Biology unit 1 AQA.

Units 1-6 

1 - Causes of disease.

2- Enzymes and the digestive system.

3- Cells and movement in and out of them.

4 - Lungs and lung disease.

5 - The heart and heart disease.

6 - Immunity.

  • Created by: Maddy
  • Created on: 20-12-10 10:47

1.1 Pathogens

  • Microorganism is a general term for a single celled organism that is too small to be seen with a microscope.
  • Disease causing microorganisms are called pathogens.
  • Disease is a malfunction to the body or mind which has an adverse affect on healh and it has social, physical and mental aspects.
  • For a microorganism to be considered a pathogen it must:
  • - gain entry to the host
  • - colonise the tissues of the host
  • - resist the defences of the host
  • - cause damage to the host's tissues.
  • When a pathogen colonises the host's tissues an infection results, disease occurs when an infection leads to recognisable symptoms in the host. When a pathogen is transferred from one individual to another it is known as transmission.
  • Pathogens normally get into the body by penetrating one of the organisms interfaces with the environment.
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  • An interface is a surface or boundry linking two systems, in this case linking the internal environment of the body with the external environment. One of these interfaces is the skin, however as the skin form a thick continuous layer, it is an effective barrier to infection. Hence invasion normally occurs when the skin is broken. This may happen as a result of cuts or abrasions or through the bites of insects and other animals. Some interfaces of the body have evolved to allow exchange of material between the internal and external environments. As a result, the body linings at theses points are thin, moist (hence sticky), have a large surface area and are well supplied with blood vessels. Interfaces with the body include:
  • - The gas exchange system, many pathogens enter the body through the gas exchange surfaces. 
  • - The digestive system, food and water may carry pathogens into the stomach and intestines via the mouth.
  • To help prevent the entry of pathogens the body has a number of natural defences:
  • - a mucous layer the covers exchange surfaces and forms a thick sticky barrier that is difficult to penetrate.
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  • - the production of enzymes that break down pathogens.
  • - the production of stomach acid that kills microgranisms.
  • Pathogens affect the body in two main ways 
  • - by damaging host tissues, sometimes the sheer number of pathogens causes damage e.g. preventing the tissues from functioning properly.
  • - by producing toxins, many bacterial pathogens produce toxins.
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1.2 Data and Disease

  • Epidemiology is the study of the incidence (number of cases) and the pattern of a disease with a view to finding the means of preventing and controlling it.
  • Epidemiologists collect data on disease and look for a relationship between these diseases and the various factors in peoples lives who have them.
  • Correlation doesn't always mean causation. 
  • External influences could have indirectly affected the results.
  • Always consider the following factors:
  • - Has the right factor been measured and have the correct questions been asked?
  • - How were the data gathered, were the methods reliable?
  • - Do the researchers have a vested interest in the results?
  • - Repeats?
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1.3 Lifestyle and Health

  • Risk is a measure of a probability that damage to health will occur as a result of a given hazard.
  • Risk has two concepts:
  • - The probability that a hazardous event will occur.
  • - The consequences of that hazardous event.
  • Risk is measured by comparing the likelihood of harm occurring in those exposed to a hazard to those who aren't exposed to it.
  • Our lifestyle can expose us to environmental and carcinogenic factors that put us at risk of contracting cancer. The specific lifestyle factors that contribute to cancer include:
  • - smoking
  • - diet
  • - obesity
  • - physical activity
  • - sunlight
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  • Coronary heart disease is the largest cause of death in the UK.
  • Factors we can control:
  • - smoking -  smokers are two to six times more likely to suffer from CHD.
  • - high blood pressure - stress, diet, lack of exercise all increase blood pressure.
  • - cholesterol - these can be kept lower by including fewer saturated fatty acids in       the diet.
  • - obesity - a BMI of over 25 increases the risk of CHD.
  • - diet - high levels of salt increase blood pressure, high levels of saturated fatty         acids increase cholesterol concentration. 
  • - physical activity - aerobic exercise can lower blood pressure and blood                   cholesterol.
  • Factors that can reduce the chances of getting CHD and cancer:
  • - giving up smoking
  • - taking regular aerobic exercise
  • - avoid becoming overweight
  • - reduce salt and saturated fatty acid intake
  • - increase the intake of dietary fibre and antioxidants in the diet.
  • - keep alcohol consumptions within same limits.
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2.1 Enzymes and digestion

The human digestive system is made up of a long muscular tube and its associated glands. The glands produce enzymes that break down large molecules into small ones ready for absorption. The digestive system provides an interface with the environment as food substances enter the body through it. 

Major parts of the digestive system

  • The oesophagus carries food from the mouth into the stomach. It is therefore adapted for transport rather than absorption or digestion; it is hence made up of a thick muscular wall. 
  • The stomach is a muscular sac with an inner layer that produces enzymes. It's role is to store and digest food especially proteins. It has glands which produce enzymes to digest protein. Other glands in the stomach wall produce mucus. This is to prevent the stomach being digested by its own enzymes. 
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  • The small intestine is a long muscular tube. Food is further digested in the small intestine by enzymes produced by its walls and by glands that pour their secretions into it. The inner walls of the small intestine are folded into villi, which gives them a large surface area. This surface area of these villi is further increased by millions of tiny projections called microvilli, on the epithelial cell of each villus, This adapts the small intestine for is purpose of absorbing the products of digestion into the bloodstream.
  • The large intestine absorbs water. Most of the water that is reabsorbed comes from the secretions of the many digestive glands. Food therefore becomes drier and thicker in consistency and forms faeces. 
  • The rectum is the final section of the intestines. The faeces are stored here before periodically being removed via the anus in a process called egestion.
  • The salivary glands are situated near the mouth. They pass their secretions via a duct into the mouth. The secretions contain the enzyme amylase, which breaks down starch into maltose. 
  • The pancreas is a large gland situated below the stomach. It produces a secretion called pancreatic juice. It contains proteases to digest proteins, lipase to digest lipids and amylase to digest starch.
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Digestion takes place in two stages:

  • Physical breakdown
  • Chemical digestion
  • Physical breakdown, if the food is large it is broken down into smaller pieces by means of structures such as the teeth, This makes it possible to ingest food and it always provides a larger surface area for chemical digestion. Food is always churned by muscles in the stomach wall and this breaks the food up also. 
  • Chemical digestion, breaks down large insoluble molecules into smaller more soluble ones. It is carried out by enzymes which function by hydrolysis. More than one enzymes is needed to break down a large molecule as enzymes are specific.
  • - carbohydrases break down carbohydrates to monosaccharides.
  • - lipases break down lipids to glycerol and fatty acids
  • - proteases break down proteins into amino acids. 
  • The small intestine absorbs these products into the blood stream. These molecules are incorporated into body tissues and used in processes within the body. This process is called assimilation. 
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2.2 Carbohydrates and monosaccharides

Carbon atoms very readily form bonds with other carbon atoms and this allows a sequence of carbon atoms with various lengths to be built up.

Each individual molecule that makes up a chain is called a monomer. The carbon atoms of these monomers join to form longer chains. These longer chains of repeating monomer units are called polymers.Most polymers are made up of the elements carbon, hydrogen, oxygen and nitrogen. In carbohydrates the basic monomer unit is sugar. A single monomer is called a monosaccharide.  

Monosaccharides have the general formula (CH2O)n where n can be any number between 3 and 7. The best known monosaccharide is glucose. This molecule is a hexose (6-carbon sugar) and has the formula. C6H12O6. The atoms of carbon, hydrogen and oxygen can be  rearranged in many different ways The atoms actually form a ring. 

All monosaccharides and some disaccharides are reducing sugars. Reduction is a chemical reaction involving the gain of electrons. A reducing sugar is a sugar that can donate electrons to (or reduce) another chemical, in this case Benedict's reagent. The test for a reducing sugar is therefore known as Benedict's test. Benedict's reagent is an alkaline solution of copper(II) sulphate. When a reducing sugar is heated with Benedict's reagent it forms an insoluble red precipitate of copper(I) oxide. The test is carried out as follows: 

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  • Add 2cm3 of the food sample being tested. If it is not already in liquid form first grind it up with water. 
  • Add an equal amount of Benedict's reagent.
  • Heat in a water bath for 5 minutes.

If a reducing sugar is present an orange-brown colour is formed. 

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2.3 Carbohydrates - disaccharides and polysacchari

When combined in pairs monosaccharides from a disaccharide. For example:

  • Glucose linked to glucose forms maltose 
  • Glucose linked to fructose forms sucrose
  • Glucose linked to galactose forms lactose

When the monosaccharides join a water molecule is removed and the reaction is hence called a condensation reaction. The bond that is formed is called a glycosidic bond. When water is added to a disaccharide, it breaks the glycosidic bond releasing the monosaccharides. This is called hydrolysis (the addition of water that causes break down)

Some disaccharides are reducing sugars (maltose) where as some are non reducing sugars (sucrose) they are called non reducing sugars as they don't change colour of Benedict's reagent when they are heated with it. In order to detect a non reducing sugar it must first be broken down into its monosaccharide components. This process is carried out as follows: 

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  • If the food sample is not already in liquid form it must first be ground up in water.
  • Add 2cm3 of the food sample to 2cm3 of Benedict's Reagent in a test tube.
  • Place the test tube in a gently boiling water bath for 5 minutes. If the Benedict's solution doesn't change colour (it remains blue) then a reducing sugar is not present.
  • Add another 2cm3 of the food sample to 2cm3 of dilute hydrochloric acid in a test tube and place the test tube in a gently boiling water bath for 5 minutes. The dilute hydrochloric acid will hydrolyse any disaccharide present into its constituent monosaccharides.
  • Slowly add some sodium hydrogencarbonate solution to the test tube in order to neutralise the hydrochloric acid (Benedict's reagent doesn't work in acidic conditions.) Check that the solution is alkaline with pH paper.
  • Re-test the resulting solution with 2cm3 of Benedict's reagent and heat it in a gently boiling water bath for 5 minutes. 
  • If a non reducing sugar was present the solution will now turn an orange-brown colour. This is due to the reducing sugars that were produced from hydrolysis of the non reducing sugar. 
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Polysaccharides are polymers that are formed together by combining many monosaccharide molecules. The monosaccharides are combined with glycosidic bonds formed as a result of a series of condensation reactions. As polysaccharides are very large molecule they are insoluble. This feature makes them suitable for storage. When they are hydrolysed, polysaccharides break down into disaccharides and then into monosaccharides. 

Starch is easily detected with its ability to change the colour of the iodine in potassium iodide from yellow to blue-black. The test is carried out as room temperature as follows:

  • Place 2cm3 of the sample being tested into a test tube or put add 2 drops of the sample into a depression of a spotting tile. 
  • Add 2 drops of iodine solution and shake or stir.
  • The presence of starch is indicated by a blue-black colouration. 
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2.4 Carbohydrate digestion

Because enzymes are specific, it takes more than one enzyme to completely break down a large molecule. These enzymes are usually produced by different parts of the digestive system. This is because each enzyme works at its optimum rate at different pH levels. It is important that enzymes are produced in the correct sequence. This is true of starch digestion.

Firstly the enzyme amylase is produced in the mouth and the pancreas. Amylase hydrolyses the alternate glycosidic bonds of the starch molecule to produce the disaccharide maltose. The maltose is in turn hydrolysed by a second enzyme (maltase) into the monosaccharide alpha glucose. Maltase is produced by the lining of the small intestine. 

In humans the process takes place as follows:

  • Food is taken into the mouth and chewed by the teeth. This breaks it into smaller pieces giving it a larger surface area.
  • Saliva enters the mouth through the salivary glands and is thoroughly mixed with the food during chewing. 
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  • This saliva contains salivary amylase. This starts hydrolysing any starch in the food to maltose. It also contains mineral salts that help maintain the pH around neutral. This is the optimum pH for the salivary amylase to work.
  • The food is swallowed and enters the stomach, where the conditions are acidic. The acid deneutralises the amylase and prevents further hydrolysis of the starch.
  • After a time the food is passed into the small intestine, where it mixes with the secretion with the pancreas called pancreatic juice. 
  • The pancreatic juice contains pancreatic amylase. This continues the hydrolysis of any remaining starch into maltose. Alkaline salts are produced by both the pancreas and the intestinal wall to maintain the pH at around neutral so the amylase can function. 
  • Muscles in the intestinal wall push the food along the small intestine. Its epithelial lining produces the enzyme maltase. The maltase hydrolyses the maltose from starch break down into alpha glucose. 

In addition to the digestion of maltose, there are two other common disaccharides  in the diet that need to be broken down: sucrose and lactose.

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  • sucrose - In natural foods, sucrose is usually contained within cells and these must be physically broken down by the teeth in order to release it. The sucrose passes through the stomach and into the small intestine, whose epithelial lining produces the enzyme sucrase. Sucrase hydrolyses the single glycosidic bond in the sucrose molecule to produce two monosaccharides that make up sucrose, glucose and fructose.
  • lactose - lactose is the sugar found in milk and hence in milk products.It is digested in the small intestine, whose epithelial lining produces the enzyme lactase.Lactase hydrolyses the glycosidic bond that links glucose and galactose monosaccharides that make up lactose.

Milk is the only food of young babies and so they produce relatively large amounts of lactase. As milk forms a much smaller part of the diet in adults, the production of lactase naturally diminishes during childhood. However, in some people this reduction is so great that they end up producing little or no lactase. 

Modern storage and distribution methods mean that adults are now consuming more and more milk products in greater quantities. As a result some people don't produce sufficient lactase to digest all of the lactose they consume. When the undigested lactose reaches 

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the small intestine, microorganisms break it down, giving rise to a large volume of gas. This may result in bloating, nausea, diarrhoea and cramps. Some people with this condition cannot consume milk or milk products at all, while others can only consume a little. Lactose intolerance can be managed by avoiding foods containing lactose. The main difficultly is taking in sufficient calcium. This can be resolved by adding the enzyme lactase to milk before drinking it. 

In babies the condition is rare but serious. These babies need to be fed special non-milk food that is rich in calcium and vitamin D.

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2.5 Proteins

Proteins are very large molecules.

Amino acids are the basic monomer units which combine to make up a polymer called a polypeptide. Polypeptides can be combined to form proteins. Every amino acid has a central carbon atom to which are attached four different chemical groups:

  • Amino group (NH2
  • Carboxyl group (COOH), an acidic group
  • Hydrogen atom (-H)
  • R group - a variety of different chemical groups, each amino acid has a different R group. 

Amino acid monomers can combine to form a dipeptide. This is done with the removal of a water molecule in a condensation reaction. This is done by removing an -OH from the carboxyl group of one amino acid with an -H from the amino group of another amino acid, The two amino acids become linked by a bond called a peptide bond. This is formed between the carbon atom of one amino acid and the nitrogen atom from the other amino acid. A peptide bond of 

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a dipeptide can be broken down by hydrolysis to give its constituent amino acids. 

Through a series of condensation reactions, many amino acids monomers can be joined together in a process called polymerisation. The resulting chain is called a polypeptide. The sequence of amino acids in a polypeptide chain forms the primary structure of any protein. There are almost limitless number of possible combinations of primary protein structures. It is the primary structure of any protein that determines its shape and hence its function. A change in just a single amino acid in this primary sequence can lead to a change in the shape of the protein and may stop it from carrying out its function. A protein's shape is very specific to its function. 

The linked amino acids that make up a polypeptide possess both -NH groups and -C=O groups on either side of every peptide bond. The hydrogen of the -NH group has an overall positive charge where as the oxygen in the -C=O group has an overall negative charge. Hence these two groups readily form weak hydrogen bonds. This causes the long polypeptide chain to be twisted into a 3D shape, e.g. an alpha helix. 

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The alpha helices of the secondary protein can be twisted and folded even more to give the complex and often unique 3D structure of each protein. This is known as the tertiary structure. This structure is maintained by a number of different bonds including:

  • disulfide bonds - these are fairly strong and so can't be broken easily. 
  • ionic bonds - these are formed between any carboxyl and amino groups that are not involved in forming peptide bonds.
  • hydrogen bonds - these are numerous but can be broken easily. 

It's the 3D structure of a protein that is important when it comes to how it functions. It makes each protein distinctive and allows it to be recognised and to recognise other molecules. 

Large proteins often form complex molecules containing a number of different polypeptide chains linked in various ways. There may also be a non-protein group (called a prosthetic group) associated with the molecules (e.g. an iron containing haem group in haemoglobin. 

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The most reliable test for proteins is the Biuret test. The biuret test detects peptide bonds. The test is performed as follows:

  • Place the a sample of the solution in a test tube and add an equal volume of sodium hydroxide solution at room temperature. 
  • Add a few drops of very dilute (0.05%) cooper(II) sulphate and mix gently.
  • A purple colouration indicates the presence of peptide bonds and hence a protein. If no protein is present the solution remains blue.
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2.6 Enzyme action

Enzymes are globular proteins that act as catalysts. Catalysts alter the rate of a chemical reaction without undergoing permanent changes themselves. They can be reused repeatedly and are therefore effective in small amounts.

Let us consider a typical chemical reaction:

sucrose+water = glucose+fructose

For reactions like this to take place naturally a number of conditions have to be met:

  • The sucrose and water molecules must collide with sufficient energy in order for to alter their atom arrangement to form glucose and fructose. 
  • The energy of the products must be less than that of the substrates.
  • An initial boost of energy is needed (activation energy).

The activation level must be overcome in order for the reaction to take place. Enzymes work by lowering the activation level for reactions to take place. This enables some metabolic processes to occur rapidly at the human body temperature of 37 degrees.

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Although an enzyme molecule is large overall, only a small region of it is functional. This is known as the active site and this is made up of a relatively small number of amino acids. The active site is a small hollow depression within the much larger enzyme molecule. The molecule on which the enzyme acts upon is called the substrate. This fits neatly into the depression to form a enzyme-substrate complex. The substrate molecule is held in the active site by bonds that temporarily form between certain amino acids of the active site and groups on the substrate molecule. 

A scientific model is where scientists try to explain their observations by producing a representation of how it works. One model proposes that enzymes work in the same way that a key operates a lock. This has been generated from the fact that each key has a specific shape which can only operate one lock. In a similar way, the substrate will only fit the active site of one particular enzyme. This model is supported by the observation that enzymes are specific in the reactions that they catalyse. This is known as the lock and key model.

One limitation of this model is that the enzyme is considered to be a rigid structure. However it has been observed that other molecules can bind to the 

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enzyme in places other than the active site. In doing so, they altered the activity of the enzyme. It's structure is not rigid but flexible. Because of this an alternative model has been proposed called the induced fit model.

Rather than being a rigid lock the induced fit model proposes that the enzyme changes it shape slightly to fit the profile of the substrate. The enzyme is flexible and moulds itself around the substrate in the same way a glove moulds itself to the shape of a hand. They have a certain general shape but it alters slightly. It explains that the enzyme puts a strain on the substrate that distorts a particular bond and consequently lowers the activation energy needed to break the bond. 

This model explains:

  • How other molecules can affect enzyme activity
  • how the activation energy is lowered

Any change in the enzyme's environment is likely to change its shape.

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2.7 Factors affecting enzyme action

For an enzyme to work it must:

  • Come into contact with the substrate molecule.
  • Have an active site which fits the substrate.

To measure the progress of an enzyme catalysed reaction we usually measure its time course. This can be done by:

  • measuring the rate of the formation of the products of the reaction
  • or measuring the rate of the disappearance of the substrate.
  • At first there is a lot of substrate.
  • It is very easy for substrate molecules to come into contact with the empty active sites of the enzyme molecules.
  • All enzyme active sites are filled and the substrate is rapidly broken down into its products. 
  • The amount of substrate decreased as it is broken down resulting in an increase in the amount of product.
  • As the reaction proceeds their is less and less substrate and more and more product.
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  • It becomes more difficult for the substrate molecules to come into contact with the enzyme molecules as there are fewer substrate molecules and the product molecules may get in the way of the substrate molecules and prevent them reaching an active site.
  • Hence it takes longer for the substrate molecules to be broken down by the enzyme.
  • The rate of reaction continues to slow until there is so little substrate that any further decrease in concentration can't be measured.
  • The graph flattens out as all the substrate has been used up and so no new product can be formed.

A rise in temperature increases the kinetic energy of molecules. Molecules move around more rapidly and collide more often. In an enzyme catalysed reaction, this means that the enzyme and substrate molecules come together more often in a given time which increases the rate of reaction. Further rise in temperature causes the hydrogen and other bonds in the enzyme to break causing the enzyme and its active site to change shape. At first this causes the substrate to fit less easily into the active site of the enzyme slowing the rate of reaction. At some point (usually around 60 degrees) the enzyme is so disrupted that is stops

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working altogether. It is said to be denatured. Denaturation is a permanent change and once it has occurred the enzyme can't function again. Many enzymes in the human body have an optimum temperature of 40 degrees. However our body temperatures have evolved to be 37 degrees The reasons for this are.

  • The advantages of increased metabolic rate are offset by the additional energy we need to maintain a higher body temperature.
  • Other proteins can become denatured at higher temperatures
  • At higher temperatures any further increase can cause the enzymes to become denatured.

The pH of a solution is its measure of it hydrogen ion concentration. Each enzyme has an optimum pH. A change in pH changes the effectiveness of the enzyme. The pH affects how an enzyme works in the following ways:

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  • A change in pH alters the charges on the amino acids that make up the active site of the enzyme. As a result the substrate can no longer become attached to the enzyme and the enzyme-substrate complex can no longer be formed.
  • A change in pH causes the bonds that maintain the enzyme's tertiary structure to break. The enzyme therefore changes shape. These changes alter the shape of the active site and the substrate can no longer fit in. The enzyme has been denatured. 

Even small changes in the pH change the arrangement of the active site of an enzyme. The arrangement of the active site is partly determined by the hydrogen and ionic bonds between -NH2 and -COOH groups of the polypeptides that make up the enzyme. The change in H+ ions affects this bonding, causing the active site to change shape. As pH fluctuations are relatively small they are far more likely to reduce an enzyme's activity rather than denature it. 

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If the amount of enzyme is fixed at a certain level and the amount of substrate is slowly added, the rate of reaction increases in proportion to the amount of substrate that is added. At a low substrate concentration the enzyme molecules only have a limited number of substrate molecules to collide with and therefore the active sites of the enzymes are not working to full capacity. As more substrate concentration is added the active sites gradually become filled and are working up to full capacity. At this point any further increase of substrate concentration won't have any affect on the rate of reaction as the rate of reaction has reached it's Vmax. When there is excess substrate the rate of reaction levels off. 

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2.8 Enzyme Inhibition

Enzyme inhibitors can either directly or indirectly interfere with the functioning of an active site of an enzyme and thereby reducing it's activity. There are two types of reversible inhibitors:

  • Competitive inhibitors - they bind to the active site of the enzyme.
  • Non competitive inhibitors - bind to any part of the enzyme other than the active site.

Competitive inhibitors have an molecular shape similar to that of the substrate. This allows them to occupy the active site of an enzyme. Hence they compete with the substrate for the available active sites. It is the difference between the concentration of the substrate and the concentration on the inhibitor as to the affect the inhibitor has on enzyme activity. If the substrate concentration is increased, the effect on enzyme activity isn't as great. A competitive inhibitor is not permanently bound to the active site of the enzyme so when it leaves, another molecule can take its place. Sooner or later all the substrate molecules will occupy an active site but the greater the concentration of the inhibitor the longer this will take. 

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Non competitive inhibitors attach themselves to the enzyme at a site which isn't the active site. Upon attaching to the enzyme the inhibitor alters the shape of the enzyme's active site in such a way that substrate molecules can no longer occupy it, and so the enzyme can't function. As the substrate and inhibitor aren't competing for the same site, an increase in substrate concentration does not decrease the effect of the inhibitor.

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3.1 Investigating the structure of cells

A cells structure is only apparent when it is seen under the microscope. 

Microscopes are instruments which magnify the image of an object. A simple convex glass can act as a magnifying glass but such lenses work more effectively in a compound light microscope. The relatively long wavelength of the light rays means that a light microscope can only distinguish between two objects if they are 0.2um apart, or further. This limitation can be overcome by using a beam of electrons rather than beams of light. With their shorter wavelengths, the beam of electrons in the electron microscope can distinguish between two objects if they are 0.1nm apart or further. 

magnification = size of image/size of object.

The resolution, or resolving power, of a microscope is the minimum distance apart that two objects have to be in order to appear as two separate objects. Whatever the type of microscope, the resolving power depends on the the wavelength and form of radiation used. In a light microscope it is about 0.2 um. Greater resolution means greater clarity, the image produced is more clear and precise.

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Increasing the magnification will increase the size of an image but it doesn't always increase the resolution. Every microscope has a limit of resolution, up to this point an increase in magnification will reveal more detail but beyond this point the image will just appear blurry.

In order to study the structure and function of various organelles that make up cells, it is necessary to obtain large numbers of isolated organelles. Cell fractionation is the process where cells are broken up and the different organelles they contain are separated out. Before cell fractionation can begin, the tissue is placed in a cold, isotonic, buffered solution for the following reasons:

  • cold to reduce enzyme activity that might break down the organelles. 
  • isotonic to prevent organelles bursting or shrinking as a result of osmostic gain or lass of water. An isotonic solution is one that has the same water potential as the original tissue,
  • buffered to maintain a constant pH.

There are two stages to cell fractionation.

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Cells are broken up in a homogeniser. This releases the organelles from their cells. The resultant fluid (known as homogenate) is then filtered to remove any complete cells and large pieces of debris. 


Ultracentrifugation is the process by which the fragments in the filtered homogenate are separated in a machine called an ultracentrifuge. This spins tubes of homogenate at a very high speed in order to create a centrifugal force. In animal cells this takes place as follows:

  • The tube of filtrate is placed in the ultracentrifuge and spun at a slow speed. 
  • The heaviest organelles (the nuclei) are forced to the bottom of the tube where they form a thin sediment or pellet.
  • The fluid at the top of the tube (supernatant) is removed, leaving just the sediment of the nuclei.
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  • The supernatant is transferred to another tube and spun in the ultracentrifuge at a faster speed than before.
  • The next heaviest organelles (the mitochondria) are forced to the bottom of the tube.
  • The process is continued in this way so that, each increase in speed, the next heaviest organelle is sedimented and separated out.

Organelle to be separated out  Speed of centrifugation  Duration (min)

Nuclei                                              1000                                   10

Mitochondria                                    3500                                   10

Lysosomes                                      16500                                   20

Ribosomes                                       100000                                60

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3.2 The electron microscope

Light microscopes have a poor resolution as a result of the relatively long wavelength of light. In the 1930s a microscope was developed using a beam of electrons instead of light. This is called an electron microscope and it has two main advantages:

  • The electron beam has a very short wavelength and the microscope has a high resolving power.
  • As electrons have a negative charge, the beam can be focused using electron magnets.

Because electrons are absorbed in air, a near-vacuum has to be created within the chamber of an electron microscope in order for it to work effectively. 

There are two types of electron microscope:

  • The transmission electron microscope (TEM)
  • The scanning electron microscope (SEM)
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The transmission electron microscope consists of an electron gun that produces a beam of electrons that is focused on the specimen by a condenser electromagnet. In the TEM the beam passes through a thin section of the specimen. Parts of this specimen absorb electrons and therefore appear dark. Other parts of the specimen allow electrons to pass through and so appear bright. An image is produced on a screen and this can be photographed to give a photomicrograph. The resolving power of a TEM is 0.1nm, although problems during preparation mean that this can't always be achieved. The main limitations of a TEM are:

  • The whole specimen must be in a vacuum and so living specimens can't be observed.
  • A complex staining process is required and even then the image is still in black and white.
  • The specimen must be extremely thin.
  • The image may contain artefacts. 

In the TEM the specimens must be extremely thin to allow electrons to penetrate. The result is therefore a 2-D image. A series of sections can be taken and a 3-D image can be built from this.

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The scanning electron microscope has all the same main limitations as the TEM, with the exception that the specimens don't need to be extremely thin as electrons don't penetrate. The SEM directs a beam of electrons on to the surface of the specimen from above, rather than below. The beam is then passed back and forth across a portion of the specimen in a regular pattern. The electrons are scattered by the specimen and the pattern of this scattering depends on the contours of the specimens surface. We can build up a 3D image by computer analysis of the pattern of scattered electrons and secondary electrons produced. The SEM has a resolving power of 20nm.

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3.3 Structure of an epithelial cell

Each cell can be regarded as a metabolic compartment, a separate place where the metabolic processes of that cell occurs. Epithelial cells are eukaryotic cells. Eukaryotic cells have a distinct nucleus and posses membrane bounded organelles.


The nucleus is the most prominent feature of a eukaryotic cell, such as an epithelial cell. The nucleus contains the organisms hereditary material and controls the cell's activities. They are usually spherical and between 10-20um in diameter. The nucleus has a number of parts:

  • The Nuclear envelope is a double membrane that surrounds the nucleus. Its outer membrane is continuous with the endoplasmic reticulum of the cell and often has ribosomes on its surface. It controls the entry and exit of materials in and out of the nucleus and contains the reactions taking place within it.
  • Nuclear pores allow the passage of large molecules, such as messenger RNA, out of the nucleus. There are around 3000 in each nucleus, each 40-100nm in diameter.
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  • The Nucleolus is a small spherical body within the nucleoplasm. It manufactures ribosomal RNA and assembles the ribosomes.
  • Chromatin is the DNA found within the nucleoplasm. This is the diffuse form that chromosomes take up when they are not dividing. 
  • Nucleoplasm is the granular jelly like material that makes up the bulk of the nucleus.

The functions of the nucleus are to:

  • Act as a control centre of the cell through the production of messenger RNA and hence protein synthesis.
  • Manufacture ribosomal RNA and ribosomes.
  • Retain the genetic material of the cell in the form of DNA or chromosomes. 

The mitochondrion

Mitochondria are rod shaped and are 1-10um in length. They are made up of the following structures:

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  • A Double membrane surrounds the organelle, the outer one controlling the entry and exit of materials. The inner one is folded to form extensions known as cristae.
  • Cristae are shelf like extensions of the inner membrane, some extend across the whole width of the mitochondrion. These provide a large surface area for the attachment of enzymes involved in respiration.
  • The matrix makes up the remainder of the mitochondrion. It is a semi rigid material containing protein, lipids, and traces of DNA that allows the mitochondria to control the production of their own proteins. The enzymes involved in respiration are found in the matrix.

The mitochondria are the sites of certain stages of respiration (Kreb's cycle and phosphorylation pathway) They are therefore responsible for the production of the energy-carrier molecule, ATP, from carbohydrates. Because of this, the number and size of mitochondria, and the number of their cristae, all increase in cells that have a high level of metabolic activity and therefore need a plentiful supply of ATP. Epithelial cells use a lot of energy in the process of absorbing substances from the intestines by active transport.

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Endoplasmic reticulum

The endoplasmic reticulum is an elaborate, three-dimensional system of sheet like membranes, spreading through the cytoplasm of the cells. It is continuous with outer nuclear membrane. The membranes enclose flattened sacs called cisternae. There are two types of endoplasmic reticulum:

Rough endoplasmic reticulum (RER) has ribosomes present on the outer surfaces of the membranes. Its functions are to:

  • Provide a large surface area for the synthesis of proteins and glycoproteins
  • Provide a pathway for the transport of materials, especially proteins throughout the cell.

Smooth endoplasmic reticulum (SER) lacks ribosomes on its surface and it often more tubular in appearance its functions are to:

  • Synthesise, store and transport lipids
  • Synthesise, store and transport carbohydrates.
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Cells that need to manufacture and store large quantities of lipids, proteins or carbohydrates have very extensive endoplasmic reticulum.

Golgi apparatus

The golgi apparatus occurs in almost all eukaryotic cells and is similar in structure to the smooth endoplasmic reticulum except it is more compact. It consists of a stack of membranes that make up flattened sacs (cisternae) with small rounded hollow structures called vesicles. The proteins and lipids produced by the ER are passed through the golgi apparatus in a strict sequence. The golgi modifies these proteins often adding non protein components such as carbohydrate to them. It also 'labels' them allowing them to be accurately sorted and sent to their correct destination. Once sorted the modified proteins and lipids are transported in vesicles which are regularly pinched off the ends of Golgi cisternae. These vesicles move to the cell surface, where they fuse with the membrane and release their contents to the outside. 

The functions of the Golgi apparatus are to:

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  • add carbohydrate to proteins to form glycoproteins. 
  • produce secretory enzymes such as those produced by the pancreas.
  • secrete carbohydrates, such as those used to making cell walls in plants.
  • transport, modify and store lipids.
  • form lysosomes

The golgi apparatus is well developed in secretory cells, such as epithelial cells that line the intestines. 


Lysosomes are formed when vesicles produced by the Golgi apparatus contain enzymes such as proteases and lipases. As many as 50 such enzymes can be contained in a single lysosome. Up to 1.0um in diameter, lysosomes isolate these potentially harmful enzymes from the rest of the cell before releasing them, either to the outside or into a phagocytic vesicle within the cell. 

The function of lysosomes is to:

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  • break down material ingested by phagocytic cells such as white blood cells. 
  • release enzymes to the outside of the cell (exocytosis) in order to destroy material around the cell. 
  • digest worn out organelles so that the useful chemicals they are made of can be reused. 
  • completely break down cells after they have died (autolysis)


Ribosomes are small cytoplasmic granules found in all cells. They may occur in the cytoplasm or be associated with RER. There are two types depending on the cells in which they are found:

  • 80S type - found in eukaryotic cells around 25nm in diameter
  • 70S type - found in prokaryotic cells, are slightly smaller

Ribosomes have two subunits - one large and one small, each of these contains ribosomal RNA and protein. Despite their small size, they occur in vast numbers. Ribosomes are important in protein synthesis.

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Microvilli are finger like projections of the epithelial cell that increase its surface area to allow more efficient absorption.

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3.4 Lipids

Lipids are a varied group of substances that share the following characteristics:

  • They contain carbon, hydrogen and oxygen
  • The proportion of oxygen to carbon and hydrogen is smaller than in carbohydrates.
  • They are insoluble in water.
  • They are soluble in solvents such as alcohol or acetone.

The main groups of lipids are triglycerides (fats and oils), phospholipids and waxes. 

The main role of lipids is in plasma membranes. Phospholipids contribute to the flexibility of membranes and the transfer of lipid-soluble substances across them. Other roles of lipids include:

  • an energy source - when oxidised lipids provide more than twice the energy as the same mass of carbohydrate. 
  • waterproof coating - Lipids are insoluble in water and therefore useful as a waterproofing.
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  • insulation - Fats are slow conductors of heat and when stored beneath the body surface they help to retain heat. 
  • protection - Fat is often stored around delicate organs.

Fats are solid at room temperature where as oils are liquid. Triglycerides have three fatty acids combined with a glycerol. Each fatty acid forms a bond with the glycerol in a condensation reaction. Hydrolysis of the triglyceride therefore provides three fatty acids and glycerol

As the glycerol molecule in all triglycerides is the same, the differences in the properties of different fats and oils come from the variations in the fatty acids. All fatty acids have carboxyl group -COOH with a hydrocarbon chain attached. If the chain has no carbon-carbon double bonds it is said to be saturated (because all the carbon atoms are linked to the maximum number of hydrogen atoms). If the chain has one carbon-carbon double bond it is said to be mono unsaturated. If the chain has more than one carbon-carbon double bond then it is said to be poly unsaturated.

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Phospholipids are similar to lipids except for the fact that one of the fatty acid molecules is replaced by a phosphate molecule. Fatty acids repel water (are hydrophobic) where as phosphate molecules attract water (are hydrophilic). A phospholipid is therefore made up of two parts:

  • a hydrophilic head, which interacts with water 
  • a hydrophobic tail, which orients itself away from water, but mixes readily with fat.

Molecules that have two ends that behave differently in this way are said to be polar. When these polar phospholipid molecules are placed in water they position themselves so that the hydrophilic heads are as close to the water as possible and the hydrophobic tails are as far away from the water as possible.

Test for lipids

The test for lipids is known as the emulsion test and it is carried out as follows:

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  • Take a completely dry and grease free test tube.
  • Add 2cm3 of the food sample being tested.
  • Add 5cm3 of ethanol
  • Shake the tube thoroughly to dissolve any lipid in the sample
  • A cloudy white colour indicates the presence of a lipid.

The cloudy colour is due to any lipid in the sample being finely dispersed to form an emulsion. Light passing through this emulsion is refracted as it passes from oil droplets to water droplets making it appear cloudy. 

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  • Take a completely dry and grease free test tube.
  • Add 2cm3 of the food sample being tested.
  • Add 5cm3 of ethanol
  • Shake the tube thoroughly to dissolve any lipid in the sample
  • A cloudy white colour indicates the presence of a lipid.

The cloudy colour is due to any lipid in the sample being finely dispersed to form an emulsion. Light passing through this emulsion is refracted as it passes from oil droplets to water droplets making it appear cloudy. 

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3.5 The cell surface membrane

All membranes around and within cells (inc. cell organelles) have the same basic structure and are know as plasma membranes.


Phospholipids form a bilayer sheet. They are important components in the cell surface membrane because:

  • One layer of phospholipids has its hydrophilic heads pointing inwards (interacting with the water in the cell cytoplasm).
  • The other layer of phospholipids has its hydrophilic heads pointing outwards (interacting with the water outside the cells)
  • The hydrophobic tails of both phospholipid layers point towards the centre of the membrane, protected as it were from water on both sides. 

Lipid soluble material moves through the membrane via the phospholipid portion. The functions of the phospholipids in membranes are to:

  • Allow lipid soluble substances to enter and leave the cell
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  • prevent water soluble substances from entering and leaving the cell
  • make the membrane flexible


The proteins of the cell surface membrane are arranged more randomly than the regular pattern of the phospholipids. They are embedded in the phospholipid bilayer in two main ways.

  • Extrinsic proteins occur either on the surface of the phospholipid bilayer or they are partly embedded in it but they never extend completely across it. They act to either give mechanical support to the membrane or, in conjunction with glycolipids, as cell receptors for molecules such as hormones. 
  • Intrinsic proteins completely span the phospholipid bilayer from one side to the other. Some act as carriers to transport water soluble material across the membrane while others act as enzymes. 
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The functions of the proteins in the membrane are to:

  • Give structural support
  • Act as carriers, transporting water soluble material across the membrane
  • act as receptors (e.g. for hormones)
  • allow active transport across the membrane by forming ion channels. 
  • help cells adhere together
  • form recognition sites by identifying cells

Fluid-mosaic model

The arrangement of the cell surface membrane is known as a fluid mosaic model for two reasons:

  • fluid because the phospholipid molecules can move relative to one another. This gives the membrane a flexible structure that is constantly changing in shape.
  • mosaic because the proteins are embedded in the phospholipid bilayer vary in shape, size and pattern.
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3.6 Diffusion

The energy required for diffusion comes from the inbuilt motion of the particles rather than from an external source. 

  • All particles are constantly in motion due to the kinetic energy that they possess.
  • This motion is random 
  • Particles are constantly bouncing off one another as well as off other objects.

Diffusion is the net movement of molecules from a region of higher concentration to a region of lower concentrations.

  • When there is no diffusion gradient particles will still be in random motion this is called a dynamic equilibrium.

Rate of diffusion

There are a number of different factors that affect that rate at which molecule diffuse:

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  • the concentration gradient, the greater the difference in concentration on either side of the exchange surface the faster the rate of diffusion
  • the length of the diffusion pathway, the thinner an exchange surface the larger the rate of diffusion
  • the area over which diffusion takes place the larger the surface area the faster the rate of diffusion.

Diffusion is proportinal to: (surface area x difference in concentration) / length of diffusion pathway

This is not wholly applicable to cells as diffusion can also be affected by:

  • the nature of the plasma membrane, (its composition and number of pores)
  • the size and nature of the diffusing molecule, e.g. small molecules diffuse faster than larger ones.

Facilitated diffusion

Facilitated diffusion is a passive process, it relies purely on the kinetic energy of the diffusing molecules. There is no external input on energy. It occurs down a

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concentration gradient. It occurs at specific points on the plasma membranes where there are special protein molecules. They form water filled channels across the membrane. These allow water soluble molecules to pass through. The channels are selective, opening only in the presence of a specific molecule. If that particular molecule isn't present then the channels remain closed. 

An alternative form of facilitated diffusion involves carrier proteins which span the plasma membrane. When a particular molecule that is specific to the protein is present it binds with the protein. This causes it to change shape in such a way that the molecule is released to the inside of the membrane. 

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3.7 Osmosis

Osmosis is the passage of water from a region where it has a higher water potential to a region where it has a lower water potential through a partially permeable membrane.

Cell surface membranes and other plasma membranes are all partially permeable. (They are permeable to water molecules and a few other small molecules but not to larger molecules.

A solute is any substance that is dissolved in a solvent (e.g. water) the solute and the solvent together form a solution. Water potential is measured in units of pressure, usually kilopascals (kPa). Water potential is the pressure created by water molecules. Pure water is said to have a water potential of 0.

One way of finding the water potential of cells or tissues is to place them in a series of solutions of different water potentials. Where there is no net gain or less of water from the cells or tissues, the water potential inside the cells or tissues must be the same as the external solution.

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A partially permeable plasma membrane separates two solutions.

  • The one on the left has a low concentration of solute molecules while the one on the right has a high concentration of solute molecules.
  • Both the solute and water molecules are in random motion due to the kinetic energy that they possess.
  • The partially permeable membrane only allows water molecules across it and not solute molecules.
  • The water molecules diffuse from the left hand side to the right.
  • At the point where the water potential on both sides of the plasma membrane is equal, a dynamic equilibrium is reached.

The highest value of water potential is 0.

Animal cells (e.g. red blood cells) contain a variety of solutes dissolved in the watery cytoplasm. If a red blood cell is placed in pure water it will absorb water by osmosis. Cell surface membranes are very thin (7nm) and even though they are flexible, they can't stretch to any great extent. The cell surface will break, bursting the cell and releasing its contents (in red blood cells this is heamolysis). To prevent this happening, animal cells are normally bathed in a liquid which

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has the same water potential as the cells. If a red blood cell is placed in a solution with a water potential lower than its own, water leaves by osmosis and the cell shrinks and becomes shrivelled.

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3.8 Active Transport

Active transport allows cells to exchange molecules against a concentration gradient. Metabolic energy is required for the process. Once inside the cell the molecules are prevented from leaking back by the barrier of the cell surface membrane's bilayer. In this way a different environment is maintained on either side of the membrane.

Active transport is the movement of molecules into or out of cell from a region of lower concentration to a region of higher concentration using energy and carrier molecules.

It differs from passive forms of transport in the following ways:

  • Energy in the form of ATP is needed
  • Materials are moved against a concentration gradient
  • Carrier protein molecules which act as 'pump's are involved.
  • The process is very selective with specific substances being transported.

Active transport uses ATP in one of two ways:

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  • by using ATP directly to move molecules
  • by using a concentration gradient that has already been set up by direct active transport. This is also known as co-transport.

Direct active transport of a single molecule is described below:

  • The carrier proteins span the cell surface membrane and accept the molecules to be transported on one side of it. 
  • The molecules bind to receptors on the channels of the carrier protein.
  • On the inside of the cell, ATP binds to the protein, causing it to split to form ADP and a phosphate molecule. As a result, the protein molecule changes shape and opens to the opposite side of the membrane.
  • The molecules are then released to the other side of the membrane.
  • The phosphate molecule is released from the protein and recombines with ADP to form ATP.
  • This causes the protein to revert back to its original shape, ready for the process to be repeated. 
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3.9 Absorption in the small intestine

Glucose is absorbed through the walls of the small intestine. These are folded and possess finger like projections called villi. They have thin walls lined with epithelial cells, on the other side of which is a network of blood capillaries. The villi considerably increase the surface area of the small intestine and therefore accelerate the rate of absorption.

Villi are situated at the interface between the lumen of the intestines and the blood and other tissues inside the body. They are part of a specialised exchange surface adapted for the absorption of the products of digestion. Their properties increase the efficiency of absorption in the following ways:

  • They increase the surface area for diffusion
  • They are thin walled thus reducing the diffusion pathway. 
  • They are able to move and so help to maintain a diffusion gradient.
  • They are well supplied with blood vessels so that blood can carry away absorbed molecules and hence maintain a diffusion gradient. 

The epithelial cells lining the villi also possess microvilli. These are finger like projections of the cell surface membrane about 0.6um in length. They are collectively termed as the 'brush border'.

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Role of diffusion in absorption

Diffusion is the net movement of molecules from a region of higher concentration to a region of lower concentration.

As carbohydrates are being digested continuously, there is normally a greater concentration of glucose within the small intestine than in the blood. There is therefore a concentration gradient down which glucose diffuses from inside the small intestine into the blood. Given that the blood is constantly being circulated by the heart, the glucose absorbed into it is continuously being removed by cells as they use it up during respiration. This helps maintain the concentration gradient between the inside of the small intestine and the blood. 

The villi contain muscles that regularly contract and relax, mixing the contents of the small intestine. This ensures that, as glucose is absorbed from the food adjacent to the villi, new glucose rich food replaces it. This also helps to maintain a concentration gradient and allows diffusion to continue. 

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Role of active transport in absorption 

At best, diffusion only results in the concentrations either side of the intestinal epithelium becoming equal. Meaning that all the available glucose can't be absorbed in this way and some may pass out of the body. This doesn't happen because glucose is also being absorbed by active transport meaning that all the glucose is absorbed into the blood.

The actual mechanism by which glucose is absorbed into the blood by active transport is called co transport as two molecules are involved. It entails glucose being drawn into the cells along with sodium ions that have been actively transported out by the sodium - potassium pump. It takes place in the following manner:

1) Sodium ions are actively transported out of the epithelial cells, by the sodium potassium pump, into the blood. This takes place in one type of protein carrier molecule found in the cell surface membrane of the epithelial cells. 

2) There is now a much higher concentration of sodium ions in the lumen of the intestine then inside the epithelial cells. 

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3) The sodium ions diffuse into the epithelial cells down this concentration gradient through a different type of protein carrier (co-transport protein) in the cell surface membrane. As the sodium ions flood back in through this second carrier protein, they couple with the glucose molecules which are carried into the cell with them. 

4) The glucose passes into the blood plasma by facilitated diffusion using another type of carrier protein. 

Both sodium ions and glucose molecules move into the cell, but while sodium ions move down their concentration gradient, the glucose molecules move up their concentration gradient. It is the sodium concentration gradient, rather than ATP directly, that powers the movement of glucose into the cell. This makes it an indirect form of active transport. 

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3.10 Cholera

The agent that causes cholera is a curved rod shaped bacterium known as Vibrio cholerae. It is characterised by the presence of flagellum at one end. Bacteria are examples of prokaryotic cells.

  • Prokaryotic cells, have no true nucleus only a diffuse area of nuclear material with no nuclear envelope where as eukaryotic cells have a distinct nucleus with a nuclear envelope. 
  • Prokaryotic cells have no nucleolus where as eukaryotic cells have a nucleolus.
  • Prokaryotic cells have circular strands of DNA but no chromosomes where as eukaryotic cells have chromosomes present in which DNA is located. 
  • Prokaryotic cells have no membrane bounded organelles where as eukaryotic cells have membrane bounded organelles. 
  • Prokaryotic cells have no chloroplasts, only photosynthetic regions in some bacteria where as eukaryotic cells have chloroplasts present in plants and algae. 
  • Prokaryotic cells have smaller ribosomes (70S type) where as in eukaryotic cells the ribosomes are larger (80S type).
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  • Prokaryotic cells have no endoplasmic reticulum or associated golgi apparatus and lysosomes where as eukaryotic cells have endoplasmic reticulum present along with golgi apparatus and lysosomes.
  • Prokaryotic cells have a cell wall made out of peptidoglycan where as eukaryotic cells have a cell wall made mostly out of cellulose. 

Structure of a bacterial cell

  • Cell wall - physical barrier that protects against mechanical damage and excludes certain substances.
  • Capsule - protects bacterium from other cells and helps groups of bacteria to stick together for further protection. 
  • Cell surface membrane - acts as a differentially permeable layer which controls the entry and exit of chemicals. 
  • Flagellum - aids movement of the bacterium because of it's rigid, corkscrew shape and rotating base help the cell spin through fluids.
  • Circular DNA - Possess the genetic information for the replication of bacterial cells.
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  • Plasmid - Possess genes that aid the survival of bacteria in adverse conditions. e.g. by producing enzymes that break down antibodies

Bacteria range from 0.1 to 10um in length. All bacteria possess a cell wall made out of peptidoglycan. This is a mixture of polysaccharides and peptide bonds. Many bacteria further protect themselves by secreting a capsule of mucilaginous slime around this wall. Flagella occur in certain types of bacteria. Their rigid corkscrew shape and rotating base enable bacteria to spin through fluids. 

Inside the cell wall is the cell surface membrane, within which is the cytoplasm that contains 70S ribosomes. Ribosomes synthesise proteins. Bacteria store food reserves as glycogen granules and oil droplets.The genetic material in bacteria is in the form of circular strands of DNA. Separate from these are smaller circular pieces of DNA called plasmids. They can reproduce themselves independently and may give the bacterium resistance to harmful chemicals, such as antibiotics.

How the cholera bacterium causes disease

The main symptoms of cholera are diarrhoea and consequently dehydration. 

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Vibrio cholerae is transmitted by the ingestion of water, or food that has been contaminated with faecal material containing the pathogen. One ingested it causes the disease in the following ways:

  • Almost all vibrio cholerae bacteria ingested by humans are killed by the acidic conditions in the stomach. However a few may survive.
  • When the surviving bacteria reach the small intestine they use their flagella to propel themselves, in a corkscrew like fashion, through the mucus lining of the intestinal wall. 
  • They then start to produce a toxic protein. This protein has two parts. One part binds to specific carbohydrate receptors on the cell surface membrane. As only the epithelial cells of the small intestine have these specific receptors, this explains why the cholera toxin only affects this region of the body. The other, the toxic part, enters the epithelial cells. This causes the ion channels of the cell surface membrane to open, so the chloride ions that are normally contained in the epithelial cells flood into the lumen of the intestine. 
  • The loss of chloride ions from the epithelial cells raises their water potential, while the increase of chloride ions in the lumen of the intestine lowers its water potential. Water therefore flows from the cells into the lumen.
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  • The loss of ions from the epithelial cells establishes a concentration gradient. Ions therefore move by diffusion into the epithelial cells, from the surrounding tissues, including the blood. This in turn establishes a water potential gradient that causes water to move by osmosis from the blood and other tissues into the intestine.
  • It is this loss of water from the blood and other tissues, into the intestine that causes the symptoms of cholera, namely diarrhoea and dehydration. 
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3.11 Oral rehydration thearpy

What causes diarrhoea?

Diarrhoea is an intestinal disorder in which watery faeces are produced frequently. The causes include:

  • damage to the epithelial cells, lining the intestine,
  • loss of microvilli due to toxins
  • excessive secretion of water due to toxins. 

As a result of diarrhoea excessive fluid is lost from the body and insufficient fluid is taken in to make up for this loss.

What is oral rehydration thearpy?

To treat diarrhoeal diseases it is vital to rehydrate the patient. Just drinking water is ineffective because:

  • Water is not being absorbed from the intestine.
  • The drinking of water does not replace the electrolytes that are being lost from the epithelial cells of the intestine. 
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What is required is a suitable mixture of substances that can be safely taken into the mouth and which will be absorbed by the intestine. There is more than one carrier protein in the cell surface membranes of the epithelial cells that absorb sodium ions. A rehydration solution has to be developed that uses these alternative pathways. As sodium ions are absorbed the water potential of the cell falls and water enters the cells by osmosis. Therefore a rehydration solution has to contain:

  • Water to rehydrate the tissues
  • Sodium to replace the sodium ions lost from the epithelium of the intestine and to make optimum use of the alternative sodium-glucose carrier proteins. 
  • Glucose to stimulate the uptake of sodium ions from the intestine and to provide energy.
  • Potassium to replace lost potassium ions and to stimulate appetite.
  • other electrolytes such as chloride and citrate ions to help prevent electrolyte imbalance. 
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4.1 Structure of the human gas exchange system

All aerobic organisms require a constant supply of oxygen to release energy in the form of ATP during respiration. The carbon dioxide produced in this process needs to be removed as its build up could be harmful to the body.

The volume of oxygen that has to be absorbed and the volume of carbon dioxide that must be removed is large in mammals because:

  • they are relatively large organisms with a large volume of cells.
  • they maintain a high body temperature and therefore have high metabolic and respiratory rates.

As a result mammals have evolved specialised surfaces called lungs, to ensure efficient gas exchange between the air and their blood.

Mammalian lungs

The lungs are the site of gas exchange and they are located inside the body because:

  • air is not dense enough to support and protect these delicate organs.
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  • they would otherwise lose a great deal of water and dry out.

The lungs are supported by the ribcage. The ribs can be moved by the muscles between them. This enables the lungs to be ventilated by a tidal stream of air, thereby ensuring that the air within them is constantly replenished. The main parts of the human gas exchange system and their structure and functions are described below:

  • The lungs are a pair of lobed structures made up of a series of highly branched tubules, called bronchioles, which end in tiny air sacs called alveoli.
  • The trachea is a flexible airway that is supported by rings of cartilage. The cartilage prevents the trachea collapsing as the air pressure inside falls when breathing in. The tracheal walls are made up of muscle lined with ciliated epithelium and goblet cells. The goblet cells produce mucus that traps dirt particles and bacteria from the air breathed in. The cilia move the mucus, with with dirt and microorganisms, up to the throat, from where it passes down the oesophagus into the stomach.
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  • The bronchi are two divisions of the trachea, each leading to one lung. They are similar in structure to the trachea and, like the trachea, they also produce mucus to trap dirt particles and have cilia that move the dirt-laden mucus towards the throat. The larger bronchi are supported by cartilage, although the amount of cartilage is reduced as the bronchi get smaller.
  • The bronchioles are a series of branching subdivisions of the bronchi. Their walls are made of muscle lined with epithelial cells. This muscle allows them to constrict so that they can control the flow of air in and out of the alveoli. 
  • The alveoli are minute air sacs with a diameter between 100um and 300um, at the end of bronchioles. They contain collagen and elastic fibres, and they are lined with epithelium. The elastic fibres allow the alveoli to stretch as they fill with air when breathing in. They then spring back during breathing out in order to expel carbon dioxide rich air. The alveolar membrane is the gas exchange surface. 
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4.2 The mechanism of breathing

To maintain diffusion of gases across the alveolar epithelium, air must be constantly moved in and out of the lungs. We call this process breathing or ventilation. When the air pressure of the atmosphere is greater than that of the air pressure in the lungs, air is forced into the alveoli. This is called inspiration. When the air pressure in the lungs is greater than that of the atmosphere, air is forced out of the lungs. This is called expiration. The pressure changes in the lungs are brought about by the movement of two sets of muscles.

  • the diaphragm, which is a sheet muscle that separates the thorax from the abdomen. 
  • the intercostal muscles which lie between the ribs. There are two types of intercostal muscles: the internal intercostal muscles, whose contraction leads to expiration and the external intercostal muscles, whose contraction leads to inspiration.                                                                      


Breathing in is an active process (it uses energy) and it occurs as follows:

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  • The external intercostal muscles contract, while the internal intercostal muscles relax.
  • The ribs are pulled upwards and outwards, increasing the volume of the thorax.
  • The diaphragm muscles contract, causing it to flatten, which also increases the volume of the thorax. 
  • The increased volume of the thorax results in reduction of pressure in the lungs.
  • Atmospheric pressure is now greater than pulmonary pressure and so air is forced into the lungs.


Breathing out is a largely passive process and it occurs as follows:

  • The internal intercostal muscles contract, while the external intercostal muscles relax.
  • The ribs move downwards and inwards, decreasing the volume of the thorax
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  • The diaphragm muscles relax, making it return to its upwardly domed position, again decreasing the volume of the thorax.
  • The decreased volume of the thorax increases the pressure in the lungs.
  • The pulmonary pressure is now greater that that of the atmosphere, and so air is forced out of the lungs,

Pulmonary Ventilation

Pulmonary ventilation is the total volume of air that is moved into the lungs during one minute. To calculate it we multiply two factors:

  • tidal volume, which is the volume of air normally taken in at each breath when the body is at rest.
  • ventilation,  breathing rate per minute.

Pulmonary ventilation is expressed as dm3min-1

Pulmonary ventiliation (dm3min-1) = tidal volume (dm3) x ventilation (min-1) 

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4.3 Exchange of gases in the lungs

The site of gas exchange in mammals is the epithelium of the alveoli. These alveoli are minute air sacs To ensure a constant supply of oxygen to the body a diffusion gradient must be maintained at the alveolar surface.

Essential features of exchange surfaces

To enable effective transfer of materials across them by diffusion or active transport, exchange surfaces must have the following characteristics:

  • They have a large surface area to volume ratio to speed up the rate of exchange.
  • They are very thin to keep the diffusion pathway short and so allow materials to cross rapidly.
  • They are partially permeable to allow selected materials to diffuse easily.
  • There is movement of the environmental medium, e.g. air to maintain a diffusion gradient.
  • There is movement of the internal medium, e.g. blood to maintain a diffusion gradient.
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Ficks Law:

Diffusion is proportional to: (surface area x difference in concentration) / length of diffusion path

Being thin this specialised exchange surfaces are easily damaged and therefore are often located inside an organism for protection. Therefore the organism needs to have means of moving the external medium over the exchange surface (means of ventilating the lungs)

Role of the alveoli in gas exchange

The total surface area of alveoli is around 70m2. Each alveolus is lined with epithelial cells. Around each alveolus is a network of blood capillaries, so narrow that red blood cells are flattened against the thin capillary walls in order to squeeze through. These capillaries have walls that are only a single layer of cells thick. Diffusion of gases between the alveoli and the blood is very rapid because:

  • red blood cells are slowed as they pass through pulmonary capillaries, allowing more time for diffusion.
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  • The distance between the alveolar air and red blood cells is reduced as red blood cells are flattened against the capillary walls.
  • The walls of both the alveoli and capillaries are very thin and therefore the distance over which diffusion takes place is short. 
  • Alveoli and pulmonary capillaries have a very large surface area.
  • Breathing movements constantly ventilate the lungs, and the action of the heart constantly circulates the blood around the alveoli. Together these ensure that a steep concentration gradient is maintained. 
  • Blood flow through the pulmonary capillaries maintains a concentration gradient. 
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4.4 Lung disease - pulmonary tuberculosis

Causes and symptoms

Tuberculosis is caused by one of two rod shaped bacterium: Mycobacterium tuberculosis and mycobacterium bovis. The symptoms of pulmonary tuberculosis initially include a persistent cough, tiredness and a loss of appetite that leads to weight loss. As the disease develops, fever and coughing up of blood may occur. 


Pulmonary tuberculosis is spread through the air by droplets, released into the air when infected individuals cough, sneeze, laugh or talk. Mycobacterium tuberculosis is a resistant bacterium that can survive several weeks once the droplets have dried. It normally takes close contact with an infected individual over a period of time to transmit the bacteria. TB can also be spread from cows to humans because M.bovis infects cattle, and as a result milk may contain the bacterium. Some groups are at greater risk of contracting TB. These include people who:

  • Are in close contact with infected individuals over long periods.
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  • work or reside in long term care facilities where relatively large numbers of people live close together,
  • are from countries where TB is common
  • have reduced immunity.

Examples of groups with reduced immunity:

  • the very young or very old
  • those with AIDS
  • People with other medical conditions that make their body less resistant to diseases
  • Those undergoing treatment with immunosuppressant drugs
  • the malnourished
  • alcoholics or injecting drug users
  • the homeless

Causes of infection

Once mycobacterium tuberculosis has been inhaled by someone who is not immune to it, the infection follows a particular course.

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  • The bacteria grow and divide within the upper regions of the lungs where there is a plentiful supply of oxygen.
  • The body's immune system responds and white blood cells accumulate at the site of infection to ingest the bacteria, 
  • This leads to inflammation and enlargement of the lymph nodes that drain that area of the lungs. This is called primary infection and usually occurs in children.
  • In a healthy person there are few symptoms if any, and the infection is controlled within a few weeks. However some bacteria usually remain.
  • Many years later these bacteria may re emerge to cause a second infection of TB. This is called post primary response and usually occurs in adults.
  • This infection also arises in the upper regions of the lungs but is not so easily controlled.The bacteria destroy the tissue of the lungs. This results in cavities and, where the lung repairs itself, scar tissue. 
  • The sufferer coughs up damaged lung tissue containing bacteria, along with blood. Without treatment TB spreads to the rest of the body and can be fatal. 

Preventing the spread of TB largely depends on public services. These services are a compromise of current scientific understanding of TB and public, political and economic circumstances. 

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4.5 Lung disease - fibrosis, asthma and emphysema

The alveolar of the lungs is the interface at which gas exchange takes place. To be efficient , this exchange surface needs to be thin, have a large surface area and be constantly ventilated. It follows that any factor that adversely affects one or more of these features will reduce the efficiency of gas exchange.

Pulmonary fibrosis

Pulmonary fibrosis arises when scars form on the epithelium of the lungs, causing them to become irreversible thickened. To diffuse respiratory gases, the linings of the alveoli need to be thin. In patients with fibrosis, oxygen cannot diffuse into the blood as efficiently because the diffusion pathway has been considerably lengthened and the volume of air that the lungs can contain has been considerably reduced. The fibrosis also reduces the elasticity of the lungs. The expulsion of air when breathing out is due to the lungs springing back and to achieve this lungs have to be elastic. Fibrosis makes it difficult to breathe out and therefore ventilate the lungs. The effects of fibrosis on lung function along with an explantion of their causes are listed below:

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  • shortness of breath is due to the considerable volume of the air space within the lungs becoming occupied by fibrosis tissue. This means that less air and hence oxygen is being taken into the lungs at each breath. In addition the thickened epithelium of the alveoli means that the diffusion pathway is increased and so diffusion of oxygen into the blood is extremely slow. The loss of elasticity makes ventilating the lungs very difficult. This makes it hard to maintain a diffusion gradient across the exchange surface. 
  • Chronic, dry cough occurs because the fibrosis tissue creates an obstruction in the airways of the lungs. The body's relax reaction is to try to remove the obstruction by coughing. Since the tissue is more or less immovable, nothing is expelled and the cough is described as dry.
  • Pain and discomfort in the chest are the consequence of pressure and hence damage, from the mass of fibrous tissue in the lungs and further damage from scarring due to coughing. 
  • Weakness and fatigue results from the reduced intake of oxygen into the blood. This means that the release of energy by cellular respiration is reduced, leading to tiredness.
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Asthma is an example of a localised allergic reaction. Some of the most common allergens that stimulate asthma are pollen, animal fur and the faeces of house dust mite. It can also be triggered (or made worse) by a range of factors: air pollutants, exercise, cold air, infection, anxiety and stress. One or more of these allergens causes white blood cells on the linings of the bronchi and bronchioles to release a chemical called histamine. This in turn has the following affects:

  • The lining of these airways becomes inflamed.
  • The cells of the epithelial lining secrete larger quantities of mucus. 
  • Fluid leaves the capillaries and enters the airways
  • The muscle surrounding the bronchioles contracts and so constricts the airways.

Overall there is a much greater resistance to the flow of air in and out of the alveoli. This makes it difficult to ventilate the lungs and so maintain a diffusion gradient across the exchange surface. The symptoms of asthma and their explanations are given below:

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  • Difficulty in breathing is due to the constriction of the bronchi and bronchioles, their inflamed linings and the additional mucus and fluid within them. 
  • A wheezing sound when breathing is caused by the air passing through the very constricted bronchi and bronchioles. 
  • A tight feeling in the chest is the consequence of not being able to ventilate the lungs adequately because of the constricted bronchi and bronchioles. 
  • Coughing is a reflex response to the obstructed bronchi and bronchioles in an effort to clear them. 

Asthma tends to run in families. The number of asthmatics continues to rise. 


One in every five smokers will develop the crippling lung disease called emphysema. The disease develops over a period of 20 years or so and it is virtually impossible to diagnose until the lungs have been irreversibly damaged. Healthy lungs contain large quantities of elastic tissue made of elastin. The tissue stretches when we breathe in and springs back when we breathe out. In a patient with emphysema, the elastin has been permanently stretched and the lungs are no longer able to force air out of the alveoli. 

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The surface area of the alveoli is reduced and they sometimes burst. As a result little if any exchange of gases can take place across the stretched and damaged air sacs.

The symptoms of emphysema and their explanations are detailed below:

  • Shortness of breath results from difficultly in exhaling air due to the loss of elasticity in the lungs. If the lungs cannot be emptied of much of their air, then it is difficult to inhale fresh air containing oxygen and so the patient feels breathless. The smaller alveolar surface area leads to reduced levels of oxygen in the blood and so the patient tries to increase the oxygen supply by breathing more rapidly. 
  • Chronic cough is the consequence of lung disease and the body's effort to remove damaged tissue and mucus that cannot be removed naturally because the cilia on the bronchi and bronchioles have been destroyed. 
  • Bluish skin colouration  is due to low levels of oxygen in the blood as a result of poor gas diffusion in the lungs.
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5.1 Structure of the heart

The heart is a muscular organ that lies in the thoracic cavity behind the sternum. It operates continuously and tirelessly throughout the life of the organism.

Structure of the human heart 

The pump on the left side of the heart deals with oxygenated blood from the lungs, while the pump on the right side of the heart deals with de oxygenated blood from the body. Each pump has two chambers:

  • The atrium  is thin walled, elastic and stretches as it collects blood. It only has to pump blood a short distance to the ventricle and therefore has a thin muscular wall.
  • The ventricle has a much thicker wall as it has to pump blood some distance, either to the lungs or to the rest of the body. 

The blood has to pass through tiny capillaries in the lungs in order to present a large surface area for the exchange of gases. In doing so there is a very large drop in pressure and so if we only had only had one pump, the blood flow to the rest of the body would be very slow.

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Because the right ventricle pumps blood to the lungs (a distance of only a few centimetres) is has a thinner muscular wall than the left ventricle. The left ventricle has a thick muscular wall enabling it to create enough pressure to carry blood to the extremities of the body. 

Between each atrium and ventricle are valves that prevent the back flow of blood into the atria when the ventricles contract. There are two sets of valves. 

  • the left atrioventricular (bicuspid) valves, formed of two cup shaped flaps on the left side of the heart. 
  • the right atrioventricular (tricuspid) valves, formed of three cup shaped flaps on the right side of the heart.

Each of the four chambers of the heart is served by large blood vessels that carry blood towards of away from the heart. The ventricles pump blood away from the heart and into the arteries. The atria receive blood from the veins. 

Vessels connecting the heart to the lungs are called pulmonary vessels. The vessels are connected to the four chambers are therefore as follows:

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  • The aorta is connected to the left ventricle and carries oxygenated blood to all parts of the body except the lungs.
  • The vena cava is connected to the right atrium and brings de oxygenated blood back from the tissues of the body. 
  • The pulmonary artery is connected to the right ventricle and carries de oxygenated blood into the lungs, where its oxygen is replenished and its carbon dioxide is removed.
  • The pulmonary vein is connected to the left atrium and brings back oxygenated blood from the lungs.

Supplying the heart muscle with oxygen

Although oxygenated blood passes through the left side of the heart, the heart does not use this oxygen to supply its own respiratory needs. The heart is supplied by its own blood vessels, called the coronary arteries, which branch of the aorta shortly after it leaves the heart.

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Could you please tag it to the exam board it s for,thanks

Abbas M.M


this was very helpful! thanks a ton maddy! are you a teacher or student? 

would you have notes for lungs and lung disease or heart or immunity please?

i was wondering if you have the full notes for Unit 2-The variety of living organisms ?




I'm a student retaking biology unit 1 and unit 2 in january and so all the topics will be covered before then. 



This stuff is really good. Thank you!

would you have the rest of the notes for 4.3, 4.4 , 4.5 and 5 and 6? i would really appreciate that.


good luck in your exams!

Zoe Alford


These notes are really great :) thank you!



Maddy ur a star!

could u upload all of 5 and 6 please? U have by far the best notes on the internet for Bio :D



this is really good thanks :D im struggling with bio and these have helped alot! 



Thank you it really helped just what i needed

hope you exams go well

Abbas M.M


thank you for the update! do u have more notes on heart n immunity please? i would really appreciate that.



Hey..Thank you soo muchhh...dese notess r awesome.. just wat i needed for me to do better in my retakes...:D



Hello Thank you for these notes! May I ask how do you convert the texts into audio files please?

Katy Martin


These are brilliant! thanks for putting them up!



could you please do unit 2? these are excellent!! :)

Rebecca Harvey


wow these notes are amazing do you have the notes for unit 2 by any chance these are the best resource i can find!

thanks so much!




hey please do unit two, these are banging






Amazing!!!!!!!!! This goes into detail about everything...thankyou..this will save me so much time =)

carl willett


These are amazing :) so far the best thing ive found to help me revise :) feel more confident after reading these !!!!



thankyou so much, these are brilliant! what grade did you get, just out of interest? :)



thankyou so much, these are brilliant! what grade did you get, just out of interest? :)



These are perfect! Do you have any unit 2 resources? :) 



There appears to be no chapter 6 notes?



how comes i cant print then? :(



so if i know everything on these cards and nothing more, what grade should i expect to get anyone?

Also thanks for the notes :)



duncan, it's about exam technique, learning these on its own would probably get you a E or D. practise papers as much as you can, learn mark schemes, and read the examiner's reports. that would move the grade up to C.B and A if you learn as much as you can. but im no expert

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