast variety of different lifestyles and survival methods.

They have no mitochondria, the cell membrane is the site of energy release.The DNA is in a single loop rather than chromosomesOutside the cell membrane is a cell wall and often a slime capsule for protectionThere may be a flagellum to help the bacterium move. size – they are much smallerAll bacteria are prokaryotes – they have no nucleus membrane, just an area that the DNA occupies

Bacteria cell

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Examples of Bacteria

Streptococcus pyogenesThese spherical bacteria are common inhabitants of the throat. Sometimes they can cause strep throat or even more serious disease like necrotizing fasciitis (commonly called flesh-eating bacteria)

Bacteria Structure

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cytoplasm

Cell wall Cell membrane

flagellum

Slime capsule

RNA/ DNA

NutritionBacteria may be parasitic (feeding off other organisms) or saprophytic. Bacteria feed by extra-cellular digestion. They secrete enzymes outside their cell membrane and cell wall. The enzymes digest the food into small particles that can be absorbed through the cell membrane. This is similar to fungi feeding.

RespirationRespiration is the process of obtaining energy by chemically breaking down food, In animals and plants, oxygen is needed to break down the food into carbon dioxide, water and energy. This is called aerobic respiration. Most bacteria respire aerobically, while others do not need oxygen (and may even be killed by it). This type of respiration is called anaerobic respiration.

Anaerobic respiration

harmful useful

>Gangrene - foul-smelling discharge, dead tissue, and gas formation within the tissue

>yoghurt production >production of biogas>waste processing >electricity generation

Aerobic respiration

harmful useful

>Food rotting – sour milk

>Nitrogen fixing bacteria>Cheese production>GE insulin production

RespirationRespiration is the process of obtaining energy by chemically breaking down food, In animals and plants, oxygen is needed to break down the food into carbon dioxide, water and energy. This is called aerobic respiration. Most bacteria respire aerobically, while others do not need oxygen (and may even be killed by it). This type of respiration is called anaerobic respiration.

ExcretionBacteria excrete waste products. Sometimes these are harmful and are known as toxins. A disease-causing bacterium is called a pathogen.

Reproduction• Happens when one bacteria cell reaches its

maximum size and divides into two identical cells

• This division is called BINARY FISSION

• Some bacteria can divide every fifteen minutes

Parent cellParent cellParent cellParent cell DNA copiedDNA copiedDNA copiedDNA copied Cell dividesCell dividesCell dividesCell divides

Two Two identical identical new cells new cells are madeare made

Two Two identical identical new cells new cells are madeare made

Conditions needed for bacterial growth

Bacteria need the following conditions for growth:

Energy – in the form of food

Moisture

Warmth – cooling bacteria reduces their growth rate, but does not usually kill them. Refrigerators and freezers preserve food by slowing down the growth of bacteria.

Oxygen – For aerobic bacteria only. Oxygen may kill anaerobic bacteria.

pH – bacteria grow better under the right conditions of pH (acidity or alkalinity). Bacteria grow well on the human skin, as it is slightly acidic.

Nutrient recyclingBacteria and fungi decompose (break down) dead plants and animals into simpler materials that can be used by plants. That is why bacteria and fungi are often referred to as decomposers.

In the carbon cycle, micro-organisms break down dead plants and animals, releasing carbon dioxide and water. The carbon dioxide is absorbed by plants and used in photosynthesis. Minerals present in the dead material return to the soil.

In the nitrogen cycle, micro-organisms break down animal and plant proteins into nitrate ions, which can be absorbed directly by plants.

Nitrogen Cycle

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Carbon Cycle

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USING FUNGI TO...make wine & beer

• The microbe used in beer & wine making is a fungus called YEAST

• The YEAST makes alcohol by anaerobic respiration or FERMENTATION

• In WINE-MAKING, the YEAST uses the SUGAR in the fruit for FERMENTATION

• In BEER-MAKING, the YEAST uses the SUGAR in the malted barley for FERMENTATION

GLUCOSEGLUCOSE CARBON DIOXIDECARBON DIOXIDE + WATER+ WATER+ OXYGEN+ OXYGEN

Food ProductionMicro-organisms play essential roles in the manufacture of such foods as bread and cheese, and also in the brewing and wine making industries.

USING BACTERIA TO…make yoghurt

YOGHURT IS MADE:

From milk that has had bacteria added to itBy BACTERIAL FERMENTATIONWhen bacteria feed on the Lactose (sugar) in the

Milk and makes LACTIC ACID and water

Stages in yoghurt production

STEP PROCESS WHAT MICROBE DOES

1 Milk is pasteurised This is to reduce the amount of unhelpful bacteria in the milk

2 Milk is cooled and bacteria are added

Two yoghurt-making bacteria are added

3 Yoghurt is incubated This is to encourage the bacteria to grow and divide by binary fission

4 Flavour is added The lactic acid made by the bacteria gives the yoghurt its “tangy” taste… just add fruit!

Yoghurt making

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The milk is pasteurised for 10 minutes at 95°C. This kills the bacteria in the milk. The milk is then homogenised to make sure none of the parts of milk separate out. The milk is then cooled and kept in a fermentation tank at 43°C. Yoghurt starter culture containing the two bacteria, streptococci and lactobacilli is added. This is called inoculation.

The mixture is incubated at this temperature for 4 to 6 hours. During this time the bacteria grow, reproduce and use lactose sugar for respiration. They excrete lactic acid as a waste product of their respiration. The lactic acid changes the flavour of the yoghurt and coagulates the proteins in the milk to form yoghurt.

When the amount of lactic acid in the yoghurt gets to 0.9% the tank is cooled down to 22°C. Fruit and flavour may be then added then the yoghurt is packaged. It is then cooled and stored in a fridge at 5°C. storage at this temperature slow down the activity of any bacteria in the yoghurt so it lasts longer.

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Complete the following table to describe the key steps in the yoghurt making processKey step Description of what happens in each step

Pasteurised

Homogenised

Inoculation

Incubated

Packaged

Stored

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Complete the following table to describe the key steps in the yoghurt making processKey step Description of what happens in each step

Pasteurised 10 minutes at 95°C, kills harmful bacteria already in the milk

Homogenised Shaken up so milk doesn’t separate out in its parts (water, cream, fat etc) Cooled and kept at 43°C

Inoculation A starter culture of useful bacteria is added to the milk

Incubated Kept warm at 43°C for 4 to 6 hours which is the ideal growing conditions for the bacteria

Packaged Cooled down to 22°C, fruit and flavour added and put into packs for selling

Stored Kept in a fridge at 5°C so bacteria does not grow any more and the yoghurt lasts longer

Stages in wine making

STEP PROCESS WHAT MICROBE DOES

1 Grapes crushed

Yeast on the grape skins is mixed in with the juice of the fruit

2 Juice & skins are left at 25oC.

Yeast on grape skins uses the sugar in the fruit juice to make alcohol and carbon dioxide gas - fermentation

3 Wine is stored in barrels for up to 18mths

Fermentation stops before the wine is put in barrels so the microbe doesn’t do anything in this step.

Infectious Diseases - Definitions

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Disease – a pathological condition of body parts or tissues characterized by an identifiable group of signs and symptoms.

Infectious disease – disease caused by an infectious agent such as a bacterium, virus, protozoan, or fungus that can be passed on to others.

Infection – occurs when an infectious agent enters the body and begins to reproduce; may or may not lead to disease.

Pathogen – an infectious agent that causes disease.Host – an organism infected by another organism.Virulence – the relative ability of an agent to cause

rapid and severe disease in a host.

Transmission of Infectious Diseases

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Agents that cause infectious diseases can be transmitted in many ways.Through the airThrough contaminated food or

waterThrough body fluidsBy direct contact with

contaminated objectsBy animal vectors such as

insects, birds, bats, etc.

Courtesy of VOA

Chinese students wearing masks during a

SARS outbreak

Courtesy of CDC

Aedes aegypti mosquito Known to transmit

Dengue fever

Classification of Infectious Disease

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By durationAcute – develops and runs its course quickly.Chronic – develops more slowly and is usually less severe,

but may persist for a long, indefinite period of time.Latent – characterized by periods of no symptoms between

outbreaks of illness.By location

Local – confined to a specific area of the body.Systemic – a generalized illness that infects most of the

body with pathogens distributed widely in tissues.By timing

Primary – initial infection in a previously healthy person.Secondary – infection that occurs in a person weakened by

a primary infection.

Production of poisons, such as toxins and enzymes, that destroy cells and tissues.

Direct invasion and destruction of host cells.

Triggering responses from the host’s immune system leading to disease signs and symptoms.

Courtesy of CDC

Human Immunodeficiency Virus. HIV-1 virions can

be seen on surface of lymphocytes.

How Infectious Agents Cause Disease

• Vaccines• Antimicrobial drugs• Good personal hygiene and

sanitation• Protection against

mosquitoes • Quarantine

Reducing the Spread of Infectious Diseases