# NCEA Level 1 Science/Life processes
## Introduction

Microorganisms or microbes are tiny living things that are found all around us. They are usually too small to be seen with the naked eye. Three of the main groups of microorganisms are:
* Bacteria
* Fungi
* Viruses

## Structure of Bacteria, Fungi and Viruses
### Bacteria

Bacteria (singular: bacterium) are a large group of unicellular microorganisms. They are extremely tiny thus they can not be seen individually unless viewed through an electron microscope. When cultured on agar, the bacteria grow as colonies that contain many individual cells. These colonies appear as spots of varying size, shape and colour, depending on the microorganism.
Bacterium typically occur in the following forms:
* cocci (spherical)
* bacillus (rod)
* spirillum (spiral)
Bacteria are commonly rod-shaped or spherical (cocci). An example of the structure of a bacillus (rod-shaped) bacterium is shown on the right.
* Nuclear material (DNA) – controls the cell's processes
* Cytoplasm – fluids that hold the internal structure
* Cell membrane – controls the movement of substances in and out of the cell
* Cell wall – maintains the shape of the bacterium
Some bacteria have the following additional parts:
* capsule – a hard and rigid protective layer
* slime layer – a soft and slimy layer
* flagella (singular: flagellum) – helps with movement of the bacterium.
Many bacteria do not exist alone. They will exist in chains or groups – many individuals joined together.

### Fungi

There are a variety of fungi:
* yeast – tiny, single celled fungi used in bread-making due the CO$_2$ byproduct of respiration
* mould – A fungi made of many threads. Grows on exposed food sources
* mushrooms and toadstools – a large fungi that grows in soil
It is composed of the following structures:
* sporangium- part of a fungus that produces spores
* spores – reproductive cells produced by a fungus
* hyphae – fine root-like threads that break down and absorb food

### Viruses

Viruses are extremely tiny and are much smaller than a bacterium cell. There are a variety of different types of viruses. In year 11, we will learn about the phage virus. This type of virus infects the E. Coli bacterium which is a usually harmless. The bacterium can be found in the lower intestine of animals.
The phage virus composes of the following parts:
* Genetic material (DNA or RNA) – controls the virus' processes
* Protein case – protects the virus
* Tail fibre – a hollow tube which genetic material passes through during infection
* Sheath – irreversibly binds the virus onto the bacterium resulting in its contraction and the tail fibre being pushed into the bacterium

## Culturing Microorganisms

When culturing or growing microorganisms in a laboratory, a petri dish can be used. An agar plate containing nutrients necessary for growth is placed inside this petri dish. Agar is a jelly-like substance derived from seaweed.
Only two out of the three main groups of microorganisms can be cultured:
* Bacteria
* Fungi
Viruses can not be cultured on an agar plate because they need a live host. Exposure to the virus once it has reached high levels can be extremely dangerous as all viruses are pathogenic.

### Bacteria

Steps to culturing bacteria:
    1. Sterilise a petri dish by using boiling water or a disinfectant.
    2. Add a food source to boiling agar and pour the agar into the petri dish. It will eventually set into a jelly-like substance. Close the plate to prevent other microbes from contaminating it.
    3. Repeat steps 1 to 3 for another petri dish to act as a control to confirm that the dish was sterile.
    3. Test whether a surface contains bacterium by rubbing a cotton bud or an inoculating loop onto a surface and gently wiping it onto the sterile agar plate. This is called inoculation.
    4. Seal the petri dish with sellotape to prevent contamination.
    5. Place the dish upside down into an incubator at around 30-40°C for 3-5 days to incubate the bacteria. Ensure that it remains upside down to prevent condensation build up.
Millions of bacteria will be seen as greasy spots or colonies. Do not open the petri dish as this will expose yourself to the bacteria. After this experiment, ensure that the petri dish is destroyed properly by either burning or killing the bacteria inside a microwave before disposing it.

### Fungi

Fungi, like bacteria can be cultured on agar plates. They need the following conditions to reproduce successfully:
* Warmth – best around 30-40°C
* Moisture – Fungi are living things thus need moisture
* Oxygen – required for respiration
* Food – a food source is needed in order to get glucose
Similarly, fungi can be cultured by exposing a petri dish to air for an amount of time before sealing the dish, or by placing bread near a window sill. After 3-5 days, fungi should appear as fuzz and sporangia should be seen as black dots.
An example of a large fungi is a mushroom or a toadstool. Mushrooms can grow in soil and are edible. Toadstools, however, are poisonous.

## Life processes of microorganisms

A common guide to defining life is MRS GREN.
* MOVEMENT
* RESPIRATION
* SENSITIVITY
* GROWTH
* REPRODUCTION
* EXCRETION
* NUTRITION
Bacteria and fungi have all of the above life processes thus are considered to be alive. Viruses are thought by most scientists to be alive but some disagree because they do not feed, respire (breath) and excrete (expel waste).

### Bacteria
#### Nutrition

Bacteria are a consumer in the food chain thus it needs to get its glucose from plant or animal matter. Unlike humans, a bacterium is an individual cell. This means that it must feed by extracellular digestion.
Extracellular digestion involves enzymes being allowed out through the cell membrane and being secreted onto food molecules. The enzymes catalyse (break down) the food into molecules small enough to be absorbed into the bacterium. Since the digestion is done outside of the cell, it . Bacteria which are parasitic feed off living matter.

#### Growth

Bacteria grow bigger by using nutrients gained through digestion of food and energy released through respiration. When cells reach about optimum size, they split into two.

#### Respiration

All living things respire in order to convert glucose into energy (note – respiring is not the same as breathing – respiration is a chemical reaction which takes place within cells).
Aerobic bacteria use oxygen in their respiration process. Their reaction is:
Anaerobic bacteria do not use oxygen in respiration thus are less efficient and produce ethanol as a product.
The by-product of anaerobic bacteria can be useful. Yeast (fungi), and anaerobic bacteria is useful in baking and fermentation (making wine).
Most bacteria do not require oxygen but will use it if it is available. Some bacteria require it, but most bacteria will use oxygen if it is available, but they can also undergo anaerobic respiration.

#### Excretion

Humans excrete by producing faeces, carbon dioxide and water. Aerobic bacteria release carbon dioxide and water. Anaerobic bacteria release alcohol and carbon dioxide.
Most saprophytic bacteria excrete usable nutrients. Pathogenic bacteria excrete toxins (strong poisons) and also some glucose products.

### Nutrition

Fungi practise extracellular digestion in order to respire. The hyphae release enzymes onto the food source. The enzymes break down the food into food molecules which are then absorbed by the hyphae. The glucose from this is used in respiration.

#### Growth

Fungi grow bigger through the nutrients absorbed by extracellular digestion. As they get taller, sporangia appear and eventually, the sporangia will become so large that it bursts.

#### Respiration

Aerobic fungi use oxygen in their respiration process. Their reaction is:
Anaerobic fungi do not use oxygen in respiration thus are less efficient and produce alcohol as a product.
An example of anaerobic fungi is yeast which is useful in baking.

#### Reproduction

Reproduction follow the above process. A mature sporangia bursts releasing a huge number of spores. These spores land on a food source and grow hyphae. Within 3-5 days, sporangia appears and soon, they become mature releasing spores. The cycle repeats.

#### Excretion

Saprophytic fungi digest dead plant and animal matter and release nutrients.

### Viruses

The main function viruses perform is reproduction. They do not grow, feed, respire or excrete.

#### Reproduction

Phage viruses reproduce in the lytic cycle. They follow the following stages:
* Penetration
    To infect the cell, the virus must enter through the cell membrane and (if present) cell wall. It attaches its tail fibre onto the surface and injects its genetic material (DNA and RNA). In doing this, the cell is infected with the virus.
* Biosynthesis
    A host cell cannot differentiate between the proteins of itself and a virus. This is exploited by DNA viruses which uses this to destroy the host's cell DNA and replaces it with its own DNA. Then biosysnthesis or the manufacturing of virus parts occur. First enzymes are produced to trick the cell into manufacturing viral parts. Genetic material (DNA) is first manufactured and in the later stages, the protein coat (head and tail).
* Maturation and lysis
    Once many copies of the viral components have been made, they are assembled into complete viruses. The phage then produces an enzyme that breaks down the bacteria cell wall and allows fluid to enter. The cell eventually becomes filled with viruses (typically 100-200) and liquid, and bursts. The new viruses are then free to infect other cells.And They Reproduce Themselves

## Effects of microorganisms

The following bacteria and fungi are saprophytic microbes. They feed off dead plant and animal matter and are helpful in a variety of ways. Some can:
* Decompose dead matter to provide nutrients for plants
* Help the digestive system
* Produce foods or drugs

### Nutrient Recycling

The nutrient cycle is the course traced by any particular life-essential substance such as carbon and nitrogen as it moves through the physical (air, water, rocks) or biological (plants or animals) environment.
Decomposers such as bacteria and fungi play an important role in these cycles. Decomposers breakdown dead plant and animal matter such as animal wastes, releasing nutrients that return into the environment.
In humans and animals, bacteria help in the digestive system. A common intestinal bacterium is the E. coli bacterium. It is vital in processing vitamins in the digestive systems however some strains are pathogenic (disease causing). New Zealand city councils use them in water testing to determine whether a beach or river is safe to swim in.

#### Carbon Cycle

The carbon cycle is the cycle of carbon usage through the earth’s ecosystem. The cycle begins with photosynthesis where plants use CO$_2$ to produce sugars. This carbon is either incorporated in the plants tissue as carbohydrates, proteins and fats or is released during respiration. Herbivorous animals eat these plants and most of the carbon is released during their respiration while the remaining is stored in their animal tissue. Carnivores receive the carbon in the herbivore's animal tissue when they feed on them. Eventually, the carbon compounds are broken down by decomposers and are released as CO$_2$ during the decomposer's respiration process, ready to be used again by plants.

#### Nitrogen Cycle

The nitrogen cycle is a natural cycle in which nitrogen from the air enters the soil, becomes part of a living organism before returning to the atmosphere. The element nitrogen is part of protein molecules which are important in cell processes. Air is composed of 78% nitrogen however, nitrogen is unreactive thus it needs to be converted to a chemically usable compound in order to be used by a living organism. This is done through the nitrogen cycle, where nitrogen gas is converted to ammonia or nitrates. Plants absorb the nitrate compounds in the soil and animals eat these plants containing nitrogen.

##### Nitrogen Fixation

Nitrogen fixation is the biological process in which molecular nitrogen found in the air is converted into a usable chemical compound which is essential for plant growth.
The most common soil micro-organisms capable of nitrogen fixation is symbiotic (close association between plants and animals) nitrogen fixing bacteria found as nodules (lumps) on the roots of legumes (plants that have pods (fruits or roots)). These fix nitrogen into nitrate ions (NO$_3$$^-$). Legumes that have these nitrogen-fixing bacteria living on their roots such as clover, beans, alfalfa, lupines and peanuts are able to use nitrogen almost directly.
Nonsymbiotic or free-living bacteria fix much smaller amounts of nitrogen.

##### Denitrification

Naturally, some bacteria denitrify nitrogen compounds into atmospheric nitrogen gas, completing the cycle. However, humans have intruded into this natural nitrogen process resulting in either less nitrogen in the process or overloading the system.

### Food production

Some micro-organisms can be helpful in food production.

##### Dairy

Some bacteria can be used in dairy production to make yoghurt due to its action with milk. Bacteria convert the lactose (milk sugar) into lactic acid in their respiration process. Acids are sour; this means that the lactic acid gives unflavoured yoghurt a sour taste. The lactic acid appears as curd (solid or semi-solid part of milk) which is separated from the milk. When yoghurt is eaten, the bacteria colonises their intestinal tract of the consumer, helping with digestion.
lactose (milk sugar) → lactic acid
Similarly when muscles of the human body respire, they need oxygen. In the absence of oxygen, respiration happens with glucose forming into lactic acids, which is thought to be the cause of cramps.

##### Baking and fermentation

Fermentation is the process in which yeast, a type of fungus, is used to raise bread and make alcohol.
The respiration process of anaerobic fungi can be written as:
Sugar → alcohol + carbon dioxide
In baking, yeast causes the dough to rise when it releases bubbles of carbon dioxide gas. The other by-product is alcohol thus sweeteners may be added to the bread to remove its soapy taste. Most of the alcohol evaporates during baking.
With alcoholic beverages, the yeast converts the crushed grains into ethyl alcohol and carbon dioxide. Fermentation stops when the amount of alcohol is too great for the yeast to handle.

### Disease in living things

Harmful microbes are called pathogens. Pathogenic fungi and bacteria feed off living matter. They excrete wastes called toxins which are strong poisons. All viruses are pathogens as they reproduce on a live host, resulting in the death of the cell when it bursts open.
Infectious disease can be spread in many ways:
* coughing or sneezing
* contact with discharge of an infected person
* contact with body fluids (e.g. blood, saliva)
* contaminated food or water

#### Immune system

The human body defends the body from invading organisms that may cause disease. The human immune system is responsible for destroying foreign substances (antigens) that enter into the body.
There are two forms of defence:
* Innate defence (first line protection)
* Adaptive defence (second line protection)
The first line defence system (innate) uses barriers such as skin and mucus (slimy secretion) which line all parts of the body as well as protective chemicals such as enzymes in saliva that destroy bacteria.
The second line defence (adaptive) use specialised white blood cells which attack specific foreign invaders. They retain a memory of infections so they can respond quickly the next time the organism attacks.
If the immune system overtakes the bacterium’s reproduction so that the disease is under control, then it has successfully defended the body from the bacterium. Once the foreign invader is destroyed by this combination of actions, the immune system is will respond more effectively to the invasion of that specific microbe. If it neutralises a specific bacterium completely before it causes disease, immunity to that bacterium is said to exist.
If a pathogen reproduces more rapidly than it is destroyed, then symptoms will develop. If the pathogen's reproduction overtakes the immune system's capability to respond, then the person will die.

##### Chemical defences

Many chemicals substances have been developed to combat pathogens.
| Antiseptics or disinfectants | Chemical agents that destroy or halt the reproduction of pathogenic micro-organisms. They can be applied to living tissue to clean scratches or wounds. |
| Antibiotics | A naturally produced chemical agent that kills bacteria. |
| Vaccines | A substance containing a weakened or dead pathogenic microbe given to stimulate the immune system to produce antibodies against that type of disease. |

#### Bacteria

Here is a list of common diseases caused by bacterial infection:
Various micro-organisms, including certain fungi and some bacteria, excrete chemical substances that are toxic to specific bacteria. These substances, (e.g. penicillin) are known as antibiotics; they either kill the bacteria or prevent them from growing or reproducing. Before penicillin (the first antibiotic) was discovered, bacterial infection was a major cause of human death.
There now is a variety of different antibiotics.

##### Resistance

The number of pathogenic bacterial strains that have become resistant to first line antibiotics has increased dramatically. This has resulted in an increased dosage of antibiotics required to kill them or the use of second line antibiotics.
This resistance is due to the misuse of antibiotics.
Inappropriate usage :
| Protecting against diseases | Physicians that prescribe antibiotics to prevent infection occurring. |
| Inappropriate treatment | Treating a viral infection with antibiotics. |
| Use on poultry and livestock | This promotes drug resistance and can contaminate meat with drug resistant bacteria such as salmonella. |

#### Fungi

Parasitic fungi digest living tissue of plants or animals. The preferred conditions for the reproduction of these microbes are a warm and damp environment. This is why they occur in warm and moist parts of the human body.
Common fungal diseases :
| Athletic's foot (tinea pedis) | Infection of the skin of the foot. It is highly contagious and may spread to other parts of the body. |
| Ringworm (tinea) | Infection of the skin, scalps, or nails. Some infections cause a red eruption that spreads at the circumference as it heals in the centre. The infection usually causes burning and itching. |
| Thrush | Infection of the mouth and vagina. Causes a white discharge. |

#### Viruses

All viruses are pathogenic as they destroy the cell when it bursts open. Viruses mutate quickly. An infection of the cold or flu virus can keep recurring because the virus has mutated enough to prevent the immune system from recognising it. Antibiotics do not kill viruses; however the immune system can treat most cases of viral infection.

##### HIV

AIDS (Acquired Immune Deficiency Syndrome) is a relatively new disease that was first diagnosed in the early 1980s. In 1983, scientists first isolate the virus that caused this disease and called it Human Immunodeficiency Virus (HIV). HIV, which destroys some common types of white blood cells, is transmitted through blood or bodily secretions such as semen. Patients lose the ability to fight infections, often dying from being infected with another pathogenic microbe. It is estimated that 25 million people have already died from this pandemic.
Once the immune system stops working, symptoms of AIDS develop as the body can no longer defend itself. These include weight loss, fatigue, headaches, fevers and recurring infections.

## Factors affecting life processes

Various factors affect the different life processes of microorganisms.

### Temperature

The ideal temperature for reproduction of microbes is around 20-40°C. At this temperature, bacteria can reproduce once every 20 minutes. Temperatures above 100°C will kill all microbes. Freezing will not kill microbes, it will stop its reproduction. Microbes will continue to reproduce in a refrigerator, only at a slower rate.

### Moisture

Water is a limiting factor in the growth of bacteria. Bacteria are about 80-90% water thus they need water to grow. If too much water passes into or out of a bacterial cell, the cell dies.
For example, if a bacterial cell is placed in a highly concentrated solution of salt water, water begins to pass out of a cell and into the salt water. The cell begins to shrink and is unable to carry on normal life functions. It cannot grow and will eventually die.

### Nutrients

In order to respire, bacteria and fungi need food. These combined with oxygen (aerobic respiration) or without (anaerobic) form carbon dioxide and water (aerobic) or carbon dioxide and alcohol (anaerobic).
When nutrients run out, the reproduction of bacteria or fungi stops and they begin to die out.
Aerobic and Anaerobic are both inside of the cell. The aerobic means 'with oxygen' and anaerobic means 'without oxygen'.

### pH

The pH (acidity or alkalinity) of the environment affects the survival of bacteria and fungi since they do not have any mechanism to adjust their internal pH. Microbes survive at around a neutral pH. Microbes will not survive in conditions too acidic or too basic.

### Oxygen availability

The availability of oxygen affects the respiration of aerobic bacteria or fungi. Without oxygen such as in vacuum packaging, microbes will not survive.

#### Terminology

* inoculate: Transferring a microbe into a petri dish
* extracellular digestion: The breaking down of food by enzymes occurring outside of the cell
* enzyme: A chemical produced by a cell for digestion
* pathogen: Microbes that causes disease
* saprophyte: A microbe that feeds on dead matter
* aerobic: Microbes that use oxygen during respiration
* anaerobic: Microbes that do not use oxygen during respiration
* hyphae: Fine root-like threads used for feeding by fungi
* spores: Reproductive cells of fungi
* sporangium: A part of a fungi that produces spores
* toxin: Poisonous substances released by microbes
* disinfectant: Chemicals applied onto living tissue that kills microbes
* antibiotic: Substance taken internally to kill bacteria
* binary fission: How bacteria reproduce
BE WARNED: Please do not use this information for tests/exams as the information may not be correct.
* ↑ https://www.khanacademy.org/science/high-school-biology/hs-energy-and-transport/hs-cellular-respiration/a/hs-cellular-respiration-review