As Biology

As level Biology notes
Unit 1 – Biology and Disease

By Jonathan Curtis

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Contents
As level Biology notes........................................................................................................1 Contents...............................................................................................................................2 Section 1.1: Causes of Disease - Pathogens......................................................................4 Section 1.2: Epidemiology..................................................................................................6 Section 1.3: Lifestyle and Health........................................................................................7 Section 2.1: Enzymes and Digestion................................................................................10 Section 2.2: Carbohydrates – Monosaccharides..............................................................11 Section 2.3: Carbohydrates – disaccharides and polysaccharides. .................................13 Section 2.4 – Carbohydrate digestion...............................................................................14 Section 2.5 – Proteins.......................................................................................................15 Section 2.6 – Enzyme action............................................................................................17 Section 2.7 – Factors affecting enzyme action.................................................................18 Section 2.8 – Enzyme inhabitation...................................................................................19 Section 3.1 – Investigating the structure of cells.............................................................20 Section 3.2 – The electron microscope.............................................................................22 Section 3.3 – Structure of epithelial cells.........................................................................23 Section 3.4 - Lipids...........................................................................................................25 Section 3.5 – The cell surface membrane.........................................................................26 Section 3.6 - Diffusion.....................................................................................................28 Section 3.7 – Osmosis.......................................................................................................29 Section 3.8 – Active transport .........................................................................................30 Section 3.9 – Absorption in the small intestine................................................................31 Section 3.10 – Cholera .....................................................................................................32 Section 3.11- Oral rehydration therapy ...........................................................................33 Section 4.1 – Structure of the human gas-exchange system............................................34 Section 4.2 – The mechanism of breathing......................................................................36 Section 4.3 – Exchange of gas in the lungs .....................................................................37 Section 4.4 – Pulmonary tuberculosis..............................................................................39 Section 4.5 – Fibrosis, asthma and Emphysema .............................................................42 Section 5.1 – The heart and heart disease.........................................................................44 Section 5.2 – The cardiac Cycle ......................................................................................47 Section 5.3 – Heart Disease..............................................................................................51 Section 6.1 – Defence mechanisms .................................................................................53 Section 6.2 – Phagocytosis...............................................................................................54 Section 6.3 – T cells and cell-mediated immunity...........................................................55 Section 6.4 – B cells and humoral immunity ..................................................................56 Section 6.5 – Antibodies...................................................................................................57 Section 6.6 – Vaccination ................................................................................................58 Section 7.1 – Investigating Variation...............................................................................60 Section 7.2 – Types of variation ......................................................................................62 Section 8.1 – Structure of DNA........................................................................................63 Section 8.2 – The triplet code ..........................................................................................66 Section 8.3 – DNA and Chromosomes.............................................................................68 Section 8.4 – Meiosis and Genetic Variation ..................................................................71 Section 9.1 – Genetic Diversity........................................................................................73 Section 10.1 – Haemoglobin.............................................................................................74 Section 10.2 – Oxygen dissociation curves .....................................................................75 Section 10.3 – Starch, glycogen and cellulose ................................................................76 Section 10.4 - Plant cell structure.....................................................................................77 Page 2 of 114

Section 11.1 – Replication of DNA..................................................................................78 Section 11.2 – Mitosis......................................................................................................80 Section 11.3 – The cell cycle............................................................................................83 Section 12.1 – Cellular organisms....................................................................................85 Section 13.1 – Exchange between organisms and their Environment ............................87 Section 13.2 – Gas exchange in single celled organisms and insects .............................88 Section 13.3 – Gas exchange in Fish................................................................................89 Section 13.4 – Gas exchange in the leaf of a plant .........................................................90 Section 13.5 – Circulatory system of a mammal ............................................................91 Section 13.6 – Blood vessels and their functions ............................................................93 Section 13.7 – Movement of water through roots ...........................................................95 Section 13.8 – Movement of water up stems ..................................................................97 Section 13.9 – Transpiration and factors affecting it.......................................................98 Section 13.10 – Limiting water loss in plants .................................................................99 Section 14.1 – Classification .........................................................................................100 Section 15.1 - Genetic comparisons using DNA and proteins ......................................104 Section 15.2- Courtship behaviour ................................................................................105 Section 16.1 – Genetic variation in bacteria ..................................................................106 Section 16.2+16.3 – Antibiotics/Antibiotic use and resistance.....................................109 Section 17.1 – Species diversity ....................................................................................112 Section 17.2 – Species diversity and Human activities .................................................113

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Section 1.1: Causes of Disease - Pathogens
• • • • • • • • • • Health – A state of physical and mental well-being, free from disease. Disease – An abnormal condition of an organism that impairs bodily functions and is associated with specific symptoms. Non-infectious – Sometimes called disorders and can be caused by a broad range of environmental factors. They cannot be transferred. Infectious – Caused by pathogens Inherited – due to a mistake or alternation in the genetic make-up e.g. down syndrome, cystic fibrosis, Huntington’s disease etc. Nutritional deficiency – caused by inadequate or unbalanced diet or by overeating E.g. scurvy, obesity, rickets, etc. Psychological disorders – diseases causing changes in the working of the brain E.g. schizophrenia. Social/self induced – Influenced by living conditions or personal behaviour e.g. lung cancer, STIs, etc. Degenerate – wholly/partly caused by aging. Organs and tissue may not work as well due to slower cell renewal and repair. Environmental – Abnormal bodily reaction caused by the environment e.g. U.V rays.

Note: many diseases can be caused by multiple factors. Most microbes are harmless Pathogen –disease causing microbe. Infection – process by which a pathogen enters and establishes it’s self. • • • • Communicable disease – spread via close proximity or contact. Non-Communicable – disease caused by food/drink or animal vectors e.g. mosquitoes. Interface – where internal and an external environment meet. Skin – Difficult to penetrate, thick and water proof. Platelets quickly produce scabs.

Interfaces are adapted for absorption but also make it easier for pathogens to pass through. Gas exchange – airborne pathogens

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Digestive System – Disease in contaminated food or water.

Defences
Gas exchange – thick/sticky mucus traps pathogens. Celia that is on the epithelial cells work together to remove microbes. Digestive system – concentrated HCl kills microbes. Protease also kills microbes. Fungi – Opportunistic pathogens. Fungal toxins are called mycotoxins. Viruses – Invade bodily cells in order to reproduce thus preventing the host cell functioning as normal. It kills bodily cells and rarely produces toxins. Bacteria reproduction is called binary fusion. Endemic – a disease that is always present in the population. Epidemic – when a new disease spreads rapidly through the population. Pandemic – when an outbreak occurs on a global basic.

Robert Koch
1. Bacteria present when disease is present. 2. It must be possible to isolate and grow the microbe. 3. When cultured, they are introduced to a healthy host to see if it is infected. 4. It should be possible to isolate the microbes from the new host.

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Section 1.2: Epidemiology
Is the study of patterns in diseases and the various factors that effect the spread of disease. A correlation is different causal link. Strong, positive correlation A positive correlation will occur when an increase in one variable, causes a increase in another. In order for the correlation to be “strong”, there must be little spread in the data.

Weak correlation

A weak correlation occurs when there is a wide spread of data shown in the graph.

Negative Correlation A negative correlation will occur when an increase in one variable causes a decrease in another.

How to prove a link • • • Wide samples must be used. Data must be analysed over long periods of time. Variables must be controlled.

Demographic Transition Explains how the population changes over time e.g. from high birth rate. Page 6 of 114

Section 1.3: Lifestyle and Health
• • • • Risk – A measure of probability that damage to health will occur as a result of a given hazard. We need to look at probability that a hazard will occur as a consequence of the hazardous event. If the consequence of the hazard is high and the probability is low, there is little cause for concern. A major concern is when both are high.

Measuring risk • • • • • • • • • • • 0% (no harm will occur) 100% (will defiantly occur) A timescale is needed to give the data more weight. Risk must be relative. Cancer – Cell division in an uncontrollable fashion. This continues if there are nutrients. Cancer cells cease to function normally. Carcinogen – Cause the DNA to mutate. They are cancer causing agents. Most mutated cells are destroyed. One mutated cell can cause a mass of mutated cells. Benign – does not move from the point of origin. Usually harmless, however can cause problems depending on where it grows. Maligment – grow faster and can spread throughout the body. Can have its own blood supply. The process of moving to another area of the body is called metastasis. Not fully understood how cancer starts. Age + = more likely. Genetics can cause approximately 5% of cancers. Tumour producing genes (oncogenes). Lifestyle factors can expose you to more carcinogens. Page 7 of 114

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More you smoke, higher the risk. Diet – low fat, high fibre, fruit etc. Radiation, uv light and xrays are carcinogens. Physical activity – exercise reduces the risk. Alcohol – increases risk. Hormones – high level of sex hormones can increase risk.

Treatments • • • • • Prevention is better than cure. Early diagnosis. Surgical removal – Easiest when the tumour is benign. Chemotherapy – using drugs to kill cells in the body. Effects all cells that divide rapidly. Radiotherapy – ionising radiation that destroys tissue. Healthy cells suffer less so there are little side-effects.

Future treatments • • Hyperthermia may destroy cancer because the immune system is better at detecting cancer cells. It may be possible to create drugs which can locate genes which are responsible for mutating and causing each type of cancer.

Smoking • • Heavy smoking over a long period of time will drastically increase the risk of developing lung cancer. There is a strong correlation, but not a causal link.

Conclusive evidence • • • Tar in cigarettes contains Benzopyrene (carcinogen) Cancer cells were looked at and scientist found that mutations occurred in 3 places in the DNA. The gene that mutates is called a tumour suppressor gene.

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This is still not a causal link because smoking does not defiantly cause cancer, even though it is very likely to be the cause. It is only a correlation because it is a multi-factorial disease.

Coronary Heart Disease • • • • • • • • • • • • Largest cause of death in the U.K Occurs when one of the arteries supplying heart tissue with oxygen is blocked. Heart respires anerobically when there is a blood clot. Anaerobic respiration does not release enough energy. Heart attack – myocardial infarction. Blood clot – thrombus Process of a blood clot forming is called thrombosis. If this happens to coronary arteries it is called coronary thrombosis. Smoking narrows blood vessels, thus increase blood pressure. High blood pressure increase the rate at which cholesterol is deposited. Exercise can lower blood pressure. Diets high in saturated fats will increase the risk of developing coronary heart disease.

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Section 2.1: Enzymes and Digestion
• • Glands produce enzymes that are used to break down large molecules into smaller ones that are ready for abortion. The digestive system provides an interface between the body and the environment because it allows food to pass through it.

Major parts of the digestive system

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The Oesophagus is made up of a thick muscular wall and is adapted so that food can pass down it easily from the mouth to the stomach. Therefore it used for transport, as appose to digestion. The stomach is a muscular sac with an inner layer that produces enzymes. Its roles are to store and digest food (especially proteins). There are glands within it that produce enzymes to digest protein. Mucus is also produced in the stomach by glands. The mucus prevents the stomach being digested by its own enzymes. The small intestine is a long muscular tube. Food is further digested by enzymes in the small intestine. The enzymes enter the small intestine through its walls and through glands. The inner walls of the small intestine are folded into villi, giving them a larger surface area. The surface area of villi is further increased by millions of tinier projections called microvilli. The microvilli are found on the epithelial cells of each villus. This adapts the small intestine so that it can absorb substances into the blood stream. The large intestine absorbs water. Often the water is reabsorbed by the secretion of digestive glands. Because there is little water within the large intestine, the food becomes drier, thus forming faeces. The rectum is where faeces is stored before it is removed through the anus in a process called egestion.

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The salivary glands are positioned near the mouth. They pass there secretion via a duct into the mouth. This secretion will contain the enzyme amylase. The pancreas is a large gland situated near the stomach. It secretes pancreatic juice. This contains protease, lipase and amylase.

There are two stages of digestion; physical breakdown and chemical absorption.

Physical breakdown
Large pieces of food are broken down into smaller pieces by processes such as chewing and the churning of food in the stomach. This makes it possible to not only absorb food but to increase its surface area, thus making it easier for chemical absorption.

Chemical digestion
Chemical digestion is the process of breaking down large molecules into smaller ones so that they can be absorbed. This is carried out by enzymes. Enzymes function by hydrolysis. Hydrolysis is the process of splitting up molecules by adding water to the bonds that hold them together. The general term for these enzymes is hydrolases. Because enzymes are specific, more than one is needed to break down a large molecule. Usually, an enzyme will break down a molecule into smaller sections. These smaller sections are then hydrolysed into even smaller molecules by additional enzymes. Carbohydrases break starch molecules down until they become monosaccharides. Lipase breaks down lips into glycerol and fatty acids. Protease breaks protein down to amino acids. Once these molecules have been broken down to become even smaller molecules such as monosaccharides, they are absorbed into the body and are often built up again to form larger molecules again. These new molecules are incorporated into body tissue or are used in processes within the body. This is called assimilation.

Section 2.2: Carbohydrates – Monosaccharides

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Carbohydrates are carbon molecules (carbo) combined with water molecules (hydrate).

Life based on Carbon
• • Carbon atoms are able to readily form bonds with other carbon atoms Life on earth is based on the versatile carbon atom.

The making of Large molecules
• • Carbohydrates are long chains made up of individual molecules called monosaccharides. A pair of monosaccharides is called a disaccharide and several monosaccharides joined together is called a polysaccharide.

Monosaccharides
• • • Monosaccharides are soluble and have the general formula (CH20)n. N can be any number from 3 -7. Glucose is a hexose because it has 6 carbon atoms and has the formula C6H12O6 Even though it has the same chemical formula, the hydrogen and oxygen atoms can be arranged in many different ways. Glucose Galactose Fructose

Glucose is the most common sugar. Although its molecular arrangement is often shown as a straight line, its atoms form a ring.

Galactose has the same chemical formula as glucose. However on the left of the diagram you can see how the Hydroxide and hydrogen atoms are arranged differently to glucose.

Fructose has a very different structure to glucose and is often used as a sweetener.

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Section 2.3: Carbohydrates – disaccharides and polysaccharides.
Disaccharides
When combined in pairs monosaccharides form disaccharides. • • • Glucose with glucose forms maltose Glucose with fructose forms sucrose Glucose linked with Galactose forms lactose. • When two monosaccharides join together a water molecule is removed. This is called a condensation reaction. In order to break the bond, water is added to the molecule in a process called hydrolysis. The bond holding the two monomers together is called a glycosidic bond. A glycosidic bond is an oxygen atom.

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Polysaccharides
• • • • Polysaccharides are long chains of monosaccharides combined together through glycosidic bonds. Because they are very long molecules, they are often insoluble. This means that they are very suitable for storage. When hydrolysed, polysaccharides break down into disaccharides or monosaccharides. Some polysaccharides such as starch are not used for storage, but instead are used to give support to plant cells.

Test for non-reducing sugars
To test for a non reducing sugar it must first be hydrolysed then added to Benedict’s reagent.

Test for starch
To test for starch, add potassium iodine solution. If starch is present, the iodine will turn from yellow to blue-black.

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Section 2.4 – Carbohydrate digestion
• • • • • • • • • • • • • • • It usually takes more than one enzyme to break down a large molecule. Food is physically broken down by teeth to increase surface area. Normally one enzyme breaks a large molecule into smaller sections, and then other enzymes break these down to monomers. Firstly the enzyme “amylase” is produced in the mouth by salivary glands, where the pH is kept at neutral by mineral salts. This enzyme breaks starch into maltose by hydrolysing the glycosidic bonds holding the molecule together. Once the food is swallowed, the enzyme is destroyed by the stomach acid where the pH is around 2. This means that no more starch can be digested. After the stomach, food passes into the small intestine where it mixes with pancreatic juices. The pancreatic juice contains pancreatic amylase which hydrolyses the remaining starch. Alkaline salts are produced by the intestine wall and the pancreas to maintain the pH at neutral so that the enzymes can work efficiently. The epithelial lining of the intestine produces the enzyme maltase. This breaks maltose into glucose. Sucrase which is produced by the epithelial lining breaks down sucrose into fructose and glucose. People who are lactose intolerant do not produce enough lactase to break down the lactose found in milk. When undigested lactose enters the small intestine, bacteria digest it and produce lots of gas. This can cause stomach cramps, nausea and diarrhoea. For new born babies, milk makes up the majority of their diet. To overcome the problem of lactose intolerance amongst children, lactose can be pre-digested before consumption.

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Section 2.5 – Proteins
• • • Each organism has numerous proteins that differ from species to species. The structure of one protein molecule differs from that of all other protein molecules. Proteins are the most important molecules for life.

Structure of amino acids There are 4 main parts that make up the general structure of an amino acid. There is: The amino group (NH2) this is a basic part of the molecule where it gets the name amino. The carboxyl group (COOH) this is an acid group. The hydrogen atom (H) The r group, this can be a variety of chemicals. Each amino acid has a different r group. The formation of a peptide bond Through the same process by which monosaccharide join to make disaccharides and polysaccharides, amino acids can join together to form dipeptides. They create a water molecule by combining the OH from the carboxyl group of one amino acid with the hydrogen atom of another amino acid. When there is a repeating sequence of amino acids joined by a peptide bond it is called a polypeptide chain. Primary Structure After many condensation reactions (removal of water molecules to form a peptide bond), many monomers are joined together in a process called polymerisation. The chain of many amino acids is called a poly peptide. This repeating sequence of amino acids in a polypeptide chain is known as the primary structure.

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Secondary structure The secondary structure is formed when the -C=O (which has a overall negative charge) is attracted to the hydrogen atom (which has an overall positive charge). This causes the long chain to twist in on its self creating a coil known as a alpha helix.

Tertiary Structure The secondary structure, which is an alpha helix can be further twisted and folded forming a unique 3D structure for each protein. It is formed by several different types of bonds. Disulphide bond – fairly strong, not easily broken down. Ionic bonds – formed by the carboxyl and amino groups. They are weaker than disulphide bonds. A change in pH can affect an ionic bond. Hydrogen bonds – there are many of these however they are easily broken down.

Quaternary Structure This structure appears when a number of complex molecules containing polypeptide chains that are linked in various ways are associated with non-protein molecules called prosthetic groups.

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Section 2.6 – Enzyme action
• • • • • • • • • All enzymes are globular proteins → spherical in shape Control biochemical reactions in cells They have the suffix "-ase" Intracellular enzymes are found inside the cell Extracellular enzymes act outside the cell Enzymes are catalysts → speed up chemical reactions Reduce activation energy required to start a reaction between molecules Substrates (reactants) are converted into products Reaction may not take place in absence of enzymes (each enzyme has a specific catalytic action) • • • • Enzymes catalyse a reaction at max. rate at an optimum state The substrate and the enzyme must collide with sufficient energy. Enzymes work by lowering the activation energy required to start a reaction Once the substrate is inside the active site, the enzyme changes shape slightly, distorting the molecule in the active site, and making it more likely to change into the product. • It's a bit more complicated than that though. Although enzymes can change the speed of a chemical reaction, they cannot change its direction, otherwise they could make "impossible" reactions happen and break the laws of thermodynamics. • When a substrate (or product) molecule binds, the active site change shape and fits itself around the molecule, distorting it into forming the transition state, and so speeding up the reaction. This is sometimes called the induced fit mechanism.

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Section 2.7 – Factors affecting enzyme action
Measuring enzyme-catalysed reactions
• • To measure the progress of an enzyme-catalysed reaction, its time course is measured. This is how long it takes to run its course. The two “events” most frequently measured are the volume of gas produced during a reaction and the disappearance of a substrate.

Effect of Temperature •
Enzymes have an optimum temperature at which they work fastest. For mammalian enzymes this is about 40°C, but there are enzymes that work best at very different temperatures, e.g. enzymes from the arctic snow flea work at -10°C, and enzymes from thermophilic bacteria work at 90°C. The rate of reaction doubles, approximately almost every ten degrees. The rate of reaction will increase as temperature increases. Then, once it reaches its optimum temperature it will begin to decrease as the temperature rises due to the active site being denatured. The thermal energy breaks the hydrogen bonds holding the secondary and tertiary structure of the enzyme together, so the enzyme (and especially the active site) loses its shape to become a random coil.

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Effect of pH •
• Enzymes have an optimum pH at which they work fastest. For most enzymes this is about pH 7-8 (physiological pH of most cells), but a few enzymes can work at extreme pH, such as protease enzymes in animal stomachs, which have an optimum of pH 1. The pH affects the charge of the amino acids at the active site, so the properties of the active site change and the substrate can no longer bind. For example a carboxyl acid R groups will be uncharged a low pH (COOH), but charged at high pH (COO-).

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Section 2.8 – Enzyme inhabitation
Inhibitors inhibit the activity of enzymes, reducing the rate of their reactions. They are found naturally, but are also used artificially as drugs, pesticides and research tools. There are two kinds of inhibitors. Competitive inhibitor • • A competitive inhibitor molecule has a similar structure to the normal substrate molecule, and it can fit into the active site of the enzyme. It therefore competes with the substrate for the active site, so the reaction is slower. It is the difference between the concentration of the inhibitor and the concentration of the substrate that determines the affect it has on the enzymes activity. The inhibitor is not permanently bonded to the active site so once it leaves a substrate molecule can take its place. Eventually all the substrate molecules will be in the active sites. However, depending on the concentration of the inhibitor, the longer this will take.

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Non-competitive inhibitors • Non-competitive inhibitors do not fit into the active site but instead they bind to another part of the enzyme molecule, changing the shape of the whole enzyme, including the active site, so that it can no longer bind substrate molecules. Inhibitors that bind fairly weakly and can washed out are sometimes called reversible inhibitors, while those that tightly and cannot be washed out are called irreversible inhibitors. Poisons like cyanide, heavy metal ions and some insecticides are all non-competitive inhibitors. Non-competitive inhibitors therefore simply reduce the amount of active enzyme (just like decreasing the enzyme concentration). be bind

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Section 3.1 – Investigating the structure of cells
Microscopy Lenses work more effectively if they are in a compound light microscope. Light waves a have a relatively long wavelength; therefore, they can only distinguish between objects that are at least 0.2micrometers apart. Beams of electrons have shorter wavelengths and are therefore able to distinguish between objects as close as 0.1nm apart. Magnification When viewed under a microscope, the material seen in called an image. Magnification tells you how many times bigger the image is in relation to the actual size of the object. It can be found using the following formula: Magnification=size of image/size of object The previous formula can also be rearranged to find the size of an object. Size of object=size of image/magnification Resolution The resolving power of a microscope is the minimum distance two objects can be apart in order for them to appear as separate items. The greater the resolution, the greater the clarity of the image that is produced. Cell fractionation Cell fractionation is the process where cells are broken up and the different organelles they contain are separated out. Before fractionation begins, the cells are but in a solution that is: Cold – to reduce enzyme activity that might break down the organelles. Isotonic – to prevent organelles bursting or shrinking as a result of osmotic gain or loss of water. An isotonic solution is one that has the same water potential as the original tissue. Buffered – to maintain a constant pH Homogenation Cells are broken up by a homogeniser that releases the organelles. The fluid is called a homogenate. It is then filtered to remove complete cells and large pieces of debris.

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Ultracentrifugation Ultracentrifugation is the process by which the homogenate is separated in a machine called a centrifuge. The spins tubes of the homogenate, creating a centrifugal force that forces the mixture to separate. • • • • • The tube of filtrate is placed in the ultracentrifuge and spun at a slow speed. The heaviest organelles such as the nucleus are forced to the bottom where they form a thin sediment. The fluid at the top, called the supernatant is removed, leaving just the sediment of nuclei at the bottom. The supernatant is then put in another tube where it is spun at an even higher speed than before. The next heaviest organelles (mitochondria) are forced the bottom and the process continues until all the organelles are separated.

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Section 3.2 – The electron microscope
Electrons have a shorter wavelength than light and so they have a greater resolving power. As electrons are negatively charged, the beam can be focused using an electromagnet. Because electrons are absorbed by molecules in the air, a near vacuum must be created within the chamber of an electron microscope for it to work effectively. There are two types of electron microscope: - Transmission electron microscope and scanning electron microscope. Transmission electron microscope The TEM consists of a gun that fires electrons which are focused onto the specimen be a condenser electromagnet. Some of the electrons are absorbed by the specimen and appear dark on the image, other parts allow the electrons through and so appear light. This produces an image of the specimen. The image that appears on screen is called a photomicrograph. Because the process takes place in a vacuum, living specimens cannot be observed. A complex staining process is required and even then the image is only in B&W. The specimen must be extremely thin. Artefacts may appear on the image, these appear as a result of the way the specimen is prepared. Scanning electron microscope All the limitations of the TEM apply to the SEM but the specimen does not have to extremely thin as the electrons do not penetrate. The beam of electrons is directed over the surface of the specimen in a regular pattern. The electrons bounce on the contours of the specimen and are scattered. The scattering of the electrons can be analysed and from this an image can be produced using a computer. The SEM has a lower resolving power than the TEM (20nm) but is still ten times better than a light microscope.

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Section 3.3 – Structure of epithelial cells
Epithelial cells are eukaryotic cells. Eukaryotic cells have a distinct nucleus and a membrane that surrounds each organelle. The function of an epithelial cells is top absorb and secrete The nucleus The nucleus controls the cells activities and contains hereditary material. • The Nuclear envelope is a double membrane that surrounds the nucleus. Its outer membrane is continuous with the endoplasmic reticulum and often has ribosomes on its surface. It can control the substances entering and leaving the nucleus.

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Nuclear pores allow the passage of large materials into and out of the nucleus. Nucleoplasm is granular jelly like material that makes up the bulk of the nucleus. Chromatin is the DNA found within the nucleoplasm This is the diffuse form chromosomes take up when the cells is not dividing. The nucleolus is small spherical body within the nucleoplasm. It manufactures ribosomal RNA and assembles ribosomes.

The mitochondria • A double membrane surrounds the organelle, the outer one controlling the entry and exit of material. The inner membrane inner membrane is folded to form extensions known as cristae. Cristae are shelf like extensions of the inner membrane. These provide a large surface area for the attachment of enzymes during respiration.

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of DNA that allows the mitochondria to control the production of its own proteins. The enzymes involved in respiration are found in the matrix. Mitochondria are responsible for the production of the energy-carrier molecule ATP. Because of this, high numbers of mitochondria are found in cells where there is a high level of metabolic activity. Endoplasmic Reticulum Rough endoplasmic reticulum – has ribosomes present on the outer surface of the membranes. Its functions are to: a) provide a large surface area for the synthesis of proteins and glycoproteins, b) provide a pathway for the transport of materials, especially proteins throughout the cell. Smooth endoplasmic reticulum lacks ribosomes on its surface and is often more tubular in appearance. Its functions are to: a) synthesise, store and transport lipids, b) synthesise store and transport carbohydrates. Golgi Apparatus The Golgi apparatus is similar to the SER in structure but is more compact. It consists of a stack of membranes that form flattened sacks, or cisternae with small rounded hollow structures called vesicles. The proteins and lipids produced in the ER are passed through the Golgi apparatus in strict sequence. The Golgi apparatus modifies these proteins often by adding non-protein structures to them such as carbohydrates. It is also labels them so they can be sorted and sent to their correct destination. Once sorted and modified, proteins are transported in vesicles which are regularly removed from the edge of the Golgi cisternae. These vesicles move to the cell membrane where they fuse and release their contents to the outside. Lysosomes

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Lysosomes are formed when a vesicle contains enzymes. Lysosomes isolate potentially dangerous enzymes from the rest of the cell before releasing them outside of the cell or into phagocytic vesicles within the cell. Lysosomes digest worn out organelles so that the useful chemicals they are made of can be reused. They can completely break down cells after they have died. (Autolysis) Ribosomes Ribosomes occur in either the cytoplasm or the RER. There are two types depending on which cell they are found in: 80S Type – found in eukaryotic cells, is around 25nm in diameter. 70S Type – found in prokaryotic cells, is slightly smaller. Microvilli Microvilli are finger like projections of the epithelial cells. There function is to increase the surface area for diffusion.

Section 3.4 - Lipids

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Lips 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 organic solvents such as alcohol and acetone.

Roles of lipids Phospholipids contribute to the flexibility of membranes and the transfer of lipidsoluble substances across them. In addition to this, lipids can be used as: An energy source. Lipids can provide more than twice the energy of carbohydrate. Waterproofing. Lipids are insoluble in water and are therefore suitable for waterproofing. Insulation. Fats are slow conductors of heat, kept under skin to retain heat in the body. Protection. Often stored around delicate organs. Triglycerides are so called because they have three fatty acids (tri) combined with glycerol (glyceride). Each fatty acids combines with glycerol in a condensation reaction. CH2OH + HOOC  CH2OOC + H2O
(Glycerol) + (fatty acid)

Phospholipids Phospholipids are similar to lipids except that the fatty acid is replaced with a phosphate molecule. Fatty acid molecules repel water whereas phosphate molecules are attracted to water. Test for lipids 1. Take a dry, grease free test tube. 2. Take 2cm^3 of the sample being tested and add 5cm^3 of ethanol. 3. Shake the test tube and dissolve the lipids. 4. Add 5cm^3 of water and shake gently. 5. A cloudy white colour indicates the presence of a lipid.

Section 3.5 – The cell surface membrane

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The cell-surface membrane is a plasma membrane that surrounds that surrounds cells and forms a boundary between the cytoplasm and the environment. Phospholipids Phospholipids are important in cell surface membranes because: • • One layer of phospholipids has its hydrophilic head pointing inwards towards the water in the cytoplasm. The other has its head pointing outwards, interacting with the water surrounding the cell. The hydrophobic tales point inwards.

The function of phospholipids in the cell-membrane are to: allow lipid-soluble substances to enter and leave the cell, Prevent water-soluble substances entering and leaving the cell, Make the membrane more flexible. Proteins The proteins in the phospholipids bilayer are arranged randomly in two main ways: Extrinsic proteins – appear on the surface or partially imbedded. They provide mechanical support or when in conjunction with glycolipids, act as cell receptors for molecules such as hormones. Intrinsic proteins – Span the phospholipids bilayer. Some transport water soluble molecules across the membrane others are enzymes. Protein molecules in the membrane allow active transport by forming ion channels for sodium, potassium, etc. Fluid-mosaic model of the cell surface membrane Fluid - because the phospholipids molecules can move relative to each other, giving it a flexible structure. Mosaic – because the proteins are imbedded in the structure in a similar way that stones are imbedded in a mosaic.

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Section 3.6 - Diffusion
Diffusion is defined as the net movement of molecules or ions from a region where they are more highly concentrated to one where their concentration is lower. All particles are constantly in motion due to the kinetic energy that they posses. The motion is random and there is no set pattern to the way they move. Rate of diffusion • • • • • The greater the difference in concentration, the greater the rate of diffusion The larger the area of an exchange surface, the greater the rate of diffusion. The thinner the exchange surface, the faster the rate of diffusion. The nature of the plasma membrane; its composition and the number of pores. The size and nature of the diffusing molecule. For example smaller molecules diffuse faster than big ones.

Diffusion is proportional to: surface area x difference in concentration Length of diffusion path Facilitated diffusion Facilitated is a passive process as it only relies on the kinetic motion of particles. Facilitated diffusion can only occur at specific point along the plasma membrane where there are special protein molecules. The proteins for special water filled channels. The channels only open for specific molecules. This allows water soluble ions and molecules to pass through. Such molecules such as glucose and amino acids would take much longer to diffuse through the phospholipids bilayer. When a molecule that is specific to the carrier protein is present, the carrier protein changes shape, causing it to release the molecule on the other side of the plasma membrane. Page 28 of 114

Section 3.7 – Osmosis
Osmosis is defined as 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. Water potential is measured in Pascal’s. Under standard conditions of temperature (25c), pure water is said to have a water potential of 0. Water with a solute dissolved in it will have a water potential that is less than 0. Water molecules move from one side where the water potential is higher (less negative) across a partially permeable membrane to another side where the water potential is lower (more negative). The water moves along a water potential gradient. At the point where the water potentials on either side of a partially permeable membrane are equal, a dynamic equilibrium is established and there is no net movement of water. Osmosis in animal cells If a red blood cell is place in pure water it will absorb water by osmosis because it has a lower water potential. The cell-surface membrane will eventually burst if too much water enters the cells. To prevent cells bursting due to too much water entering the cells, cells are often bathed in solutions where the water potential outside the cell is the same as the water potential inside the cell. This is called an isotonic solution. A hypotonic solution is one where the concentration outside is greater than the concentration inside. A hypertonic solution is one where the water potential outside the cell is lower than the water potential inside the cell.

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Section 3.8 – Active transport
Active transport allows cells to exchange molecules against a concentration gradient. Metabolic energy is required for this process. Active transport is the movement of molecules or ions into or out of a cell from a region of lower concentration to a region on higher concentration using energy and carrier molecules. Metabolic energy is needed in the form ATP. Carrier molecules which act as “pumps” are involved. • Active transport uses ATP in two main ways: by using ATP to directly move molecules. • • • • By using a concentration gradient that has already been set up by direct active transport. This is known as co-transport. The carrier molecules accept molecules or ions to be transport on one side of it. The molecules of the ions bind to the receptors on the channels of the carrier protein. On the other side of the membrane ATP bind to the carrier protein causing it to split into ADP and a phosphate molecule. This as a result, causes the carrier protein to change shape, releasing the molecule onto the other side. The phosphate molecule then recombines with the ADP to form ATP again, which causes the carrier protein to revert back to its original shape.

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Occasionally, the molecule or ion is moved into the cell at the same time as a different one is being removed from it. One example of this is the sodiumpotassium pump Sodium ions are actively taken in by the cell whilst potassium ones are actively removed from the cell.

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Section 3.9 – Absorption in the small intestine
Villi and Microvilli Villi have walls lined with epithelial cells. Villi are situated at the interface between the lumen of the intestines and the blood and other tissues inside the body. Their properties increase the efficiency of absorption because: • • • • They increase the surface area for diffusion They are very thin walled, thus reducing the distance over which diffusion takes place. They are able to move and so maintain a concentration gradient They are well supplied with blood vessels so that the blood can carry away absorbed molecules and hence maintain a diffusion gradient.

The epithelial cells possess Microvilli which further increase the surface area for diffusion. They are situated on the cell surface membrane. Villi contain muscles which move the food ensuring the glucose is absorbed from the food adjacent to the villi, new glucose rich food replaces it, thus maintains a concentration gradient for diffusion. Role of active transport in absorption The way in which most glucose is absorbed from small intestine is an example of cotransport. 1. Sodium ions are actively transported out of the epithelial cells by the sodium potassium pump. 2. There is now a much higher concentration of sodium ions in the lumen than in the cells. 3. The sodium ions diffuse into the cells down a concentration gradient. As they flood back into the cells, they are coupled with glucose molecules which are drawn in with them. 4. The glucose diffuses into the blood through a carrier protein. It is the sodium ion concentration, rather than the ATP directly, that powers the movement of glucose into the cell.

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Section 3.10 – Cholera
Structure of a bacteria cell The bacterium that causes cholera is called Vibrio Cholerae. • • • • All bacteria possess a cells wall that is made up of peptidoglycan. This is a mixture of polysaccharides and peptides. Many bacteria also protect themselves by producing a capsule of mucilaginous slime around this wall. Flagella occur at certain types of bacteria. Inside the cell-surface membrane is the cytoplasm that contains ribosomes that are smaller than the ones found in eukaryotic cells. (70s type) Bacteria store food as glycogen granules and oil droplets. The genetic material of a bacterium is found in the form of a circular strand of DNA. Separate from this are smaller circular pieces of DNA, called plasmids.

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How the cholera bacterium causes disease Almost all Vibrio cholerae bacteria ingested by humans are killed by the low pH in the stomach but many can still survive, especially if the pH is above 4.5. When the bacteria enter the lumen of the small intestine they use their flagella to propel themselves through the mucus lining of the intestinal wall. They then start to produce a toxic protein. The protein has two parts: one part binds to the carbohydrate receptors of the intestinal epithelial cells, whereas the other part enters the epithelial cells. The causes the ion channels of the cell-surface membrane to open, that the chloride ions that are normally contained within the epithelial cells flood into the lumen of the intestine. The loss of chloride ions from cells increases the water potential in the cell, but lowers the water potential outside the cells. This causes water to move into the small intestine. The loss of ions from the cells establishes a concentration gradient. Ions move by diffusion into the epithelial cells. This establishes a water potential gradient that causes water to move by osmosis from the blood and other tissues into the small intestine.

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Section 3.11- Oral rehydration therapy
What causes diarrhoea? • • • Damage to the epithelial cells in the lining of the small intestine Loss of Microvilli due to toxins Excessive secretion of water due to toxins

What is oral rehydration therapy? Drinking water to treat diarrhoea is ineffective because: Water is not being absorbed by the intestine. Indeed, as in the case of cholera, water is actually being lose from cells. The drinking water does not replace electrolytes that are being lost from cells of the intestine. As sodium ions are being absorbed, the water potential falls and water enters the cells by osmosis. A rehydration solution should therefore contain: • • • • • Water – to rehydrate tissues Sodium – to replace the ions lost from the epithelium of the small intestine and to make optimum use of the 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

The solution must be given regularly and in large amounts whilst the person has the illness.

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Section 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 volume of oxygen that needs to be absorbed and the volume of carbon dioxide that needs to be removed is large in mammals because there is a large volume of respiring cells. Mammals must also maintain a high temperature and therefore have high metabolic and respiratory rates. Lungs provide efficient surface area for effective gas exchange. Mammalian Lungs • Lungs are kept inside the body because air is not dense enough to support and protect these delicate structures. In addition to this, keeping them inside the body prevents loss of water and so they will not dry out easily. The lungs are a pair of lobed structures made up of a series of bronchioles, which end in tiny sacs called alveoli. The trachea (windpipe) branches into two smaller airways: the left and right bronchi, which lead to the two lungs. The left lung is longer, narrower, and has a smaller volume than the right lung it shares space in the left side of the chest with the heart. The right lung is divided into three lobes and each lobe is supplied by one of the secondary bronchi. It has an indentation, called the cardiac notch, on its medial surface for the apex of the heart. The left lung has two lobes. The bronchi themselves divide many times before branching into smaller airways called bronchioles. These are the narrowest airways – as small as one half of a millimeter across. The larger airways resemble an upside-down tree, which is why this part of the respiratory system is often called the bronchial tree. The airways are held open by flexible, fibrous connective tissue called cartilage. Circular airway muscles can dilate or constrict the airways, thus changing the size of the airway. At the end of each bronchiole are thousands of small air sacs called alveoli. Together, the millions of alveoli of the lungs form a surface of more than 100 square meters. Within the alveolar walls is a dense network of tiny blood vessels called capillaries. The extremely thin barrier between air and capillaries allows

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oxygen to move from the alveoli into the blood and allows carbon dioxide to move from the blood in the capillaries into the alveoli. • Each lung is enclosed by a double-layered serous membrane, called the pleura. The visceral pleura is firmly attached to the surface of the lung. At the hilum, the visceral pleura is continuous with the parietal pleura that lines the wall of the thorax. The small space between the visceral and parietal pleurae is the pleural cavity. It contains a thin film of serous fluid that is produced by the pleura. The fluid acts as a lubricant to reduce friction as the two layers slide against each other, and it helps to hold the two layers together as the lungs inflate and deflate. The lungs are soft and spongy because they are mostly air spaces surrounded by the alveolar cells and elastic connective tissue. They are separated from each other by the mediastinum, which contains the heart. The only point of attachment for each lung is at the hilum, or root, on the medial side. This is where the bronchi, blood vessels, lymphatics, and nerves enter the lungs.

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Section 4.2 – The mechanism of breathing
To maintain a steep concentration gradient, air must be constantly moved into and out of the lungs. The process of breathing is called ventilation. Air pressure in the atmosphere is greater than the air pressure in the lungs, air is drawn in. This is known as inspiration. When air pressure in the lungs is greater than the air pressure of the outside atmosphere, air is forced out. This is called expiration. There are two types of intercostals muscles that lie between the ribs. There is internal muscles and external muscles. During inspiration, the external muscles contract. During expiration, the external muscles relax and the internal muscles contract.

Inspiration
Inspiration is an active process (requires energy) In order to respire, the internal muscles relax whilst the external muscles contract. The ribs, as a result move upwards and outwards, thus increasing the volume. The diaphragm muscle contracts, and flattens. This further increases the volume. Due to the increase in volume, the air pressure drops, and is then lower than the air pressure outside of the lungs. Due to this, air is drawn in.

Expiration
Normally, breathing out is a passive process (requires no energy) this is because the force of gravity and the recoil of elastic muscle fibres pull the rib cage downwards and inwards. The internal muscles contract while the external muscles relax, this decreases the volume. The diaphragm relaxes and moves back into its domed shape. This further decreases the volume. The decrease in volume causes an increase in pressure and so air is pushed out.

Pulmonary Ventilation Pulmonary ventilation = tidal volume x ventilation rate (dm^3min^-1) (dm^3) (min^-1) Page 36 of 114

Section 4.3 – Exchange of gas in the lungs
Gas exchange is the process by which 02 moves enters the blood and CO2 moves out. Cellular respiration creates a constant demands for oxygen. The movement of O2 is independent of the movement of CO2. Diffusion occurs when there is a difference in concentration. Particles move down a concentration gradient. Breathing in air when there is a high concentration of CO2 can be lethal even when there is a rich supply of oxygen. CO2 will not diffuse out if the concentration is higher outside the lungs. Gas exchange surface - where gas enters and leaves the lungs. Single cell organisms can use there cell membrane as a surface for gas exchange. Many organisms have developed specialised gas exchange structures called lungs. Alveoli Mammals exchange respiratory gases mainly through the alveoli. Each alveoli is approximately 75 – 300 micrometers across. The delicate surface area is protected from damage by being tucked away inside the chest. Ficks law Rate of diffusion = surface area of the membrane x difference in concentration length of diffusion path Having a vast number of capillaries is very important. Walls of the alveoli are very thin and close together. This allows for efficient gas exchange. Cells in the alveoli wall are flattened with only a thing layer of cytoplasm between the cell membranes. This reduces the distance for diffusion. The lumen of the capillary is so narrow that the red blood cells slow down as the pass through it. They are flattened against the alveoli. This brings haemoglobin very close to the alveoli air.

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The inner surface of the alveoli wall is covered in water, this is because the plasma membranes of its cells are permeable to water. The film of water slows down the rate of diffusion because it has increased the distance the gases need to travel. For a membrane to be permeable to oxygen it must also be permeable to water. Epithelium and endothelium Epithelial cells – cells from epithelium tissue that lines the internal and external cavity. Endothelium is a specialised type of epithelium that lines the inner surface of blood vessels. Alveoli structure The wall of the alveoli is made of epithelial cells. Surfactant Surfactant prevents the alveoli from collapsing or sticking together. Alveoli must be kept open to increase their surface area. Lung surfactant reduces the surface tension so that the alveoli remain open.

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Section 4.4 – Pulmonary tuberculosis
Tb is an infectious disease caused by an airborne, rod-shaped pathogen called mycobacterium tuberculosis. Most commonly affects the lungs, causing pulmonary TB. Almost any part of the body can be infected by the pathogen (extra pulmonary tb). TB is the leading cause of death from bacterial infection. The disease affects almost 1.7 billion people world wide. It kills approximately 2 million people each year. It is the biggest killer of women of reproductive age. It has an extremely slow growth rate. Divides once every 16-20 hours. Droplets of MTB can remain suspended in air for several hours. It is very resistant, can survive several weeks in dry state. Can survive week disinfectants. When a person coughs or sneezes, droplets of water are expelled and may contain the bacteria. The disease only develops if the bacterium reaches the alveoli. TB is referred to as invasive because it enters and spreads into tissue. Contracting TB Most people with tb only exhale a few bacteria in each breath. You can only contract the disease after prolonged exposure. People who are most at risk are: People who have HIV Those taking immune suppressant drugs Those under going cancer treatment The very young/old Those who live in LDCs Those who inject drugs or drink too much alcohol Skin test – the doctor would inject a very dilute extract of the bacterium into your skin. If the person has been exposed to the TB bacterium, the immune response will cause an area of inflammation.

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Treatment MTB is a bacterium that can be treated with antibiotics. Most TB is curable using a combination of 4 different types of antibiotics. The antibiotics are affective against most strains of the bacteria. The drug is taken for 6 – 9 months. Symptoms Persistent cough Chest pain Coughing up blood Chill + fever Night sweat Loss of appetite Unexplained weight loss Fatigue Death – occurs when the sufferer has lost too much weight. When you are most at risk When you are in regular contact with those who have the disease When your immune system is compromised, the bacteria could break out of the tubercles in the alveoli. They can then affect other regions of the lungs. If the bacterium enters the blood, other areas of the body can be infected. This is called active tuberculosis. Bacteria destroy the lung tissue, resulting in cavities and scar tissue where the lungs repair. The loss of S.A can reduce the efficiency of gas exchange. Fluid collects in the lungs and breathing becomes difficult. Disease progression Your immune system kills the bacteria and no further symptoms are experienced. Immune system responds, bacteria are then engulfed by a type of white blood cell called macrophages which do not actually destroy the bacteria. Tb bacteria have a cell wall made of a complex, waxy material that protects it from the macrophages. The infection can lead to inflammation and enlargement of the lymph nodes responsible for that area of the lung.

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After 3 – 6 weeks another white blood cell called T-lymphocytes arrive at the site and activate the macrophages so they can destroy the bacteria. Lysosomes in the macrophages contain enzymes that break down the waste materials. In a healthy person there are few, if any symptoms and the infection is controlled within a few weeks. Active TB The bacteria can multiply within the macrophages and eventually cause the cell to burst, releasing the bacteria. These bacteria are then engulfed by more macrophages and the cycle continues.

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Section 4.5 – Fibrosis, asthma and Emphysema
Infection Can be caused by environmental agents such as asbestos, silica and some gases Exposure to ionising radiation Autoimmune response to inhaling gas containing bacterial,, fungal or animal products. Often linked with occupation Most contaminants that reach the bronchi and brochioles are trapped in the mucus. Air laden with fine dust is drawn into the alveoli where there is no celia to sweep away the particles. White blood cells near the alveoli are called alveoli macrophages. They engulf bacteria and foreign particles. Pulmonary fibrosis Occurs when scars form on the epithelium causing them to become irreversibly thickened. Patients suffering from the disease cannot diffuse oxygen into their blood as efficiently. Diagnosed by a lung biopsy The fibrous tissue also reduces the elasticity of the lungs. This makes it harder to ventilate the lungs. Shortness of breath – occurs due to the lack of oxygen diffusing into the blood as a result of the lengthened pathway and shallower concentration gradient. Chronic dry cough – bodies reflex to try and remove fibrous tissue. However, the tissue is virtually irremovable. Pain and discomfort in the chest – caused by the pressure and damage caused by the tissue. Asthma Allergens cause a chemical called histamine to be produce, which causes the airways to become thickened. The lining of these airways become inflamed Goblet cells secrete more mucus. Fluid leaves capillaries and enters the lungs. The muscles surrounding the bronchi and bronchioles contract

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Difficulty breathing – due to constriction of airways A wheezing sound when breathing – caused by air passing through restricted airways A tight feeling in the chest – consequence of not being able to ventilate the lungs properly Emphysema In emphysematous tissue the elastin has become permanently stretched and the lungs are no longer able to force all the air out of the alveoli. Shortness of breath – air cannot be ventilated as effectively. This causes the concentration gradient to become shallower. As a result, the rate of diffusion is reduced and less gas exchange will take place. Chronic cough – bodies reflex to try and remove damaged tissue. Bluish skin colouration – due to the lower levels of oxygen within the blood as a result of poor gas exchange

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Section 5.1 – The heart and heart disease
• • • • Mammals are too large to rely on diffusion. They need a circulatory system to move substances around the body. Blood moves down pressure gradients, from high to low pressure. The heart produces the main pressure gradient, although contractions of skeletal muscles also push blood along veins.

The circulatory system • • • Mammals have a double circulatory system as blood passes through the twice on one complete circulation of the body. The pulmonary circulation pumps blood to the lungs to be oxygenated. The systemic circulation pumps oxygenated blood to every other part of the body that uses oxygen.

The human heart • • • Lies in the thoracic cavity Consists mainly of cardiac muscle Its pumping action ensures that fresh supplies of oxygen and nutrients are constantly being supplied to all living cells of the body. It is divided into a left and right side by a septum.

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Pericardium • • The heart is covered by a double layer of tough, inelastic membranes which form the pericardium. Pericardium fluid is secreted by the membranes and reduces friction, allowing them to move freely over each other.

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This sac, protects the heart, anchors its surrounding structures and prevents overfilling of the heart with blood.

Heart Chambers • • • • The right side pumps oxygenated blood; the left side pumps oxygenated blood. Each side has two chambers. The two upper chambers are called the atria and the two lower chambers are called the ventricles. The atria receive blood from veins. The ventricles pump blood into arteries.

The right side of the heart • • • • • The right atrium receives deoxygenated blood from the systemic circulation through the vena cava. Each atrium is elastic so it can stretch as it fills up with blood. Atria have only a thin muscular wall as they only need to pump blood a short distance to the ventricle. The right ventricle pumps deoxygenated blood through the pulmonary artery, to the pulmonary circulation. The pulmonary artery is the only artery to carry deoxygenated blood.

Left side of the heart • • • • The left atrium receives oxygenated blood from the pulmonary vein. The pulmonary vein is the only vein to carry oxygenated blood. The left ventricle pumps oxygenated blood through the aorta into the systemic circulation. Ventricle walls are thicker than that of the atria as they have to pump blood over a greater distance.

Ventricles • • The right ventricle pumps blood to the lungs where the left ventricle has to pump blood to the whole body. Although the volume of blood they hold is the same, the left ventricle has a thicker muscular wall. Page 45 of 114

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A thicker muscular wall will allow a stronger contraction to push blood further.

Valves • • • • • There are 4 valves in the mammalian heart; one between each atrium and ventricle, and one at the base of each artery leading from the ventricles. The tricuspid valve between the right atrium and the right ventricle has three flaps. The bicuspid valve between the left atrium and the left ventricle has two flaps. The pulmonary semi-lunar valve is between the right ventricle and the pulmonary artery. The aortic semi lunar valve is between the left ventricle and the aorta.

How valves work • • • • • They prevent the back flow of blood. Valves in the heart are designed to open when there is high pressure forcing the blood on the correct direction. If high pressure forces the blood in the wrong direction, the valves shut. Thin tendons join to the edges of the valve flaps to the wall of each ventricle. These tendons to not stretch, they stop the valves turning inside out.

Cardiac Muscle • • A special type of muscle, unlike other muscles it never fatigues. Does not tolerate a lack of oxygen or nutrients and soon dies if its supply of blood is cut off.

Coronary arteries • Some of the bloody leaving the left ventricle goes to the coronary arteries. These arteries branch out to supply the thick heart muscle with oxygen and nutrients. • The coronary arteries are much narrower than many other arteries and so can become blocked more easily.

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Section 5.2 – The cardiac Cycle
• • • • The 4 chambers in the heart are constantly contracting and relaxing in a definite sequence. The cardiac cycle is the sequence of stages that take place in one heart beat. When a chamber is contracting it is in systole. When it is relaxing it is in diastole.

The stages of the cardiac cycle • • • • • There are three stages of the cardiac cycle: atrial systole and ventricular systole and diastole. Atrial systole refers to the contracting of the atrial myocardium (heart muscle). Ventricle systole refers to the contraction of the ventricular myocardium. Between heart beats the myocardium of both atria and ventricles are relaxed. This is known as diastole. Both sides of the heart contract together. This means that the atria will contract and relax at the same time and so will the two ventricles.

Diastole • • • Ventricular and atrial myocardium relaxes at the same time. Blood returning to the heart fills the atria. The higher pressure in the atria than the ventricles, forces the atrioventricular valves to open. Even though the atria aren’t contracting, blood flows from the atria to the ventricles.

Atrial systole • • • • • The myocardium of both atria contract. This raises the pressure in the atria, pushing more blood into the ventricles. The atrioventricular valves open. More blood passes through these valves into the ventricles. Both semi-lunar valves are closed. Page 47 of 114

Ventricular Systole • • • • • • • • The myocardium of both ventricles contract The atria are relaxed The ventricles continue to fill with blood This quickly raises the pressure of the ventricles higher than that of the atria. Both atrioventricular valves are forced closed When the pressure of the ventricles exceeds that of the arteries, the pulmonary and aortic valves are forced open. Blood is pushed out of the heart into the pulmonary artery and aorta. The semi-lunar valves close, stopping blood moving back into the heart.

Pressure changes • • • The events of the cardiac cycle create pressure changes. Pressure changes are responsible for moving blood through the heart and into the systemic and pulmonary circulations. Valves open or close when the balance of pressure on opposite sides of the valves changes.

Controlling the cardiac cycle • Myogenic contractions are contractions originating from within the muscle, rather than by the nervous system. Myogenic contractions of the myocardium are largely responsible for the cardiac cycle. The cardiac cycle starts at the sinoatrial node (SA node). The SA node is a group of cells found out the top of the right atrium which acts as a natural pacemaker and initiates the heart beat.

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The rate at which the SA node produces the waves determines the heart rate. The heart rate can also be controlled by nervous impulses and hormones such as during exercise and adrenalin.

Starting the Cardiac cycle • • • • The SA node produces waves of electrical impulses called cardiac impulses. The impulses are not carried by nervous tissue but by specialised muscle fibres called purkinje fibres. This tissue conducts the impulses throughout the atria, stimulating the myocardium of the atria to contract. The contraction spreads outwards and downwards, from the top of the atria, squeezing blood towards the ventricles.

Continuing the cardiac cycle • The electrical activity cannot pass from the walls of the atria to the walls of the ventricles, because it is stopped by a wall of fibrous tissue called the atrioventricular system. This stops the waves of the atrial muscle contraction continuing through the ventricle muscles as the blood would be forced to the bottom of the heart. There is only one location where the impulse can travel from atrium to ventricle – through the atrioventricular node. (av node) The AV node is another specialised group of cells. The cells in the AVN can conduct electricity but only shortly after a slight delay. The delay allows time for the atria to complete their cycle.

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Contraction of the ventricles • • • From the AVN two specialised bundles of purkinje tissue run down the atrioventricular septum and up the ventricular wall. Bundles of his conduct electrical impulses rapidly down the atrioventricular septum, to the bottom of the heart. These fibres stimulate the muscles of the ventricles to contract rapidly, from the base of the heart upwards.

The heart beat Page 49 of 114

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First heart beat sound “lub” occurs when the atrioventricular valves close. Second heart sound “dub” occurs when the semi lunar valves close.

Cardiac output • • • • • The volume of blood from ventricles in one minute. Measured in DM^3min^-1 The volume pumped by both ventricles pumped is the same. The cardiac output depends on two features: how quickly the heart is beating, and the stroke volume (amount of blood in one beat). Cardiac output =heart rate (min^-1) X stroke volume (dm^3)

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Section 5.3 – Heart Disease
Atheroma is the build up of fatty deposits that can impair blood flow. If blood flow to the heart muscle is interrupted it can cause a myocardial infarction. Atheroma Begins as fatty streaks which are deposits of white blood cells that have taken up low density lipoproteins These streaks enlarge to form an irregular patch, or athermanous plaque. Athermanous plaques are made up of cholesterol, fibres and dead muscle cells. Thrombosis If an Atheroma breaks through the endothelium of the blood vessel, it forms a rough surface that interrupts the otherwise smooth flow of blood. This may cause a thrombus (blood clot), that will stop the flow of blood. The region of tissue deprived of blood due to the thrombus will not be able to respire as a result of no oxygen, glucose and other nutrients being transported to the tissue. Aneurysm Atheromas that form thrombosis can weaken artery wall, causing them to swell to form a balloon like, blood filled structure called an aneurysm. Myocardial infarction Occurs when the hear stops beating, otherwise known as a heart attack. Smoking Carbon monoxide combines easily, but irreversibly with haemoglobin, thus reducing the oxygen carry capability of the blood. In order to supply tissue with the same amount of oxygen the heart must work harder, thereby increasing blood pressure. Nicotine stimulates the production of adrenalin which will increase heart rate and blood pressure. Blood pressure If the blood pressure in the arteries is high, the heart must work harder to pump blood into them.

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High blood pressure in the arteries means there is more chance of an aneurysm forming and bursting causing a haemorrhage. To resist the high pressure the walls of the arteries tend to become thickened and may harden, restricting blood flow. Blood Cholesterol High density lipoproteins remove cholesterol from tissue and transport it to the liver for excretion. They help protect arteries against heart disease. Low density lipoproteins which transport cholesterol from the liver to the tissue, including the artery walls, which they infiltrate, leading to the development of Atheroma and hence a heart attack. Diet High levels of salt raise blood pressure. High levels of saturated fat increase low density lipoprotein levels and hence blood cholesterol concentration. Foods that act as antioxidants, e.g. vitamin c, reduce the risk of heart disease, and so does non-starch polysaccharide (dietary fibre).

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Section 6.1 – Defence mechanisms
Defence mechanisms Non-specific – mechanisms that do not distinguish between one type of pathogen and another, but respond to all of them in the same way. These mechanisms act immediately and take two forms: A) barrier of entry B) phagocytosis Specific – Mechanisms that do distinguish between different pathogens. The response is less rapid but provides long lasting immunity. The response involves a type of white blood cell called a lymphocyte and can take two forms: A) cell mediated response (T-lymphocytes) B) Humoral responses (B-Lymphocytes) Recognising your own cells Lymphocytes must be able to distinguish between pathogens and the bodies own cells. If they did not, they would destroy the body’s tissue. Defence Mechanisms

Non specific
Response is immediate and the same for all

Specific
Response is slower and is specific to each pathogen

pathogens

Physical barrier

Phagocytosis

Cell mediated response. Tlymphocytes

Humoral response Blymphocyte s

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T-lymphocytes already exist within the body. There is over 10 million different types of T-lymphocytes. Given that there are so many different types of lymphocyte in the body. There is a high probability that when a pathogen enters the body the antigen on its surface will be complementary to a specific lymphocyte. There are very few of each lymphocyte so response to an infection is slow.

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Section 6.2 – Phagocytosis
There are two different types of white blood cells. There are phagocytes and lymphocytes. Phagocytes ingest and destroy pathogens by a process called phagocytosis. Barriers of entry • • • A protective covering – The skin covers the body’s surface, creating a barrier that is hard for pathogens to penetrate. Epithelia covered in the mucus – Many epithelia produce mucus. In the lungs pathogens are often caught in the mucus and moved by the cilia. Hydrochloric acid in the stomach – Provides a low pH that denatures the pathogens enzymes.

Phagocytosis • • • • • • Pathogens are engulfed by phagocytes in the form of vesicles which are formed on the cell-surface membrane. Chemical products of the pathogen act as attractants which draw the phagocyte towards it. Phagocytes attach themselves to the surface of the pathogen. They engulf the pathogen to form a vesicle known as a “phagosome”. Enzymes within the Lysosomes join with the phagosome and release their contents. The enzymes within the Lysosomes digest the pathogen. The soluble products of the pathogen are absorbed into the cytoplasm of the phagocyte

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Section 6.3 – T cells and cell-mediated immunity
Antigens An antigen is any part of an organism or substance that is recognised as foreign and stimulates a response from the immune system. Antigens are normally proteins that are part of the organism’s cell-surface membrane. Lymphocytes B –Lymphocytes are associated with humoral immunity i.e. immunity involving antibodies that are present in the body’s fluids, or “humour”. T – Lymphocytes are associated with cell-mediated immunity i.e. immunity involving body cells. Both types of lymphocytes are formed from stem cells in the bone marrow. Cell-mediated immunity T – Lymphocytes can distinguish foreign material from the bodies own tissue because: Phagocytes have engulfed and broken down a pathogen and have presented some of its antigens on its own cell-surface membrane. Body cells that have been invaded by a virus also manage to present some of the virus’ antigens on its surface as a sign of distress. Cancer cells also present antigens on its cell-surface membrane. T-Lymphocytes only respond to antigens that are attached to a body cell. This type of response is called “cell-mediated immunity”. A) Pathogens invade body cells or are taken in by phagocytes. B) The phagocyte places the antigen on its own cell-surface membrane. C) Receptors on certain T helper cells fit exactly onto these antigens. D) This stimulates other T cells to divide rapidly by osmosis to form a clone. E) The cones T cells: a) Develop into memory cells that provided rapid response in the future. b) Stimulate phagocytes to engulf the bacteria by phagocytosis. c) Stimulate b cells to divide d) Kill infected cells T cells do not kill cells by phagocytosis. Instead, they produce a protein that makes a hole in the pathogen or infected cells. The hole then makes the cell freely permeable to all substances and quickly dies as a result.

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Section 6.4 – B cells and humoral immunity
Humoral immunity is so called because it involves antibodies which are soluble in the blood and tissue fluid, also called “humour”. A typical pathogen may have more than one type of antigen on its surface. Toxin molecules will also act as an antigen. Each B cell develops into two different types of cell: Plasma cells secrete antibodies directly. They only live for a few days but produce more than 2000 antibodies every second. This is known as the primary immune response Memory cells live for decades in some cases. When they encounter the same antigen they divide rapidly into plasma cells and more memory cells. The memory cells provide long term immunity. This is known as the secondary immune response. 1. The surface antigens of the invading pathogen are taken up by the B cells. 2. The B cells process the antigens and present them on their surface. 3. T helper cells attach to the processed antigens and B cells thereby activating them. 4. The B cells are now activated to divide by mitosis to give a clone of the plasma cells. 5. The cloned plasma cells produce antibodies that exactly fit the antigens on the pathogens surface. 6. The antibodies attach to antigens on the pathogens and destroy them. This is the primary immune response. 7. Some B cells develop into memory cells. These can respond to future infections by the same pathogen by dividing rapidly and developing into plasma cells that produce antibodies. This is the secondary immune response. Antigenic Variability The antigens that pathogens are made of, and the ones they produce are constantly changing, this is known as antigenic variability. This explains why it is possible to get the same diseases more than once. Influenza for example has many different strains and so when a new strain enters the body, its antigens are not complimentary to the antigens or the memory cells produced from the last infection. Due to this the most use its primary immune response.

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Section 6.5 – Antibodies
Antibodies are proteins synthesised by B cells. Antibodies react with antigens by binding with them. Structure Antibodies are made up of four different polypeptide chains.

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The chains of one pair are long and are called heavy chains, while the other pair have shorter chains and are called light chains. Antibodies have a binding site that is very specific to the antigen once together they form and antigen-antibody complex The binding site is different for all antibodies and is known as the variable region. The rest of the antibody is the same and is called the constant region. Monoclonal antibodies A pathogen entering the body is likely to have hundreds of different antigens on its surface. Each antigen will induce a different B cells to divide and clone its self. Each clone will produce a different antibody known as a polyclonal antibody. Antibodies that can be isolated and cloned are called monoclonal antibodies. Monoclonal antibodies have a number of uses such as: The separation of a chemical from a mixture Immunoassay- this is the method of calculating the amount of substance in a mixture. It is used in pregnancy testing kits, testing for drugs in the urine, and detecting the immunodeficiency virus (aids test) Cancer treatment – it is possible to manufacture monoclonal antibodies that will attach themselves to cancer cells. They will then activate a cytotoxic drug that will kill cells. This drug will only be activated by cells to which the antibody is attached. Transplant surgery – Even with close matching the transplanted tissue will experience some rejection from the T – cells. Monoclonal antibodies can be used to knock out these T – Cells.

Section 6.6 – Vaccination
Passive immunity is produced by the introduction of antibodies into individuals from an outside source. As the antibodies are not being produced by the individuals themselves, they are not being replaced when they are broken down in the body and so the immunity is generally short-lived. Active immunity is produced by stimulating the production of antibodies by the individuals own immune system. In is generally long-lasting.

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Vaccination is the injection of a substance into the body with the intention of stimulating active immunity. Features of a successful vaccination program • • • • • • The success of a vaccination program depends on a number of factors: A suitable vaccine must be economically available in sufficient quantities There must be very few if any unpleasant side effects from the vaccine. Means of producing, storing and transporting the vaccine must be available. There must be the means of administrating the vaccine at the right time. It must be possible to vaccinate the vast majority of the vulnerable population.

Why vaccination does not eliminate a disease • • • • • Vaccination fails induce immunity amongst some individuals. Individuals may develop the disease immediately after vaccination but before their immunity levels are high enough to prevent it. Pathogens may mature rapidly so that their antigens change suddenly rather than gradually. This is due to the antigenic variability. There may be many varieties of a particular pathogen. Certain pathogens can hide from the body’s immune system by hiding themselves with cells or by living in places that are out of reach.

The problems of controlling cholera and tuberculosis by vaccination • • • • Cholera is an intestinal disease and is not easily reached by the immune system. The antigens on the cholera surface change rapidly. The increasing amounts of people with HIV has led to more people having impaired immune systems and so are more likely to contract TB. The proportion of elderly people in the population is increasing. These people have less effective immune systems and so vaccination is less effective at stimulating immunity.

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Section 7.1 – Investigating Variation
If one species differs from another it is called interspecific variation. If each member of a species differs from one another it is called intraspecific variation. Making measurements

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Biologists often take measurements of some aspect of a living thing. However, all living organisms differ in some way. Sampling – involves taking measurements of individuals, selected from the population of organisms which is being investigated. • • Sampling bias – The selection process may be biased, possibly due to the investigator making unrepresentative choices, either deliberately or unwittingly. Chance – Even if sampling bias is avoided, the individuals chosen may, by pure chance be unrepresentative.

To prevent sampling being biased, random sampling should be carried out instead. One method is to: 1. Divide the study area into a grid of numbered lines. 2. Using numbers generated by a computer to obtain a series of coordinates 3. Take sample at the intersection of each set of coordinates. The affect of chance cannot be removed however it can be minimised by using large sample sizes and analysing the data collected at the end to determine the affect chance had and to what degree it influenced the data. Causes of variation Genetic differences – due to differences in the genes of each individual organism Genetic differences occur due to: Mutations – sudden changes to genes and chromosomes may, or may not, be passed on to the next generation. Meiosis – Special form of nuclear division, forms gametes. This mixes up all the genetic material before it is passed into the gametes, all of which are different. Fusion of gametes – In sexual reproduction the offspring inherit some characteristics of each parent and are therefore different from both of them. Which gamete fuses with which at fertilisation are a random process which further adds variety to the offspring. Environmental differences In most cases variation is due to the combined effects of both genetic differences and environmental influences. As a result it is very difficult to draw conclusions about the causes of variation in any particular case.

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Section 7.2 – Types of variation
Variation due to genetic factors Where variation is the result of genetic factors organisms fit into a few distinct forms and there are no intermediate types. Variation can be represented on a bar chart of pie graph. Variation due to environmental influences

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Some characteristics of organisms grade into one another, forming a continuum. Environmental factors play a major role in determining where on the continuum an organism actually lies. If we take these data and plot them on a graph we obtain a bell-shaped curve known as a normal distribution curve. Mean and standard deviation Mean – measurement of the maximum height of the curve. The mean provides an average value that can be used when comparing one sample with another. It does not however, provide any information about the range of values within the sample. Standard deviation – Is a measurement of the width of the curve. It gives an indication of the range of values either side of the mean. A standard deviation is the distance from the mean to the point where the curve changes from being convex to concave. Calculating standard deviation 1. Calculate the mean value (x bar). 2. Subtract the mean value from the measurement values. For example if the mean is 9 and one of the measurement values is 6, do 6-9. 3. Square all the numbers obtained in step 2 to make them positive. 4. Add all the square numbers together and divide by the number of measurements. 5. Square root the number obtained in step 4, to get the standard deviation.

Section 8.1 – Structure of DNA
DNA – deoxyribonucleic acid It is a type of nucleic acid; it is the molecule of which our genes are made of. Why is DNA important? Its structure enables it to play a key role in two essential features of all living organisms.

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Inheritance – ensuring that DNA is passed on, unaltered, onto the next generation and protein synthesis. DNA structure DNA molecules are huge: each molecule consists of two interconnected chains or stands. Each chain is sing and unbranched These polynucleotide strands are twisted to for a double helix. What is DNA made of? Each strand of DNA is made of repeated subunits called nucleotides. The phosphate and sugar molecule make the backbone of the DNA molecule. What are nucleotides? DNA is called a polynucleotide. Nucleotides are nitrogen containing, organic molecules that play a vital role in every organisms life. They occur singly (mononucleotides), in twos (dinucleotides), or in thousands (polynucleotides). The nucleotides of DNA Each nucleotide has three components: 1. An organic nitrogenous base: adenine, thymine, cytosine, or guanine. 2. The pentose (5 carbon) sugar deoxyribose 3. A phosphate group The structure of the nucleotides The nucleotides in each strand of DNA are held together by the bonds between deoxyribose of one nucleotide, and the phosphate group of the next. This forms a “sugar-phosphate backbone” with the base petruding outwards. The bases are attached to the backbone. Nucleotides are joined together by a condensation reaction. The reaction occurs between the deoxyribose sugar and the phosphate group.

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The bonds linking the two nucleotides are called covalent phosphodiester bonds. The bond can be broken down by hydrolysis. DNA bases Adenine = A Thymine = B Cytosine = C Guanine = G As there are four different bases, there four different types of nucleotides in a DNA molecule. Bonding between DNA strands All the atoms in the nucleotides that make up each chain have no free covalent bond site. Hydrogen bonds are formed between the organic bases of each polynucleotide strand. The hydrogen bonds are between the hydrogen atoms of a base in one chain and the nitrogen and oxygen atoms in another chain. Hydrogen Bonds Hydrogen bonds are weaker that phosphate covalent bonds. Individually, hydrogen bonds are weak, but in a combination they can be strong. Hydrogen bonds break and reform, allowing strands to separate during replication and protein synthesis. Base pairing rule If the nucleotide contains adenine it bonds with thymine. Nucleotides containing cystine, bond with guanine. Three hydrogen bonds are formed between G and C Two hydrogen bonds are formed between A and T Reason for pairing Hydrogen bonding only occurs between certain bases. G and A have a double ring structure and are longer molecules. C and T have a sing ring structure and are shorter. Each run on the ladder must be the same length so long molecules bond with short molecules. Complementary bases

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A and T are complementary bases. There are equal amounts of A and T and C and G DNA and variety What differs between DNA is the proportion and sequence of bases. The four different types of nucleotides can join in an infinite number of ways. The Double helix DNA is similar to twisted ladder Each complete turn has ten base pairs Because of the complementary pairing, the sequence of bases along a polynucleotide chain determines he sequence along another. DNA strands A polynucleotide has two distinct ends: a 3 prime end and a 5 prime end. At the 3’ end, carbon 3 of the deoxyribose is closest to the end. Each of the two polynucleotide chains is anti-parallel, that is, they run in opposite directions.

Section 8.2 – The triplet code
Genes are sequences of nucleotides at a fixed position on a strand of DNA that specify a sequence of amino acids that form the primary structure of a protein. Genetic code The order of bases in an organisms DNA The order of bases determines what amino acid is produced.

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Each gene carries the code for a specific polypeptide. Making proteins DNA codes for amino acids that form the primary structure of a protein. Each protein has a unique tertiary structure due to its sequence of amino acids. All proteins are made from the 20 amino acids. Different numbers and sequences of these amino acids produce an almost limitless range of proteins. Determining amino acid sequences Each is amino acid is determined by the sequence of bases in the gene. Each code has three bases – triplet code. Amino acids Three bases can code for 64 different amino acids. As there are only 20 amino acids, most amino acids have more than one code. We say the degenerate code. Coding – non coding Much of the DNA is Eukaryotic cells does not code for polypeptides. Some non – coding DNA is found within a gene, some found between genes. Non coding regions – introns Coding regions – exons Splicing The introns are spliced out by enzymes. The remaining exons code for amino acids. Joining amino acids Peptide bonds between amino acids, forming polypeptides Genetic code summary Triplet – each of the 20 amino acids used to make proteins is represented by a base triplet in DNA. Non – overlapping: each base is part of only one triplet and is therefore involved in specifying only one amino acid.

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Linear DNA – is always read from 5’ to 3’ Degenerate There are more base triplets than amino acids. Some amino acids have more than one code. Almost universal: the base triplet that codes for a particular amino acid in humans also codes for the same amino acid in most other living organisms.

Section 8.3 – DNA and Chromosomes
Eukaryotic DNA • • • Is linear and forms chromosomes Found in the nucleus of cells. Is larger than prokaryotic DNA

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• •

A single eukaryotic cell has many different molecules of DNA called chromosomes. Mitochondria + Chloroplasts DNA does not have histones.

Prokaryotic DNA • • • • Forms a closed loop and is circular. Found in the cytoplasm Found in a region of the cell called a nucleoid The DNA of prokaryotic cells is smaller than the DNA in eukaryotic cells. This is because the cell is smaller and so is less complex; ergo it does not need as many genes. It is not organised into chromosomes. Does not contain non-coding DNA Many cells contain smaller circular pieces of DNA called plasmids.

• • •

Chromosomes • • • • • Human cells has 46 chromosomes (23 pairs) The chromosomes are only visible when the nucleus divides. Each chromosome is made of one DNA molecule Chromosomes are thicker and shorter than individual DNA molecules; therefore it is possible to see them under electron microscopes. Each chromosome carries the DNA for a large number of polypeptides.

The structure of polypeptides • • • • Composed of DNA and histones DNA and histones forms chromatin Nucleosomes are the basic structural unit of chromatin. Nucleosomes consist of a DNA molecules wrapped around a ball of 8 histone molecules. Page 69 of 114

• Alleles • • • •

Chromatin takes up special stains and is visible in a non-dividing nucleus.

Genes come in more than one form. Alleles are different version of the same gene. Chromosomes come in pairs and so there are two copies of the same gene. As we have two of each gene we have two alleles for each gene.

Homologous Chromosomes • • • • • • The members of each pair of chromosomes have the same shape, size and code for the same genes. One chromosomes comes from the mother (maternal), the other from the father (paternal). We call the members of each pair, homologous chromosomes. Cells with pairs of homologous chromosomes – are called diploid cells. Cells with one chromosome from a homologous pair are called haploid cells. Gametes are haploid cells.

Chromosomes and genes • • • • The largest chromosome can contain approximately 8000 genes, whereas the smallest contains approximately 300. Each gene has a specific position on a chromosome called its locus. Different genes are active in different cells. Changes in the genetic code can mean that a particular protein is not produce, is not produced properly or is produced in the wrong amounts.

Karyotyping • A karyotype is a photograph of a person’s chromosomes arranged in order of size.

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• • •

Sex chromosomes are the 23rd pair. The other 22 chromosomes are called autosomes Karyotyping is used to spot chromosomal disorders

Section 8.4 – Meiosis and Genetic Variation
The division of the nucleus occurs in two ways: Mitosis – produces two daughter nuclei with the same number of chromosomes as the parent cell and as each other. Meiosis – produces four daughter nuclei, each with half the number of chromosomes as the parent cell. Why is meiosis necessary?

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When two gametes fuse to give rise to new offspring there chromosomes pair with each other. The number of chromosomes in a gamete is a haploid number; therefore when they fuse the diploid number of the cell is restored. Meiosis allows for genetic material from both the mother and the father to be passed on. The process of meiosis First Division – Homologous chromosomes pair up and their chromatids wrap around each other. Crossing over occurs, where equal proportions of each chromatid are exchanged. At the end of this first stage, the homologous pair would have separated, leaving just one chromosomes in the daughter cell. Second division – During the second division, each chromosome separates into two chromatids. Each of which will enter the daughter cells. At the end of meiosis two there will be 4 new cells. In humans each cell will have 23 chromatids. Meiosis brings about genetic variation by independent segregation of homologous chromosomes and recombination of homologous chromosomes by crossing over. Gene – section of DNA that codes for a polypeptide Locus – Position of a gene of a chromosome Allele – One of the different forms of a gene Independent Segregation of Homologous Chromosomes When homologous chromosomes line up, they do so randomly. One of each pair will go into the daughter cell. Because the chromosomes line up randomly, the combination of chromosomes that go into the daughter cell is also random. Variety from new genetic combinations Independent segregation brings about genetic variation because although the homologous chromosomes have the same genes, the alleles differ. The random distribution, and consequent independent assortment, of these chromosomes produces different genetic combinations. Genetic recombination by crossing over 1. The chromatids of each pair twist around one another 2. During the twisting process, tensions are created causing portions of the chromatids to break off.

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3. These portions of chromatids then join on to the homologous partner. 4. Usually equivalent portions of chromosomes are exchanged. 5. In this way new genetic combinations are achieved.

Section 9.1 – Genetic Diversity
Genetic Diversity • • • • Similarities and differences amongst organisms may be defined in terms of the variation in DNA. Hence it is the differences in DNA that lead to the vast differences in genetic diversity on earth All members of the same species have the same genes, yet differ in terms of the two alleles they will posses for each gene. The greater the number of alleles for genes, the greater the genetic diversity within a species If there is a lot of genetic diversity within a species there is more chance that the species will be able to cope with changes to the environment. This is due to the

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fact that because there are more alleles, there is therefore a greater probability that there are members within the species that have the characteristics required to adapt to a certain change in the environment. Selective Breeding • • • • Selective breeding, or artificial selection, involves selecting individuals with desired characteristics and using them to parent the next generation. Offspring without desired characteristics may be killed or prevented from breeding Due to this, alleles with unwanted characteristics are bread out of the population. Selective breeding is used to produce high yielding breeds of domestic animals and strains of plants.

The founder affect • • • • Occurs when a few individuals colonise a region The few individuals will possess fewer alleles and may not be representative of the whole population. The new group will show less variation, yet may be genetically distinct from the original population. In time this new population may become a separate species.

Genetic Bottlenecks • • • Occurs when a species suffers a dramatic drop in numbers The few survivors will possess few alleles than the original population therefore there is less genetic diversity. As these individuals become re-established, the genetic diversity of the population will be restricted.

Section 10.1 – Haemoglobin
Haemoglobin molecules Primary Structure – Consists of four polypeptide chains Secondary Structure – Chains are coiled into a helix Tertiary Structure – Polypeptide chain is folded into a precise shape, important for its ability to hold oxygen Quaternary Structure – All four polypeptides are chained to form an almost spherical model. Each polypeptide is associated with a “haem” group (Fe2+) Page 74 of 114

Each Fe ion can combine with a single oxygen molecule, therefore allowing a total of four O2 molecules to be carried. The role of Haemoglobin • • • • • • Transportation of oxygen Haemoglobin must be able to: Readily associate with oxygen at the surface where gas exchange takes place Readily dissociate from oxygen at respiring tissues Haemoglobin can change its affinity for oxygen under certain condition Its shape changes in the presence of certain substances such as carbon dioxide. When carbon dioxide is present, its shape changes so that its affinity for oxygen decreases and so can dissociate from the oxygen molecule more readily.

Why have different haemoglobins? Haemoglobin with a high affinity for oxygen – takes up oxygen more readily but releases it less easily. Haemoglobin with a low affinity for oxygen – takes up oxygen less easily but releases it more readily. An organism living in an environment where there is little oxygen, should have haemoglobin with a high affinity for oxygen, thus making it easy to take up oxygen. This is provided that it has a low metabolic rate and therefore does not need to give up its oxygen as easily to respiring tissues. An organism with a high metabolic rate needs to give up its oxygen more readily to tissues, and so haemoglobin with a low affinity for oxygen is necessary. This is provided that the organism lives in an oxygen rich environment. Why do organisms have haemoglobin with different affinities for oxygen? Different sequence of amino acid changes the shape of the molecules and there for its ability to hold oxygen.

Section 10.2 – Oxygen dissociation curves
At different partial pressures, haemoglobin may not absorb oxygen evenly. At low concentrations of oxygen, the Fe groups are close together, thus making it difficult to absorb oxygen. Once one oxygen molecule is absorbed, the polypeptide chains move away making it easier for more oxygen molecules to be absorbed The graph shows that a small decrease impartial pressure can lead to a lot of oxygen being dissociated. • The further to the left the curve is, the greater its affinity for oxygen Page 75 of 114

•

The further to the right, the lower its affinity for oxygen

The affects of Carbon dioxide concentration In the presence of CO2, haemoglobins affinity for oxygen is reduced. At the gas exchange surface, there is a low concentration of CO2 because it is diffusing out of the blood. This causes haemoglobins affinity for oxygen to increase, thus allowing for O2 to be absorbed more easily. The curve therefore shifts to the right. At respiring tissue the level of CO2 is greater, the haemoglobin therefore has a lower affinity for oxygen, it releases its O2 more readily to respiring cells, and the curve shifts to the right. When CO2 dissolves, it lowers the pH of the blood. A low pH can reduce haemoglobins affinity for oxygen. Loading, transporting and unloading oxygen • • • • • At the gas exchange surface, CO2 is constantly being removed. The pH is higher due to low CO2 concentrations. High pH changes the shape so that oxygen can be easily absorbed. In tissues, CO2 is produced by respiring cells, thus lowering pH. The haemoglobin molecule changes shape in such away that its affinity for oxygen is reduced. Haemoglobin then releases its O2 into respiring cells.

High rate of respiration  more CO2 produced  lower pH  greater haemoglobin changes shape  oxygen unloaded more readily  more oxygen available for respiration.

Section 10.3 – Starch, glycogen and cellulose
Starch • • • Starch is polysaccharide that is found in many parts of plants in the form of grains. Large amounts are found in seeds as an energy store. It is an important component of food and is the major energy source of most diets. Starch is made up of long chains of alpha glucose molecules. The chain is unbranched and winds into a coil making the molecule very compact. The main role of starch is energy storage.

•

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• • •

It is insoluble and therefore does not cause osmosis to occur. It is compact, allowing more to be stored in a small space. When hydrolysed, alpha glucose can easily be used in respiration.

Glycogen • • • • Glycogen is similar to starch however it is highly branched and made up of shorter chains. In animals it is stored as grains in the muscles and the liver. Because it is made up of shorter chains, it is more readily hydrolysed. Glycogen is found in animal cells, but never in plant cells.

Cellulose • • • Cellulose differs from starch and glycogen in that it is made up of beta glucose rather than alpha glucose. This produces fundamental differences in its structure. The reason for this is that in beta glucose the position of the –H and the –OH group is reverse. When glycosidic bonds form between these molecules the result is that the – CH2OH group on each beta glucose molecule alternates from being above and below the chain Rather than forming a coiled chain like starch, cellulose forms straight chains that run parallel to one another, allowing for hydrogen bonding to occur. Although each hydrogen bond is on its own weak, because there are many hydrogen bonds, the chains are held tightly together. Cellulose molecules are grouped together to form microfibrils which in turn make parallel groups called fibres. Cellulose is major component in plant cell walls. It is strong and prevents the cell from bursting due to osmosis. It achieves this by exerting and inwards pressure that stops the influx of water.

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Section 10.4 - Plant cell structure
Leaf palisade cells Function – Photosynthesis Main features of its function include: • Long, thin cells that form a continuous layer for photosynthesis • Numerous chloroplasts that are arranged in the most effective way for absorbing the maximum amount of light • A large vacuole that ensures that the cytoplasm and chloroplasts are at the edge of the cell Chloroplasts The main features of chloroplasts are:

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• •

•

The chloroplast envelope is a double plasma membrane that surrounds the organelle. It is highly selective in what it allows to enter and exit. The grana are stacks of 100 disc – like structures called thylakoids. Within the thylakoids is the photosynthetic pigment called chlorophyll. Some thylakoids have tubular like extensions that join up with thylakoids of adjacent grana. The grana are where the first stage of photosynthesis takes place. The stroma is a fluid –filled matrix where the second stage of photosynthesis takes place. Within the stroma are a number of other structures such as starch grains.

Chloroplasts are adapted to their function in the following ways The granal membrane allows a large surface area for the attachment of chlorophyll, electron carriers and enzymes that carry out the first stage of photosynthesis. These chemicals are attached the membrane in ordered fashion. The fluid of the stroma possesses all the enzymes required for the second stage of photosynthesis. Chloroplasts contain both DNA and ribosomes so they can quickly manufacture some of the proteins needed for photosynthesis. Cell wall • • • Contains microfibrils of cellulose Consist of a number of polysaccharides such as cellulose There is a thin layer called the middle lamella, which marks the boundary between adjacent cell walls and cements cells together.

Functions of cellulose cell wall are: • Provides strength and prevents cell from bursting due to osmotic gain. • Mechanical strength to plant as a whole • Allows water to pass along it and so contributes to the movement of water through a plant.

Section 11.1 – Replication of DNA
Why is DNA replication needed? • • • • • Multi-cellular organisms are constantly loosing cells which need to be replaced. More cells are also needed when the organism grows. Extra cells are only produced when the parent cell divides. New cells must contain the same genetic information as the parent cell. To achieve this, DNA must be able to replicate its self exactly.

Replicated chromosomes

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Following the replication of DNA, a chromosome appears to double its structure composed of two chromatids. The chromatids are identical as the DNA in the original chromosomes has replicated exactly. The two chromatids are temporarily held together by a centromere. The replicated chromosomes has twice the DNA as the regular chromosomes, but still only counts as being one chromosome. The chromatids become separated when the cell divides. Stages of DNA replication Stage 1 Strands of DNA separate The double helix structure of the DNA molecule partially unwinds An enzyme called Helicase breaks hydrogen bonds between complementary basis. The two strands are now separate Stage 2 Free nucleotides bond with the complementary basis exposed on each poly nucleotide. Large numbers of nucleotides are made in the nucleus and are attracted to the exposed basis. Hydrogen bonds form between complementary basis and as a result the strand builds up into a sequence of nucleotides. Stage 3 Nucleotides bond together Bonds have already formed between bases. Through condensation reactions, an enzyme called DNA polymerase forms covalent phosphodiester bonds between the deoxyribose of on nucleotide and the phosphate group of the next. The DNA molecule rewinds into a double helix and the process is complete. Leading and lagging strands Nucleotides can only be joined together in the 5’ to the 3’ On the leading strand, nucleotides can be added continuously in the same direction as the movement of the replication fork. On the lagging strand, continual synthesis is not possible, so small fragments of DNA are constructed. These fragments are linked together by DNA ligase. Origins of replication – replication forks

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The origins of replication are the points where replication begins DNA molecules are very long and so it would take too long if it started at one end and moved along the molecule. Instead, the double helix opens up and is replicated at a number of different sites. Replication forks resemble branching prongs where DNA Helicase is separating DNA into single strands. Semi conservative replication Each DNA molecules is formed from an intact strand from the original DNA and are newly synthesised. Both new DNA molecules are identical to one another and to the original molecule. Evidence for DNA replication Intact DNA acts as a template Mixture of nucleotides DNA polymerase ATP for energy New DNA molecules were formed that contained the same proportions of bases. Strong indication that DNA can copy its self by base pairing Alternative to semi-conservative The conservative model: parental DNA remains intact and the new molecule is built from completely new material. The dispersive model: proposes the new DNA molecules consist of sections of both old and new DNA, interspersed along each strand.

Section 11.2 – Mitosis
When a cell divides to make new cells, the DNA must be copied exactly into each cell. To do this, the parent cell divides by mitosis Why are new cells needed? For growth of a zygote into a multicellular organism

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Differentiation and repair: worn out or damaged cell tissues must be replaced by cells that do the same job. Therefore the new cells must have the same structure, function and genetic information as the original cell they are replacing. Asexual reproduction: offspring are genetically identical to the parent, such as in bacteria amoeba and non flowering plants. Daughter cells Mitosis results in each daughter nucleus having the same number and same type of chromosomes as the parent nucleus. Each chromosome contains one molecules of DNA, therefore each daughter nucleus contains exactly the same amount and the same type of DNA as the other daughter cell and parent nucleus. DNA replication is needed Daughter nuclei are identical because the DNA replicates. The chromosomes that were single stranded become a double structure. Each structure is chromatid, each chromatid in the two chromatids that make up a chromosome are called sister chromatids. Chromatids are held together by a centromere. The centromere The centromere is a constricted region of the chromosome that is made up of two components. A specific sequence of DNA bases that is not transcribed, but which is required for the segregation of chromatids A protein based structure called a kinetochore to which spindle fibres attach Mitotic cell division Two main stages Division of nucleus, mitosis Cell divides cytokinesis Mitosis is a continuous process although it is described in 4 stages. Prophase By the start of prophase, DNA has replicated and so chromosomes have a double structure.

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The chromatin condenses, forming chromosomes that are tightly coiled and appear shorter and thicker. As soon as the chromosomes condense, the DNA becomes inactive. • • • • Sister chromatids - attach to the centromere Nuclear envelope breaks down Spindle apparatus appear Nucleolus disappears

Metaphase • • • Chromosomes align at the centre of the cell Spindle fibres appear from the poles of the cell and attach to the centromere One sister chromatid of each chromosome is attached by spindle fibres to one pole the other is attached to the other pole.

Anaphase • • • • • Involves splitting of the centromere The separation of the chromatids Spindle fibres pull chromatids to opposite poles of the cell. Chromatids are now referred to as chromosomes. BY the end of anaphase there are two groups of chromosomes. One at each pole Each group contains one chromatid from each pair of sister chromatids.

Telophase • • • • Nuclear envelope reforms around daughter nucleus. Nucleoli appear in each daughter nucleus. Chromosomes become long and thin until they’re a mass of chromatin fibres and can no longer be seen with a microscope. Telophase marks the end of mitosis. The original nucleus has divided into two genetically identical daughter nuclei. Next the cell must divide into two.

Cytokinesis • • • • Cytokinesis is when the plasma membrane forms a constriction across the centre of the cell. This becomes narrower and narrower finally dividing the cytoplasm into two cells. The result is two daughter cells. Some cells such as those of the muscles divide their nuclei without cytokinesis.

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Cytokinesis in plants In plant cells, a cell plate is formed in the centre of cells. This grows outwards and fuses with the cell wall, forming the two new cell walls and separating the two daughter plant cells. Key features of mitosis • • • • Only one nuclear division Two daughter cells formed Daughter cells are diploid Daughter cells are identical

Section 11.3 – The cell cycle
The cell cycle is the sequence of events that take place in dividing eukaryotic cells. In actively dividing eukaryotic tissues, the new cells formed by mitosis grow before replicating their DNA and dividing by mitosis again. The 2 events covered in already are only short parts of the cell cycle.

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Prokaryotic cell division Prokaryotes do not divide by mitosis but instead by binary fission. Binary fission is different because it cannot be divided into phases because prokaryotes do not have a nucleus and a centromere. Why do cells need replacing? Cells are constantly being scraped off of the lining of the gut, billions of red blood cells are replaced each day and are lost from the surface of the skin. The daughter cells are genetically identical to the parent cell. The four main phases Once in the cell cycle, a non embryonic cell goes through four main phases then divides by cytokinesis. The first 3 phases (G1 S and G2) are often grouped together and called interphase. The 4th phase is mitosis. Each part of the cell cycle involves specific cell activities. A cell that has formed due to cell division is initially have the size of the parent cell with only half the number of organelle as the parent cell, therefore must enlarge and synthesis new organelles. Phases of the cell cycle G1 phase of interphase The cell is active growing and increases in size Nucleotides and histones are produced Proteins are produced from which organelles will be synthesised Cellular checks are made to ensure that the DNA is in good enough condition to be replicated. If it is not, the cell is terminated. S phase – synthesis of DNA DNA is replicated and combines with newly formed histones to double the amount of chromatin in the nucleus. Chromosomes are now duplicated The amount of DNA remains at this “double level” until cytokinesis because until then the DNA is contained within the cell. G2 phase Organelles are replicated Proteins are made to create spindle apparatus that will separate chromosomes during mitosis and synthesis.The cell continues to grow in size. M phase Chromatids are separated and go into daughter nuclei The nucleus divides before cytokinesis The cytoplasm divides to form new cells.

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Length of the cell cycle The length of the cell cycle is important because it determines how quickly an organism can multiply or grow or replace damaged cells. The duration of the cell cycle varies greatly from organism to organism and from cell to cell. DNA replication is generally faster in simpler organisms with smaller genome. In humans, the whole cycles takes approximately 24hours How to prepare slides Onion roots are often used as their cells are rapidly dividing and so the will be many cells in different phases. The tips must be squashed so that they form a thin single layer that easily allows the light to pass through it. Chromosomes must be treated with a stain to be made visible. Mitosis and cancer Most cells only divide by mitosis when required to do so. The process is carefully controlled by genes Eukaryotic cells normally divide when triggered to enter the cell cycle by one or more chemical factors. Non-dividing ells are not considered to be in the cell cycle – G0 phase. Nerve cells are permanently in G0 phase Genes controlling cell division might mutate, causing cells to enter the cell cycle when there is no need to control growth/repair. Cancer and the cell cycle Most mutated cells that are undergoing unwanted cell division are destroyed by phagocytes. Sometimes the protective mechanisms break down and rogue, mutated cells remain in the cell cycle. These cells continue to divide out of control and form a malignant tumour or cancer. Cancer treatments Effective cancer treatments require early diagnosis. Treatments work by blocking some part of the cell cycle. Problems with treatments Cancer treatments do not just stop cancer cells. Cancer drugs target all rapidly dividing cells that have a short or absent G0 phase. Cancer cells are damaged the most as they are the fastest dividing.

Section 12.1 – Cellular organisms
Making a multicellular organism All organisms start life as a zygote, formed during fertilization when a sperm and egg nuclei fuse.

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The cell goes through a series of mitotic cell cycles to form two cells, then four, etc. This resulting in a multicellular organism with cells genetically identical to the original single cell Cells formed during early mitotic division form a hallow ball of cells known as a blastocyst A blastocyst consists of an inner cellular mass surrounded by a layer of cells. These inner cells are called stem cell and will eventually give rise to nearly all the different adult cells. Forming different cell types All of out cells have the same DNA but they differ in how these instructions are used. Not all genes work in all cells – only a few genes are switched on I any one cell, the rest are switched off. Because different genes are expressed, this determines the size and the shape of the cell and how many of each organelle are produced. Cells in different positions in an embryo develop in different ways to form tissues. Embryonic stem cells There are different types of stem cells with varying abilities of differentiation, but those taken from the blastocyst are called embryonic stem cells. They can develop into and of the 200 different cells that make up the human body. Because they can develop into any tissue, embryonic stem cells have the ability to be used in the treatment of degenerate diseases and growing new organs. Injection of stem cells could hopefully lead to regeneration of healthy tissues. Adult stem cells An adult stem cells I thought to be an undifferentiated cells, found amongst differentiated cells in a tissue or organ that can its self and can differentiate to yield some or all of the major specialised cell types of the tissue/organ. The primary roles of an adult stem cell in a living organism are to maintain and repair the tissue in which they are found. These adult stem cell generally remain inactive until needed. Specialised cells They have been differentiated They have lost the ability to carry out other functions. Stem cells become specialised when the genes required for a particular function are switched on and all others are switched off. One a cell becomes specialised it is usually unable to make other types of cells. Connective tissue: adds support and strength to the body. Epithelial tissues: Lines the body surfaces, the surfaces of organs or organ cavities and tubes. Muscle tissue: moves the body or body parts. Nerve tissues: enables quick communication between body parts.

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Organs Organs are structures within an organism that are made of at least two types of tissue. Each tissue performs its own function and is essential to the overall function of the organ. The skin is the largest organ within the human body; other organs include the heart, liver, kidneys, etc. Organ system An organ system is comprised of two or more different organs working together to a common function.

Section 13.1 – Exchange between organisms and their Environment
The size and metabolic rate of an organism will affect the amount of each material that needs to be exchanged. This will therefore influence the type of exchange surface and transport system that has evolved. Materials that are exchanged between the organism and the environment include: • Respiratory gases Page 87 of 114

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Nutrients (glucose, fatty acids, amino acids, vitamins and minerals) Excretory products (urea, carbon dioxide)

Exchange can happen in two ways 1. Passively – requires no energy (diffusion, osmosis) 2. Actively – Energy is required (Active transport) For exchange to be affective, the surface area to volume ration of the organism must be high. Organisms have evolved in the following ways so that they can provide all their cells with the material necessary in an affective manor: • • A flattened shape means that no cell is ever far away from the exchange surface (e.g. a flat worm) A specialised exchange surface, for example the lungs which has a large surface area, and therefore increases the S.A: Vol. ratio.

Features of specialised gas exchange surfaces Exchange surfaces have the following characteristics: • • • • • Large surface are to volume ratio to increase the exchange rate. Very thin so that diffusion distance is short Partial permeable so that only certain materials can diffuse across Movement of the environmental medium to maintain concentration gradient (e.g. air) Movement of internal medium to maintain concentration gradient (e.g. blood)

Diffusion can be explained with fick’s law. Diffusion is proportional to surface area X difference in concentration gradient Length of diffusion

Section 13.2 – Gas exchange in single celled organisms and insects
Gas exchange in single celled organisms Single - celled organism have large S.A to Vol. ratio and so gases exchange through their cell surface membrane.

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For cells that have a cell wall, the cell wall does not affect the diffusion of gases as it is completely permeable. Gas exchange in insects Terrestrial insects have a problem where they loose water through the surface of their bodies and so easily become dehydrated. To inhibit water loss, terrestrial organisms usually have the following two features: Water proof coverings over their body surfaces. In the case of insects this is a waterproof cuticle. Small surface area to volume ratio to minimise the area over which water is lost Insects gave developed an internal system of tubes called trachea The trachea has strengthened rings for support. The trachea branches into smaller tubes called tracheoles. Gases move into and out of the respiratory system in the following ways. • Along diffusion gradient – During respiration, oxygen at the end of the tracheoles is reduced. This sets up a diffusion gradient where oxygen in the atmosphere moves towards where there is less oxygen, i.e. the tracheoles. Carbon dioxide is also produced during respiration which sets up a diffusion gradient that moves in the opposite way. Ventilation – The movement of muscles in insects cause mass movements in air into and out of the trachea. This speeds up gas exchange as it maintains a diffusion gradient between the two mediums. Gases enter and leave the trachea through small pores called spiracles. Spiracles are often closed to prevent water loss. Spiracles open periodically to allow gas exchange. For diffusion to be affective the pathway needs to be short. This has limited the size of insects.

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Section 13.3 – Gas exchange in Fish
Fish have specialised gas exchange surface – the gills. Structure of the gills

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They made up of gill filaments Gill filaments are stacked up in a pile. At right angle are structures called lamellae which increase the surface area for gas exchange. Water is taken in through the mouth and forced over the gills. Blood flows in the opposite direction to the water that moves over the gills. This is known as counter current flow.

The counter current flow • The counter current flow ensure that there is a concentration gradient maintained between the two mediums so that gas exchange can take place at a fast rate. Blood that is already well loaded with oxygen meets water, which has its maximum concentrations of oxygen. Therefore diffusion from water to blood takes place. Blood with little to no oxygen meets water with most of its oxygen removed. However oxygen diffuses from water to the gills regardless. There is a consistent rate of diffusion from the water to the lamella. Due to the counter current flow approx 80% of the available oxygen is absorbed. Without it the maximum amount would be 50% as there would be no diffusion gradient.

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Section 13.4 – Gas exchange in the leaf of a plant
When photosynthesis is taking place, although some carbon dioxide comes from respiring cells, most of it needs to be taken directly from the air. In the same way, some

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oxygen from photosynthesis is used in respiration but most of it diffuses out of the plant. When photosynthesis is not taking place, oxygen diffuses into the leaf because it is constantly being used by cells during respiration. Om the same way carbon dioxide produced by respiration diffuses out. Structure of a plant leaf and gas exchange No living cell is far from the external air, and therefore a source of oxygen and carbon dioxide. Diffusion takes place in the gas phase, which makes it more rapid than if it was in water. There is a short diffusion pathway. No specialised transport system is required for moving the respiratory gases in leaves. Leaves have the following adaptations for gas exchange: • • • A thin, flat shape that provides a large surface area Many small pores called stomata, which are found mostly in the lower epidermis of the leaf. Numerous, interconnecting air spaces that occur throughout the mesophyll

Stomata • • • • • Stomata are pores which occur mainly but not exclusively on the lower epidermis of the leaf. Each stoma is composed of two specialised cells called “guard cells”. Guard cells can open and close the stomatal pore. Due to this, they have the ability to control the rate of gaseous exchange. This means they are able to prevent water loss

Section 13.5 – Circulatory system of a mammal

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Diffusion is only adequate for the movement of substances over a short distance. In order to move substances a long distance, a specialised transport system is required. Why large organisms need a transport system A transport system is required to take materials from cells to exchange surfaces and from exchange surfaces to cells. Materials have to be transported from the environment to cells. They also need to be transported to different parts of the organism. Whether or not a specialised transport system is required depends on the S.A to vol. ratio and how active the organism is. Features of a transport system • • • • • • • Common features include: A suitable medium for carrying materials e.g. blood because it is water based and so substances can dissolve. A form of mass transport by which the medium is moved A closed system of tubular vessels that contains the transport medium A mechanism that moves the transport medium creates a pressure difference. A mechanism to maintain mass flow in one direction e.g. valves A means of controlling the transport medium

Transport system in mammals Mammals have a double circulatory system which means blood travels twice through the heart I one complete circuit. When blood travels through the lungs is pressure is reduced. By going back to the heart to be pumped once more, its pressure increases, allowing it to travel around the body. With out going back to the heart the pressure would be low and so blood would take longer to circulate the body. Substances are quickly delivered to the rest of the body, which is necessary as mammals have a high metabolic rate. Although transport systems move materials a over longer distance, the final part involves diffusion into cells. The final phase where materials pass from the blood to the cells and vise versa is rapid because it takes place over a large surface area, across short distances and down a steep concentration gradient.

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Section 13.6 – Blood vessels and their functions
Structure of blood vessels There are 4 different types of blood vessels: 1. Arteries – carry blood away from the heart 2. Arterioles – smaller arteries that control blood flow to capillaries 3. Capillaries – tiny vessels linked to arterioles 4. Veins – Carry blood back to heart Arteries, arterioles and veins have the same basic structure which includes: • A tough outer layer - resist pressure changes • A muscular layer – Contract to control blood flow • Elastic layer – maintains blood pressure by stretching and springing back • Endothelium – smooth to prevent friction and thin to increase diffusion • Lumen – central cavity through which blood flows Artery structure and function • • Muscular layer is thicker than veins – smaller arteries can be constricted and dilated to control blood flow Elastic layer is relatively thick compared to veins – Pressure in arteries is high so that it can reach extremities. The wall stretches (systole) then recoils back (diastole). Stretching and recoiling helps maintain pressure and creates smooth pressure surges. Thickness of the wall is large – prevents vessel from bursting There are no valves – Blood is under constant high pressure and does not move back.

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Arteriole structure and function • • Muscle layer is thicker than that of arteries – contraction of muscle layer narrows the lumen and so constricts blood flow and helps control the blood flow into capillaries. Elastic layer is thinner than that of arteries – The pressure in arterioles is lower than in arteries.

Vein structure related to function • Muscle layer is thin – constriction does not control the movement of blood into capillaries because blood is moving away from tissues.

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Elastic layer is relatively thin – pressure in veins is low and so the blood vessel will not burst. In addition the pressure is to low to create a recoil action The overall thickness of the wall is small – No need for the wall to be thick as the pressure within veins is small. Also, it allows veins to be flattened thus aiding blood flow There are valves throughout – prevents back flow of blood because pressure is low. When body muscles contract, veins are compressed pressurising blood within them. Valves ensure that the pressure directs blood toward the heart.

Capillary structure and function Walls consist only of lining layer – short diffusion pathway Numerous and highly branched – increased surface area Narrow diameter – permeate tissues Narrow lumen – pushes red blood cells which reduces diffusion pathway There are spaces between the lining – allows white blood cells to escape Tissue fluid and its formation Blood pumped by the heart passes through arteries, then arterioles then finally narrower capillaries. This creates a hydrostatic pressure at the arteriole end of the capillaries. Hydrostatic pressure forces tissue fluid out of the blood plasma. This however is apposed by two forces. • • Hydrostatic pressure outside of capillaries Lower water potential of the blood due to its contents e.g. proteins causes water from tissue fluid to move back into the capillary.

The overall affect means that there is only a small pressure that pushes small molecules out of the capillaries. This is called ultra filtration Return of tissue fluid • • • • Loss of tissue fluid in capillaries reduces hydrostatic pressure. When blood reaches the venous end its hydrostatic pressure is less than that outside of the capillary. Tissue fluid is then forced back into the capillaries. Osmotic forces from proteins in the blood pull water back.

Some tissue fluid travels back via the lymphatic system. The content of the lymphatic system is moves by hydrostatic pressure of tissue fluid leaving capillaries, and contraction of body muscles that creates pressure changes. Valves also ensure the fluid moves in one direction.

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Section 13.7 – Movement of water through roots
Uptake of water by root hair cells Root hair cells are the exchange surface of plants. They absorb water and mineral ions. Plants are always loosing water by transpiration and so this must be replaced. Each root hair is a long, thin extension of the root epidermal cell. They are efficient exchange surfaces because: • They have a large surface area for rapid diffusion of water. • They have a thin surface area, and therefore short diffusion pathway. The water potential in root hair cells is very low due to the sugars and amino acids dissolved in them, this causes the water in the soil, which has a much higher water potential to move into the cell by osmosis. Water moves through the plant by the following pathways: • The apoplastic pathway • The symplastic pathway The apoplastic pathway • • As water is drawn in through the endodermal cells, it pulls more water along with it. This is a result of waters cohesive properties due to it being a polar molecule. The water moves through the cellulose cells walls.

The symplastic pathway Water moves through the cytoplasms of cells of the cortex by osmosis. Water moves through small pores called plasmodesmata. The process happens in the following way: • Water enters by osmosis and increases the water potential of the root hair cell. • Water then moves via osmosis to the first cell of the cortex. • This cell then has a higher water potential than the neighbouring cell, further into the root. The water then moves by osmosis.

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A water potential gradient is set up along the cells of the cortex; this carries water through the cytoplasm of cells to the endodermis.

Passage of water into xylem Water travelling by the apoplastic pathway eventually reaches the Casparian strip where it is prevented from travelling further by the waterproof band. Water is then forced into living cells where is joins water travelling via the symplastic pathway. • • Active transport of salts in the most likely way by which water moves into the xylem Endodermal cells actively transport salts into the xylem which sets up a water potential gradient. If water in to move into the xylem it must first enter the cytoplasm of endodermal cells. This is explains why water from the apoplastic pathway is forced into the cytoplasm of cells by the Casparian strip. Water moving into the xylem via osmosis creates a force called root pressure.

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Evidence of root pressure includes the following: • The pressure increases with a rise in temperature and decreases with a fall in temperature. • Metabolic inhibitors, for example Cyanide stop active transport and therefore cause root pressure to cease. • A decrease in oxygen for respiration decreases root pressure.

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Section 13.8 – Movement of water up stems
Water leaves plants by evaporating and moving out through the stomata Movement of water through stomata When the stomata are open, water molecules diffuse out into the surrounding air. Water that leaves the stomata via evaporation is replaced by water evaporating from the cell wall of mesophyll cells. Plants can control there rate of transpiration by opening/closing stomata. Movement of water across the cells of a leaf Water that evaporates from mesophyll cells is replaced by water reaching the mesophyll cells from the xylem through the apoplastic/symplastic pathway. For the symplastic pathway, the water movement occurs because: • Mesophyll cells loose water to the air spaces • These cells now have a lower water potential, water enters by osmosis. • The loss of water from neighbouring cells lowers their water potential • They then take water from their neighbouring cell Movement of water up the stem through the xylem Movement of water up xylem is due to root pressure and cohesion tension Cohesion theory operates as follows: • Water leaves as a result of transpiration • Due to hydrogen bonds, water molecules stick together. • Water forms a continuous unbroken pathway across mesophyll cells and xylem • As water evaporates, water molecules are drawn up behind it. • Water is pulled up due to transpiration. This is called transpiration pull. Evidence to support cohesion theory includes: 1. Change in diameter of tree trunks in relation to the rate of transpiration. When transpiration rate is high, there is negative pressure in the xylem and so the trunk shrinks.

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2. If a xylem vessel is broken and air enters it, water can no longer be drawn up. This is because the continuous chain of water molecules joined by cohesion is broken. 3. When the xylem is broken, water does not leak out. Transpiration pull is a passive process. No additional metabolic energy is required. In addition xylem vessels are composed of dead cells.

Section 13.9 – Transpiration and factors affecting it
The role of transpiration Materials such as minerals and ions are moved around the plant dissolved in water This water is carried up the plant by transpiration pull Without transpiration, water would not be so plentiful and the transport of materials would not be so rapid. Factors affecting transpiration Light Carbon dioxide diffuses in to leaves through the stomata so that it can be used in photosynthesis. Photosynthesis takes place during the day, so the stomata are open when there is a high light intensity (leaves photosynthesising) and close when there is a low light intensity (leaves not photosynthesising). Temperature Temperature affects the water potential of air and how fast water molecules move An increase in temperature increases the kinetic energy of water molecules. These molecules will then have enough energy to change from its liquid state to its gaseous state, hence evaporating. A rise in temperature decreases the amount of water air can hold. Rise in temperature; rise in transpiration rate. Humidity When humidity is high (when there is a large amount of water in a given volume of air) the water potential of the air is high, and so water evaporates at a slower rate because the osmotic gradient is decreased. Air movement Water that has evaporated accumulates around the leaf and so the water potential gradient is decreased. If air is being moved away from the leaf by wind a concentration gradient is maintained. To summarise this, if there is little air movement there is likely to be a smaller water potential gradient and therefore slower transpiration rate. When there is a lot of air movement, a water potential gradient is maintained and so transpiration occurs quicker.

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Although transpiration is thought of as a passive process, the energy that drives it comes from the sun. This is due to the fact that the sun provides the heat energy and the light, both of which are factors affecting transpiration rates.

Section 13.10 – Limiting water loss in plants
The adaptation of an efficient gas exchange surface, contradict the plants ability to retain water, and so plants have adapted in other ways to limit water loss. Xerophytic plants Plants that have adapted to limit water loss are called, “xerophytes”. Xerophytic plants have adaptations to not only limit water loss, but also store and increase the uptake of water also. Examples of these modifications include: A thick cuticle – Plants that have leaves with a waxy cuticle can still loose water through the upper epidermis. To compensate for this, Xerophytes have a thicker cuticle. The thicker the cuticle, the lower the amount of water loss Rolling up of leaves – Leaves can wrap up so that their lower epidermis is enclosed within the leaf. This creates a region of air that gets saturated with water molecules and increases in water potential. Once the water potential is the same as within the leaf, there is no net movement of water out of the plant. Hairy leaves – hairs on the lower epidermis trap moisture in the air and so reduce the water potential gradient inside and outside of the leaf, thus lowering the rate of water loss. Stomata in pits and grooves – These just like the hairs on the lower epidermis of leaves trap air and so decrease the water potential gradient inside and outside of the leave. This lowers the rate at which water is lost. A reduced surface are to volume ratio of leaves – by having leaves that are small and roughly circular in cross section, the surface area to volume ration can be considerably be reduced. This however contradicts the

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plants ability for photosynthesis and so a compromise must be met between the two requirements.

Section 14.1 – Classification
What is classification? Classification is the grouping together of things on the basis of features that they have in common. We classify things so that we can make sense of the world around us and to know where to find things we want. To classify all the organisms that w know about, the system must be universal – it has to be usable by biologist anywhere in the world. The we use is based on dividing living organisms into species. What is a species? A group of organisms similar to each other with similar features that can interbreed to produce fertile offspring, and that are reproductively isolated from other species. If an organism is fertile it is capable of producing offspring. Occasionally two different species can interbreed to produce organisms known as hybrids. The parents of the hybrids are still separate species as they occupy different habitats and are usually reproductively isolated. Biological classification systems Can be either natural or artificial Artificial classification The grouping of an organism based on characteristics such as colour, size, etc Does not necessarily effect the evolutionary relationship of an organism. Natural classification Attempt to group organisms according to their natural relationship Reflects the way in which different groups are thought to have evolved Classifies species into a hierarchy in which smaller groups are contained within larger groups with no overlaps. Relationships are based on the homologous characteristics, with similar evolutionary origins regardless of their functions in the adult of a species. Phylogenic relationships

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Most classification in use today are natural and aim to reflect the Phylogenic relationships – that is, the historical/evolutionary relationships between organisms. Phylogeny is putting organisms into groups that reflect their evolutionary history A Phylogenic tree shows the evolutionary relationship between organisms. Phylogenic Trees The closer the branches, the closer the evolutionary relationship Hierarchy system Uses Phylogenic relationship to group organisms Modern biology places each organism into a taxa: a series of groups arranged in a hierarchy. Each group is called a taxon and contains organism sharing some basic features indication they have a common ancestry. The study of a classification is called taxonomy Taxa • • • • • • • Kingdom Phylum Class Order Family Genus Species

They are listed in descending order of size – species is the most exclusive group containing the fewest organisms. Kingdom Is the largest taxon Contains the most organisms, with the fewest features in common There are five kingdoms: 1. Prokaryotae 2. Protoctista 3. Fungi 4. Animalia 5. Plantae Page 101 of 114

Kingdom Prokaryotae • • • Cells lack true nuclei Cells have circular DNA Cells to not have membranes around organelles

Example: bacteria Organisms in other kingdoms have cells with true nuclei, chromosomes and membrane bound organelles.

Kingdom Protoctista Very diverse, contains most organism that do not belong in other kingdoms. May be sub divided in the future due to the diverse mix of organisms • • • • All protocistians have eukaryotic cells Some posses’ cells walls, chlorophyll and can even photosynthesise Others have no cell walls and are motile. Some are unicellular; others consist of billions of cells.

Kingdom Fungi • • • • • • Common features Non-cellulose wall Are non photosynthetic Eukaryotic cells Secrete enzymes to digest organic materials outside their cells and absorb the products of digestion. Usually feed on dead organic material but some feed on living hosts Example, yeast, mushrooms.

Kingdom Animalia • • • • Are multicellular Have eukaryotic cells with no cell walls Develop from blastocyst Most animals: Ingest food into their digestive system, and are motile.

Kingdom Plantae • • • • All plants: Multicellular have eukaryotic cells with a cellulose cell wall Are photosynthetic Examples: mosses, ferns conifers

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Viruses are not included in the classification system as they are acellular Autotrophs – make their own food Hetrotrophs – Consume food Phylum The kingdom Animalia contains approx. 10 phyla. Class Classes include mammalia, reptilia, and anphibia. Order Mammalian order includes primates, carnivores, etc. Family Primate families include hominidue. Genus Species that are very similar to each other are places in the same genus. Both the species and the genus are used when naming the organisms. Species Homosapiens are the only existing species of the genus “homo” Binomial system Is used to name organism based on the system devised by Swedish naturalist Carl Linnaeus Is a universal system, laid down by international codes; never a matter of personal opinion. Latin or Greek names are used Each organism is given a name with two words. The first word is the generic name, the name of the genus and begins with an uppercase letter. The second word is the name of the species and it begins with an uppercase letter.

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The two words must be printed in italic when typed or underlined if handwritten to show that it is the biological name.

Section 15.1 - Genetic comparisons using DNA and proteins
Comparing the DNA and proteins of different species it is possible for scientists to determine the evolutionary relationships between them Comparison of DNA base sequences When a species gives rise to another species through evolution, the two species will be very similar genetically. Species that are more closely related will show fewer differences in their DNA compared to species that are less closely related. DNA hybridisation • • • • • • • • • • • • • When DNA is heated, the hydrogen bonds between the complementary stands break, causing them to separate. When they cool they reform. DNA between two species can be compared in the following manor: DNA is purified, extracted and cut into short pieces DNA from one species is labelled with a fluorescent radioactive tracer. It is then mixed with the DNA of the other species. The mixture is then heated so that the strands separate. The mixture is cooled allowing strands with complementary bases to join Some of the double strands formed with contain one strand for each species. They can be identified because they are 50% labelled The hybrid stands are separated out and the temperature increase in stages At each temperature the degree to which the two strands are still linked together is measured If the two species are closely related they will share many complementary bases The more complementary bases, the more h bonds The greater the number of h bonds the higher the temperature required for separation The closer the species are related, the higher the temperature needed

Comparison of amino acid sequences in proteins The sequence of amino acids in proteins is determined by the DNA. The degree of similarity in the amino acid sequence is of the same protein in two species will therefore reflect how closely related they are.

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Immunological comparisons of proteins The proteins of different species can be compared using immunological techniques. The principle behind this methods is the fact that antibodies of one species will respond to specific antigens on proteins.

Section 15.2- Courtship behaviour
The behaviour of members of the same species is more alike than members of different species. It is therefore possible for animals to identify each other by observing their behaviour. Why is courtship behaviour necessary? It is important to ensure that mating is successful and that the offspring have the maximum chance of survival. Courtship behaviour ensures this by enabling individuals to: • Recognise members of their own species - ensures that mating only takes place within the same species so that offspring are fertile. • Identify a mate that is capable of reproducing – both partners need to be sexually mature and fertile. • Forms a pair bond – leads to successful mating and raising of offspring • Synchronise mating – takes place when there is a maximum chance of the sperm and egg meeting Females have cycles during which they are only fertile for brief periods of time. It is therefore important that during this time, the female seeks out a male who she can mate with. The actions of a male act as a stimulus to the female, who if she is receptive will respond with another stimulus to the male to carry out a further action. The longer the courtship ritual lasts, the more likely it is at being successful. If at one point, one partner fails to respond correctly, the sequence is ended.

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Section 16.1 – Genetic variation in bacteria
Bacterial DNA Double stranded Contains two types of DNA Most bacterial DNA is organised into large circular molecules (as appose to linear DNA molecules found in eukaryotic cells). Some bacterial DNA is found as plasmids these are small circular molecules of DNA, separate from the main DNA. Bacterial reproduction Reproduce asexually through binary fission In theory all of springs should be clones, but in reality there is still genetic variation which can lead to antibiotic resistance. Binary fission is also known as vertical gene transmission Changes to DNA Like the DNA of all cells, bacterial DNA can also mutate Mutation – changes in the sequence of bases. Changing the base sequence leads to a different amino acid being coded for and therefore a different polypeptide is produced. Mutations generally happen during DNA replication. Factors that induce DNA replication are called mutagens. Mutation A change of a single nucleotide base pair is a point of mutation Different types of mutation Substitution – The replacement of one nucleotide Deletion – loss of a nucleotide Insertion – Extra nucleotide added Duplication – A certain portion a nucleotide sequence of a gene is replicated. Inversion – The reversal of nucleotide sequence in a gene. Harmful mutation

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Most are harmful Man mutation result in a change in the shape of a protein so that the protein cannot function. Mutations that affect large sections of a gene are often lethal. Silent neutral mutations Some mutations have no effect because the mutation has occurred in a non-coding part of DNA The mutation may also produce a different codon for the same amino acid. The alternative amino acid sequence may not affect the proteins shape/function. Beneficial mutations Very occasionally a mutation occurs that changes the phenotype so that an organism has a better chance of surviving and reproducing. Although rare, beneficial mutations are bound to happen sooner or later if there are a large number or organisms. As there are so many bacteria and they reproduce so quickly, even a rare event such as a beneficial mutation is likely to happen in a relatively short time. Conjunction Conjunction is another way in which bacteria increase their genetic variation.

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The donor cell produces a thin production called a “pilus” that connects the two cells. The pilus retracts to draw the cells closer together. The donor cell has replicated one of its plasmids The plasmid is altered by an enzyme to make it linear. Once the plasmid has been transferred to the recipient cell, the ends of the plasmid rejoin and become circular again. The plasmids in each bacterial cell then replicate to become double stranded. Their connection via pilus is broken and each cell is free to conjugate with other cells. Conjugation is also known as horizontal gene transmission.

Section 16.2+16.3 – Antibiotics/Antibiotic use and resistance
What is an Antibiotic? An antibiotic is a substance produced by a microorganism that is capable of destroying or inhibiting the growth of another organism. Antibiotics are not affective against viruses Antibiotics are known as secondary metabolites as they are not essential for the growth or reproduction of the organism that is producing them, but may give the producer a selective advantage. Producing antibiotics According to the strict definitions, only microorganisms produce antibiotics, however the term is generally used to include a wide rage of chemicals that damage pathogens. • Antibiotics often include:

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Chemicals produced by microorganism, animals and plants. Chemicals such as penicillin which is produced naturally but altered chemically to make them more affective Chemicals such as chloramphemiol originally produced naturally but now entirely synthesised.

Types of antibiotics Antibiotics that kill bacteria are called bactericidal antibiotics. Some antibiotics, known as bacteriostatic antibiotics, do not kill the bacteria, but stop them from reproducing. How antibiotics work Antibiotics work by interfering with some metabolic functions of microorganisms. There are three main ways antibiotics can do this: 1. Disrupt cell wall synthesis 2. Disrupt DNA replication 3. Disrupt protein synthesis Disrupting cell wall synthesis Antibiotics weaken the cell wall and cause osmoticlysis. Cell walls are made up of long chains of peptidoglycan molecules and allow the bacteria to tolerate osmotic influx of water. Just as in plant cells, bacterial cells become turgid when in a watery environment with higher water potential than they have. The cell contents push against the cell wall, which can stretch, so it prevents expansion of the cell and halts further entry of water. The antibiotics inhibit the synthesis of peptide links that bind molecules together. The cell wall becomes so weak that the bacteria burst when water enters the cell by osmosis. These antibiotics only work on bacteria that are actively growing and have no effect on bacteria lying dormant in the body. Disrupt DNA replication These antibiotics disrupt the synthesis of nucleic acids, so DNA is not replicated. Bacteria are not killed but cell division is halted. Disrupt protein synthesis These antibiotics either inhibit protein synthesis or promote the synthesis of abnormal proteins. The antibiotics bind to the bacterial ribosomes but do not affect eukaryotic ribosomes which are larger. The bacterial cells cannot synthesis enzymes and structured proteins. How bacteria resist antibiotics Remember that bacterial DNA can mutate Page 110 of 114

A mutation is the change of base sequence in a gene that results in a new protein produced. This new protein could be an enzyme that is able break down the antibiotic before it has a chance to kill the bacteria. Antibiotics do not cause mutations Antibiotic resistance most often results from mutations in the plasmid DNA Passing on antibiotic resistance Bacteria can pass on resistance in two ways, binary fission/conjugation Binary fission – Both the plasmid and the larger circular DNA in the bacterium replicate prior to cell division. If a plasmid has a mutation that gives the bacteria resistance to an antibiotic, when the cell divides, each daughter cell will receive the gene for resistance. Conjugation – Bacteria can also pass and receive plasmids from other bacteria in the process called conjugation. A plasmid conferring antibiotic resistance can pass from one bacterium to another Conjugation can also occur between members of the same species. Conjugation is the main reason why some bacteria have become resistant to antibiotics. Antibiotic resistant strains An antibiotic resistant strain is a whole population that has become resistant to an antibiotic. A gene for antibiotic resistant gene is only beneficial where there the bacteria are exposed to the antibiotic; hence there is a selection pressure that kills off the bacteria without the gene, leaving only the resistant bacteria. Natural selection The frequency of the allele for resistance consequently increases and will continue to increase with each succeeding generation of the bacteria, until an antibiotic resistant strain has been produced. This antibiotic resistant strain is a result of natural selection. Overuse of antibiotics may have provided an increased selection pressure in favour of resistant bacteria. Multiple resistance A bacterium can accumulate several plasmid DNA via conjugation that give it resistance. An antibiotic strain can be produced by natural selection if the population was exposed to several antibiotics. The greater the amount of antibiotics used, the greater the chance that mutant bacteria will have multiple resistance. These bacteria will have an advantage over the other bacteria and will out-compete the normal variety. MRSA

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Resistant to several antibiotics Because of its multiple resistances, infections caused by this bacterium are difficult to treat, so the focus is on preventing transmission. MRSA is found on many individuals skin without any ill effects but these people could pass the bacterium to somebody else via skin to skin contact. If the bacterium gets inside the body it can cause deadly infections. Absolute cleanliness is particularly important in wards where patients may have open wounds. Anyone in contact with patients is required to wash their hands.

Section 17.1 – Species diversity
Biodiversity is the term given to describe the variety in the living world. • • • Species diversity – refers to the number of different species and the number of individuals of each species within anyone community Genetic diversity – refers to the variety of genes possessed by the individuals that make up any one species Ecosystem diversity – refers to the rand of different habitats within a particular area

Species diversity has two components: 1. The number of different species in a given area 2. The proportion of the community that is made up of an individual species Species diversity is calculated using the index that follows: d=N(N-1)

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Σn(n-1) Where: • • • • d = species diversity index N = total number of organisms of all species n = total number of organisms of each species Σ = the sum of Number (n) found in habitat X 10 10 10 10 10 Σn(n-1) N(n-1) 10(9)=90 10(9)=90 10(9)=90 10(9)=90 10(9)=90 450 Number (n) found in habitat Y 3 5 2 36 4 Σn(n-1) N(n-1) 3(2)=6 5(4)=20 2(1)=2 36(25)=1260 4(3)=12 1300

Species A B C D E

Habitat X: d = 50(49) 450 =5.44 Habitat Y: d =50(49) 1300 =1.88 Habitat X has a higher value for d and therefore has more species diversity

Section 17.2 – Species diversity and Human activities
The impact of providing more food at a lower cost as resulted in less biodiversity. Agriculture and deforestation are two examples of processes carried out by humans that have the affect of lower biodiversity. Impact of agriculture • • • • Ecosystems develop overtime, becoming more complex communities with many individuals of many different species; this therefore means that they have increased in species diversity. Selective breeding has reduced the genetic variation of certain species and therefore reduced the variety of alleles in the population. Any particular area can only support a certain amount of biomass, therefore these areas must be occupied by the species the farmer feels is most desirable. This means that smaller areas are only available for other species.

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Species will compete for the resources around and many will not survive. In addition pesticides are used to kill off these species as they can affect crop growth. The overall affect is that the species diversity is lowered.

Impact of deforestation Forests provide numerous habitats where species have become adapted to live. Deforestation is the permanent clearing of forests and the conservation of the land to other uses such as agriculture. The most serious consequence of deforestation is the loss of bio diversity where many species are killed each year as a result. Species diversity is reduced due to deforestation because: • Habitats are destroyed • Species are not adapted to live anywhere else • The organism in the species will not survive as a result • This note only reduces the amount of organisms in a species, but also reduces the number of different species. • The overall affect is a reduction in the species diversity for the given area.

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