5.15a Genetically Modified Plants

1. Maize
- it is damaged by the larvae of the european cork borer. This causes 20% loss of crop yield.

2. In a bacterium that we will call Bt, there is a chromosome and on that chromosome there is a gene.
- when the gene is switched on it produces Bt toxin and this is known to kill the cork borer larvae.
- what can we do to get this toxin into maize to protect it from the european cork borer?

3. Take restriction enzymes to the gene of the Bt and chop the gene out
- so we only get the Bt gene for the toxin.

4. This is transferred to the cells of the maize plant.
- This is not easy and the technique used currently, involves a 'gene gun'.
- It involves taking tiny particles of gold, that is coated in the Bt gene, and firing it at a high velocity at the plant cell
- introduces the Bt gene to the interior of the plant cell. The Maize cell gets the gene and once switched on, it can switch on the Bt toxin --> killing the larve
- This gives the Maize resistance to damage caused by the cork borer.

5.14 Humulin

- the bacterial cell (E.Coli) has been transformed by the addition of recombinant DNA.
- the black circle, in the image, represents the plasmid DNA and the yellow dot, in the image, represents the human DNA (insulin gene in this instance)
- a culture of this bacteria (large population) will be injected into the fermenter.
- necessary to provide the culture nutrient, necessary to control the temp. and the pH and also the gases that are in the fermenting chamber.
- by creating the optimal temperature for bacterial growth, we will see this population increase and we will see the bacteria manufacture the protein insulin by switching on the gene for insulin.
- the bacteria inside the fermenter will manufacture the insulin protein from the nutrient provided (amino acids)
- it will be necessary to remove the product and carry out purification (many processes required for human use) - this is called Downstream processing
- the genetically engineered human insulin is called 'Humulin'

5.13b Hosting Recombinant DNA

- Recombinant DNA - mixture of human gene and bacterial plasmid
- it is necessary to transfer the structure into the host cell
- in this instance, the host is a virus and inside is the nucleic acid such as DNA or RNA and around it is the protein cell
- the first thing is: remove the nucleic acid from the virus. Only the capsid protein shell is needed
- the plasmids are taken up by the virus and acts as a vector recombinant DNA. It is going to help transfer the DNA into the host cell.
- the reason why we choose the virus is because the virus, known as the phage, infects bacterial cells.
- it is able to attach to the cell membrane of the bacteria and insert the recombinant DNA into the host cell.
- at the end of the process, we have a bacterial cell which now contains the recombinant DNA including the human gene for insulin.
- the bacteria has its own DNA plus DNA from another organism. This combination is known as 'Transgenic'

5.13a Recombinant DNA

1. Plasmind.
- they are found in bacterial cells
- they are a ring of DNA
- particularly small and dont carry many genes

2. Virus.
- it has a protein shell called a capsid and inside will be a nuclic acid. Possible DNA or RNA.
- it has no other cellular components. no cytoplasm, no nucleus, no other structures like this

3. Human Chromosome
- it is the length of DNA.
- the human chromosome is made of DNA
- the gene codes for the protein insulin which is a hormone controlling blood sugar levels

- the restriction enzyme is selected that can cut the DNA on two sides. Essentially, we are cutting out the gene for insulin
- the enzymes are called 'restriction enzymes'
- once the gene is cut, we progress to the stage where the plasmid is cut with exactly the same restriction enzyme
- this leaves the ring structure of the plasmid, broken.
- introduced into the cut plasmid, is the human insulin gene, remembering that the plasmid and the human gene is composed of DNA
- we leave the plasmid with the human gene inserted inside and necessary to complete the process by applying the second enzyme which is called the 'DNA ligase' enzyme which will join the DNA.
- this combination of the human gene and the plasmid DNA is known as 'Recombinant DNA'

5.11 Breeding Animals

- The animal in the video is a cow. The desired characteristic is milk yield.
- The earliest farmers notice that a few cows will produce a small amount of milk each time. around 50 ml each time that they are milked.
- Other cows, a few, will produce 150 ml of milk
- Most cows produce 100 ml of milk.
- The farmer will collect all the milk
- He chooses the cows that make 150 ml of milk to become his breeding cows.
- In the next generation of cows, we find out that a few cows produce 100 ml of milk, very few produce 200 ml of milk and the majority produce 150 ml of milk
- The farmer selects his breeding cows from the one that produce 200 ml to become the breeding population
- perhaps, in the next generation, a few cows will produce 150 ml of milk, most cows will produce 200 ml and few produce 250 ml
- as we progressively select, we change the desired characteristic. We are able to develop the desired characteristic by selective breeding
- for this to work, milk yield must be genetic - under the control of genes.

5.10 Breeding Plants

- In the image, the plant is rice. On the rice there are rice grains
- the number of rice grains are under the control of genes
- the farmer wants to improve the number of rice granes per plant which would lead to the increase in yield
- Some plants have six grains per stem whilst others have 8 grains per stem as well as others that have 10 grains per stem
- the farmer decides to harvest the one with 6 and 8 grains and use the one with 10 grains for planting
- in the next generation of rice, the number of grain increases to 8 grains per stem, 10 grains per stem and 12 grains per stem.
- he harvests 8 grains and 10 grains and selects the one with 12 grains for planting and breeding
- this way, the number of grains of rice on each plant gradually increases --> therefore, the yield increases.
- this is an example of selective breeding and can be applied to most characteristics of the plant.

5.9 Fish Farming

- fish is an attractive product for farmers because:
1. they have low fat and high protein
2. they are efficient at turning their nutrient into fish mass

Pros:
- fish faming allows us to control the quality of water = clean
- we can control predator's
- we can reduce pests
- we can also reduce diseases

- By controlling all these factors, we contribute to an increase in yield of fish.
- However, where you have a high density of fish, there is a possibility of transmission of disease.
- Because of this, some fish farmers have taken to using antibiotics and is a concern to human health
- The abundance of fish within the fish farm also makes pests common and therefore, some fish farmers use pesticides - this is also a cause of concert amongst humans.

5.8 Fermenter

- Fermenter = the reaction vessel in which fermentation occurs.
- the vessel is usually built of metal, e.g. copper, steel, etc.
- normally, there is another steel jacket inside the first steel jacket
- in between the two jackets, there is water = cooling jacket. once a fermentation gets going, it produces heat and the water cools down the reaction so it occurs at optimum conditions.
- the fermenter needs to be clean and therefore, there is an inlet. Steam goes through the inlet and it will be sterilizing the fermenter between fermentations.
- within the fermenter, there is a heating plate to raise the temperature.
- the heater and the cooling jacket allows us to control the optimum conditions for fermentation.
- there is a tap/pipe work to insert nutrients
- there is a temperature probe = it will tell us whether to deploy the heater or the cooling jacket
- the reaction require addition of organisms, therefore, there will be another tap for it.
- a pH probe is also required - to monitor and keep it at the optimum temperature to get the maximum rate of reaction
- to stir the reaction, a motor is required and this will agitate the mixture, stopping it from clumping together

- the idea of the fermenter is to create a reaction centre in which we control the optimum growth conditions for the micro-organism so that it will be able to produce the product that we are looking for
- at the end of the reaction, the important thing is to find a way to drain off the product which would then go on to the process called down stream processing which involves purification

5.7 Yogurt

- The process starts with a cow and milk is produced
- Pathogens such as TB bacillus is removed from the milk through the process called pasteurisation
- The milk sugars are converted into lactic acid, this is brought about by incubating the milk at 45 - 46 degrees and to add lactobacillus (lactobacillus produce the enzymes that break down the milk sugar, lactose into lactic acid)
- The acid will result in a lower pH (acidic conditions) and this causes milk proteins. The milk proteins then solidifies. The solidification is 'yogurt'

5.5 Beer Production

- the beer is largely: Ethanol - an alcohol molecule
- Anaerobic respiration: glucose --(yeast)--> ethanol + carbon dioxide
- yeast is able to supply the enzymes to bring about the conversion
- the ethanol is flavoured by the addition of plants (e.g. Hops)
- glucose comes from starch in a two-step process
- Starch --(enzyme: amylase)--> maltose --(enzyme: maltase)--> glucose
- the source of the starch are things like: barley seeds, wheat seeds and sometimes rice
- malting: breaking starch down to maltose through the germination of the seed
- yeast brings about the anaerobic respiration of glucose, ethanol and carbon dioxide

5.4b Biological Control

example of biological control - not using pesticide:
- In Australia, the prickly pear cactus, which was the pest, of north america was introduced to gardens
- it escaped into the countryside
- it flourished under the Australian climate and the ecosystem
- the cactus started to cover a deal of agricultural land and was necessary to get rid of it
- there was no natural herbivore of the cactus and was necessary to introduce an alien species from another country = a moth which feeds on the cactus, known as Cactoblastis
- the moth was introduced and had no competitors = able to eat away at the cactus and remove it from the agricultural land of Australia

Pros:
- There are no toxic chemicals involved
- this leads to less impact on man/wildlife

Cons:
- not 100 percent effective
- often difficult to control - there is always a danger that the introduced species will find alternative pray on which to feed and will not die out once the pest has been removed
- difficult to match a predator to the prey

5.4a Pesticides

- monoculture = large fields of crops, all of the same type.
- this could be fields of wheat, barley, potato, rice, etc. and tend to be susceptible to pests.
- they use the crops as their own food source --> reduces productivity of farming = loss of food and financial impact on the farmer
- to over come this: Pesticides are used (these are chemicals designed to kill the pests)

PESTICIDES
Pros:
- They are chemicals = easy to obtain
- Easy to apply, not difficult for the farmer to spray it
- They are very effective

Cons:
- The chemicals are toxic = kill other plants and animals other than the pests and may be harmful to humans
- Bio-accumulation = the pesticide builds up through the food chain causing problems for animals in the higher tropic levels (e.g. DDT)
- mutation in the pest often leads to resistance = the pesticide must be applied in higher concentration and therefore, more toxic or no longer works and have to find an alternative for the pesticide.

5.3 Fertilisers

- the growth of the plant can be achieved in farming by the application of fertilisers to the soil
- fertilisers normally take the forms of Nitrates, Phosphates or both.
- these compounds go down into the soil and taken up from the roots. It is then moved into the transpiration stream up to the leaf and used in the leaf. (nitrates go on to form proteins, phosphates are involved in DNA and membrane structure)
- the fertilisers can be divided into two groups: organic and artificial

1. Organic fertilisers
- produced from animal waste on farms, e.g. cow faeces
- collected by the farmer and goes through the process of decomposition and fermentation
- it forms a substance known as 'slurry'
- it is applied to the fields, giving the crop plants a supply of nitrate and phosphate to promote growth




2. Artificial fertilisers
- take forms of chemicals that are synthetically produced
- Potassium Nitrate and Ammonium Nitrate - can be bought by farmer
- applied to the field
- go into solution in the soil water and this will release the nitrates
- promotes growth in the same way as organic compounds




problems caused through the fertilisers
- leaching: if the nutrients in the fertilisers aren't taken up, they could be washed out of the soil by the rain and enter streams and rivers. This then causes eutrophication
- Eutrophication: process that takes place when freshwater is enriched by nutrients, especially nitrates and phosphates

5.2 Crop Yield

- This is related to the rate of photosynthesis CO2 + H20  --(light, enzyme reaction)--> C6H12O6 (turned into starch and stored by the plant) + 02

1. Increasing the concentration of Carbon dioxide. CO2 = substrate
- increasing the concentration of the substrate and the rate of reaction will increase
- the rate of photosynthesis will increase = higher yield up to a point.
- the optimum point will give the greatest yield of product

1. Increasing the temperature
- as we increase the temperature we get an increase in the rate of reaction and the yield increases
- this only continues until it reaches the optimum temperature.

- if we increase the temperature and the concentration of carbon dioxide we will experience the increase in rate of photosynthesis and the yield. They both have limits
- increase temperature in a greenhouse also has other affects:
1. avoiding frost damage
2. providing constant temperatures
- both contribute to the increase yield

5.1 Glasshouses

Glasshouses / Greenhouses
- it is constructed on a framework and all of the surfaces are glass --> allows light to penetrate through to the interior.

Polythene tunnels
- usually a frame work with polythene on the surface
- Polythene allows light to penetrate through to the interior as well
- Associated with market gardening and used in less-developed countries because cheaper than the glass
- it is adjustable and can be taken down and replaced much more regularly than the glasshouse

How it works:
1. start: solar radiation - initial source of energy in the form of light
2. light penetrates through the glass into the internal surfaces
3. the light is absorbed by surfaces  inside the glasshouse e.g. soil, wooden bench surfaces, plants, etc.
4. the surfaces then re-emit the energy as heat
5. the heat warms the air - raising the average kinetic energy = temperature increases
6. the warm air is trapped. It would cool at the upper surface and then sink to the floor to be re-warmed by the surfaces within the glasshouse

- Warm air ---> increase in crop yield
1. the higher temps in the glasshouse lead to optimum temperatures for enzyme reactions (including photosynthesis)
2. provides constant temperatures throughout the growing year ---> constant production
3. prevention of loss of water vapour. The crops dont dry out  - have a constant supply of water.
4. avoid frost damage (particularly to seedlings in the spring time)
5. it is warmed by the burning of fossil fuels
---> 1. increase in CO2 levels inside the glasshouse --> increase the concentration of the substrate for photosynthesis = more product and more growth
---> 2. inefficient burning of fossil fuels --> ethene ---> it stimulates fruit ripening

2.89 Hormones

2.89 understand the sources, roles and effects of the following hormones: ADH, adrenaline, insulin, testosterone, progesterone and oestrogen.


This is the Endocrine system.
Endocrine glands --Hormone travels though blood)--> Target --> Effects
The hormonal system also coordinates the body and the hormones are chemicals produced by glands. Small amounts of the chemicals are carried around the body by blood and tells different parts of the body what to do.


ADH:
ADH --> Pituitary gland ---> collecting duct ---> Increases absorption of water into the blood stream
- produced in the pituitary gland
- controls the level of water in your body
- causes kidney tubules to reabsorb more water into the blood stream


Adrenaline:
Adrenaline ---> Adrenal glands --> Heart (one of the targets - many more) --> Increase Heart rate
- produced in the adrenal glands
- it is released during excitement, stress or fear
- helps the body prepare for action by:
1. Glycogen is converted to glucose in the liver --> more glucose reaches the muscles as a source of energy for the rapid contractions needed for sudden action
2. Heart rate increases --> more oxygen and glucose delivered to muscles for energy release.
3. Bronchioles widen --> more air reaches lungs
4. Blood vessels go the gut and other organs narrow --> more blood to be diverted to more life-saving organs
5. Blood vessels to the brain and muscles widen --> more glucose and oxygen delivered to these organs
6. Hairs are raised --> makes furry animals look larger 


Insulin:
Insulin --> Pancreas --> Liver --> storage of glucose (reduce blood sugar levels) 
- secreted by the pancreas
- controls blood sugar levels 


Glucagon
Glucagon --> Pancreas --> Liver --> put sugar into kidney


Testosterone:
Testosterone --> Testis --> Testis (sperm) --> Sperm cell mature
- produced in the testes
- develops male features during puberty


Progesterone:
Progesteron --> Ovary --> Uterus --> maintains the lining of the uterus
- produced in the ovaries 
- prepares the womb so it could receive a fertilized egg 
- works with oestrogen for menstrual cycle


Oestrogen:
Oestrogen --> Ovary --> Uterus --> makes the lining of the uterus
- produced in the ovaries 
- develops female features during puberty
- works with progesterone for menstrual cycle

2.88 Skin

2.88 describe the role of the skin in temperature regulation, with reference to sweating vasoconstriction and vasodilation

- Homeostasis is the act of keeping conditions steady inside the body.

- It is important to keep the body temperature at 37 oC because enzymes work best at this temperature. Any slight change int he conditions can slow down or stop the enzyme from working.

- The skin controls the temperature within our body.

- Temperature is one of the factors controlled by the negative feedback system as well as blood sugar the water levels. If there are any changes in the surrounding environment, the system will try to minimize the changes.
- Stimuli: blood temperature
- Receptor/co-ordinator: Hypothalamus
- Effector: Skin
- Latent heat of evaporation

When the temperature is low - cold:

- There is less sweating

- Hair erection - when the hair muscles contract and this traps a thicker layer of air --> cuts down more on heat loss

- Vasoconstriction - the capillaries narrow and therefore, carry less blood --> more heat kept inside the body

- There is insulation from a layer of fat underneath the skin 

- Shivering releases extra heat from increased respiration

When the temperature is high - hot:

- More sweating for evaporation ---> reduces the amount of heat

- Hairs lie flat - hair muscles relax and less air is trapped close to the skin ---> more heat lost by radiation

- Vasodilation - the capillaries widen and therefore, carry more blood ---> the heat can be transferred out of the body via conduction and radiation.

- There is no shivering.

2.87 Focusing

2.87 understand the function of the eye in focusing near and distant objects, and in responding to changes in light intensity


- Most of the bending of the light rays are done by the cornea.
- The shape of the lens is controlled by the ciliary muscles


Looking at a distant object:
- the ciliary muscles relax
- the suspensory ligaments tightens
- the lens is pulled into a thin shape
- the distant object is then focused on the retina


Looking at a near object:
- the ciliary muscles contract
- the suspensory ligaments slackens
- the elastic lens goes fatter
- the near object is focused on the retina


In bright lights: the circular muscles contract and the radial muscles relax --> the pupil becomes smaller and less light enters the eyes


In dim lights: the circular muscles relax and the radical muscles contract ---> the pupil becomes bigger and more light enters the eyes

2.86 The Eye

2.86 describe the structure and function of the eye as a receptor

- The eyes are moved by 3 pairs of eye muscles.
- Light enters the eye through the transparent cornea and passes through the pupil (the pupil is surrounded by the coloured iris). The conjunctiva, a delicate, transparent layer at the front of the cornea is kept moist by tear glands.

Cornea - It is a curved band of strong, clear tissue that is on the surface of the eye. The cornea focuses the light onto the retina.
Epithelium - Provides a thin protective layer from the cornea and heals quickly when disturbed.
Iris - A muscle that controls the size of the pupil. The coloured part of the eye.
Pupil - The black circular area in the middle of the eye that controls the amount of light reaching the retina.
Retina - This is a membrane on the inner wall of the eye. It is similar to the film in a camera - it changes light into images that are transferred to the brain via the optic nerve. It is an inner light-sensitive layer that contains rod cells that work in dim light and cone cells that detect colour and details.
Sclera - Provides protection and is the outer white coat of the eye.
Lens - This is a natural lens behind the pupil that changes shape to allow the eye to focus. It focuses light onto the retina. When aging, the natural lens hardens and results in the loss of reading vision.
Choroid - A black layer containing lots of blood vessels
Vitreous humour - Transparent jelly-like substance that supports the back of the eye
Yellow Spot / Fovea - most sensitive part of the retina
Blind Spot - where the optic nerve attaches to the eye and there are no light-sensitive cells here
Optic Nerve - Carries nerve impulses away to the brain
Suspensory ligaments - holds the lens in place
Aqueous humour - Watery liquid filling the front of the eye
Ciliary muscle - changes the thickness of the lens when it is focusing

2.83 - 2.85

2.83 recall that the central nervous system consists of the brain and spinal cord and is linked to sense organs by nerves

The nervous system controls your actions. It coordinates different parts of your body so that they work together and are able to bring about the correct responses.
The nervous system consists of the brain and the spinal cord - both are made up of delicate nervous tissue.
The central nervous system is connected by different parts of the body by nerves which are made up of lots of neurons.
Sense organs are our receptors and the instructions are sent along sensory neurons to the central nervous system.

2.84 understand that stimulation of receptors in the sense organs sends electrical impulses along nerves into and out of the central nervous system, resulting in rapid responses

The messages that nerves carry are called nerve impulses - they are electrical signals. They pass very quickly along the axon of the neuron. Some of the axons have a fatty sheath around them that insulates the axon and makes the impulse travel along faster. The motor neuron carries signals from the central nervous system to the muscles and this controls the response. Sensory neurons carries signals into the central nervous system.
The electrical nerve impulses are very fast enabling a fast response and therefore known as 'rapid responses'

2.85 describe the structure and functioning of a simple reflex arc illustrated by the withdrawal of a finger from a hot object

A reflex is a type of response that are there to protect you where it happens very quickly without thinking. You do this automatically.

The flowchart of co-ordination in a reflex system is:

stimulus (hot flame) ---> receptor (in this case, fingertip - it has a pain sensor) ---> sensory neuron ---> coordinator (Central Nervous System) ---> Motor neuron ---> effector (muscles) ---> response

The stimulus is the hot flame, the receptor is the heat sensor in the skin. The impulse travels to the spinal cord along the sensory neuron and in the spinal cord, the impulse is passed on to the relay neuron. From this, the impulse then goes to the motor neuron and then into a muscles in the arm. The muscle is the effector and it contracts to remove the hand from the hot object. This action is known as the response.

2.82 Communication

1st Diagram
- example is a motor nerve. The orange part would be embedded in the spine and at the other end, it would connected to the effector (most likely a muscle)
- the electrical impulse (or the nerve impulse) is carried a long inside the nerve down the orange structure from the cell body to the end known as the synoptic knob where it connects to the muscle.
- this can be up to a metre long. A single cell is shown in orange.
- the long structure is known as the axon.
- in mammals, the axon is surrounded by the Schwann cell - contains a great deal of fat and form a Myelin Sheath.
- this is one way of linking our co-ordinator to our effector

2nd Diagram
- the endocrine system
- involves the endocrine gland that produces a chemical known as a hormone (they can be proteins or steroids). example of this is Adrenal gland
- the hormone is secreted into the blood. Adrenaline is secreted by the Adrenal gland into the blood and travels to the target tissue (or target organ) and then it will have an effect.
- hormones can have multiple targets and bring about multiple effects contrasting with the nerve system.

- a comparison between communication based on nerves and communication based on hormones needs to be drawn
e.g. the nerve impulses are fast
hormones are relatively slow

2.77b Thermoregulation

- Negative feedback loop = method of control or maintaining constant conditions. (in humans, this is the idea of our fixed point, our constant body temperature = 37 - 38 degrees)
- In order for it to work we have receptors of body temperature (internal conditions) = Hypothalamus - region of the brain
- Hypothalamus responds to a stimulus = the temperature of the body and the temperature of the blood.
- Body temperature feeds into the brain --> it is compared to the theoretical level of control. If the temperature needs to be altered, it is brought about through the action of the effector such as the skin.
- The response would either be an increase or decrease in the body temperature.
- This feedback to the hypothalamus on the basis of the input, a new output would be produced.

- One of the major components of the skin for the control of body temperature are:
+ sweat glands
+ Capillary network - it allows blood to move closer or further away from the surface of the skin.
- In the graph, x axis is time and the y axis is the 37/38 regulation point.

In a hot environment:
- If body temp. increases, the input to the hypothalamus stimulates responses in the skin which bring about cooling
- One of the responses is sweating.
- Another is when the blood flow to the surface of the skin increases. The blood vessels dilate and widen. This increases the exchange of heat to the outside of the body by processes such as the evaporation of sweat and radiation - vasodilation
- Hairs flat
- This brings the cooling of the blood and brings the body temp back to the fixed level.

In a cold environment:
- Our body temperature will fall. This feeds to the hypothalamus and switches on and brings about regulation to increase the body temperature such as shivering, raised hairs and vasoconstriction.

2.77a Thermoregulation

- Homeostasis = Homeo (refers to the idea that something being the same) stasis (refers to a fixed point or a set of conditions) --> The idea that conditions are kept the same or constant.
- Homeothermic = maintaining the same temperature.
- Some organisms (e.g. mammals) when the environmental temperature either increases or decreases, then their body temperature remains constant.
- These are Homeothermic organisms that carry out the process of Thermoregulation (an example of Homeostasis)
- Other organisms body temperature vary with the environmental temperature.
- Mammals maintain a constant body temperature because:
+ Enzymes work best at the optimum temperature.
+ The optimum temperature for the enzyme reaction is the approx. the same as the temperature that which the mammals maintain their body conditions.

2.76 Sensitivity

- Characteristics of life:
M.R.S.G.R.E.N.
- S = Sensitivity. This is the characteristic in which organisms respond to changes in the environment.
- Type of change in the environment:
+ changes in light levels
+ Temperature
+ Pressure levels
+ Chemicals
- To be able to detect the changes in the environment, organisms need to have receptors. In order to respond to the changes in the environment, organisms need to have effectors (eg. muscles and glands)
- The response that ensures that the organisms is able to survive the changes in the environment.