AS Biology part 2

PROTEINS

Proteins are made up of long chains of amino acids. A dipeptide bond is formed when two amino acids join together. A polypeptide if formed when more than two amino acids join together. Proteins are made uop of one or more polypeptide. Different amino acids have different variable groups. All amino acids have the same general structure - a carboxyl group (-COOH) and an amino group (-NH2) attached to a carbon atom. The only difference between different amino acids is the variable group they contain.

AMINO ACIDS

Amino acids are joined together by peptide bonds to form dipeptides and polypeptides. They are formed during a condesation reaction, which means water is removed to join the amino acids together.

STRUCTURE OF PROTEINS

Primary Structure - this is the sequence of amino acids in the polypeptide chain. The polypeptides are held together by peptide bonds. Secondary Structure - Hydrogen bonds form between the amino acids in the chain. This makes it automatically coil into an alpha helix. Tertiary Structure - The coiled or folded chain of the amino acids is further coiled and folded. More bonds forn between different parts of th epolypeptide chain such as: disulfide, ionic and hydrogen bonds. For proteins make from a single polypeptide chain, the tertiary structure forms their final 3D shape. Quarternary Structure - Large protein molecules often form complex molecules containing a number of individual polypeptide chains that are linked in various ways. There may also be non-protein (prosthetic) groups associated with molecules, which as the iron containing heam group in heamoglobin.

A protein's shape is closely related to its function. E.g. insulin's function is to make cells take up glucose from the blood. It's a compact protein, which makes it easy to transport around the body in the blood, so it can carry out its function effectively.

FUNCTIONS OF PROTEINS

Enzymes are usually roughly spherical in shape due to the tight folding of the polypeptide chains. They're soluble and often have roles in metabolism, e.g. some of the enzymes break down large food molecules and other enzymes help to make large molecules. Antibodies are involved in the immune response. They're made up of two short polypeptide chains and two long polypeptide chains bonded together. Antibodies have variable regions - the amino acid sequences in these regions vary greatly. Transport Proteins are present in cell membranes. They contain hydrophilic and hydrophobic amino acids, which cause the protein to fold up and form a channel. These proteins transport molecules and ions across cell membranes. Structural Proteins are physically strong. they consist of long polypeptide chains lying parallel to each other with cross-links between them. Structural proteins include keratin and collagen.

CARBOHYDRATES - MONOSACCHARIDES

Most carbohydrates are large, complex molecules composed of long chains of monosaccharides. Singlemonosaccharides are still called carbihydrates. Glucose is s monosaccharide with six carbons atoms in each molecule. Glucose's structure is related to its function as the main energy source in plants and animals. Its structure makes it soluble so it can be easily transported. Its chemical bonds contain a lot of energy.

CARBOHYDRATES - DISACCHARIDES

Monosaccharides join together to form disaccharides. They are joined by the process of condensation which removes a molecule of water and forms a glycosidic bond. A hydrogen on one monosaccharide binds to a hydroxyl group on the other, releasing a molecule of water. To break teh bond you would just have to add water to the disaccharide - hydrolysis.

Monosaccharides Disaccaride

Glucose + Glucose = Maltose

Glucose + Fructose = Sucrose

Glucose + Galactose = Lactose

CARBOHYDRATES - POLYSACCHARIDES

A polysaccharide is formed when two or more monosaccharides join together. They join together in the same way as monosaccharides.

LIPIDS - TRIGLYCERIDE

A triglyceride is made of one molecule of glycerol and three fatty acids. Fatty acid molcules have long tails made of hydrocarbons. The tails are hydrophobic. This makes the lipids insoluble in water. All fatty acids consist of tha same basic structure,, but the hydrocarbon chain varies - the r group.

SATURATED AND UNSATURATED LIPIDS

There are two kinds of lipid - saturated and unsaturated. Saturated lipids are mainly found in animal fats and unsaturated lipids are found in mostly plants. Unsaturated lipids melt at lower temperatures than unsaturated ones. This is because saturated lipids don’t have any double bonds between their carbon atoms and unsaturated lipids do have double bonds.

PHOSPHOLIPIDS

Phospholipids are pretty similar to triglycerides except a phosphate group replaces one of the fatty acid molecules. The phosphate group is hydrophilic. The fatty acid tails are hydrophobic. This is important in the cell membrane.

BENEDICT'S TEST FOR SUGARS

Sugar is general term for monosaccharides and disaccharides. All sugars can be classified as reducing or non-reducing. To test for sugars you use the benedict's test. The test differs depending on the type of sugar you testing for.

REDUCING SUGARS

Reducing sugars include all monosaccharides (glucose) and some disaccharides (maltose). You add Benedict's reagant to to a liquid sample and heat it. Make sure the solution doesn't boil. If the test's positive it will form a coloured precipitate. The colour changes from: Blue - Green - Yellow - Orange - Brick Red. The higher the concentration of reducing sugar the further the colour change goes - you can use this to compare the amount of reducing sugars in different solutions.

BENEDICT'S TEST FOR SUGARS - NON-REDUCING

To test for non-reducing sugars, like sucrose, first you have to break them down into monosaccharides. You do this by boiling the test solution with dilute hydrochloric acid and then neutralising it with sodium hydrogencarbonate. Then just carry out the Benedict's test as you would for a reducing sugar. Annoyingly, if the result is positive the sugar could be reducing or non-reducing. To check it's non-reducing you need to do the reducing sugar test too - to make sure its not a reducing sugar.

IODINE TEST FOR STARCH

Just add iodine dissolved in ptassium iodide solution to the test sample. It starch is present, the sample will change from browny-orange to a dark, blue-black colour. If there's no starch, it stays browny-orange.

BIURET TEST FOR PROTEINS

There are two stages to this test:

1) The test solution needs to be alkaline, so first you add a few drops of soduim hydroxide solution.

2) Then you add some copper sulphate solution.

• If the protein is present a purple layer forms.
• If there's no protein, the solution will stay blue.

Enzymes catalyse metabolic reactions in your body. Even your phenotype is due to enzymes that catalyse the reactions that cause growth and development. Enzymes action can be intracellular - within cells, or extra cellular - outside cells. Enzymes are globular proteins. They have an active site, which has a specific shape. The active site is the part of the enzyme where the substrate binds.

ENZYMES LOWER THE ACTIVATION ENERGY OF A REACTION

In a chemical reaction, a certain amount of energy needs to be supplied to the chemicals before the reaction will start - activation energy - it's often provided as heat. Enzymes lower activation energy, often making reactions happen at lower temperatures than normal. This speeds up the rate of reaction. When a substrate fits into the enzyme's active site it forms an enzyme-substrate complex - this lowers the activation energy. Here's two reasons why: If two substrates need to be joined, being attached to the enzyme holds them close together, reducing any repulsion between the molecules so they can bond more easily. If the enzyme is catalysing a breakdown reaction, fitting into the active site puts a strain on the bonds in the substrate, so the substrate breaks up more easily.

INDUCED FIT MODEL

The induced fit model helps to explain why enzymes are so specific and only bond to one particular substrate. The substrate doesn't only have to be the right shape to fit the active site, it has to make the active site change shape in the right way as well.

ENZYMES ARE VERY SPECIFIC

Enzymes usually only catalyse one reaction. This is because only one substrate will fit into the active site. The active site's shape is determined by the enzyme's tertiary structure, which is determined by the enzyme's primary structure. Each different enzyme has a different tertiary structure and so a different shaped active site. If the substrate shape doesn't match the active site, the reaction won't be catalysed. If the tertiary structure of a protein is altered in any way, the shape of the active site will change. This means the substrate won't fit into the active site and 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 is determined by a gene. If a mutation occurs in the gene, it could change the tertiary structure of the enzyme produced.

FACTORS AFFECTING ENZYME ACTIVITY - TEMPERATURE

Like any chemical reaction, the rate an enzyme works at increases when the temperature increases. More heat means more kinetic energy, so molecules move faster. This makes the enzymes more likely to collide with the substrate. The energy of these collisions also increases, which means each collision is more likely to result in a reaction. But, if the temperature is too high, the reactions stops beacuse the enzymes denature. The rise in temperature makes the enzyme's vibrate more. If the temperature goes above a certain level, the vibration breaks some of the bonds that hold the enzyme in shape The active site changes shape and teh enzyme and substrate no longer fit together. At this point, the enzyme is denatured - it no longer functions as a catalyst.

FACTORS AFFECTING ENZYME ACTIVITY - pH

All enzymes have an optimum pH value. Mosthuman enzymes work at pH 7 - neutral, but there are some exceptions. Pepsin, for example, works best at pH 2. Above and below optimum pH, the H+ and OH- found in acids and alkalis mess up the ionic and hydrogen bonds that hold the enzyme's tertiary structure in place. This make the active site change shape, so the enzyme is denatured.

FACTORS AFFECTING ENZYME ACTIVITY - SUBSTRATE CONCENTRATION

The higher the substrate concentration, the faster the reaction - more substrate means more collisions between substrates and enzymes are more likely. This is only true up until a saturated point. After that, there are so many substrate molecules that the that all the enzyme's active sites are full and adding more substrate makes no difference.

Cholera is caused by a bacterial pathogen. Pathogens cause disease by producing toxins and damaging cells. If pathogens successfully enter an organism's body the can cause disease in two ways:

Production of toxins

Many bacteria release toxins into the body. For example, the bacterium that causes tetanus produces a toxin that blocks the function of certain nerve cells, causing muscle spasms. The bacterium that causes cholera produces toxins that upsets the exchange of substances in and out of cells.

Cell Damage

Pathogens can physically damage the host cell by: Rupturing them to rupturing them to release nutrients (proteins etc.) inside them. Breaking down nutrients inside the cell for their own use. This starves and eventually kills the cell. Replicating inside the cells and bursting them when they're released, e.g. some viruses do this.

Cholera bacteria produce a toxin that affects chloride ion exchange.

1) The toxin causes chloride ion channel proteins in the plasma membrane of the small intestine epithelial cells to open.

2) Chloride ions move into the lumen of the small intestine. The build up of chloride ions lowers the water potential of the lumen.

3) Water moves out of the blood, across the epithelial cells and into the lumen by osmosis (to even up the water concentration).

4) The massive increase in water secretion into the lumen leads to really, really, really bad diarrhoea - causing the body to become extremely rehydrated

ORAL REHYDRATION SOLUTIONS

Oral Rehydration Solutions (ORS') are used to treat diarrhoeal diseases.

People suffering from diarrhoeal diseases like cholera need to replace all the fluid that they've lost in diarrhoea. The quickest way to do this is by inserting a drip into a person's vein. However, not everywhere in the world has access to drips so ORS' are used instead.

Oral Rehydration Solutions (ORS')

1) An oral rehydation solution is a drink that contains large amounts of salts and sugars dissolved in water. Sodium ions are included to increase glucose absorption via co-transport. Getting the concentration of an ORS right is essential for effective treatment. An ORS is a very cheap treatment and the people administrating it don't need much training, This makes it perfect to treat people in developing countries.

ORS are so important in treating diarrhoeal disease that research into development of new, improved ORS is always being carried out. But before an ORS can be put into use it has to be tested to show that is more effective than the old one and that it's safe. This is done by clinical testing on humans. Diarrhoeal diseases mostly affect children, so many trials involve children. Parents decide whether the child will participate in the trial - some people think this is un ethical. But scientist believe the treatment must be trialled on children if it's to be shown effective to a disease that mainly affects children. Clinical trials usually involve a blind trial. This is where some patients who are admitted to the hospital with diarrhoeal diseases are given the standard ORS and others are give the new ORS. This gives opportunity for comparison. It's called a blind trial because the patients don't know which treatment they've been given. Some people don't agree with this - they think the people have the right to know and decide on the treatment they're going to have. Scientists argue that a blind trial is important to eliminate any bias that may effect the data as a result of the patients knowing which treatment they've received. When a new ORS is first trialled, there's no way of knowing whether it'll be better than the current ORS - there's a risk of the patient dying when the original, better treatment was available.

PATHOGENS

Pathogens need to enter the body to cause disease. They get in through an organism's interface, e.g. nose, eyes, a cut. An organism has three main interfaces where the pathogen can enter: 1) Skin - If you damage your skin, pathogens can enter your bloodstream from the surface. 2) Digestive System - If you eat or drink food that contains pathogens, most of them will be killed by the acidic conditions in the stomach. However, come may survive and pass into the intestines where they invade cells of the gut wall and cause disease. 3) Gas-Exchange System - If you breathe air that contains pathogens, most of them will be trapped in mucus lining the lung epithelium. These cells have cillia that beat and move the mucus up the trachea to the mouth, where they are removed. Unfortunately, some pathogens are able to reach the alveoli where they can invade cells and cause disease

If a pathogen enters the body, the immune system responds. An immune response is the body's reaction to a foreign antigen. Antigens are molecules found on the surface of cells. When a pathogen invades the body, the antigens on its cell surface are identified as foreign, which activates cells in the immune system.

A phagocyte is a type of white blood cell that carries out phagocytosis. They're found in the blood and in tissues and are the first cells to respond to a pathogen inside the body. A phagocyte recognises the antigens on a pathogen. The cytoplasm of the phagocyte moves round the pathogen, engulfing it. The pathogen is now contained in a phagocytic vacuole in the cytoplasm of the phagocyte. A lysosome fuses with the phagocytic vacuole. The lysosomal enzymes break down the pathogen. The phagocyte then presents the pathogen's antigen. It sticks the antigens on its surface to activate other immune system cells.

T-CELLS

A T-cell is another type of white blood cell. Their surface is covered in receptors. The receptors bind to antigens presented by the phagocytes. Each T-cell has a different receptor on its surface. When the receptor on the surface of a T-cell meets a complimentary antigen, it bind to it - so each T-cell will bind to a different antigen. This activates the T-cell - it divides and differentiates and different types of T-dells that carry out different functions: Some activated T-cells releases substances to activate B-cells. Some attach to antigens on a pathogen and kill the cell. Some become memory cells.

B-CELLS

B-cells are another type of white blood cell. They're covered with antibodies. Antibodies are proteins that bind to antigens to form an antigen-antibody complex. Each B-cell has a different shaped antibody on its surface. When the antibody on the surface of a B-cell meets a complimentary shaped antigen, it binds to it - so each B-cell will bind to a different antigen. This, together with substances released from T-cells, activates the B-cell. The activated B-cell divides, by mitosis, into plasma and memory cells.