AA--PPDDFF WWaatteerrmmaarrkk DDEEMMOO:: PPuurrcchhaassee ffrroomm wwwwww..AA--PPDDFF..ccoomm ttoo rreemmoovvee tthhee wwaatteerrmmaarrkk http://www.mrothery.co.uk/ Mark Rothery's Biology Web Site A level biology resources past paper questions coursework help A level biology resources past paper questions coursework help WELCOME: This site is mainly for AQA(B) AS & A2 (A level) Biology, content is reached from the module links below. There are extensive notes, summaries and past paper questions. Other resources can be found in each module's resource centre. AS & A2 Module1 Biochemistry, cells, cell transport, exchange, enzymes & digestion. Module2 Genetic code, cell cycle, sexual reproduction & gene technology. Module3 Transport, breathing & heartbeat control, energy & exercise. Photosynthesis, respiration, homeostasis, nervous coordination, muscles, Module4 inheritance, variation, and evolution & classification. Energy flow through ecosystems, material cycles, studying ecosystems, Module5 dynamics of ecosystems and human activities. Patterns of behaviour, reproductive behaviour, pregnancy, human growth Module8 and development, human populations and health. PowerPoints -------------------------------------------------------------------------------------------------------------------------------------------- T N K Q OPIC OTES EY FACTS UESTIONS Some are best printed & answered Cut down versions on paper then checked. Newer Q's can be answered online. Tests Properties Q1 Q2 Q3 Q4 Q5 Q6 BIOCHEM Notes Carb. Notes MCQ CELLS Notes All Q1 Q2 Q3 Q4 MCQ EXCHANGE Notes All Q1 Q2 Q3 Q4 ENZYMES Notes Q1 Q2 Q3 DIGESTION Notes Fungi Human Q1 Q2 Q3 Q4 Notes TECHNIQUES M/scope exam board specification for module one resource centre revision quiz on module one Email link [email protected] BIOCHEMISTRY Contents Water Carbohydrates Lipids Proteins At least 80% of the mass of living organisms is water, and almost all the chemical reactions of life take place in aqueous solution. The other chemicals that make up living things are mostly organic macromolecules belonging to the 4 groups proteins, nucleic acids, carbohydrates or lipids. These macromolecules are made up from specific monomers as shown in the table below. Between them these four groups make up 93% of the dry mass of living organisms, the remaining 7% comprising small organic molecules (like vitamins) and inorganic ions. GROUP NAME MONOMERS POLYMERS % DRY MASS Proteins amino acids polypeptides 50 nucleic acids nucleotides polynucleotides 18 carbohydrates monosaccharides polysaccharides 15 GROUP NAME COMPONENTS LARGEST UNIT % DRY MASS lipids fatty acids + glycerol Triglycerides 10 The first part of this unit is about each of these groups. We'll look at each of these groups in detail, except nucleic acids, which are studied in module 2. WATER Water molecules are charged, with the oxygen atom being slightly negative and the hydrogen atoms being slightly positive. These opposite charges attract each other, forming hydrogen bonds. These are weak, long distance bonds that are very common and very important in biology. Water has a number of important properties essential for life. Many of the properties below are due to the hydrogen bonds in water. • Solvent. Because it is charged, water is a very good solvent. Charged or polar molecules such as salts, sugars and amino acids dissolve readily in water and so are called hydrophilic ("water loving"). Uncharged or non-polar molecules such as lipids do not dissolve so well in water and are called hydrophobic ("water hating"). • Specific heat capacity. Water has a specific heat capacity of 4.2 J g-1 °C-1, which means that it takes 4.2 joules of energy to heat 1 g of water by 1°C. This is unusually high and it means that water does not change temperature very easily. This minimizes fluctuations in temperature inside cells, and it also means that sea temperature is remarkably constant. • Latent heat of evaporation. Water requires a lot of energy to change state from a liquid into a gas, and this is made use of as a cooling mechanism in animals (sweating and panting) and plants (transpiration). As water evaporates it extracts heat from around it, cooling the organism. • Density. Water is unique in that the solid state (ice) is less dense that the liquid state, so ice floats on water. As the air temperature cools, bodies of water freeze from the surface, forming a layer of ice with liquid water underneath. This allows aquatic ecosystems to exist even in sub- zero temperatures. • Cohesion. Water molecules "stick together" due to their hydrogen bonds, so water has high cohesion. This explains why long columns of water can be sucked up tall trees by transpiration without breaking. It also explains surface tension, which allows small animals to walk on water. • Ionization. When many salts dissolve in water they ionize into discrete positive and negative ions (e.g. NaCl Na+ + Cl-). Many important biological molecules are weak acids, which also ionize in solution (e.g. acetic acid acetate- + H+). The names of the acid and ionized forms (acetic acid and acetate in this example) are often used loosely and interchangeably, which can cause confusion. You will come across many examples of two names referring to the same substance, e.g.: phosphoric acid and phosphate, lactic acid and lactate, citric acid and citrate, pyruvic acid and pyruvate, aspartic acid and aspartate, etc. The ionized form is the one found in living cells. • pH. Water itself is partly ionized (H O H+ + OH- ), so it is a source of protons (H+ ions), and indeed 2 many biochemical reactions are sensitive to pH (-log[H+]). Pure water cannot buffer changes in H+ concentration, so is not a buffer and can easily be any pH, but the cytoplasms and tissue fluids of living organisms are usually well buffered at about neutral pH (pH 7-8). CARBOHYDRATES Carbohydrates contain only the elements carbon, hydrogen and oxygen. The group includes monomers, dimers and polymers, as shown in this diagram: Monosaccharides All have the formula (CH O) , where n is between 3 and 7. The most common & important 2 n monosaccharide is glucose, which is a six-carbon sugar. It's formula is C H O and its structure is shown 6 12 6 below or more simply Glucose forms a six-sided ring. The six carbon atoms are numbered as shown, so we can refer to individual carbon atoms in the structure. In animals glucose is the main transport sugar in the blood, and its concentration in the blood is carefully controlled. There are many monosaccharides, with the same chemical formula (C H O ), but different structural 6 12 6 formulae. These include fructose and galactose. Common five-carbon sugars (where n = 5, C H O ) include ribose and deoxyribose (found in nucleic 5 10 5 acids and ATP). Disaccharides Disaccharides are formed when two monosaccharides are joined together by a glycosidic bond. The reaction involves the formation of a molecule of water (H O): 2 This shows two glucose molecules joining together to form the disaccharide maltose. Because this bond is between carbon 1 of one molecule and carbon 4 of the other molecule it is called a 1-4 glycosidic bond. This kind of reaction, where water is formed, is called a condensation reaction. The reverse process, when bonds are broken by the addition of water (e.g. in digestion), is called a hydrolysis reaction. • polymerisation reactions are condensation reactions • breakdown reactions are hydrolysis reactions There are three common disaccharides: • Maltose (or malt sugar) is glucose & glucose. It is formed on digestion of starch by amylase, because this enzyme breaks starch down into two-glucose units. Brewing beer starts with malt, which is a maltose solution made from germinated barley. Maltose is the structure shown above. • Sucrose (or cane sugar) is glucose & fructose. It is common in plants because it is less reactive than glucose, and it is their main transport sugar. It's the common table sugar that you put in tea. • Lactose (or milk sugar) is galactose & glucose. It is found only in mammalian milk, and is the main source of energy for infant mammals. Polysaccharides Polysaccharides are long chains of many monosaccharides joined together by glycosidic bonds. There are three important polysaccharides: Starch is the plant storage polysaccharide. It is insoluble and forms starch granules inside many plant cells. Being insoluble means starch does not change the water potential of cells, so does not cause the cells to take up water by osmosis (more on osmosis later). It is not a pure substance, but is a mixture of amylose and amylopectin. Amylose is simply poly-(1-4) glucose, so is a straight chain. In fact the chain is floppy, and it tends to coil up into a helix. Amylopectin is poly(1-4) glucose with about 4% (1-6) branches. This gives it a more open molecular structure than amylose. Because it has more ends, it can be broken more quickly than amylose by amylase enzymes. Both amylose and amylopectin are broken down by the enzyme amylase into maltose, though at different rates. Glycogen is similar in structure to amylopectin. It is poly (1-4) glucose with 9% (1-6) branches. It is made by animals as their storage polysaccharide, and is found mainly in muscle and liver. Because it is so highly branched, it can be mobilised (broken down to glucose for energy) very quickly. Cellulose is only found in plants, where it is the main component of cell walls. It is poly (1-4) glucose, but with a different isomer of glucose. Cellulose contains beta-glucose, in which the hydroxyl group on carbon 1 sticks up. This means that in a chain alternate glucose molecules are inverted. This apparently tiny difference makes a huge difference in structure and properties. While the a1-4 glucose polymer in starch coils up to form granules, the beta1-4 glucose polymer in cellulose forms straight chains. Hundreds of these chains are linked together by hydrogen bonds to form cellulose microfibrils. These microfibrils are very strong and rigid, and give strength to plant cells, and therefore to young plants. The beta-glycosidic bond cannot be broken by amylase, but requires a specific cellulase enzyme. The only organisms that possess a cellulase enzyme are bacteria, so herbivorous animals, like cows and termites whose diet is mainly cellulose, have mutualistic bacteria in their guts so that they can digest cellulose. Humans cannot digest cellulose, and it is referred to as fibre. Other polysaccharides that you may come across include: • Chitin (poly glucose amine), found in fungal cell walls and the exoskeletons of insects. • Pectin (poly galactose uronate), found in plant cell walls. • Agar (poly galactose sulphate), found in algae and used to make agar plates. • Murein (a sugar-peptide polymer), found in bacterial cell walls. • Lignin (a complex polymer), found in the walls of xylem cells, is the main component of wood. LIPIDS Lipids are a mixed group of hydrophobic compounds composed of the elements carbon, hydrogen and oxygen. They contain fats and oils (fats are solid at room temperature, whereas oils are liquid) Triglycerides Triglycerides are commonly called fats or oils. They are made of glycerol and fatty acids. Glycerol is a small, 3-carbon molecule with three hydroxyl groups. Fatty acids are long molecules with a polar, hydrophilic end and a non- polar, hydrophobic "tail". The hydrocarbon chain can be from 14 to 22 CH units long. The 2 hydrocarbon chain is sometimes called an R group, so the formula of a fatty acid can be written as R- COOH. • If there are no C=C double bonds in the hydrocarbon chain, then it is a saturated fatty acid (i.e. saturated with hydrogen). These fatty acids form straight chains, and have a high melting point. • If there are C=C double bonds in the hydrocarbon chain, then it is an unsaturated fatty acid (i.e. unsaturated with hydrogen). These fatty acids form bent chains, and have a low melting point. Fatty acids with more than one double bond are called poly-unsaturated fatty acids (PUFAs). One molecule of glycerol joins togther with three fatty acid molecules to form a triglyceride molecule, in another condensation polymerisation reaction: Triglycerides are insoluble in water. They are used for storage, insulation and protection in fatty tissue (or adipose tissue) found under the skin (sub-cutaneous) or surrounding organs. They yield more energy per unit mass than other compounds so are good for energy storage. Carbohydrates can be mobilised more quickly, and glycogen is stored in muscles and liver for immediate energy requirements. • Triglycerides containing saturated fatty acids have a high melting point and tend to be found in warm-blooded animals. At room temperature they are solids (fats), e.g. butter, lard. • Triglycerides containing unsaturated fatty acids have a low melting point and tend to be found in cold-blooded animals and plants. At room temperature they are liquids (oils), e.g. fish oil, vegetable oils. Phospholipids Phospholipids have a similar structure to triglycerides, but with a phosphate group in place of one fatty acid chain. There may also be other groups attached to the phosphate. Phospholipids have a polar hydrophilic "head" (the negatively-charged phosphate group) and two non-polar hydrophobic "tails" (the fatty acid chains). This mixture of properties is fundamental to biology, for phospholipids are the main components of cell membranes. • When mixed with water, phospholipids form droplet spheres with the hydrophilic heads facing the water and the hydrophobic tails facing each other. This is called a micelle. • Alternatively, they may form a double- layered phospholipid bilayer. This traps a compartment of water in the middle separated from the external water by the hydrophobic sphere. This naturally- occurring structure is called a liposome, and is similar to a membrane surrounding a cell. Waxes Waxes are formed from fatty acids and long-chain alcohols. They are commonly found wherever waterproofing is needed, such as in leaf cuticles, insect exoskeletons, birds' feathers and mammals' fur. Steroids Steroids are small hydrophobic molecules found mainly in animals. They include: • cholestero l, which is found in animals cell membranes to increase stiffness • bile salts , which help to emulsify dietary fats • steroid hormones such as testosterone, oestrogen, progesterone and cortisol • vitamin D, which aids Ca2+ uptake by bones. PROTEINS Proteins are the most complex and most diverse group of biological compounds. They have an astonishing range of different functions, as this list shows. • structure e.g. collagen (bone, cartilage, tendon), keratin (hair), actin (muscle) • enzymes e.g. amylase, pepsin, catalase, etc (>10,000 others) • transport e.g. haemoglobin (oxygen), transferrin (iron) • pumps e.g. Na+K+ pump in cell membranes • motors e.g. myosin (muscle), kinesin (cilia) • hormones e.g. insulin, glucagon • receptors e.g. rhodopsin (light receptor in retina) • antibodies e.g. immunoglobulins • storage e.g. albumins in eggs and blood, caesin in milk • blood clotting e.g. thrombin, fibrin • lubrication e.g. glycoproteins in synovial fluid • toxins e.g. diphtheria toxin • antifreeze e.g. glycoproteins in arctic flea • and many more! Proteins are made of amino acids. Amino acids are made of the five elements C H O N S. The general structure of an amino acid molecule is shown on the right. There is a central carbon atom (called the "alpha carbon"), with four different chemical groups attached to it: • a hydrogen atom • a basic amino group • an acidic carboxyl group • a variable "R" group (or side chain)