Biology Unit 1 Notes 3.1.

1 Pathogens Pathogens include bacteria, viruses and fungi Disease can result from the pathogenic microorganisms penetrating any of an organisms interface with the environment. These interfaces include the digestive and gas-exchange systems and the skin Digestive system: Eat/drink food containing pathogens Most skilled by acidic conditions of the stomach Some may survive and pass into the intestines where they can invade cells of the gut wall and cause disease

Gas Exchange System: Skin: Damage skin Pathogens on the surface can enter your bloodstream The blood clots at the area of damage to prevent pathogens from entering Some may get in before the clot forms Breathe in air containing pathogens Most will be trapped in a layer of mucus lining the lung epithelium These cells have cilia that beat and move the mucus up the trachea to the mouth where it is removed Some pathogens reach the alveoli where it can invade cells and cause damage

Pathogens can cause diseases by damaging the cells of the cost and by producing toxins Cell Damage: Pathogens can physically damage host cells by Rupturing them to release nutrients inside them Breaking down nutrients inside of the cell to their own use, starves and eventually kills the cell Replicating inside the cells and bursting them when they are released

Production of Toxins: Bacteria releases toxins into the body E.g. Tetanus bacteria produces toxins that blocks the function of certain nerve cells causing muscle spasms

Lifestyle Lifestyle can affect human health Risk Factors for Cancer: Smoking mouth, throat and lung cancer Excessive exposure to sunlight skin cancer Excessive alcohol intake liver cancer

Risk Factors for Coronary Heart Disease: Poor Diet diet high in saturated fats or salts increase the risk Smoking Leads to high blood pressure, which can damage the heart and the Lack of exercise blood vessels, increasing the risk Alcohol intake

Changes in lifestyle may also be associated with a reduced risk of contracting these conditions. Reducing the risk of Cancer and Coronary Heart Disease Giving up smoking Avoiding becoming overweight Reducing salt intake Reducing intake of cholesterol and saturated fats Taking regular aerobic exercise Keeping alcohol consumption within limits Increase the intake of dietary fibre and antioxidants

3.1.2 The Digestive system Oesophagus: the tube that takes food down to the stomach using waves of muscle contractions called peristalsis. Mucus is secreted from the tissues in the walls, to lubricate the foods passage downwards. Stomach: is a small sac. It was lots of folds allowing the stomach to expand. The entry and exit into the stomach is controlled by the sphincter muscles. The stomach walls produce gastric juice, which helps break down food. Gastric juice is made up of HCL and pepsin and mucus. Pepsin hydrolyses proteins into smaller polypeptide chains. It only works in acidic conditions. Peristalsis of the stomach turns food into an acidic fluid called chyme

Large Intestines: absorbs water salts and minerals. It has a folded wall this provides a large surface area for absorption. Bacteria that decompose some of the undigested nutrients are found in the large intestines

Rectum: faeces are stored in the rectum and then pass through the sphincter muscles at the anus during defecation

Small Intestines: has 2 main parts the duodenum and the ileum. Chyme is moved along the small intestines by peristalsis. In the duodenum, bile and pancreatic juice neutralise the acidity of the chyme and break it down into smaller molecules. In the ileum the small, soluble molecules are absorbed through the structures called villi that line the gut wall. Molecules absorbed by diffusion, facilitated diffusion and active transport.

The salivary glands: they secrete saliva that consists of mucus, mineral salts and salivary amylase. Salivary amylase breaks down starch into maltose. Saliva also helps to lubricate food, making it easier to swallow. The Pancreas: releases pancreatic juice into the duodenum through the pancreatic duct. Pancreatic juice contains amylase, trypsin chymotrypsin and lipase. It also contains sodium hydrogencarbonate which neutralises the acidity of hydrochloric acid from the stomach. Digestion is the process in which large molecules are hydrolysed by enzymes to produce smaller molecules that can be absorbed and assimilated

Proteins Proteins have a variety of functions within all living organisms

Condensation and the formation of peptide bonds linking together amino acids to form polypeptides. Primary Structure- sequence of amino acid in the polypeptide chain Secondary Structure- polypeptide chain does not remain flat and straight. Hydrogen bonds form between the amino acids in the chain, this makes it automatically coil into an alpha helix or fold into a beta pleated sheet. Tertiary Structure- the coiled or folded chain of amino acids is often coiled and folded further. More bonds form between the different parts of the polypeptide chain. For proteins made form single polypeptide chain, the tertiary structure forms their final 3D shape. Quaternary Structure- some proteins are made of several different polypeptide chains held together by bonds. The quaternary structure is the way these polypeptide chains are assembled together. For proteins made from more than 1 polypeptide chain, the quaternary structure is the proteins final 3D shape. Functions of Proteins: Enzymes- spherical in shape due to tight folding of the polypeptide chains. They are soluble and have roles in metabolism e.g. some enzymes break down large food molecules and others help to make large molecules. Antibodies- are involved in the immune response. They are made up of two light and two heavy polypeptide chains bonded together. Antibodies have variable regions the amino acid sequence s in these regions vary greatly Transport Proteins are present in all cell membranes, they contain both hydrophilic and hydrophobic amino acids, which causes the protein to fold up and form a channel. These proteins transport molecules and ions across membranes. Structural Proteins physically strong, consist of long polypeptide chains lying parallel to each other with cross links between them.

Test For Protein: add biuret solution (blue), positive turn lilac

Enzyme Action Enzymes are catalysts lowering activation energy through the formation of enzyme-substrate complexes. Lock and Key: this is where the substrate fits into the enzyme in the same way that a key fits into a lock. Induced Fit: active site will change to fit the substrate. Provides a better explanation of specific enzyme properties. Enzyme Properties Enzymes are very specific, usually only catalyse one reaction, this is because only one substrate will fit into the active site. The active sites shape is determined by the enzymes tertiary structure. Each different enzyme has a different tertiary structure and so a different shaped active site. If the substrate does not match the active site the reaction wont be catalysed. If the tertiary structure of a protein is changed, the shape of the active site will be changed, this means that the substrate wont fit in to the active site and that the enzyme will no longer be able to carry out its function. The tertiary structure of an enzyme may be altered by changes in pH or temperature. The primary structure of a protein in determined by a gene. If a mutation occurs in that gene, it could change the tertiary structure of the enzyme produced. Factors affecting enzyme activity: Temperature more heat means more kinetic energy so molecules move faster, more likely for collisions to occur, energy of the collisions also increase which means each collision is more likely to result in a reaction but if the temperature is too high the reaction stops pH above or below the optimum pH, will affect the ionic and hydrogen bonds that hold the enzymes tertiary structure together, this makes the active site change shape so the enzyme is denatured Concentration higher the concentration the faster the reaction, more substrate molecules means that it is likely for more collisions to occur. This will only work until the saturation point adding anymore substrate wont help because all the active sites will be full. Inhibitors prevent enzyme activity, bind to the enzyme Competitive similar shape to the substrate, compete with substrate molecules to fit into the active site but no reaction takes place, they block the active site so no substrate molecule can fit in. Non-Competitive bind to the enzyme away from the active site, causes the active site to change shape so the substrate no longer fits in. Increasing the concentration of the substrate will have no effect because the inhibitors are not competing.

Carbohydrate Digestion Biological molecules such as carbohydrates and proteins are often polymers and are based on a small number of chemical elements. All carbohydrates contain elements carbon, hydrogen and oxygen. Monosaccharaides are the basic molecular units of which carbohydrates are formed. The linking of alpha glucose by glycosidic bonds formed by condensation reactions to form maltose and starch.

Sucrose is a disaccharide formed by condensation glucose and fructose Lactose is a disaccharide formed by condensation of glucose and galactose. Lactose intolerance Lactase is a sugar found in milk. Its digested by an enzyme called lactase, found in the intestines. If you dont have enough enzyme lactase, you wont be able to break down lactose in milk properly a condition called lactose intolerance. Undigested lactose is fermented by bacteria and can cause a whole host of intestinal complaints such as stomach cramps, excessive flatulence and diarrhoea. Reducing Sugar Test: Add benedicts solution, positive turns brick red Non- Reducing Sugar Test: Add HCl, boil, add sodium to neutralise, then add Benedicts, positive brick red. Starch Test: Add iodine, positive turns blue/black

3.1.3 Cells Plasma Membrane found on the surface of animal cells and just inside the cell wall of plant cells and prokaryotic cells, made up of proteins and lipids. Regulates the moment of substances into and out of the cell, has receptor molecules on it which allow it to respond to chemicals like hormones. Microvilli folds in the plasma membrane. They are found on cells involved in process like absorption e.g. epithelium cells in the small intestines. They increase the surface area of the plasma membrane. Nucleus a large organelle surrounded by a nuclear envelope/ double membrane, which contains many pores. The nucleus contains chromatin and often a structure called the nucleolus. Mitochondria oval shaped, has a double membrane -> inner one is folded to form structures called cristae. Inside is the matrix, which contains enzymes involved in respiration. It is the site of aerobic respiration. Found in large numbers in cells that are very active and require lots of energy. Lysosomes a round organelle surrounded by a membrane, with no clear internal structure. Contains digestive enzymes -> these are kept separate by the surrounding membrane, and can be used to digest invading cells or break down worn out components of the cell. Ribosomes - a very large organelle that float free in the cytoplasm or is attracted to the rough endoplasmic reticulum. It is the site at which proteins are made. Smooth Endoplasmic Reticulum is a system of membranes enclosing a fluid-filled space. Synthesises and processes lipids Rough Endoplasmic Reticulum is a system of membranes enclosing a fluid space covered in ribosomes. Folds and processes proteins that have been made at the ribosomes. Golgi Apparatus a group of fluid filled sacs. It processes and packages new lipids and proteins. Also makes lysosomes. Transmission Electron microscope electromagnets focus a beam of electron transfer through the specimen.

High resolution images Only thin specimen can be used -> denser parts adsorb more electrons, which makes them
look darker Scanning Electron Microscope scan across the specimen, knocks off electrons from the specimen, gathered by a cathode ray tube to form the image. Image shows the surface of specimen and can be in 3D

Can be used on a thick specimen Lower resolution images than TEM

Magnification- how much bigger the image is than the specimen

Resolution how detailed the image is, how well a microscope distinguishes between 2 point that are close together , if it cant separate 2 point increasing magnification wont help. Cell fractionation: 1. Homogenisation breaking up the cells to release the organelles 2. Filtration through gauze to separate large cells debris or tissue debris e.g. connective tissue. Organelles are much smaller that the debris to they pass through the gauze 3. Ultracentrifugation separating the organelles, when spun at a low speed the heaviest organelles get flung to the bottom of the test tube (e.g. nuclei), they form thick sediment called a pellet. When spun at a higher speed -> mitochondria, lysosomes, ER, ribosomes Plasma Membrane Glycerol and fatty acids combine by condensation to produce triglycerides. The R group of fatty acids may be saturated or unsaturated. In phospholipids, one of the fatty acids of a triglyceride is substituted by a phosphate group. Test For Lipids: shake the test substance with ethanol for about a minute, then pour the solution into water. Positive turns cloudy. Fluid Mosaic Model phospholipids form a continuous bilayer -> fluid, phospholipids always moving. Proteins scattered like mosaic tiles. Microvilli increases the surface area of cell surface membranes Diffusion Diffusion is the passive movement of substances down a concentration gradient. Surface area, differences in concentration and the thickness of the exchange surface affect the rate of diffusion. Facilitated Diffusion: Down a concentration gradient from areas of high concentration to areas of low concentration and is passive (requires no energy). Carrier Proteins move large molecules into and out of the cell, down their concentration gradient. Different carrier proteins facilitate the diffusion of different molecules. Large molecules attach to a carrier protein in the membrane. Then the protein changes shape. This releases the molecule on the opposite side of the membrane. Protein channels for pores in the membrane for charged particles to diffuse through. Different protein channels facilitate the diffusion of different charged particles.

Properties of the Fluid Mosaic Model: 1. The membrane is a good barrier against most water soluble molecules 2. The membrane controls what enters and leaves-> protein channel and carrier proteins 3. The membrane allows cell communication-> contain receptor proteins these allow the cell to detect chemicals released from other cells. The chemicals signal for the cells to respond. Different cells have different receptors. 4. The membrane allows cell recognition 5. The membrane is fluid -> phospholipids are constantly moving, the more unsaturated fatty acids there are in the phospholipid bilayer the more fluid it is. More cholesterol molecules, the less fluid the membrane as cholesterol makes the cell membrane more rigid and prevents it from breaking up. Osmosis Osmosis is a special case of diffusion in which water moves from a solution of higher water potential to a solution of lower water potential through a partially permeable membrane. Isotonic If 2 solutions have the same water potential, they are said to be isotonic. Its balanced Active Transport Active transport uses energy to move molecules and ions across plasma membrane, against a concentration gradient. Carrier proteins:

A molecule attaches to the carrier protein, the protein changes shape and this moves the molecule across the membrane, releasing it on the other side. Energy is used from ATP to move the solute against its concentration gradient.

Co-transporters are a type of carrier protein. They bind 2 molecules at a time. The concentration gradient of one of the molecule is used to move the other molecule against its own concentration gradient.

Absorption When carbohydrates are first broken down, there is a higher concentration of glucose in the small intestines than in the blood -> this makes a concentration gradient. Glucose moves across the epithelium cells of the small intestine into the blood by diffusion. When the concentration in the lumen becomes lower that in the blood diffusion stops. The remaining is absorbed by active transport: 1. Sodium ions are actively transported out of the small intestine epithelium cells, into the blood by the sodium potassium pump. This created a concentration gradient higher concentration of sodium ions in the small intestine lumen than inside the cell. 2. This causes sodium ions to diffuse from the small intestine lumen into the cell, down their concentration gradient; this is done by sodium-glucose co-transporter proteins. 3. The co-transporter carries glucose into the cell with the sodium. Then the concentration of glucose inside the cell increases. 4. Glucose diffuses out of the cell, into the blood, down its concentration gradient through a protein channel by facilitated diffusion. Cholera The cholera bacterium is an example of a prokaryotic organism. The structure of prokaryotic cells includes: cell wall, cell-surface membrane, capsule, circular DNA, flagella and plasmid Cholera bacteria produce toxins which increase secretion of chloride ions into the lumen of the intestines. This results in severe diarrhoea. 1. This toxin causes chloride ion protein channels in the plasma membrane of the small intestines epithelium cells to open. 2. Chloride ions move it the small intestine lumen. The build-up of chloride ions lowers the water potential of the lumen. 3. Water moves out of the blood, across the epithelium cells and into the small intestine lumen by osmosis. 4. The massive increase in water secretion into the intestine lumen leads to diarrhoea causing the body to become extremely dehydrated. The use of oral rehydration solutions treats diarrhoea diseases. Replaces the fluid you have lost. ORS is a drink that contain large amount of salts and sugars dissolved in water. Sodium ions are used to increase glucose absorption into the epithelium cells in the intestines .Getting the concentration of the ORS right is essential for effective treatment. Very cheap and dont need a lot of training to administer it, so great for developing countries. Ethical Issues: Diarrhoea diseases mostly affect children and parent put them in the experiment so they have no say Blind trail people think they have the right to know if they are getting the medication

3.1.4 Lung Function

3.1.5 Heart structure and Function

3.1.6 Principles of Immunology 1) Phagocytosis 1. The phagocyte is attracted to the pathogen by chemoattractants. The phagocyte moves towards the pathogen along a concentration gradient. 2. The phagocyte binds to the pathogen 3. Lysosomes within the phagocyte migrate towards the phagosome formed by engulfing the bacterium 4. The lysosomes release their lytic enzymes into the phagosome, where they break sown the bacterium 5. The break down products of the bacterium are absorbed by the pathogen 6. Once digested the phagocyte displays the pathogen antigens on its own membrane. 2) Phagocytes activate T- Cells Some release substances to activate B- Cells Some attach to antigens on a pathogen and kill the cell

3) T-Cells activate B- Cells, Which Divide into Plasma Cells Each B-Cell has a different shaped antibody on its membrane, so different ones bind to different shaped antigens. They are also covered in antibodies. 1. When the antibody on the surface of a B- Cell meets a complementary shaped antigen, it binds to it 2. This, together with substances released form T-Cells, activate the B- Cells 3. The activated B- Cells divide into plasma cells 4) Plasma Cells make more antibodies to a specific antigen Antibody Function: Coating the pathogen to make it easier to be engulfed by the phagocyte and preventing it from entering the host cell. Binding to and neutralising toxins produced by the pathogen

Antigen: molecules found on the surface of cells Antibody: is a protein, they are made up of chains of amino acid monomers linked together by peptide bonds.

Humoral B cells and the production of antibodies form the humoral response. Cellular- the T cells and other immune system cells that they interact with e.g. phagocytes, form the cellular response. Secondary Response 1. If the same pathogen enters the body again, the immune response will produce a quicker, stronger immune response. 2. Memory B- Cells divide into plasma cells that produce the right antibody to the antigen. Memory T- Cells divide into the correct type of T- Cells to kill the cell carrying the antigen. 3. The secondary response gets rid of the pathogen before you show any symptoms Antigenic Variation When pathogen changes their surface antigens, this is called antigenic variation. This means that when you are infected a second time, the memory cells produced from the first infection will not recognise the different antigens, so the immune system has to start from scratch and carry put the primary response against the new antigen. Antigenic variation makes it difficult to develop vaccines against some pathogens. Example Influenza 1. The influenza virus cause influenza 2. Proteins on the surface of the influenza virus acts as antigens, triggering the immune systems 3. These antigens can change regularly, forming new strains of the virus. 4. Memory cells produced from infection with 1 strain of flu will not recognise other strains with different antigens, this means that your immune system produces a primary response every time you are infected with a new strains. 5. This means that you can suffer from the flu each time you get the new strain.

Vaccines provide protection for individual and populations against diseases. Vaccines contain antigens (these may be free or attached to a dead or attenuated pathogen) that cause your body to produce memory cells against a particular pathogen, without causing disease. This means you are immune without getting symptoms. Reduce the occurrence of the disease; because the people who are not vaccinated are less likely to catch the disease, this is called herd immunity. The disadvantages of taking a vaccine orally is that it could be broken down by enzymes in the gut or the molecules in the vaccine may be too big to be absorbed in to the blood. Monoclonal Antibodies are used to target specific substances and cells. E.g. cancer and pregnancy test. Monoclonal antibodies are antibodies produces from a single group of genetically identical BCells. This means that they are identical in structure. 1. A mouse is exposed to a pathogen against which an antibody is required 2. The B- Cells in the mouse produce a mixture of antibodies that can be extracted. A sample of the B- Cells are taken from the spleen 3. In order to replicate quickly, the B- Cells are mixed with cancer tumour cells 4. Detergent is added to the mixture to break down the cell surface membrane and fuse the two cells together producing hybridomas 5. The cells are separated under a microscope and each cell is cultured to form a cone of itself 6. The clones that produce the required antibody are grown on a large scale and the antibodies are extracted 7. Because these antibodies are all from the cells cloned from a single B- Cell, they are called monoclonal antibodies. Advantage: to be able to produce antibodies outside the body. Uses: Separation of a chemical from a mixture Immunoassay method of calculating the amount of a substance in a mixture Cancer Treatment monoclonal antibodies attach themselves to cancer cells, and then the antibodies can be used to activate a cytotoxic drug. This drug will only be activated by cells that the monoclonal antibody is attached to, then the cancer cell is destroyed causing little damage to other cells. Transplant Surgery monoclonal antibodies used to knock out specific T-Cells that would normally cause rejection.