Biology- OCR- B4 and B5

The reactions of photosynthesis:

• It is carried out by all green plants and some bacteria. 
• It traps the energy from sunlight and uses it to make food in the form of a type of sugar called glucose.
• The plant converts glucose into other chemicals it needs to live and grow.

The structure of the leaf (from top to bottom): 

• Cuticle (waterproof)
• Upper epidermis
• Palisade layer
• Spongy layer and the leaf vein
• Stoma, guard cells and lower epidermis.

Under the cuticle there are different layers of cells. All the cells have a large central vacuole containing sap, as well as a tough cellulose wall. Some of the cells contain also have chloroplasts that contain the green chemical chlorophyll and so can carry out photosynthesis.

Photosynthesis efficiency: 

• They are broad so that they have a large surface area to absorb light
• They are very thin so gases do not have far to travel
• They have a network of veins that support the leaf, and carry water in and glucose out
• They have stomata to allow gases to pass in and out by diffusion
• They have chlorophyll to absorb sunlight
• The air spaces inside the leaf mean that the leaf has a large internal surface area-to-volume ratio.

The top layer of the cells, the upper epidermis, has no chloroplasts and so is transparent. This means that light hitting the leaf passes straight through to the palisade mesophyll layer. This is close to to the top of the leaf and contains most of the leaf's chloroplasts. It is where most photosynthesis takes place.
The air spaces in the spongy mesophyll layer allow gases to diffuse between the stomata and the photosynthesising cells. Carbon dioxide diffuses in and oxygen diffuses out of the stomata. All the thousands of cells inside the leaf give a very large surface area for the absorption of carbon dioxide.
Apart from the guard cells, the cells from the lower epidermis do not contain chloroplast. 

Water is taken in from the soil by the process of osmosis.

Water moves in and out of plant cells through the cell wall and membrane. When the vacuole of a plant cell is filled with liquid the water pressure presses up against the cell wall. The cell is said to be turgid. The cell wall is inelastic and does not stretch so it supports the plant cell. This turgor pressure s very important in supporting plants. 
When the opposite happens and there is not enough water the cell becomes flaccid. This means they collapse inwards and the plant wilts.

Sometimes the cells lose so much water that the cell membrane may come away from the cell wall. This is called plasmolysis. 

The cell wall is permeable and so it can let in large molecules. 
The cell membrane is partially permeable, this means small molecules such as water can diffuse through but not large molecules.

Osmosis is where water moves from high water concentration (a dilute solution) to an area  of low water concentration (a concentrated solution) across a partially permeable membrane.

Animal cells do not have an inelastic cell wall, this means that when the amount of water is changed the whole cell changes shape. When the animal cells take up too much water they burst, this is called lysis. But when the cells lose water they shrink, which is called crenation.
As water leaves a plant through the stomata it is called transpiration. Water is taken up from the soil by the roots. The younger roots are covered in projections called root hairs, these increase the surface area to increase the take up of water.
The plant cannot stop losing water through transpiration, the flow of water to the leaves in the atmosphere does benefit the plant in several ways:

• it helps cool down the plant, like sweating
• it provides the leaves with water for photosynthesis
• it brings minerals up from the soil
• it makes sure cells stay turgid for support.

The plant tries to cut water loss as much as possible, it has adapted in many ways: The waxy cuticle on top stops water leaving the leaf, the small amount of stomata on top means that when sun' energy hits it small amounts of water is evaporated, the stomata are adapted by when there is a lot of light and water available , they take in water and become turgid, opening. But when light levels are low the stomata become flaccid and close, reducing water loss.

The two different transport tissues in a plant are called xylem and phloem.
Dicotyledonous is a plant with two seed leaves.

Xylem transports water and dissolved minerals. The xylem contains long thin tubes called vessels each with a hollow lumen. This means they are made from dead cells. The vessels are hollow so that water can easily pass through. Their cellulose cell wall is thickened to stop them collapsing and helps support the pant as well.
Phloem transports dissolved food substances (sugars) around the plant. Unlike the the transport of water, the food may be transported up or down the stem. It may move from the leaves where it is made to the tips of the shoots where growth happens. This movement of food substances is called translocation. The phloem is made up of columns of living cells. The cells have holes in the end walls to allow the food to pass through.

When water is lost this causes a suction for the xylem to **** up more water by the roots and the leaves. 
The rate of transpiration increases when:
-The temperature increases, light levels increase it is windy, it is dry and not very humid.
This is because, in warmer conditions, the water molecules have more energy and so evaporate faster. An increase in light causes the stomata to open allowing water out, while in windy conditions the water vapour in the air is blown away allowing more of it to evaporate and in dry conditions the air holds fewer water molecules and so more water diffuses out. 

Plants minerals: 

• Name-Magnesium
  Main source- Magnesium compounds
  Used to produce- Chlorophyll for photosynthesis
  Effect of deficiency- Yellow leaves
• Name-Nitrogen
  Main source- Nitrates
  Used to produce- Amino acids for making proteins which are needed for cell growth
  Effect of deficiency- Poor growth and yellow leaves
• Name- Phosphorous 
  Main source- Phosphates
  Used to produce- DNA and cell membranes to make new cells for respiration and growth
  Effect of deficiency- Discoloured leaves and poor flower and fruit growth
• Name-Potassium
  Main source- Potassium compounds
  Used to produce- compounds needed to help enzymes in photosynthesis and respiration
  Effect of deficiency- Poor root growth and discoloured leaves

The minerals that the plant needs are absorbed from the soil by the roots. They are dissolved in water in quite low concentrations.

The concentration of these minerals in the root hairs is much higher. This means that they cannot be taken in by diffusion. A process called active transport is needed. This process moves substances from low concentration to high concentration. This means it moves substances against the concentration gradient. It requires the energy from respiration to do this.

Because active transport uses energy from respiration, roots need oxygen in order to take up minerals by this process. Farmers try to make sure their soil is not waterlogged because this reduces the oxygen content of the soil.

In every food chain the first organism is the producer. this means it can make its own food using energy from sunlight. All other organisms are consumers, they need to take in food because they can't produce their own. 

Pyramid of numbers, the numbers of each organisms at each stage in the food chain (trophic level) is counted. Each box in the pyramid is drawn so that the area represents the number of organisms.
An alternative is the pyramid of biomass. Biomass is the mass of living material of an organism. The mass of all organisms at each level is measured  and the boxes are drawn to show the mass at each stage in a food chain.

Energy is lost from organisms through heat, egestion and energy used to grow, this explains why each chain only has four or five levels because another organism would not be able to survive on the energy that the last organism would give them.

We can use energy stored in biomass in different ways:
-We can burn wood from fast growing trees, we can produce alcohol by using yeast to ferment biomass, we can produce biogas which contains gases produced by bacteria fermenting biomass.

Intensive farming is where the farmer uses a range of fertilisers and pesticides to increase yield. 
Battery farming is where livestock are kept under controlled conditions. They are kept warm and their movement limited so they lose less energy as heat. 

Although using pesticides kills and stops the pests from eating and destroying the crop they can have affects on other wildlife. For example pesticides that are washed into a nearby lake or river can infect the fish and when a larger animal eats them it can interfere with its egg production.

Many farmers who use intensive farming grow plants in greenhouses. This is to protect them from the extremes of weather. They are usually grown in soil but not always. This is called hydroponics. Proper hydroponics means growing crops in water, but farmers may use artificial soil. This technique is beneficial to where the soil may be barren. 
The disadvantages of this is that the plants are not supported by deep soil and you need to add fertilisers to it.
The advantages are that the mineral level can be controlled and you can control diseases by adding pesticides to the water so they reach every plant. 

Organic farming avoids using chemicals, pesticides and fertilisers to boost its yield. Instead it uses different methods:
-Manure and compost to fertilise the soil,
-Crops that can fix nitrogen in the soil, such as clover, can be grown,
-Crop rotation can be used so that pests cannot build up in the soil,
-Crops can be weeded by hand,
-Farmers can vary seed planting times.

Biological control can also be used to prevent pests. The farmer will release an organism that feeds off the pest and hopefully kill them. Sometimes this can go wrong and end up affecting the whole food chain if they kill all of the pests or they themselves can become another pest.

When organic material dies it starts to break down or decay.
Organisms that break down dead organic material are called decomposers. They are very important because they allow chemical elements to be recycled. If decomposers did not do this all the chemical elements needed for this life would build up inside dead organisms.

The two main groups of decomposers are bacteria and fungi. They release enzymes on the dead organic material and then take up the partially digested chemicals.

This type of feeding is saprophytic nutrition and the bacteria and fungi are called saprophytes.

There are organisms that help the decomposers to do their job. Animals such as earthworms, maggots and woodlice feed on pieces of dead and decaying material (detritus). They are called detritivores. 

Detritivores increase the rate of decay by finely breaking up material so it has a larger surface area. This means it can be broken down faster by the decomposers.

In order for organic material to decay, several things need to be present: microorganisms, oxygen and water. Oxygen is needed for the aerobic respiration of the microbes, while water is needed to allow substances to dissolve and the chemical reaction of respiration to occur. It also needs to be warm enough.

We use food preservation to reduce the rate of decay, this can be done in different ways:
-Method-Canning.
Details-food is heated to 100 degree in a can and then sealed.
How decay is prevented- the high temperature kills the microorganisms; water and oxygen cannot get into the can after it is sealed.

-Method- Cooling.
Details- food is kept refrigerated at 5 degrees.
How decay is prevented- the low temperature slows down the growth and respiration of microorganisms.

-Method-Drying.
Details- dry air is passed over the food, sometimes, in a partial vacuum.
How decay is prevented- microorganisms cannot respire or reproduce.

And:
-Method- Freezing.
Details- food is kept in a freezer at about -18 degrees.
How decay is prevented-microorganisms cannot reproduce or respire because their chemical reactions are slowed down.

-Method- Adding salt or sugar.
Details- food is stored exposed to a high sugar or salt concentration.
How decay is prevented- the sugar or salt draws water out of the microorganisms.

-Method- Adding vinegar.
Details- the food is soaked in vinegar.
How decay is prevented- the vinegar is too acidic for the microorganisms preventing their enzymes from working.

Other methods consist of adding artificial chemicals but people complain it gives the food an unappealing taste and some think that it has side effects on their body.

The carbon cycle:
-The element carbon is the basis for all molecules that make up living organisms. Carbohydrates, proteins and fats all contain carbon. In nature, pure carbon is found as diamonds and graphite, but animals and plants cannot use this carbon.
-The main source of carbon is carbon dioxide in the air but  there is only one way that it can get into living organisms. This happens when plants photosynthesise.
-This process traps the carbon inside carbon compounds and it is then passed from organism to organism along food chains or food webs. It returns to the air in carbon dioxide when plants and animals use the carbon compounds in respiration. 
-The decomposers, bacteria and fungi in the soil, also release carbon dioxide when they use dead material for respiration.
-Sometimes dead animals and plants do not decompose but over millions of years they are changed into fossil fuels. This process of fossilisation traps carbon in coal, oil and gas. Burning (combustion) of these fossil fuels releases this carbon again as carbon dioxide.

Carbon can also be locked up by organisms in the sea. Microscopic plants use carbon dioxide in photosynthesis and marine organisms use carbon to make shells. These shells are made up of carbonates. When the organisms die the shells sink and get compressed at the bottom of the sea. They turn to limestone rock. 

Nitrogen cycle: 
-Plants and animals are surrounded by air that contains 78% nitrogen but they cannot use it directly because it is too unreactive.  
-Plants take in nitrogen as nitrates through their roots and use the nitrates to make nitrogen compounds (proteins) for growth. This protein passes along the food chain or web as animals eat plants and other animals.
-Eventually all this trapped nitrogen is released when decomposers break down nitrogen compounds in dead plants and animals.
-The nitrogen cycle is more complicated than the carbon cycle because four different types of bacteria are involved instead of just one.
-Soil bacteria and fungi , acting as decomposers, convert proteins and urea into ammonia . This is poisonous to the plants but nitrifying bacteria turn it into nitrates.
-Denitrifying bacteria turn some of these nitrates into nitrogen gas. Nitrogen-fixing bacteria that live in the roots of the plants of the pea family can make the use of nitrogen gas in the air and return it to the cycle. This is called fixing nitrogen. Lightning can also fix nitrogen.

Humans have internal skeletons called endoskeletons. Some animals, such as insects and spiders, have external spines called exoskeletons.
Internal skeletons are generally lighter, smaller and allow a greater range of movement than exoskeletons. They do not restrict growth as so much. Exoskeletons restrict growth and have to shed their skeleton to grow, making them vulnerable to predators. The human skeleton has over 200 separate bones and five different kind of joints. 
Your skeleton starts as cartilage. As you grow, the cartilage is slowly replaced by calcium salts and phosphates that turn it into bone. This is called ossification. This is why a diet with lots of calcium, phosphorus and vitamin D is important for strong bones. Your sex hormones help control the production of bone.

Osteoporosis is a disease caused by a lack of minerals and exercise making the bones weaker and softer, more prone to breaking or fracturing.  

You skeleton is consists of 206 bones which are held together by a number of joints.

• The bones of the skull form fixed joints that fit together to make the cranium and protect the brain.
• Synovial joints are moveable joints that allow different degrees of movement. In a synovial joint the ends of the bones are covered with smooth cartilage which reduces friction. The moving surfaces are lubricated by synovial fluid. This fluid is secreted by the synovial membranes which also act like an 'oil sea'.
• Your limbs are joined to your body at the shoulder and hip by ball-and-socket joints which allow circular movements in more than one plane.
• Your elbows and knees are example of hinge joints and move in one plane. Ligaments keep the hinge joint together while tendons transmit the pull of muscles to the bones.
• Your wrists and ankles contain lots of small bones that form sliding or gliding joints.
• You also have joints between your vertebrae, fingers, toes and at the ends of the ribs to which muscles are attached. These allow different ranges of movement. 

Muscles can only exert force when they contract , so they work in pairs. When you bend your arm the the biceps muscle contracts and the triceps muscle relaxes. This action is called flexion.
When you straighten your arm, the triceps contracts and the biceps relaxes.

The biceps and triceps are called antagonistic muscles because they work in opposite ways.

Your arm bending and straightening is an example of a lever.

The heart is part of a circulatory system.

Fish have a single circulatory system. Their two-chambered heart pumps deoxygenated blood to the gills. Oxygenated blood flows to the body organs and back to the heart in one continuous circuit.

Humans have a four-chambered heart powering a double circulatory system. In one circuit deoxygenated blood is pumped from the heart to the lungs, where it is oxygenated. This oxygenated blood then goes back to the heart where it is pumped to the body. Deoxygenated blood then returns to the heart continuing in the circuit.

The human heart is a double pump with four chambers, two atria and two ventricles. Both sides of the heart pump at the same time. Valves between each atrium and each ventricle stop blood flowing backwards.

The right atrium fills with deoxygenated blood from the vena cava. Blood then passes right into the right ventricle. When the right ventricle contracts it pumps deoxygenated blood along the pulmonary artery to the lungs . Oxygenated blood returns along the pulmonary vein to the left atrium. Blood enters the left ventricle which pumps it along the aorta. This is called the cardiac cycle.

Your heart muscle contractions are controlled by a pacemaker. The pacemaker produces nerve impulses. It consists of two groups of cells, the sino-atrial node (SAN) and the atrio-ventricular node (AVN). In the SAN, nerve impulses start the heartbeat by making the the right and left atria contract at the same time. This fills the ventricles with blood. The nerve impulses then reach AVN and both ventricles contract. This then forces blood out of the heart.

An electrocardiograph (ECG) can detect the electrical current produced by the pacemaker cells. The signals produced during each heartbeat are detected by electrodes placed on a person's chest. They can then be displayed on a TV screen or recorded on a paper print out.

An echocardiogram bounces ultrasound waves off the heart to show it beating. It can produce live, moving pictures of the inside of the heart as it pumps blood. 

A hormone called adrenaline stimulates your heart, when doing exercise or if you are stressed or scared, and redirects blood from your skin and digestive system to your muscles. 

The structure and functions of the components of blood:

• Plasma (liquid part of blood): Plasma contains the products of digestion, dissolved oxygen, salts, waste products (urea, CO2), hormones, clotting factors and antibodies.
• Red blood cells: Red blood cells contain haemoglobin, a protein which joins with oxygen to form oxyhaemoglobin in the lungs. It transports oxygen to the tissues and releases it when needed.
• White blood cells: Phagocytes change shape to swallow and digest bacteria. Lymphocytes include B cells that make antibodies in response to 'foreign' substances T 'killer' cells that attack bacteria and memory cells that give immunity.
• Platelets: Platelets release chemicals which, together with proteins in the plasma, are needed for blood clotting. The plasma becomes sticky and turns into jelly. This forms a clot which prevents blood loss.

Haemophilia is an inherited genetic disorder that can lead to sufferers bleeding to death. It means that they lack the factors to allow blood clotting to occur. 

Fish use gills to extract dissolved oxygen from water. 
The gills have three parts:

• gill raker that filter out objects that could damage the gills,
• the gill bar that supports the gill filaments,
• feathery gill filaments containing blood capillaries. 

As water travels between the filaments, oxygen diffuses out into the capillaries and carbon dioxide passes out into the water. 
The gill flap can pump water but not air. If a fish is removed from water, the gill filaments stick together and the fish suffocates.

In our human gaseous exchange system we take in oxygen and give out carbon dioxide. Our lungs are constructed so that oxygen and carbon dioxide are exchanged efficiently:
-The alveoli have a large surface area, usually in a compact space
-There are thin, moist permeable membranes so gases can diffuse through them easily
- There is a plentiful blood supply to unload carbon dioxide and take away oxygen.

When you breathe in, your diaphragm flattens and your ribs are pulled upwards and outwards by the intercostal muscles. This increases your chest volume and lowers the pressure inside your lungs. Air is forced into your lungs by atmospheric pressure.

When you breathe out, the elasticity of your lungs pushes most of the air out of them. Even when you breathe out as much as possible some air always stays in your airways. This is residual air. Changes in your breathing rate and lung capacity can be measured and recorded at rest and during exercise using a machine called a spirometer. 

The spirometer absorbs the carbon dioxide from your breath enabling it to measure the efficiency of gas exchange. The air entering and leaving your lungs at rest is called your tidal air. 

The organs that remove waste products are the kidneys, liver, the lungs and the skin. 
Cellular activity makes three main waste products: Water, carbon dioxide and urea.
Urea is produced when when the liver breaks down excess amino acids. Urea is removed by the kidneys.

A kidney works by the blood entering the nephron from the renal artery under pressure. It passes through a filter unit which consists of a knot of capillaries, it is called the glomerulus and it is where small molecules are filtered out of the blood under high pressure. This is called ultra-filtration.
A cup shaped capsule collects the filtrate and passes it into the kidney tubule. The first part of the tubule is folded and surrounded by more capillaries. Glucose is removed from the filtrate and out back into the blood by a process called selective reabsorption.
The filtrate continues through the kidney tubule to a region where salt and water are regulated. Here more capillaries reabsorb water and salts back into the blood. When the filtrate finally leaves the nephron, all of the glucose and most of the salt and water has been removed leaving a solution containing urea. This is urine. 

You body controls its water content by balancing its intake and output. The amount of water vapour you lose in breathing and sweating is unavoidable. It varies with activity and temperature. If you lose too much water, you feel thirsty and drink to replace the water that you have lost. If you do not drink, your pituitary gland releases ADH (anti-diuretic hormone) which makes your kidneys reabsorb more water.

Part of your nephron reabsorbs salts into the blood. This makes your blood more concentrated and creates an osmotic gradient. ADH makes your tubules more permeable to water so water passes into your blood by osmosis. When your blood is too dilute, the production of ADH is switched off. The tubules become less permeable to water so your urine output increases. This type of control is an example of negative feedback. 

Most women menstruate once every 28 days. The menstrual cycle is shown in the diagram. 
The uterus lining thickens so it is ready to receive an egg. Around day 14, an egg is released by the ovary. If the egg is not fertilised, the uterus lining breaks down and eventually passes out of the vagina as a 'period' two weeks later. The cycle then begins over again. This is controlled by four hormones: oestrogen, progesterone, follicle stimulating hormone (FSH) and luteinising hormone (LH). 

At the start of the menstrual cycle, a woman's pituitary gland releases FSH which stimulates the production of follicles. A follicle is a small sac containing an egg. As the egg develops the follicle produces oestrogen. Oestrogen stops the pituitary gland making FSH.
After she ovulates (releases an egg) the woman's pituitary gland produces LH. This makes her follicle develop into a gland called a corpus luteum. This gland makes progesterone. If the egg is not fertilised, the gland shrinks and stops making progesterone. This triggers menstruation.
During pregnancy, progesterone continues to be made, maintaining the uterus and preventing the production of FSH.